diff --git a/models/finetuned/bace/checkpoint_epoch_025/config.json b/models/finetuned/bace/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
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- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
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- "type_vocab_size": 1,
- "use_cache": true,
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diff --git a/models/finetuned/bace/checkpoint_epoch_025/merges.txt b/models/finetuned/bace/checkpoint_epoch_025/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/checkpoint_epoch_025/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
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-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
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-- 1
-O -1
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-\ C
-# N
-/ N
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-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
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-\ S
-S +1
-Cl -1
-I -1
-/ C@@H1
-S i
-/ C@H1
-/ S
-=N -1
-S e
-= P
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-\ C@@H1
-\ C@H1
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-C -1
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-B -1
-+ 3
-Cl +3
-\ NH1
-L i
-Li +1
-P H1
-1 8
-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
-1 2
-P @
-+ 2
-@@ +1
-S -1
-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
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-=S e
-S @@+1
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-1 4
--\ Ring2
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-\ F
-/ C@
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-H1 -1
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-/ P
-a +2
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-C a+2
-\ Br
-M g
-Zn +2
-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
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--/ Ring1
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-Na H1
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-Ag +1
-H1 +1
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-\ P
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-14C H1
-= 11C
-S @@
-=P @@
-Si H2
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-B H3-1
-S @
-=14C H1
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-\S +1
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-#C -1
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-N @
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-13C H1
-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/bace/checkpoint_epoch_025/model.pt b/models/finetuned/bace/checkpoint_epoch_025/model.pt
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index 34d885fdb2c94581c290984e5158af8aa821f504..0000000000000000000000000000000000000000
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index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/checkpoint_epoch_025/special_tokens_map.json
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-{
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- "single_word": false
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diff --git a/models/finetuned/bace/checkpoint_epoch_025/tokenizer.json b/models/finetuned/bace/checkpoint_epoch_025/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/checkpoint_epoch_025/tokenizer.json
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-{
- "version": "1.0",
- "truncation": {
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- "Si-1": 396,
- "SiH1-1": 397,
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- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
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- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
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- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
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- "C@ @",
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- "\\ C",
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- "= S",
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- "Na +1",
- "/ O",
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- "Branch 3",
- "\\ S",
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- "I -1",
- "/ C@@H1",
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- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
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- "P @",
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- "\\ O-1",
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- "5 I",
- "12 5I",
- "11 C",
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- "- \\",
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- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
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- "-\\ Ring2",
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- "\\ F",
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- "H1 -1",
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- "=S +1",
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- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
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- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
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- "\\ 11CH3",
- "\\C -1",
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- "Si @",
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- "Si H1-1",
- "Si H3-1",
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- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/bace/checkpoint_epoch_025/vocab.json b/models/finetuned/bace/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
-{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427}
\ No newline at end of file
diff --git a/models/finetuned/bace/config.json b/models/finetuned/bace/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/bace/merges.txt b/models/finetuned/bace/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
-Br -1
-Branch 3
-\ S
-S +1
-Cl -1
-I -1
-/ C@@H1
-S i
-/ C@H1
-/ S
-=N -1
-S e
-= P
-N -1
-Ring 3
-2 H
-P +1
-K +1
-\ C@@H1
-\ C@H1
-/ N+1
-@ @
-C -1
-# N+1
-B -1
-+ 3
-Cl +3
-\ NH1
-L i
-Li +1
-P H1
-1 8
-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
-1 2
-P @
-+ 2
-@@ +1
-S -1
-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
-/ C@
-T e
-H 2
-H1 -1
-=O +1
-N @@+1
-C +1
-=S +1
-Z n
-/ P
-a +2
-/ I
-O H1-1
-C a+2
-\ Br
-M g
-Zn +2
-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
-H3 -1
-14C H3
-B H3-1
-S @
-=14C H1
-=P H1
-=P @
-=N H1+1
-\S +1
-12 4
-C H1-1
-S r
-=S i
-124 I
-Sr +2
-#C -1
-/C -1
-N @
-/N -1
-13C H1
-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/bace/model.pt b/models/finetuned/bace/model.pt
deleted file mode 100644
index 5557f9c3c74f91a50aa359848815ba6469e3dce1..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:62289c1112babd62c4b045f6971b8dcdd42201fb5a17acf59a471db88f14a56e
-size 1022855293
diff --git a/models/finetuned/bace/special_tokens_map.json b/models/finetuned/bace/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
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- "cls_token": {
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- "rstrip": false,
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- "content": "",
- "lstrip": false,
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- "rstrip": false,
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- "sep_token": {
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- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/bace/tokenizer.json b/models/finetuned/bace/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
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- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
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- "content": "",
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- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
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- "content": "",
- "single_word": false,
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- "rstrip": false,
- "normalized": true,
- "special": true
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- "content": "",
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- {
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- "content": "",
- "single_word": false,
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- "special": true
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- "content": "",
- "single_word": false,
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- "rstrip": false,
- "normalized": true,
- "special": true
- }
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- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
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- "trim_offsets": true,
- "add_prefix_space": false
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- "decoder": {
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- "fuse_unk": false,
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- "": 1,
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- "": 3,
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- "i": 46,
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- "n": 48,
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- "#Branch1": 69,
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- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
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- "-1": 81,
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- "\\N": 90,
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- "\\C@@H1": 113,
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- "+3": 120,
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- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
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- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
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- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
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- "N@+1": 157,
- "14": 158,
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- "\\F": 161,
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- "Te": 163,
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- "SeH1": 205,
- "-/Ring1": 206,
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- "SiH2": 222,
- "H3-1": 223,
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- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
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- "14C@H1": 317,
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- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
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- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
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- "\\SeH1": 346,
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- "LiH1": 349,
- "18F-1": 350,
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- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
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- "45": 373,
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- "42K+1": 375,
- "5I-1": 376,
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- "SH0": 389,
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- "\\3H": 391,
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- "\\C-1": 393,
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diff --git a/models/finetuned/bace/tokenizer_config.json b/models/finetuned/bace/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
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- "normalized": true,
- "rstrip": false,
- "single_word": false
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- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
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diff --git a/models/finetuned/bace/train_stdout.log b/models/finetuned/bace/train_stdout.log
deleted file mode 100644
index 03c26b0ae4120b70ae323542a7cffa79f8253ca4..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/train_stdout.log
+++ /dev/null
@@ -1,91 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=binary batch_size=16 max_len=128 backbone_lr=5e-05 head_lr=1e-05 weight_decay=0.1 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bace/bace.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bace/bace_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=True seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-
- 0%| | 0/1513 [00:00, ?it/s]
- 21%|██▏ | 325/1513 [00:00<00:00, 3239.43it/s]
- 43%|████▎ | 649/1513 [00:00<00:00, 3235.14it/s]
- 66%|██████▋ | 1006/1513 [00:00<00:00, 3386.92it/s]
- 90%|█████████ | 1362/1513 [00:00<00:00, 3454.73it/s]
-100%|██████████| 1513/1513 [00:00<00:00, 3457.01it/s]
-[finetune] split sizes: train=1,210 val=151 test=152
-[finetune] train modality_non_empty: graph=1,210/1,210 text=87/1,210 kg=172/1,210
-[finetune] val modality_non_empty: graph=151/151 text=2/151 kg=8/151
-[finetune] test modality_non_empty: graph=152/152 text=23/152 kg=18/152
-[finetune] extracting labels...
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=76 val_steps=10 test_steps=10
-[finetune] initialized head: in_dim=3072 out=2
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=0.6443 val_loss=0.5344 time=20.3s tod=02:28
-[finetune] epoch 2/50: train_loss=0.5351 val_loss=0.4565 time=20.1s tod=02:29
-[finetune] epoch 3/50: train_loss=0.4530 val_loss=0.4736 time=20.2s tod=02:29
-[finetune] epoch 4/50: train_loss=0.4232 val_loss=0.3851 time=20.0s tod=02:29
-[finetune] epoch 5/50: train_loss=0.3725 val_loss=0.5440 time=20.1s tod=02:30
-[finetune] epoch 6/50: train_loss=0.3314 val_loss=0.4757 time=20.1s tod=02:30
-[finetune] epoch 7/50: train_loss=0.3265 val_loss=0.6589 time=20.1s tod=02:30
-[finetune] epoch 8/50: train_loss=0.3003 val_loss=0.4855 time=20.1s tod=02:31
-[finetune] epoch 9/50: train_loss=0.2645 val_loss=0.4110 time=20.0s tod=02:31
-[finetune] epoch 10/50: train_loss=0.2473 val_loss=0.5245 time=20.0s tod=02:31
-[finetune] epoch 11/50: train_loss=0.2134 val_loss=0.4764 time=20.1s tod=02:32
-[finetune] epoch 12/50: train_loss=0.1911 val_loss=0.5448 time=20.1s tod=02:32
-[finetune] epoch 13/50: train_loss=0.1706 val_loss=0.6041 time=20.2s tod=02:32
-[finetune] epoch 14/50: train_loss=0.1543 val_loss=0.6573 time=20.3s tod=02:33
-[finetune] epoch 15/50: train_loss=0.1514 val_loss=0.7120 time=20.2s tod=02:33
-[finetune] epoch 16/50: train_loss=0.1367 val_loss=0.5487 time=20.0s tod=02:33
-[finetune] epoch 17/50: train_loss=0.1170 val_loss=0.6278 time=20.1s tod=02:34
-[finetune] epoch 18/50: train_loss=0.1168 val_loss=0.5940 time=20.0s tod=02:34
-[finetune] epoch 19/50: train_loss=0.0957 val_loss=0.6297 time=20.2s tod=02:34
-[finetune] epoch 20/50: train_loss=0.0911 val_loss=0.7283 time=19.0s tod=02:35
-[finetune] epoch 21/50: train_loss=0.0738 val_loss=0.6790 time=20.2s tod=02:35
-[finetune] epoch 22/50: train_loss=0.0631 val_loss=0.6892 time=20.1s tod=02:35
-[finetune] epoch 23/50: train_loss=0.0577 val_loss=0.7209 time=20.1s tod=02:36
-[finetune] epoch 24/50: train_loss=0.0533 val_loss=0.8518 time=17.3s tod=02:36
-[finetune] epoch 25/50: train_loss=0.0614 val_loss=0.9262 time=13.7s tod=02:36
-[finetune] test_metrics: epoch=25 loss=1.3773 accuracy=0.7961 precision=0.7568 recall=0.8116 f1=0.7832 roc-auc=0.7974 prc-auc=0.8269
-[finetune] saved checkpoint (best roc-auc=0.7974): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bace/e0tdguei/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=0.0411 val_loss=0.7979 time=15.5s tod=02:37
-[finetune] epoch 27/50: train_loss=0.0465 val_loss=0.8770 time=20.1s tod=02:37
-[finetune] epoch 28/50: train_loss=0.0277 val_loss=0.9220 time=20.1s tod=02:37
-[finetune] epoch 29/50: train_loss=0.0290 val_loss=0.8844 time=20.1s tod=02:38
-[finetune] epoch 30/50: train_loss=0.0214 val_loss=0.9923 time=20.0s tod=02:38
-[finetune] epoch 31/50: train_loss=0.0187 val_loss=0.8791 time=20.2s tod=02:38
-[finetune] epoch 32/50: train_loss=0.0210 val_loss=0.9760 time=20.1s tod=02:39
-[finetune] epoch 33/50: train_loss=0.0211 val_loss=0.9671 time=20.0s tod=02:39
-[finetune] epoch 34/50: train_loss=0.0161 val_loss=1.0266 time=20.1s tod=02:39
-[finetune] epoch 35/50: train_loss=0.0154 val_loss=1.0887 time=20.1s tod=02:40
-[finetune] epoch 36/50: train_loss=0.0117 val_loss=1.0074 time=20.1s tod=02:40
-[finetune] epoch 37/50: train_loss=0.0072 val_loss=0.9916 time=20.1s tod=02:40
-[finetune] epoch 38/50: train_loss=0.0092 val_loss=1.0393 time=20.2s tod=02:41
-[finetune] epoch 39/50: train_loss=0.0090 val_loss=1.1473 time=20.2s tod=02:41
-[finetune] epoch 40/50: train_loss=0.0055 val_loss=1.1209 time=20.0s tod=02:41
-[finetune] epoch 41/50: train_loss=0.0060 val_loss=1.1437 time=20.2s tod=02:42
-[finetune] epoch 42/50: train_loss=0.0039 val_loss=1.2147 time=20.1s tod=02:42
-[finetune] epoch 43/50: train_loss=0.0033 val_loss=1.2128 time=20.1s tod=02:42
-[finetune] epoch 44/50: train_loss=0.0027 val_loss=1.2480 time=20.1s tod=02:43
-[finetune] epoch 45/50: train_loss=0.0019 val_loss=1.2552 time=20.1s tod=02:43
-[finetune] epoch 46/50: train_loss=0.0017 val_loss=1.2641 time=20.1s tod=02:43
-[finetune] epoch 47/50: train_loss=0.0008 val_loss=1.2660 time=20.1s tod=02:44
-[finetune] epoch 48/50: train_loss=0.0008 val_loss=1.2750 time=20.0s tod=02:44
-[finetune] epoch 49/50: train_loss=0.0005 val_loss=1.2843 time=20.1s tod=02:44
-[finetune] epoch 50/50: train_loss=0.0004 val_loss=1.2864 time=20.2s tod=02:45
-[finetune] test_metrics: epoch=50 loss=2.1284 accuracy=0.7697 precision=0.7429 recall=0.7536 f1=0.7482 roc-auc=0.7684 prc-auc=0.8042
-[finetune] checkpoint skipped (current roc-auc=0.7684 vs best=0.7974 at epoch 25)
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=2.1284 accuracy=0.7697 precision=0.7429 recall=0.7536 f1=0.7482 roc-auc=0.7684 prc-auc=0.8042
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bace/e0tdguei
-[finetune] done in 1002.9s
diff --git a/models/finetuned/bace/vocab.json b/models/finetuned/bace/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/bace/vocab.json
+++ /dev/null
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diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/config.json b/models/finetuned/bbbp/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_025/config.json
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-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
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diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/merges.txt b/models/finetuned/bbbp/checkpoint_epoch_025/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_025/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
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-c h
-Br an
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-- 1
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-\ S
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-I -1
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-/ S
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-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
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-H 3
-\ N+1
-- \
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-\ Br
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--\ Ring1
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-\ I
-/ NH1
-O +1
-13 1
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-\ C@@
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-\ C@
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-19 F
-/ 125I
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-R b
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-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
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-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
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-11C H2
-14 C@@H1
-Te H2
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-Bi +3
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-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
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-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
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-\ PH1
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-=C a
-\C H1-1
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-\S eH1
-/S eH1
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-Te H1
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-Zn -2
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-15 N
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-B@@ -1
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-- 4
-/ PH1
-/ P@@
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-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/model.pt b/models/finetuned/bbbp/checkpoint_epoch_025/model.pt
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-{
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diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json b/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json
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index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json
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-{
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- "11C@@H1": 404,
- "11C-1": 405,
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- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
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- "a n",
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- "Ring 3",
- "2 H",
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- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
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- "@ @",
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- "# N+1",
- "B -1",
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- "Cl +3",
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- "L i",
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- "1 8",
- "18 F",
- "@ +1",
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- "P @@",
- "H 0",
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- "12 5I",
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- "S @+1",
- "A s",
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- "123 I",
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- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
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- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
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- "1 9",
- "B a+2",
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- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
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- "7 6Br",
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- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
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- "=C a",
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- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
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- "8 9",
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- "= 32P",
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- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
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- "Si @",
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- "Se -2",
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- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/bbbp/checkpoint_epoch_025/vocab.json b/models/finetuned/bbbp/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
-{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427}
\ No newline at end of file
diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/config.json b/models/finetuned/bbbp/checkpoint_epoch_050/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_050/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/merges.txt b/models/finetuned/bbbp/checkpoint_epoch_050/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_050/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
-Br -1
-Branch 3
-\ S
-S +1
-Cl -1
-I -1
-/ C@@H1
-S i
-/ C@H1
-/ S
-=N -1
-S e
-= P
-N -1
-Ring 3
-2 H
-P +1
-K +1
-\ C@@H1
-\ C@H1
-/ N+1
-@ @
-C -1
-# N+1
-B -1
-+ 3
-Cl +3
-\ NH1
-L i
-Li +1
-P H1
-1 8
-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
-1 2
-P @
-+ 2
-@@ +1
-S -1
-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
-/ C@
-T e
-H 2
-H1 -1
-=O +1
-N @@+1
-C +1
-=S +1
-Z n
-/ P
-a +2
-/ I
-O H1-1
-C a+2
-\ Br
-M g
-Zn +2
-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
-H3 -1
-14C H3
-B H3-1
-S @
-=14C H1
-=P H1
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- "- 2",
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- "17 F",
- "35 S",
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- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
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- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
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- "C a",
- "C H1",
- "I +3",
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- "3 Se",
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- "Te -1",
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- "123 Te",
- "123I H1",
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- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
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- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/bbbp/checkpoint_epoch_050/vocab.json b/models/finetuned/bbbp/checkpoint_epoch_050/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/checkpoint_epoch_050/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
-{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427}
\ No newline at end of file
diff --git a/models/finetuned/bbbp/config.json b/models/finetuned/bbbp/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/bbbp/merges.txt b/models/finetuned/bbbp/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
-Br -1
-Branch 3
-\ S
-S +1
-Cl -1
-I -1
-/ C@@H1
-S i
-/ C@H1
-/ S
-=N -1
-S e
-= P
-N -1
-Ring 3
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-P +1
-K +1
-\ C@@H1
-\ C@H1
-/ N+1
-@ @
-C -1
-# N+1
-B -1
-+ 3
-Cl +3
-\ NH1
-L i
-Li +1
-P H1
-1 8
-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
-1 2
-P @
-+ 2
-@@ +1
-S -1
-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
-/ C@
-T e
-H 2
-H1 -1
-=O +1
-N @@+1
-C +1
-=S +1
-Z n
-/ P
-a +2
-/ I
-O H1-1
-C a+2
-\ Br
-M g
-Zn +2
-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
-H3 -1
-14C H3
-B H3-1
-S @
-=14C H1
-=P H1
-=P @
-=N H1+1
-\S +1
-12 4
-C H1-1
-S r
-=S i
-124 I
-Sr +2
-#C -1
-/C -1
-N @
-/N -1
-13C H1
-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/bbbp/model.pt b/models/finetuned/bbbp/model.pt
deleted file mode 100644
index a27b52e128ed17cabe4cf7875c06eb290f65abe8..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:56553557c9abbd004f18d16f7862060afa43a9b8a7b4f3a95956b77cc7e7ea27
-size 1022855293
diff --git a/models/finetuned/bbbp/special_tokens_map.json b/models/finetuned/bbbp/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/bbbp/tokenizer.json b/models/finetuned/bbbp/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
- "": 2,
- "": 3,
- "": 4,
- "\n": 5,
- "#": 6,
- "+": 7,
- "-": 8,
- ".": 9,
- "/": 10,
- "0": 11,
- "1": 12,
- "2": 13,
- "3": 14,
- "4": 15,
- "5": 16,
- "6": 17,
- "7": 18,
- "8": 19,
- "9": 20,
- "=": 21,
- "@": 22,
- "A": 23,
- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
- "O": 33,
- "P": 34,
- "R": 35,
- "S": 36,
- "T": 37,
- "Z": 38,
- "\\": 39,
- "a": 40,
- "b": 41,
- "c": 42,
- "e": 43,
- "g": 44,
- "h": 45,
- "i": 46,
- "l": 47,
- "n": 48,
- "r": 49,
- "s": 50,
- "Br": 51,
- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
- "S+1": 98,
- "Cl-1": 99,
- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
- "Se": 106,
- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
- "2H": 110,
- "P+1": 111,
- "K+1": 112,
- "\\C@@H1": 113,
- "\\C@H1": 114,
- "/N+1": 115,
- "@@": 116,
- "C-1": 117,
- "#N+1": 118,
- "B-1": 119,
- "+3": 120,
- "Cl+3": 121,
- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
- "P@": 134,
- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/bbbp/tokenizer_config.json b/models/finetuned/bbbp/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/bbbp/train_stdout.log b/models/finetuned/bbbp/train_stdout.log
deleted file mode 100644
index e6f1c4bb9d809523a6881395f093c8192e483169..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/train_stdout.log
+++ /dev/null
@@ -1,91 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=binary batch_size=32 max_len=128 backbone_lr=5e-05 head_lr=5e-05 weight_decay=0.01 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bbbp/bbbp.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/bbbp/bbbp_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=True seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-
- 0%| | 0/2039 [00:00, ?it/s]
- 21%|██ | 425/2039 [00:00<00:00, 4245.72it/s]
- 43%|████▎ | 885/2039 [00:00<00:00, 4448.82it/s]
- 67%|██████▋ | 1358/2039 [00:00<00:00, 4573.64it/s]
- 94%|█████████▍| 1923/2039 [00:00<00:00, 4995.19it/s]
-100%|██████████| 2039/2039 [00:00<00:00, 4863.36it/s]
-[finetune] split sizes: train=1,631 val=203 test=205
-[finetune] train modality_non_empty: graph=1,631/1,631 text=1,089/1,631 kg=48/1,631
-[finetune] val modality_non_empty: graph=203/203 text=151/203 kg=3/203
-[finetune] test modality_non_empty: graph=205/205 text=136/205 kg=4/205
-[finetune] extracting labels...
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=51 val_steps=7 test_steps=7
-[finetune] initialized head: in_dim=3072 out=2
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=0.4502 val_loss=0.3330 time=19.7s tod=11:10
-[finetune] epoch 2/50: train_loss=0.2497 val_loss=0.2723 time=19.6s tod=11:11
-[finetune] epoch 3/50: train_loss=0.1748 val_loss=0.3403 time=19.2s tod=11:11
-[finetune] epoch 4/50: train_loss=0.1205 val_loss=0.3844 time=19.3s tod=11:11
-[finetune] epoch 5/50: train_loss=0.0923 val_loss=0.4908 time=19.4s tod=11:12
-[finetune] epoch 6/50: train_loss=0.0617 val_loss=0.6117 time=19.3s tod=11:12
-[finetune] epoch 7/50: train_loss=0.0374 val_loss=0.5942 time=19.3s tod=11:12
-[finetune] epoch 8/50: train_loss=0.0312 val_loss=0.6833 time=19.4s tod=11:13
-[finetune] epoch 9/50: train_loss=0.0195 val_loss=0.7027 time=19.3s tod=11:13
-[finetune] epoch 10/50: train_loss=0.0168 val_loss=0.9035 time=19.5s tod=11:13
-[finetune] epoch 11/50: train_loss=0.0116 val_loss=0.6633 time=18.6s tod=11:14
-[finetune] epoch 12/50: train_loss=0.0120 val_loss=0.7813 time=19.4s tod=11:14
-[finetune] epoch 13/50: train_loss=0.0076 val_loss=0.7791 time=19.5s tod=11:14
-[finetune] epoch 14/50: train_loss=0.0072 val_loss=0.8010 time=19.4s tod=11:14
-[finetune] epoch 15/50: train_loss=0.0077 val_loss=0.9591 time=19.5s tod=11:15
-[finetune] epoch 16/50: train_loss=0.0062 val_loss=0.9107 time=19.4s tod=11:15
-[finetune] epoch 17/50: train_loss=0.0027 val_loss=0.9619 time=19.3s tod=11:15
-[finetune] epoch 18/50: train_loss=0.0032 val_loss=0.9483 time=19.7s tod=11:16
-[finetune] epoch 19/50: train_loss=0.0032 val_loss=0.9611 time=19.4s tod=11:16
-[finetune] epoch 20/50: train_loss=0.0025 val_loss=0.9530 time=19.3s tod=11:16
-[finetune] epoch 21/50: train_loss=0.0035 val_loss=0.9558 time=19.5s tod=11:17
-[finetune] epoch 22/50: train_loss=0.0024 val_loss=0.9389 time=19.4s tod=11:17
-[finetune] epoch 23/50: train_loss=0.0023 val_loss=0.9919 time=19.4s tod=11:17
-[finetune] epoch 24/50: train_loss=0.0021 val_loss=1.0150 time=19.6s tod=11:18
-[finetune] epoch 25/50: train_loss=0.0021 val_loss=1.0188 time=19.3s tod=11:18
-[finetune] test_metrics: epoch=25 loss=0.5357 accuracy=0.9073 precision=0.9595 recall=0.9161 f1=0.9373 roc-auc=0.8981 prc-auc=0.9695
-[finetune] saved checkpoint (best roc-auc=0.8981): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bbbp/9qb82eig/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=0.0017 val_loss=1.0293 time=19.4s tod=11:18
-[finetune] epoch 27/50: train_loss=0.0013 val_loss=1.0406 time=19.7s tod=11:19
-[finetune] epoch 28/50: train_loss=0.0017 val_loss=1.0474 time=19.3s tod=11:19
-[finetune] epoch 29/50: train_loss=0.0020 val_loss=1.0570 time=19.4s tod=11:19
-[finetune] epoch 30/50: train_loss=0.0015 val_loss=1.0563 time=19.6s tod=11:20
-[finetune] epoch 31/50: train_loss=0.0014 val_loss=1.0590 time=19.4s tod=11:20
-[finetune] epoch 32/50: train_loss=0.0010 val_loss=1.0643 time=19.2s tod=11:20
-[finetune] epoch 33/50: train_loss=0.0014 val_loss=1.0696 time=19.5s tod=11:21
-[finetune] epoch 34/50: train_loss=0.0012 val_loss=1.0717 time=19.4s tod=11:21
-[finetune] epoch 35/50: train_loss=0.0017 val_loss=1.0735 time=19.4s tod=11:21
-[finetune] epoch 36/50: train_loss=0.0013 val_loss=1.0781 time=19.6s tod=11:22
-[finetune] epoch 37/50: train_loss=0.0014 val_loss=1.0798 time=18.6s tod=11:22
-[finetune] epoch 38/50: train_loss=0.0009 val_loss=1.0833 time=19.5s tod=11:22
-[finetune] epoch 39/50: train_loss=0.0016 val_loss=1.0830 time=19.6s tod=11:23
-[finetune] epoch 40/50: train_loss=0.0012 val_loss=1.0843 time=19.3s tod=11:23
-[finetune] epoch 41/50: train_loss=0.0010 val_loss=1.0882 time=19.6s tod=11:23
-[finetune] epoch 42/50: train_loss=0.0011 val_loss=1.0891 time=19.3s tod=11:24
-[finetune] epoch 43/50: train_loss=0.0014 val_loss=1.0889 time=19.4s tod=11:24
-[finetune] epoch 44/50: train_loss=0.0010 val_loss=1.0939 time=19.4s tod=11:24
-[finetune] epoch 45/50: train_loss=0.0012 val_loss=1.0937 time=19.3s tod=11:25
-[finetune] epoch 46/50: train_loss=0.0010 val_loss=1.0971 time=19.5s tod=11:25
-[finetune] epoch 47/50: train_loss=0.0012 val_loss=1.0984 time=19.5s tod=11:25
-[finetune] epoch 48/50: train_loss=0.0012 val_loss=1.0978 time=19.3s tod=11:26
-[finetune] epoch 49/50: train_loss=0.0011 val_loss=1.0980 time=19.1s tod=11:26
-[finetune] epoch 50/50: train_loss=0.0010 val_loss=1.0982 time=13.3s tod=11:26
-[finetune] test_metrics: epoch=50 loss=0.5324 accuracy=0.9171 precision=0.9726 recall=0.9161 f1=0.9435 roc-auc=0.9181 prc-auc=0.9761
-[finetune] saved checkpoint (best roc-auc=0.9181): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bbbp/9qb82eig/checkpoint_epoch_050
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=0.5324 accuracy=0.9171 precision=0.9726 recall=0.9161 f1=0.9435 roc-auc=0.9181 prc-auc=0.9761
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/bbbp/9qb82eig
-[finetune] done in 976.9s
diff --git a/models/finetuned/bbbp/vocab.json b/models/finetuned/bbbp/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/bbbp/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/esol/checkpoint_epoch_025/config.json b/models/finetuned/esol/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/esol/checkpoint_epoch_025/merges.txt b/models/finetuned/esol/checkpoint_epoch_025/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_025/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
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- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
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- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
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- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/esol/checkpoint_epoch_025/vocab.json b/models/finetuned/esol/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
-{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427}
\ No newline at end of file
diff --git a/models/finetuned/esol/checkpoint_epoch_050/config.json b/models/finetuned/esol/checkpoint_epoch_050/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/esol/checkpoint_epoch_050/merges.txt b/models/finetuned/esol/checkpoint_epoch_050/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
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-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
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-/ O
-\ O
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-Branch 3
-\ S
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-Cl -1
-I -1
-/ C@@H1
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-\ C@@H1
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-@ @
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-B -1
-+ 3
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-\ NH1
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-1 8
-18 F
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-3 H
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-1 2
-P @
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-@@ +1
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-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
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-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
-/ C@
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-H 2
-H1 -1
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-N @@+1
-C +1
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-Z n
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-a +2
-/ I
-O H1-1
-C a+2
-\ Br
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-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
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-14C H3
-B H3-1
-S @
-=14C H1
-=P H1
-=P @
-=N H1+1
-\S +1
-12 4
-C H1-1
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-124 I
-Sr +2
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-/C -1
-N @
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-13C H1
-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/esol/checkpoint_epoch_050/model.pt b/models/finetuned/esol/checkpoint_epoch_050/model.pt
deleted file mode 100644
index c7053f6e4ecac583450341274eaa264133d4cdf2..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:1cea5584251eff6c83eecaee68088f28a1b3cc0048d8380c6ed78beafcb5d031
-size 1022843005
diff --git a/models/finetuned/esol/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/esol/checkpoint_epoch_050/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/esol/checkpoint_epoch_050/tokenizer.json b/models/finetuned/esol/checkpoint_epoch_050/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
- "": 2,
- "": 3,
- "": 4,
- "\n": 5,
- "#": 6,
- "+": 7,
- "-": 8,
- ".": 9,
- "/": 10,
- "0": 11,
- "1": 12,
- "2": 13,
- "3": 14,
- "4": 15,
- "5": 16,
- "6": 17,
- "7": 18,
- "8": 19,
- "9": 20,
- "=": 21,
- "@": 22,
- "A": 23,
- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
- "O": 33,
- "P": 34,
- "R": 35,
- "S": 36,
- "T": 37,
- "Z": 38,
- "\\": 39,
- "a": 40,
- "b": 41,
- "c": 42,
- "e": 43,
- "g": 44,
- "h": 45,
- "i": 46,
- "l": 47,
- "n": 48,
- "r": 49,
- "s": 50,
- "Br": 51,
- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
- "S+1": 98,
- "Cl-1": 99,
- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
- "Se": 106,
- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
- "2H": 110,
- "P+1": 111,
- "K+1": 112,
- "\\C@@H1": 113,
- "\\C@H1": 114,
- "/N+1": 115,
- "@@": 116,
- "C-1": 117,
- "#N+1": 118,
- "B-1": 119,
- "+3": 120,
- "Cl+3": 121,
- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
- "P@": 134,
- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
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- "\\ C@H1",
- "/ N+1",
- "@ @",
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- "# N+1",
- "B -1",
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- "\\ NH1",
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- "1 8",
- "18 F",
- "@ +1",
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- "=O +1",
- "N @@+1",
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- "=S +1",
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- "/ I",
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- "\\ Br",
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- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
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- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
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- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
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- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/esol/checkpoint_epoch_050/vocab.json b/models/finetuned/esol/checkpoint_epoch_050/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/checkpoint_epoch_050/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
-{"":0,"":1,"":2,"":3,"":4,"\n":5,"#":6,"+":7,"-":8,".":9,"/":10,"0":11,"1":12,"2":13,"3":14,"4":15,"5":16,"6":17,"7":18,"8":19,"9":20,"=":21,"@":22,"A":23,"B":24,"C":25,"F":26,"H":27,"I":28,"K":29,"L":30,"M":31,"N":32,"O":33,"P":34,"R":35,"S":36,"T":37,"Z":38,"\\":39,"a":40,"b":41,"c":42,"e":43,"g":44,"h":45,"i":46,"l":47,"n":48,"r":49,"s":50,"Br":51,"an":52,"ch":53,"Bran":54,"Branch":55,"Branch1":56,"=C":57,"Ri":58,"ng":59,"Ring":60,"Ring1":61,"=Branch1":62,"Branch2":63,"=O":64,"Ring2":65,"H1":66,"C@":67,"=N":68,"#Branch1":69,"C@@":70,"=Branch2":71,"C@H1":72,"C@@H1":73,"#Branch2":74,"#C":75,"Cl":76,"/C":77,"NH1":78,"=Ring1":79,"+1":80,"-1":81,"O-1":82,"N+1":83,"\\C":84,"#N":85,"/N":86,"=Ring2":87,"=S":88,"=N+1":89,"\\N":90,"Na":91,"Na+1":92,"/O":93,"\\O":94,"Br-1":95,"Branch3":96,"\\S":97,"S+1":98,"Cl-1":99,"I-1":100,"/C@@H1":101,"Si":102,"/C@H1":103,"/S":104,"=N-1":105,"Se":106,"=P":107,"N-1":108,"Ring3":109,"2H":110,"P+1":111,"K+1":112,"\\C@@H1":113,"\\C@H1":114,"/N+1":115,"@@":116,"C-1":117,"#N+1":118,"B-1":119,"+3":120,"Cl+3":121,"\\NH1":122,"Li":123,"Li+1":124,"PH1":125,"18":126,"18F":127,"@+1":128,"3H":129,"P@@":130,"H0":131,"OH0":132,"12":133,"P@":134,"+2":135,"@@+1":136,"S-1":137,"/Br":138,"-/":139,"\\Cl":140,"-/Ring2":141,"\\O-1":142,"11":143,"5I":144,"125I":145,"11C":146,"H3":147,"\\N+1":148,"-\\":149,"/C@@":150,"S@+1":151,"As":152,"/Cl":153,"11CH3":154,"=Se":155,"S@@+1":156,"N@+1":157,"14":158,"-\\Ring2":159,"14C":160,"\\F":161,"/C@":162,"Te":163,"H2":164,"H1-1":165,"=O+1":166,"N@@+1":167,"C+1":168,"=S+1":169,"Zn":170,"/P":171,"a+2":172,"/I":173,"OH1-1":174,"Ca+2":175,"\\Br":176,"Mg":177,"Zn+2":178,"Al":179,"/F":180,"Mg+2":181,"123":182,"123I":183,"13":184,"I+1":185,"/O-1":186,"-\\Ring1":187,"BH2":188,"BH2-1":189,"\\I":190,"/NH1":191,"O+1":192,"131":193,"131I":194,"=14C":195,"/S+1":196,"=Ring3":197,"\\C@@":198,"H2+1":199,"\\C@":200,"Ag":201,"=As":202,"=Se+1":203,"NH2+1":204,"SeH1":205,"-/Ring1":206,"=Te":207,"Al+3":208,"NaH1":209,"=Te+1":210,"NH1+1":211,"Ag+1":212,"H1+1":213,"NH1-1":214,"\\P":215,"14CH2":216,"13C":217,"14CH1":218,"=11C":219,"S@@":220,"=P@@":221,"SiH2":222,"H3-1":223,"14CH3":224,"BH3-1":225,"S@":226,"=14CH1":227,"=PH1":228,"=P@":229,"=NH1+1":230,"\\S+1":231,"124":232,"CH1-1":233,"Sr":234,"=Si":235,"124I":236,"Sr+2":237,"#C-1":238,"/C-1":239,"N@":240,"/N-1":241,"13CH1":242,"/B":243,"19":244,"Ba+2":245,"H4":246,"SH1+1":247,"Se+1":248,"19F":249,"/125I":250,"P@+1":251,"Rb":252,"Cl+1":253,"SiH4":254,"Rb+1":255,"=Branch3":256,"N@@":257,"As+1":258,"/Si":259,"BH1-1":260,"SH1":261,"/123I":262,"32":263,"=Mg":264,"H+1":265,"\\B":266,"SiH1":267,"P@@+1":268,"-2":269,"15":270,"17":271,"35":272,"=13CH1":273,"Cs":274,"=NH2+1":275,"=SH1":276,"MgH2":277,"32P":278,"17F":279,"35S":280,"Cs+1":281,"#11C":282,"/131I":283,"Bi":284,"\\125I":285,"=S@@":286,"\\S-1":287,"6Br":288,"7I":289,"76Br":290,"=B":291,"eH1":292,"\\N-1":293,"18O":294,"127I":295,"11CH2":296,"14C@@H1":297,"TeH2":298,"15NH1":299,"Bi+3":300,"/P+1":301,"/13C":302,"/13CH1":303,"0B":304,"10B":305,"=Al":306,"=18O":307,"BH0":308,"F-1":309,"NH3":310,"S-2":311,"Br+2":312,"Cl+2":313,"\\Si":314,"/S-1":315,"=PH2":316,"14C@H1":317,"NH3+1":318,"#14C":319,"#O+1":320,"-3":321,"22":322,"4H":323,"5Se":324,"5Sr+2":325,"75Se":326,"85Sr+2":327,"=B-1":328,"=13C":329,"@-1":330,"Be":331,"B@@":332,"B@-1":333,"Ca":334,"CH1":335,"I+3":336,"KH1":337,"OH1+1":338,"Ra+2":339,"SH1-1":340,"\\PH1":341,"\\123I":342,"=Ca":343,"\\CH1-1":344,"=S@":345,"\\SeH1":346,"/SeH1":347,"Se-1":348,"LiH1":349,"18F-1":350,"125IH1":351,"11CH1":352,"TeH1":353,"Zn+1":354,"Zn-2":355,"Al-3":356,"13CH3":357,"15N":358,"Be+2":359,"B@@-1":360,"#P":361,"#S":362,"-4":363,"/PH1":364,"/P@@":365,"/As":366,"/14C":367,"/14CH1":368,"2K+1":369,"2Rb+1":370,"3Se":371,"3Ra+2":372,"45":373,"47":374,"42K+1":375,"5I-1":376,"73Se":377,"89":378,"82Rb+1":379,"=32":380,"=32P":381,"CH0":382,"CH2":383,"I+2":384,"NH0":385,"NH4":386,"OH1":387,"PH2+1":388,"SH0":389,"SH2":390,"\\3H":391,"\\11CH3":392,"\\C-1":393,"\\Se":394,"Si@":395,"Si-1":396,"SiH1-1":397,"SiH3-1":398,"/Se":399,"Se-2":400,"\\NH1-1":401,"18FH1":402,"125I-1":403,"11C@@H1":404,"11C-1":405,"AsH1":406,"As-1":407,"14C@@":408,"Te-1":409,"Mg+1":410,"123I-1":411,"123Te":412,"123IH1":413,"135I":414,"131I-1":415,"Ag-4":416,"124I-1":417,"76BrH1":418,"18OH1":419,"22Na+1":420,"223Ra+2":421,"CaH2":422,"45Ca+2":423,"47Ca+2":424,"89Sr+2":425,"=32PH1":426,"NH4+1":427}
\ No newline at end of file
diff --git a/models/finetuned/esol/config.json b/models/finetuned/esol/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/esol/merges.txt b/models/finetuned/esol/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
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-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
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-= O
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-H 1
-C @
-= N
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-= Branch2
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-# Branch2
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-= Ring1
-+ 1
-- 1
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-N +1
-\ C
-# N
-/ N
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-\ N
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-\ O
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-I -1
-/ C@@H1
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-/ S
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-\ NH1
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-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
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-+ 2
-@@ +1
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-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
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-=S e
-S @@+1
-N @+1
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--\ Ring2
-14 C
-\ F
-/ C@
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-H 2
-H1 -1
-=O +1
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-/ P
-a +2
-/ I
-O H1-1
-C a+2
-\ Br
-M g
-Zn +2
-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
-H3 -1
-14C H3
-B H3-1
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-=14C H1
-=P H1
-=P @
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-\S +1
-12 4
-C H1-1
-S r
-=S i
-124 I
-Sr +2
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-/C -1
-N @
-/N -1
-13C H1
-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/esol/model.pt b/models/finetuned/esol/model.pt
deleted file mode 100644
index c7053f6e4ecac583450341274eaa264133d4cdf2..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:1cea5584251eff6c83eecaee68088f28a1b3cc0048d8380c6ed78beafcb5d031
-size 1022843005
diff --git a/models/finetuned/esol/special_tokens_map.json b/models/finetuned/esol/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
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- "normalized": true,
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- "single_word": false
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- "mask_token": {
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- "normalized": true,
- "rstrip": false,
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- "rstrip": false,
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- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/esol/tokenizer.json b/models/finetuned/esol/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
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- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
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- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
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- {
- "id": 2,
- "content": "",
- "single_word": false,
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- "normalized": true,
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- {
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- "normalizer": null,
- "pre_tokenizer": {
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- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
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- "trim_offsets": true,
- "add_prefix_space": false
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- "decoder": {
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- "add_prefix_space": true,
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- "model": {
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- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
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- "": 1,
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- "3": 14,
- "4": 15,
- "5": 16,
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- "8": 19,
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- "=": 21,
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- "A": 23,
- "B": 24,
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- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
- "O": 33,
- "P": 34,
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- "S": 36,
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- "e": 43,
- "g": 44,
- "h": 45,
- "i": 46,
- "l": 47,
- "n": 48,
- "r": 49,
- "s": 50,
- "Br": 51,
- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
- "S+1": 98,
- "Cl-1": 99,
- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
- "Se": 106,
- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
- "2H": 110,
- "P+1": 111,
- "K+1": 112,
- "\\C@@H1": 113,
- "\\C@H1": 114,
- "/N+1": 115,
- "@@": 116,
- "C-1": 117,
- "#N+1": 118,
- "B-1": 119,
- "+3": 120,
- "Cl+3": 121,
- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
- "P@": 134,
- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/esol/tokenizer_config.json b/models/finetuned/esol/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/esol/train_stdout.log b/models/finetuned/esol/train_stdout.log
deleted file mode 100644
index ad7f63f0bfb065ea4587adce57b9b88b02103e03..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/train_stdout.log
+++ /dev/null
@@ -1,84 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=regression batch_size=16 max_len=128 backbone_lr=1e-05 head_lr=0.0005 weight_decay=0.1 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/esol/esol.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/esol/esol_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-[finetune] split sizes: train=902 val=113 test=113
-[finetune] train modality_non_empty: graph=902/902 text=797/902 kg=31/902
-[finetune] val modality_non_empty: graph=113/113 text=101/113 kg=7/113
-[finetune] test modality_non_empty: graph=113/113 text=98/113 kg=2/113
-[finetune] extracting labels...
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=57 val_steps=8 test_steps=8
-[finetune] initialized head: in_dim=3072 out=1
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=2.1456 val_loss=0.7541 time=10.5s tod=23:34
-[finetune] epoch 2/50: train_loss=0.5921 val_loss=0.8212 time=10.6s tod=23:34
-[finetune] epoch 3/50: train_loss=0.4620 val_loss=1.0872 time=10.4s tod=23:34
-[finetune] epoch 4/50: train_loss=0.3742 val_loss=0.6175 time=10.6s tod=23:34
-[finetune] epoch 5/50: train_loss=0.3656 val_loss=0.5443 time=10.4s tod=23:34
-[finetune] epoch 6/50: train_loss=0.2373 val_loss=0.8940 time=10.4s tod=23:34
-[finetune] epoch 7/50: train_loss=0.2876 val_loss=0.7784 time=10.6s tod=23:35
-[finetune] epoch 8/50: train_loss=0.2574 val_loss=0.7644 time=10.4s tod=23:35
-[finetune] epoch 9/50: train_loss=0.1703 val_loss=0.5304 time=10.4s tod=23:35
-[finetune] epoch 10/50: train_loss=0.1926 val_loss=0.8380 time=10.4s tod=23:35
-[finetune] epoch 11/50: train_loss=0.1611 val_loss=0.5210 time=10.6s tod=23:35
-[finetune] epoch 12/50: train_loss=0.1468 val_loss=0.4703 time=10.3s tod=23:36
-[finetune] epoch 13/50: train_loss=0.1523 val_loss=0.5576 time=10.4s tod=23:36
-[finetune] epoch 14/50: train_loss=0.1304 val_loss=0.4909 time=10.6s tod=23:36
-[finetune] epoch 15/50: train_loss=0.1077 val_loss=0.5125 time=10.6s tod=23:36
-[finetune] epoch 16/50: train_loss=0.1145 val_loss=0.4894 time=10.3s tod=23:36
-[finetune] epoch 17/50: train_loss=0.1228 val_loss=0.4724 time=10.4s tod=23:36
-[finetune] epoch 18/50: train_loss=0.0919 val_loss=0.5175 time=10.6s tod=23:37
-[finetune] epoch 19/50: train_loss=0.0883 val_loss=0.4762 time=10.4s tod=23:37
-[finetune] epoch 20/50: train_loss=0.0836 val_loss=0.5046 time=8.3s tod=23:37
-[finetune] epoch 21/50: train_loss=0.0758 val_loss=0.5696 time=5.3s tod=23:37
-[finetune] epoch 22/50: train_loss=0.0667 val_loss=0.4784 time=5.3s tod=23:37
-[finetune] epoch 23/50: train_loss=0.0678 val_loss=0.4916 time=5.2s tod=23:37
-[finetune] epoch 24/50: train_loss=0.0691 val_loss=0.5081 time=5.3s tod=23:37
-[finetune] epoch 25/50: train_loss=0.0691 val_loss=0.5231 time=5.3s tod=23:37
-[finetune] test_metrics: epoch=25 loss=0.3905 mse=0.4388 rmse=0.6624 mae=0.4929
-[finetune] saved checkpoint (best rmse=0.6624): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/esol/a0w73dq7/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=0.0674 val_loss=0.4815 time=8.0s tod=23:37
-[finetune] epoch 27/50: train_loss=0.0489 val_loss=0.5125 time=10.4s tod=23:38
-[finetune] epoch 28/50: train_loss=0.0520 val_loss=0.4919 time=10.4s tod=23:38
-[finetune] epoch 29/50: train_loss=0.0428 val_loss=0.5000 time=10.6s tod=23:38
-[finetune] epoch 30/50: train_loss=0.0476 val_loss=0.5481 time=10.4s tod=23:38
-[finetune] epoch 31/50: train_loss=0.0437 val_loss=0.5889 time=10.4s tod=23:38
-[finetune] epoch 32/50: train_loss=0.0469 val_loss=0.5447 time=10.6s tod=23:39
-[finetune] epoch 33/50: train_loss=0.0351 val_loss=0.4789 time=10.3s tod=23:39
-[finetune] epoch 34/50: train_loss=0.0427 val_loss=0.4710 time=10.4s tod=23:39
-[finetune] epoch 35/50: train_loss=0.0325 val_loss=0.4598 time=10.6s tod=23:39
-[finetune] epoch 36/50: train_loss=0.0285 val_loss=0.5224 time=10.4s tod=23:39
-[finetune] epoch 37/50: train_loss=0.0315 val_loss=0.4766 time=10.3s tod=23:39
-[finetune] epoch 38/50: train_loss=0.0259 val_loss=0.4907 time=10.4s tod=23:40
-[finetune] epoch 39/50: train_loss=0.0274 val_loss=0.4913 time=10.4s tod=23:40
-[finetune] epoch 40/50: train_loss=0.0245 val_loss=0.4672 time=10.6s tod=23:40
-[finetune] epoch 41/50: train_loss=0.0238 val_loss=0.4869 time=10.4s tod=23:40
-[finetune] epoch 42/50: train_loss=0.0229 val_loss=0.4674 time=10.4s tod=23:40
-[finetune] epoch 43/50: train_loss=0.0204 val_loss=0.5000 time=10.6s tod=23:40
-[finetune] epoch 44/50: train_loss=0.0198 val_loss=0.4839 time=10.2s tod=23:41
-[finetune] epoch 45/50: train_loss=0.0180 val_loss=0.4792 time=10.5s tod=23:41
-[finetune] epoch 46/50: train_loss=0.0175 val_loss=0.4750 time=10.6s tod=23:41
-[finetune] epoch 47/50: train_loss=0.0169 val_loss=0.4856 time=10.4s tod=23:41
-[finetune] epoch 48/50: train_loss=0.0140 val_loss=0.4864 time=10.4s tod=23:41
-[finetune] epoch 49/50: train_loss=0.0142 val_loss=0.4835 time=10.6s tod=23:42
-[finetune] epoch 50/50: train_loss=0.0130 val_loss=0.4823 time=10.4s tod=23:42
-[finetune] test_metrics: epoch=50 loss=0.3251 mse=0.3635 rmse=0.6029 mae=0.4456
-[finetune] saved checkpoint (best rmse=0.6029): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/esol/a0w73dq7/checkpoint_epoch_050
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=0.3251 mse=0.3635 rmse=0.6029 mae=0.4456
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/esol/a0w73dq7
-[finetune] done in 503.2s
diff --git a/models/finetuned/esol/vocab.json b/models/finetuned/esol/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/esol/vocab.json
+++ /dev/null
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diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/config.json b/models/finetuned/freesolv/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt b/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
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-- 1
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--\ Ring1
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-\ I
-/ NH1
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-= 14C
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-P@@ +1
-- 2
-1 5
-1 7
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-=S H1
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-32 P
-17 F
-35 S
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-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
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-7 6Br
-= B
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-\N -1
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-- 3
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-7 5Se
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-- 4
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-3 Ra+2
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-4 2K+1
-5 I-1
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-8 2Rb+1
-= 32
-= 32P
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-P H2+1
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-\ 3H
-\ 11CH3
-\C -1
-\S e
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-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
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-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/model.pt b/models/finetuned/freesolv/checkpoint_epoch_025/model.pt
deleted file mode 100644
index b4c39ddfaaef7a18c0375b2bd5a792d5f81f38e7..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer.json b/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
- "": 2,
- "": 3,
- "": 4,
- "\n": 5,
- "#": 6,
- "+": 7,
- "-": 8,
- ".": 9,
- "/": 10,
- "0": 11,
- "1": 12,
- "2": 13,
- "3": 14,
- "4": 15,
- "5": 16,
- "6": 17,
- "7": 18,
- "8": 19,
- "9": 20,
- "=": 21,
- "@": 22,
- "A": 23,
- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
- "O": 33,
- "P": 34,
- "R": 35,
- "S": 36,
- "T": 37,
- "Z": 38,
- "\\": 39,
- "a": 40,
- "b": 41,
- "c": 42,
- "e": 43,
- "g": 44,
- "h": 45,
- "i": 46,
- "l": 47,
- "n": 48,
- "r": 49,
- "s": 50,
- "Br": 51,
- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
- "S+1": 98,
- "Cl-1": 99,
- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
- "Se": 106,
- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
- "2H": 110,
- "P+1": 111,
- "K+1": 112,
- "\\C@@H1": 113,
- "\\C@H1": 114,
- "/N+1": 115,
- "@@": 116,
- "C-1": 117,
- "#N+1": 118,
- "B-1": 119,
- "+3": 120,
- "Cl+3": 121,
- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
- "P@": 134,
- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
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-{
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- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/freesolv/checkpoint_epoch_025/vocab.json b/models/finetuned/freesolv/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/config.json b/models/finetuned/freesolv/checkpoint_epoch_050/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
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- ],
- "attention_probs_dropout_prob": 0.1,
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- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/merges.txt b/models/finetuned/freesolv/checkpoint_epoch_050/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
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-\ I
-/ NH1
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-- 2
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-= 13CH1
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-Mg H2
-32 P
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-35 S
-Cs +1
-# 11C
-/ 131I
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-\S -1
-6 Br
-7 I
-7 6Br
-= B
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-14 C@H1
-NH3 +1
-# 14C
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-- 3
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-4 H
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-= B-1
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-I +3
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-- 4
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-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
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-Si -1
-Si H1-1
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-/S e
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-\NH1 -1
-18F H1
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-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
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diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/model.pt b/models/finetuned/freesolv/checkpoint_epoch_050/model.pt
deleted file mode 100644
index b4db7d8c07d36db777c87860a91fdcbce7b97039..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/model.pt
+++ /dev/null
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diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
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- "cls_token": {
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diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer.json b/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
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- "truncation": {
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- "strategy": "LongestFirst",
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- },
- "padding": {
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- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
- "S+1": 98,
- "Cl-1": 99,
- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
- "Se": 106,
- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
- "2H": 110,
- "P+1": 111,
- "K+1": 112,
- "\\C@@H1": 113,
- "\\C@H1": 114,
- "/N+1": 115,
- "@@": 116,
- "C-1": 117,
- "#N+1": 118,
- "B-1": 119,
- "+3": 120,
- "Cl+3": 121,
- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
- "P@": 134,
- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/freesolv/checkpoint_epoch_050/vocab.json b/models/finetuned/freesolv/checkpoint_epoch_050/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/checkpoint_epoch_050/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/models/finetuned/freesolv/config.json b/models/finetuned/freesolv/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/freesolv/merges.txt b/models/finetuned/freesolv/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
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-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
-Br -1
-Branch 3
-\ S
-S +1
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-I -1
-/ C@@H1
-S i
-/ C@H1
-/ S
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-P +1
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-\ C@H1
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-C -1
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-\ NH1
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-Li +1
-P H1
-1 8
-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
-1 2
-P @
-+ 2
-@@ +1
-S -1
-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
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-=O +1
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-a +2
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-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
-H3 -1
-14C H3
-B H3-1
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-\S +1
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-/C -1
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-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/freesolv/model.pt b/models/finetuned/freesolv/model.pt
deleted file mode 100644
index b4db7d8c07d36db777c87860a91fdcbce7b97039..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:18d826a9910632f53115fa941647098fcfed72830b225c3d73c45a123e154d64
-size 1022843005
diff --git a/models/finetuned/freesolv/special_tokens_map.json b/models/finetuned/freesolv/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/freesolv/tokenizer.json b/models/finetuned/freesolv/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
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- "": 3,
- "": 4,
- "\n": 5,
- "#": 6,
- "+": 7,
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- "=": 21,
- "@": 22,
- "A": 23,
- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
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- "R": 35,
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- "c": 42,
- "e": 43,
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- "i": 46,
- "l": 47,
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- "s": 50,
- "Br": 51,
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- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
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- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
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- "Ring2": 65,
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- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
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- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
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- "\\C": 84,
- "#N": 85,
- "/N": 86,
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- "/C@@H1": 101,
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- "18": 126,
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- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
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- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
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- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
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- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
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- "Sr": 234,
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- "#C-1": 238,
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- "/N-1": 241,
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- "/B": 243,
- "19": 244,
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- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
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- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
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- "17F": 279,
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- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
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- "6Br": 288,
- "7I": 289,
- "76Br": 290,
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- "eH1": 292,
- "\\N-1": 293,
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- "127I": 295,
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- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
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- "=Al": 306,
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- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
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- "NH3+1": 318,
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- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
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- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
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- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
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- "# C",
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- "N H1",
- "= Ring1",
- "+ 1",
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- "N +1",
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- "# N",
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- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/freesolv/tokenizer_config.json b/models/finetuned/freesolv/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/freesolv/train_stdout.log b/models/finetuned/freesolv/train_stdout.log
deleted file mode 100644
index 183a4d5663bbb05b5adfeb7778283af490685b3b..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/train_stdout.log
+++ /dev/null
@@ -1,84 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=regression batch_size=8 max_len=128 backbone_lr=5e-05 head_lr=0.0005 weight_decay=0.01 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/freesolv/freesolv.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/freesolv/freesolv_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-[finetune] split sizes: train=513 val=64 test=65
-[finetune] train modality_non_empty: graph=513/513 text=470/513 kg=25/513
-[finetune] val modality_non_empty: graph=64/64 text=57/64 kg=6/64
-[finetune] test modality_non_empty: graph=65/65 text=61/65 kg=0/65
-[finetune] extracting labels...
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=65 val_steps=8 test_steps=9
-[finetune] initialized head: in_dim=3072 out=1
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=8.8327 val_loss=8.6622 time=13.2s tod=16:56
-[finetune] epoch 2/50: train_loss=4.4709 val_loss=8.2606 time=12.7s tod=16:56
-[finetune] epoch 3/50: train_loss=3.8963 val_loss=4.6549 time=12.9s tod=16:56
-[finetune] epoch 4/50: train_loss=2.0273 val_loss=3.4323 time=12.2s tod=16:56
-[finetune] epoch 5/50: train_loss=1.5289 val_loss=2.8464 time=12.8s tod=16:56
-[finetune] epoch 6/50: train_loss=1.3175 val_loss=2.9690 time=12.8s tod=16:57
-[finetune] epoch 7/50: train_loss=1.2857 val_loss=2.2687 time=12.7s tod=16:57
-[finetune] epoch 8/50: train_loss=1.2503 val_loss=3.5530 time=12.8s tod=16:57
-[finetune] epoch 9/50: train_loss=1.2438 val_loss=1.9285 time=12.8s tod=16:57
-[finetune] epoch 10/50: train_loss=0.9841 val_loss=1.9874 time=12.3s tod=16:57
-[finetune] epoch 11/50: train_loss=0.9595 val_loss=2.1377 time=12.7s tod=16:58
-[finetune] epoch 12/50: train_loss=0.7905 val_loss=1.8522 time=12.8s tod=16:58
-[finetune] epoch 13/50: train_loss=0.6547 val_loss=2.2271 time=12.8s tod=16:58
-[finetune] epoch 14/50: train_loss=0.6922 val_loss=1.9394 time=12.7s tod=16:58
-[finetune] epoch 15/50: train_loss=0.5703 val_loss=2.7039 time=12.9s tod=16:58
-[finetune] epoch 16/50: train_loss=0.6377 val_loss=1.4721 time=12.7s tod=16:59
-[finetune] epoch 17/50: train_loss=0.5650 val_loss=2.9902 time=12.3s tod=16:59
-[finetune] epoch 18/50: train_loss=0.4907 val_loss=2.0984 time=12.8s tod=16:59
-[finetune] epoch 19/50: train_loss=0.4697 val_loss=2.9616 time=12.8s tod=16:59
-[finetune] epoch 20/50: train_loss=0.4219 val_loss=1.2584 time=12.6s tod=17:00
-[finetune] epoch 21/50: train_loss=0.4772 val_loss=1.4099 time=12.8s tod=17:00
-[finetune] epoch 22/50: train_loss=0.3259 val_loss=1.9489 time=12.8s tod=17:00
-[finetune] epoch 23/50: train_loss=0.3399 val_loss=1.6618 time=11.3s tod=17:00
-[finetune] epoch 24/50: train_loss=0.3765 val_loss=1.7658 time=8.7s tod=17:00
-[finetune] epoch 25/50: train_loss=0.3145 val_loss=2.0268 time=8.6s tod=17:00
-[finetune] test_metrics: epoch=25 loss=1.4893 mse=1.6323 rmse=1.2776 mae=0.9874
-[finetune] saved checkpoint (best rmse=1.2776): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/freesolv/4zs7c1p0/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=0.3076 val_loss=1.5888 time=8.5s tod=17:01
-[finetune] epoch 27/50: train_loss=0.2732 val_loss=1.6552 time=10.7s tod=17:01
-[finetune] epoch 28/50: train_loss=0.2281 val_loss=1.2463 time=12.9s tod=17:01
-[finetune] epoch 29/50: train_loss=0.3385 val_loss=1.6431 time=12.3s tod=17:01
-[finetune] epoch 30/50: train_loss=0.2315 val_loss=1.0546 time=12.6s tod=17:01
-[finetune] epoch 31/50: train_loss=0.2672 val_loss=1.4163 time=12.8s tod=17:02
-[finetune] epoch 32/50: train_loss=0.1979 val_loss=1.1115 time=12.8s tod=17:02
-[finetune] epoch 33/50: train_loss=0.2258 val_loss=1.6268 time=12.8s tod=17:02
-[finetune] epoch 34/50: train_loss=0.1904 val_loss=1.4480 time=12.7s tod=17:02
-[finetune] epoch 35/50: train_loss=0.1873 val_loss=1.2501 time=12.9s tod=17:02
-[finetune] epoch 36/50: train_loss=0.1512 val_loss=1.5128 time=12.2s tod=17:03
-[finetune] epoch 37/50: train_loss=0.1381 val_loss=1.2301 time=12.8s tod=17:03
-[finetune] epoch 38/50: train_loss=0.1482 val_loss=1.5650 time=12.9s tod=17:03
-[finetune] epoch 39/50: train_loss=0.1227 val_loss=1.4072 time=12.7s tod=17:03
-[finetune] epoch 40/50: train_loss=0.1140 val_loss=1.1888 time=12.9s tod=17:04
-[finetune] epoch 41/50: train_loss=0.1237 val_loss=1.2910 time=12.7s tod=17:04
-[finetune] epoch 42/50: train_loss=0.1119 val_loss=1.5262 time=12.5s tod=17:04
-[finetune] epoch 43/50: train_loss=0.1147 val_loss=1.2782 time=12.6s tod=17:04
-[finetune] epoch 44/50: train_loss=0.0989 val_loss=1.2923 time=12.7s tod=17:04
-[finetune] epoch 45/50: train_loss=0.0900 val_loss=1.3757 time=12.8s tod=17:05
-[finetune] epoch 46/50: train_loss=0.0889 val_loss=1.4483 time=12.8s tod=17:05
-[finetune] epoch 47/50: train_loss=0.0858 val_loss=1.3142 time=12.8s tod=17:05
-[finetune] epoch 48/50: train_loss=0.0912 val_loss=1.3258 time=12.7s tod=17:05
-[finetune] epoch 49/50: train_loss=0.0762 val_loss=1.3466 time=12.4s tod=17:05
-[finetune] epoch 50/50: train_loss=0.0681 val_loss=1.3496 time=12.7s tod=17:06
-[finetune] test_metrics: epoch=50 loss=0.7098 mse=0.7796 rmse=0.8829 mae=0.6312
-[finetune] saved checkpoint (best rmse=0.8829): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/freesolv/4zs7c1p0/checkpoint_epoch_050
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=0.7098 mse=0.7796 rmse=0.8829 mae=0.6312
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/freesolv/4zs7c1p0
-[finetune] done in 630.4s
diff --git a/models/finetuned/freesolv/vocab.json b/models/finetuned/freesolv/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/freesolv/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/hiv/config.json b/models/finetuned/hiv/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/hiv/merges.txt b/models/finetuned/hiv/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
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-- 1
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-- 2
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-= 13CH1
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-\ 11CH3
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-22 3Ra+2
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-NH4 +1
diff --git a/models/finetuned/hiv/model.pt b/models/finetuned/hiv/model.pt
deleted file mode 100644
index 87b0c30b31733df3b61cb311842030ca0b163d51..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e256d9c1f34dc1d3521586b383cb58b01238a2d5229e4383cb7a0cae792fb7a8
-size 1022855293
diff --git a/models/finetuned/hiv/special_tokens_map.json b/models/finetuned/hiv/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
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- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/hiv/tokenizer.json b/models/finetuned/hiv/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
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- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
- "": 2,
- "": 3,
- "": 4,
- "\n": 5,
- "#": 6,
- "+": 7,
- "-": 8,
- ".": 9,
- "/": 10,
- "0": 11,
- "1": 12,
- "2": 13,
- "3": 14,
- "4": 15,
- "5": 16,
- "6": 17,
- "7": 18,
- "8": 19,
- "9": 20,
- "=": 21,
- "@": 22,
- "A": 23,
- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
- "O": 33,
- "P": 34,
- "R": 35,
- "S": 36,
- "T": 37,
- "Z": 38,
- "\\": 39,
- "a": 40,
- "b": 41,
- "c": 42,
- "e": 43,
- "g": 44,
- "h": 45,
- "i": 46,
- "l": 47,
- "n": 48,
- "r": 49,
- "s": 50,
- "Br": 51,
- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
- "S+1": 98,
- "Cl-1": 99,
- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
- "Se": 106,
- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
- "2H": 110,
- "P+1": 111,
- "K+1": 112,
- "\\C@@H1": 113,
- "\\C@H1": 114,
- "/N+1": 115,
- "@@": 116,
- "C-1": 117,
- "#N+1": 118,
- "B-1": 119,
- "+3": 120,
- "Cl+3": 121,
- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
- "P@": 134,
- "+2": 135,
- "@@+1": 136,
- "S-1": 137,
- "/Br": 138,
- "-/": 139,
- "\\Cl": 140,
- "-/Ring2": 141,
- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
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- "=13C": 329,
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- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
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- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
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- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/hiv/tokenizer_config.json b/models/finetuned/hiv/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/hiv/vocab.json b/models/finetuned/hiv/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/hiv/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/lipo/checkpoint_epoch_025/config.json b/models/finetuned/lipo/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
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- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/lipo/checkpoint_epoch_025/merges.txt b/models/finetuned/lipo/checkpoint_epoch_025/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
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-22 3Ra+2
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diff --git a/models/finetuned/lipo/checkpoint_epoch_025/model.pt b/models/finetuned/lipo/checkpoint_epoch_025/model.pt
deleted file mode 100644
index c85c57aae30f87c843bb1e23ab33d810869532ac..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:33b8625d3f581bd33d28f8191db5208a9932ce7f7a11403cdd343b409fe36e2f
-size 1022843005
diff --git a/models/finetuned/lipo/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/lipo/checkpoint_epoch_025/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
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- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
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- "lstrip": false,
- "normalized": true,
- "rstrip": false,
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- },
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- "rstrip": false,
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- "rstrip": false,
- "single_word": false
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- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer.json b/models/finetuned/lipo/checkpoint_epoch_025/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
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- },
- "direction": "Right",
- "pad_to_multiple_of": null,
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- "pad_token": ""
- },
- "added_tokens": [
- {
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- "content": "",
- "single_word": false,
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- "rstrip": false,
- "normalized": true,
- "special": true
- },
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- "normalized": true,
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- "use_regex": true
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- "post_processor": {
- "type": "RobertaProcessing",
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- "",
- 2
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- "cls": [
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- "model": {
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- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/lipo/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/lipo/checkpoint_epoch_025/vocab.json b/models/finetuned/lipo/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/lipo/checkpoint_epoch_050/config.json b/models/finetuned/lipo/checkpoint_epoch_050/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/lipo/checkpoint_epoch_050/merges.txt b/models/finetuned/lipo/checkpoint_epoch_050/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
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-- 1
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-- \
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-\ I
-/ NH1
-O +1
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-Si -1
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-Si H3-1
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-\NH1 -1
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-22 Na+1
-22 3Ra+2
-Ca H2
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-=32 PH1
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diff --git a/models/finetuned/lipo/checkpoint_epoch_050/model.pt b/models/finetuned/lipo/checkpoint_epoch_050/model.pt
deleted file mode 100644
index a9132c4814a1423d6bba1195c3634687d83d02cc..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:33bbc6c2499b3aeafd1c0daf364fb68847ff9a7fed370354ca735a2bac4574ff
-size 1022843005
diff --git a/models/finetuned/lipo/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/lipo/checkpoint_epoch_050/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
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- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
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- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
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- "normalized": true,
- "rstrip": false,
- "single_word": false
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- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer.json b/models/finetuned/lipo/checkpoint_epoch_050/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
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- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
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- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
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- "single_word": false,
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- "rstrip": false,
- "normalized": true,
- "special": true
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- {
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- "content": "",
- "single_word": false,
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- "special": true
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- "id": 4,
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- "normalized": true,
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- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
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- "trim_offsets": true,
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- "use_regex": true
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- "model": {
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- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/lipo/checkpoint_epoch_050/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/lipo/checkpoint_epoch_050/vocab.json b/models/finetuned/lipo/checkpoint_epoch_050/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/checkpoint_epoch_050/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/models/finetuned/lipo/config.json b/models/finetuned/lipo/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/lipo/merges.txt b/models/finetuned/lipo/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
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-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
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-S +1
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-I -1
-/ C@@H1
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-/ S
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-\ C@H1
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-\ NH1
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-Li +1
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-@ +1
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-P @@
-H 0
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-+ 2
-@@ +1
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-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
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-H 2
-H1 -1
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-/ F
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-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
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-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
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-Sr +2
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-/ B
-1 9
-B a+2
-H 4
-S H1+1
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-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
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-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/lipo/model.pt b/models/finetuned/lipo/model.pt
deleted file mode 100644
index a9132c4814a1423d6bba1195c3634687d83d02cc..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:33bbc6c2499b3aeafd1c0daf364fb68847ff9a7fed370354ca735a2bac4574ff
-size 1022843005
diff --git a/models/finetuned/lipo/special_tokens_map.json b/models/finetuned/lipo/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/lipo/tokenizer.json b/models/finetuned/lipo/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
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- "": 3,
- "": 4,
- "\n": 5,
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- "=": 21,
- "@": 22,
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- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
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- "\\": 39,
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- "s": 50,
- "Br": 51,
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- "ch": 53,
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- "=C": 57,
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- "Ring": 60,
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- "=O": 64,
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- "#Branch1": 69,
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- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
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- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
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- "Al": 179,
- "/F": 180,
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- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
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- "\\I": 190,
- "/NH1": 191,
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- "131": 193,
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- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
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- "\\P": 215,
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- "H3-1": 223,
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- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
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- "N@@": 257,
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- "/Si": 259,
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- "/13C": 302,
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- "BH0": 308,
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- "85Sr+2": 327,
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- "B@-1": 333,
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- "Ra+2": 339,
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- "Se-1": 348,
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- "18F-1": 350,
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- "Zn+1": 354,
- "Zn-2": 355,
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- "13CH3": 357,
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- "#P": 361,
- "#S": 362,
- "-4": 363,
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- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
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- "= Branch1",
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- "= O",
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- "H 1",
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- "I -1",
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- "S e",
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- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
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- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
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- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
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- "- \\",
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- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
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- "N @+1",
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- "14 C",
- "\\ F",
- "/ C@",
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- "C +1",
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- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
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- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
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- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
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- "\\ C@",
- "A g",
- "= As",
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- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
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- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
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- "18F -1",
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- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/lipo/tokenizer_config.json b/models/finetuned/lipo/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/lipo/train_stdout.log b/models/finetuned/lipo/train_stdout.log
deleted file mode 100644
index acd2e33136a7ff829af04264977e9249e5aaad87..0000000000000000000000000000000000000000
--- a/models/finetuned/lipo/train_stdout.log
+++ /dev/null
@@ -1,84 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=regression batch_size=32 max_len=128 backbone_lr=5e-05 head_lr=0.0005 weight_decay=0.1 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/lipo/lipo.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/lipo/lipo_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-[finetune] split sizes: train=3,360 val=420 test=420
-[finetune] train modality_non_empty: graph=3,360/3,360 text=1,092/3,360 kg=815/3,360
-[finetune] val modality_non_empty: graph=420/420 text=126/420 kg=99/420
-[finetune] test modality_non_empty: graph=420/420 text=134/420 kg=96/420
-[finetune] extracting labels...
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=105 val_steps=14 test_steps=14
-[finetune] initialized head: in_dim=3072 out=1
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=1.0260 val_loss=0.5933 time=37.0s tod=01:20
-[finetune] epoch 2/50: train_loss=0.4242 val_loss=0.5410 time=34.5s tod=01:20
-[finetune] epoch 3/50: train_loss=0.2867 val_loss=0.4757 time=42.7s tod=01:21
-[finetune] epoch 4/50: train_loss=0.2087 val_loss=0.4417 time=41.9s tod=01:22
-[finetune] epoch 5/50: train_loss=0.1613 val_loss=0.4787 time=43.0s tod=01:22
-[finetune] epoch 6/50: train_loss=0.1394 val_loss=0.3972 time=43.0s tod=01:23
-[finetune] epoch 7/50: train_loss=0.1148 val_loss=0.4614 time=42.9s tod=01:24
-[finetune] epoch 8/50: train_loss=0.1038 val_loss=0.4147 time=42.9s tod=01:24
-[finetune] epoch 9/50: train_loss=0.0841 val_loss=0.4036 time=43.1s tod=01:25
-[finetune] epoch 10/50: train_loss=0.0834 val_loss=0.4152 time=42.8s tod=01:26
-[finetune] epoch 11/50: train_loss=0.0781 val_loss=0.4173 time=43.1s tod=01:27
-[finetune] epoch 12/50: train_loss=0.0680 val_loss=0.4063 time=42.2s tod=01:27
-[finetune] epoch 13/50: train_loss=0.0608 val_loss=0.3898 time=42.9s tod=01:28
-[finetune] epoch 14/50: train_loss=0.0573 val_loss=0.3987 time=42.9s tod=01:29
-[finetune] epoch 15/50: train_loss=0.0568 val_loss=0.4186 time=43.0s tod=01:29
-[finetune] epoch 16/50: train_loss=0.0498 val_loss=0.4147 time=43.1s tod=01:30
-[finetune] epoch 17/50: train_loss=0.0471 val_loss=0.4005 time=43.0s tod=01:31
-[finetune] epoch 18/50: train_loss=0.0452 val_loss=0.4167 time=42.8s tod=01:32
-[finetune] epoch 19/50: train_loss=0.0440 val_loss=0.4071 time=42.9s tod=01:32
-[finetune] epoch 20/50: train_loss=0.0386 val_loss=0.4185 time=43.1s tod=01:33
-[finetune] epoch 21/50: train_loss=0.0373 val_loss=0.4106 time=36.2s tod=01:34
-[finetune] epoch 22/50: train_loss=0.0348 val_loss=0.4107 time=34.1s tod=01:34
-[finetune] epoch 23/50: train_loss=0.0337 val_loss=0.3840 time=42.9s tod=01:35
-[finetune] epoch 24/50: train_loss=0.0340 val_loss=0.3960 time=42.8s tod=01:36
-[finetune] epoch 25/50: train_loss=0.0304 val_loss=0.3962 time=42.8s tod=01:36
-[finetune] test_metrics: epoch=25 loss=0.3360 mse=0.3397 rmse=0.5828 mae=0.4434
-[finetune] saved checkpoint (best rmse=0.5828): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/lipo/ejiyn98r/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=0.0285 val_loss=0.3949 time=42.7s tod=01:37
-[finetune] epoch 27/50: train_loss=0.0268 val_loss=0.4015 time=43.0s tod=01:38
-[finetune] epoch 28/50: train_loss=0.0247 val_loss=0.3962 time=42.7s tod=01:39
-[finetune] epoch 29/50: train_loss=0.0252 val_loss=0.4017 time=42.8s tod=01:39
-[finetune] epoch 30/50: train_loss=0.0270 val_loss=0.3894 time=42.9s tod=01:40
-[finetune] epoch 31/50: train_loss=0.0240 val_loss=0.3859 time=42.0s tod=01:41
-[finetune] epoch 32/50: train_loss=0.0222 val_loss=0.3969 time=42.8s tod=01:41
-[finetune] epoch 33/50: train_loss=0.0228 val_loss=0.3901 time=42.8s tod=01:42
-[finetune] epoch 34/50: train_loss=0.0218 val_loss=0.3887 time=42.8s tod=01:43
-[finetune] epoch 35/50: train_loss=0.0197 val_loss=0.3904 time=42.9s tod=01:44
-[finetune] epoch 36/50: train_loss=0.0197 val_loss=0.4033 time=42.8s tod=01:44
-[finetune] epoch 37/50: train_loss=0.0179 val_loss=0.4006 time=43.0s tod=01:45
-[finetune] epoch 38/50: train_loss=0.0180 val_loss=0.4014 time=42.8s tod=01:46
-[finetune] epoch 39/50: train_loss=0.0173 val_loss=0.3929 time=38.0s tod=01:46
-[finetune] epoch 40/50: train_loss=0.0156 val_loss=0.3943 time=32.6s tod=01:47
-[finetune] epoch 41/50: train_loss=0.0156 val_loss=0.3950 time=35.6s tod=01:47
-[finetune] epoch 42/50: train_loss=0.0150 val_loss=0.3858 time=37.5s tod=01:48
-[finetune] epoch 43/50: train_loss=0.0142 val_loss=0.3958 time=44.4s tod=01:49
-[finetune] epoch 44/50: train_loss=0.0142 val_loss=0.3989 time=44.4s tod=01:50
-[finetune] epoch 45/50: train_loss=0.0136 val_loss=0.3931 time=44.3s tod=01:50
-[finetune] epoch 46/50: train_loss=0.0129 val_loss=0.3934 time=44.4s tod=01:51
-[finetune] epoch 47/50: train_loss=0.0132 val_loss=0.3925 time=44.4s tod=01:52
-[finetune] epoch 48/50: train_loss=0.0127 val_loss=0.3911 time=44.2s tod=01:53
-[finetune] epoch 49/50: train_loss=0.0121 val_loss=0.3897 time=44.4s tod=01:53
-[finetune] epoch 50/50: train_loss=0.0120 val_loss=0.3900 time=44.5s tod=01:54
-[finetune] test_metrics: epoch=50 loss=0.3241 mse=0.3293 rmse=0.5739 mae=0.4349
-[finetune] saved checkpoint (best rmse=0.5739): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/lipo/ejiyn98r/checkpoint_epoch_050
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=0.3241 mse=0.3293 rmse=0.5739 mae=0.4349
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/lipo/ejiyn98r
-[finetune] done in 2114.9s
diff --git a/models/finetuned/lipo/vocab.json b/models/finetuned/lipo/vocab.json
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--- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
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+++ /dev/null
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diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt b/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt
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--- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/model.pt
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--- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/special_tokens_map.json
+++ /dev/null
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-{
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diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer.json
deleted file mode 100644
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--- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer.json
+++ /dev/null
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-{
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- 1
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- "": 1,
- "": 2,
- "": 3,
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- "A": 23,
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- "L": 30,
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- "O": 33,
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- "Z": 38,
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- "a": 40,
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- "h": 45,
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- "n": 48,
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- "an": 52,
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- "3H": 129,
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- "OH1-1": 174,
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- "123I": 183,
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- "45Ca+2": 423,
- "47Ca+2": 424,
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- "=32PH1": 426,
- "NH4+1": 427
- },
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- "S e",
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- "\\ C@@H1",
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- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
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- "+ 3",
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- "\\ NH1",
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- "Li +1",
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- "1 8",
- "18 F",
- "@ +1",
- "3 H",
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- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
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- "12 3",
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- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
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- "BH2 -1",
- "\\ I",
- "/ NH1",
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- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
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- "\\ C@",
- "A g",
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- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
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- "14C H1",
- "= 11C",
- "S @@",
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- "14C H3",
- "B H3-1",
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- "B H1-1",
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- "1 7",
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- "/ 13C",
- "/ 13CH1",
- "0 B",
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- "= Al",
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- "B H0",
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- "S -2",
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- "\\S i",
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- "NH3 +1",
- "# 14C",
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- "4 H",
- "5 Se",
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- "= 13C",
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- "8 2Rb+1",
- "= 32",
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- "C H2",
- "I +2",
- "N H0",
- "N H4",
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- "Si H3-1",
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- "Se -2",
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- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/pdbbind_full/checkpoint_epoch_025/vocab.json b/models/finetuned/pdbbind_full/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/models/finetuned/pdbbind_full/config.json b/models/finetuned/pdbbind_full/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/pdbbind_full/merges.txt b/models/finetuned/pdbbind_full/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
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-Bran ch
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-R i
-n g
-Ri ng
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-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
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-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
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-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
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-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
-Br -1
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-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
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--\ Ring2
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-\ F
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-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
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-\ C@
-A g
-= As
-=Se +1
-N H2+1
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--/ Ring1
-= Te
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-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
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-Se +1
-19 F
-/ 125I
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-R b
-Cl +1
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-Rb +1
-= Branch3
-N @@
-As +1
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-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
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-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
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-7 6Br
-= B
-e H1
-\N -1
-18 O
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-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
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-1 0B
-= Al
-= 18O
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-Cl +2
-\S i
-/S -1
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-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
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-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
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-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
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-\ 123I
-=C a
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-Te H1
-Zn +1
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-13C H3
-15 N
-Be +2
-B@@ -1
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-- 4
-/ PH1
-/ P@@
-/ As
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-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
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-N H4
-O H1
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-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/pdbbind_full/model.pt b/models/finetuned/pdbbind_full/model.pt
deleted file mode 100644
index 102758e7a8d32d3985000cd9969676e9d113b026..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8b8dedbde23c4e767ffd787e61ccb7516e88bdd94c2071c2bb06be3f09a83125
-size 1022843005
diff --git a/models/finetuned/pdbbind_full/special_tokens_map.json b/models/finetuned/pdbbind_full/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/pdbbind_full/tokenizer.json b/models/finetuned/pdbbind_full/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
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- "=": 21,
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- "H": 27,
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- "i": 46,
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- "#Branch2": 74,
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- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
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- "131": 193,
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- "=14C": 195,
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- "=Ring3": 197,
- "\\C@@": 198,
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- "Ag": 201,
- "=As": 202,
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- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
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- "\\P": 215,
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- "=PH1": 228,
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- "/B": 243,
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- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
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- "SiH4": 254,
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- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
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- "=Mg": 264,
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- "-2": 269,
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- "Bi": 284,
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- "6Br": 288,
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- "Bi+3": 300,
- "/P+1": 301,
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- "NH3": 310,
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- "NH3+1": 318,
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- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
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- "85Sr+2": 327,
- "=B-1": 328,
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- "B@@": 332,
- "B@-1": 333,
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- "CH1": 335,
- "I+3": 336,
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- "Ra+2": 339,
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- "Se-1": 348,
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- "18F-1": 350,
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- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
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- "/P@@": 365,
- "/As": 366,
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- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
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- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
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- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
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- "\\ S",
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- "S i",
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- "=N -1",
- "S e",
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- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
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- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
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- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
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- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
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- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/pdbbind_full/tokenizer_config.json b/models/finetuned/pdbbind_full/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/pdbbind_full/train_stdout.log b/models/finetuned/pdbbind_full/train_stdout.log
deleted file mode 100644
index 311f4ebdcdfc122bcb5a7fd77c685c4193f4a7b6..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/train_stdout.log
+++ /dev/null
@@ -1,84 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=regression batch_size=32 max_len=128 backbone_lr=1e-05 head_lr=1e-06 weight_decay=0.001 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/pdbbind_full/pdbbind_full.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/regression/pdbbind_full/pdbbind_full_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-[finetune] split sizes: train=7,904 val=988 test=988
-[finetune] train modality_non_empty: graph=7,897/7,904 text=1,871/7,904 kg=388/7,904
-[finetune] val modality_non_empty: graph=988/988 text=231/988 kg=57/988
-[finetune] test modality_non_empty: graph=986/988 text=236/988 kg=45/988
-[finetune] extracting labels...
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=247 val_steps=31 test_steps=31
-[finetune] initialized head: in_dim=3072 out=1
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=5.5868 val_loss=2.2110 time=37.0s tod=10:21
-[finetune] epoch 2/50: train_loss=1.9830 val_loss=2.1185 time=36.5s tod=10:21
-[finetune] epoch 3/50: train_loss=1.8369 val_loss=1.9493 time=36.5s tod=10:22
-[finetune] epoch 4/50: train_loss=1.6677 val_loss=1.8721 time=36.5s tod=10:22
-[finetune] epoch 5/50: train_loss=1.5533 val_loss=1.9191 time=36.4s tod=10:23
-[finetune] epoch 6/50: train_loss=1.4599 val_loss=1.8973 time=36.5s tod=10:24
-[finetune] epoch 7/50: train_loss=1.3654 val_loss=1.8004 time=36.2s tod=10:24
-[finetune] epoch 8/50: train_loss=1.2898 val_loss=1.7818 time=36.5s tod=10:25
-[finetune] epoch 9/50: train_loss=1.2106 val_loss=1.9329 time=36.5s tod=10:25
-[finetune] epoch 10/50: train_loss=1.1396 val_loss=1.8307 time=36.5s tod=10:26
-[finetune] epoch 11/50: train_loss=1.0760 val_loss=1.8189 time=36.7s tod=10:27
-[finetune] epoch 12/50: train_loss=1.0274 val_loss=1.9702 time=36.3s tod=10:27
-[finetune] epoch 13/50: train_loss=0.9712 val_loss=1.7947 time=36.6s tod=10:28
-[finetune] epoch 14/50: train_loss=0.9133 val_loss=1.7824 time=36.5s tod=10:29
-[finetune] epoch 15/50: train_loss=0.8634 val_loss=1.8319 time=36.2s tod=10:29
-[finetune] epoch 16/50: train_loss=0.8148 val_loss=1.9180 time=36.5s tod=10:30
-[finetune] epoch 17/50: train_loss=0.7857 val_loss=1.9476 time=36.5s tod=10:30
-[finetune] epoch 18/50: train_loss=0.7387 val_loss=1.8473 time=36.6s tod=10:31
-[finetune] epoch 19/50: train_loss=0.6946 val_loss=1.8302 time=36.6s tod=10:32
-[finetune] epoch 20/50: train_loss=0.6552 val_loss=1.8975 time=36.6s tod=10:32
-[finetune] epoch 21/50: train_loss=0.6345 val_loss=1.8368 time=36.4s tod=10:33
-[finetune] epoch 22/50: train_loss=0.6189 val_loss=1.9089 time=36.4s tod=10:33
-[finetune] epoch 23/50: train_loss=0.5669 val_loss=1.9858 time=36.5s tod=10:34
-[finetune] epoch 24/50: train_loss=0.5540 val_loss=1.9184 time=36.4s tod=10:35
-[finetune] epoch 25/50: train_loss=0.5332 val_loss=1.8838 time=36.6s tod=10:35
-[finetune] test_metrics: epoch=25 loss=1.7602 mse=1.7634 rmse=1.3279 mae=1.0330
-[finetune] saved checkpoint (best rmse=1.3279): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/pdbbind_full/ntqfan0j/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=0.5093 val_loss=1.8506 time=36.6s tod=10:36
-[finetune] epoch 27/50: train_loss=0.4882 val_loss=1.8703 time=36.6s tod=10:37
-[finetune] epoch 28/50: train_loss=0.4750 val_loss=1.9481 time=36.7s tod=10:37
-[finetune] epoch 29/50: train_loss=0.4604 val_loss=1.9254 time=36.3s tod=10:38
-[finetune] epoch 30/50: train_loss=0.4280 val_loss=1.9441 time=36.4s tod=10:38
-[finetune] epoch 31/50: train_loss=0.4231 val_loss=1.9181 time=36.6s tod=10:39
-[finetune] epoch 32/50: train_loss=0.4140 val_loss=1.9401 time=36.6s tod=10:40
-[finetune] epoch 33/50: train_loss=0.3994 val_loss=1.8978 time=36.4s tod=10:40
-[finetune] epoch 34/50: train_loss=0.3918 val_loss=2.0566 time=36.4s tod=10:41
-[finetune] epoch 35/50: train_loss=0.3855 val_loss=1.9523 time=36.4s tod=10:41
-[finetune] epoch 36/50: train_loss=0.3770 val_loss=1.9759 time=36.6s tod=10:42
-[finetune] epoch 37/50: train_loss=0.3655 val_loss=1.9533 time=36.5s tod=10:43
-[finetune] epoch 38/50: train_loss=0.3534 val_loss=1.9834 time=36.6s tod=10:43
-[finetune] epoch 39/50: train_loss=0.3458 val_loss=2.0582 time=36.7s tod=10:44
-[finetune] epoch 40/50: train_loss=0.3442 val_loss=1.9665 time=36.6s tod=10:44
-[finetune] epoch 41/50: train_loss=0.3312 val_loss=1.9377 time=36.5s tod=10:45
-[finetune] epoch 42/50: train_loss=0.3235 val_loss=1.9249 time=36.7s tod=10:46
-[finetune] epoch 43/50: train_loss=0.3167 val_loss=1.9429 time=36.5s tod=10:46
-[finetune] epoch 44/50: train_loss=0.3108 val_loss=1.9271 time=36.5s tod=10:47
-[finetune] epoch 45/50: train_loss=0.3076 val_loss=1.9263 time=36.5s tod=10:47
-[finetune] epoch 46/50: train_loss=0.2961 val_loss=1.9143 time=36.6s tod=10:48
-[finetune] epoch 47/50: train_loss=0.2949 val_loss=1.9215 time=36.5s tod=10:49
-[finetune] epoch 48/50: train_loss=0.2856 val_loss=1.9664 time=36.5s tod=10:49
-[finetune] epoch 49/50: train_loss=0.2852 val_loss=1.9501 time=36.3s tod=10:50
-[finetune] epoch 50/50: train_loss=0.2774 val_loss=1.9502 time=36.4s tod=10:51
-[finetune] test_metrics: epoch=50 loss=1.8280 mse=1.8309 rmse=1.3531 mae=1.0394
-[finetune] checkpoint skipped (current rmse=1.3531 vs best=1.3279 at epoch 25)
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=1.8280 mse=1.8309 rmse=1.3531 mae=1.0394
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/pdbbind_full/ntqfan0j
-[finetune] done in 1839.9s
diff --git a/models/finetuned/pdbbind_full/vocab.json b/models/finetuned/pdbbind_full/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/pdbbind_full/vocab.json
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diff --git a/models/finetuned/sider/checkpoint_epoch_025/config.json b/models/finetuned/sider/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
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- "model_type": "roberta",
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- "use_cache": true,
- "vocab_size": 800
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diff --git a/models/finetuned/sider/checkpoint_epoch_025/merges.txt b/models/finetuned/sider/checkpoint_epoch_025/merges.txt
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--- a/models/finetuned/sider/checkpoint_epoch_025/merges.txt
+++ /dev/null
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-#version: 0.2 - Trained by `huggingface/tokenizers`
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-22 3Ra+2
-Ca H2
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-=32 PH1
-NH4 +1
diff --git a/models/finetuned/sider/checkpoint_epoch_025/model.pt b/models/finetuned/sider/checkpoint_epoch_025/model.pt
deleted file mode 100644
index 313881dbf9033030494b20f9d155e81d369caf12..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_025/model.pt
+++ /dev/null
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diff --git a/models/finetuned/sider/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/sider/checkpoint_epoch_025/special_tokens_map.json
deleted file mode 100644
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--- a/models/finetuned/sider/checkpoint_epoch_025/special_tokens_map.json
+++ /dev/null
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-{
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diff --git a/models/finetuned/sider/checkpoint_epoch_025/tokenizer.json b/models/finetuned/sider/checkpoint_epoch_025/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_025/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
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- "cls": [
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- 1
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- "decoder": {
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- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
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- "vocab": {
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- "": 1,
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- "": 3,
- "": 4,
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- "+": 7,
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- "B": 24,
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- "H": 27,
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- "O": 33,
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- "Br": 51,
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- "ch": 53,
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- "@+1": 128,
- "3H": 129,
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- "N@+1": 157,
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- "=S+1": 169,
- "Zn": 170,
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- "/I": 173,
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- "\\Br": 176,
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- "Al": 179,
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- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
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- "BH2-1": 189,
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- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
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- "H3-1": 223,
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- "=14CH1": 227,
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- "=S@@": 286,
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- "45": 373,
- "47": 374,
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- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
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- "I -1",
- "/ C@@H1",
- "S i",
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- "=N -1",
- "S e",
- "= P",
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- "Ring 3",
- "2 H",
- "P +1",
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- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
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- "O H0",
- "1 2",
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- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
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- "5 I",
- "12 5I",
- "11 C",
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- "\\ N+1",
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- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
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- "=O +1",
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- "Z n",
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- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
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- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
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- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
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- "124 I",
- "Sr +2",
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- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
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- "/ Si",
- "B H1-1",
- "S H1",
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- "= Mg",
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- "\\ B",
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- "- 2",
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- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
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- "17 F",
- "35 S",
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- "=S @@",
- "\\S -1",
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- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
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- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
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- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
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- "Te H1",
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- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
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- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/sider/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/sider/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/sider/checkpoint_epoch_025/vocab.json b/models/finetuned/sider/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/sider/checkpoint_epoch_050/config.json b/models/finetuned/sider/checkpoint_epoch_050/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/sider/checkpoint_epoch_050/merges.txt b/models/finetuned/sider/checkpoint_epoch_050/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
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-c h
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-# Branch2
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-- 1
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-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
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-\ N+1
-- \
-/ C@@
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--\ Ring2
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--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
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-A g
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-=P @@
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-- 2
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-= 13CH1
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-=S H1
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-35 S
-Cs +1
-# 11C
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-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
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-NH3 +1
-# 14C
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-- 3
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-8 5Sr+2
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-2 K+1
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-3 Ra+2
-4 5
-4 7
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-8 9
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-= 32P
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-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
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-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
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-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/sider/checkpoint_epoch_050/model.pt b/models/finetuned/sider/checkpoint_epoch_050/model.pt
deleted file mode 100644
index d5262ada0a1773d2f5142c00c258de47e32fbb41..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:da1c7d30cd890211ba9b7db75d9c59a4b465aa3ca4e8de458cad8b54e2af215d
-size 1023174845
diff --git a/models/finetuned/sider/checkpoint_epoch_050/special_tokens_map.json b/models/finetuned/sider/checkpoint_epoch_050/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/sider/checkpoint_epoch_050/tokenizer.json b/models/finetuned/sider/checkpoint_epoch_050/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
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- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
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- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
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- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
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- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
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- "continuing_subword_prefix": "",
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- "fuse_unk": false,
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- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
- "S@@": 220,
- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
- "S@": 226,
- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
- "CH1-1": 233,
- "Sr": 234,
- "=Si": 235,
- "124I": 236,
- "Sr+2": 237,
- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
- "Ba+2": 245,
- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
- "35": 272,
- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
- "35S": 280,
- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
- "\\S-1": 287,
- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
- "eH1": 292,
- "\\N-1": 293,
- "18O": 294,
- "127I": 295,
- "11CH2": 296,
- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
- "Cl+2": 313,
- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
- "C l",
- "/ C",
- "N H1",
- "= Ring1",
- "+ 1",
- "- 1",
- "O -1",
- "N +1",
- "\\ C",
- "# N",
- "/ N",
- "= Ring2",
- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
- "/ O",
- "\\ O",
- "Br -1",
- "Branch 3",
- "\\ S",
- "S +1",
- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/sider/checkpoint_epoch_050/tokenizer_config.json b/models/finetuned/sider/checkpoint_epoch_050/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/sider/checkpoint_epoch_050/vocab.json b/models/finetuned/sider/checkpoint_epoch_050/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/checkpoint_epoch_050/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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\ No newline at end of file
diff --git a/models/finetuned/sider/config.json b/models/finetuned/sider/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
- "hidden_dropout_prob": 0.1,
- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/sider/merges.txt b/models/finetuned/sider/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
-#version: 0.2 - Trained by `huggingface/tokenizers`
-B r
-a n
-c h
-Br an
-Bran ch
-Branch 1
-= C
-R i
-n g
-Ri ng
-Ring 1
-= Branch1
-Branch 2
-= O
-Ring 2
-H 1
-C @
-= N
-# Branch1
-C@ @
-= Branch2
-C@ H1
-C@@ H1
-# Branch2
-# C
-C l
-/ C
-N H1
-= Ring1
-+ 1
-- 1
-O -1
-N +1
-\ C
-# N
-/ N
-= Ring2
-= S
-=N +1
-\ N
-N a
-Na +1
-/ O
-\ O
-Br -1
-Branch 3
-\ S
-S +1
-Cl -1
-I -1
-/ C@@H1
-S i
-/ C@H1
-/ S
-=N -1
-S e
-= P
-N -1
-Ring 3
-2 H
-P +1
-K +1
-\ C@@H1
-\ C@H1
-/ N+1
-@ @
-C -1
-# N+1
-B -1
-+ 3
-Cl +3
-\ NH1
-L i
-Li +1
-P H1
-1 8
-18 F
-@ +1
-3 H
-P @@
-H 0
-O H0
-1 2
-P @
-+ 2
-@@ +1
-S -1
-/ Br
-- /
-\ Cl
--/ Ring2
-\ O-1
-1 1
-5 I
-12 5I
-11 C
-H 3
-\ N+1
-- \
-/ C@@
-S @+1
-A s
-/ Cl
-11C H3
-=S e
-S @@+1
-N @+1
-1 4
--\ Ring2
-14 C
-\ F
-/ C@
-T e
-H 2
-H1 -1
-=O +1
-N @@+1
-C +1
-=S +1
-Z n
-/ P
-a +2
-/ I
-O H1-1
-C a+2
-\ Br
-M g
-Zn +2
-A l
-/ F
-Mg +2
-12 3
-123 I
-1 3
-I +1
-/ O-1
--\ Ring1
-B H2
-BH2 -1
-\ I
-/ NH1
-O +1
-13 1
-131 I
-= 14C
-/ S+1
-= Ring3
-\ C@@
-H2 +1
-\ C@
-A g
-= As
-=Se +1
-N H2+1
-Se H1
--/ Ring1
-= Te
-Al +3
-Na H1
-=Te +1
-NH1 +1
-Ag +1
-H1 +1
-NH1 -1
-\ P
-14C H2
-13 C
-14C H1
-= 11C
-S @@
-=P @@
-Si H2
-H3 -1
-14C H3
-B H3-1
-S @
-=14C H1
-=P H1
-=P @
-=N H1+1
-\S +1
-12 4
-C H1-1
-S r
-=S i
-124 I
-Sr +2
-#C -1
-/C -1
-N @
-/N -1
-13C H1
-/ B
-1 9
-B a+2
-H 4
-S H1+1
-Se +1
-19 F
-/ 125I
-P @+1
-R b
-Cl +1
-Si H4
-Rb +1
-= Branch3
-N @@
-As +1
-/ Si
-B H1-1
-S H1
-/ 123I
-3 2
-= Mg
-H +1
-\ B
-Si H1
-P@@ +1
-- 2
-1 5
-1 7
-3 5
-= 13CH1
-C s
-=N H2+1
-=S H1
-Mg H2
-32 P
-17 F
-35 S
-Cs +1
-# 11C
-/ 131I
-B i
-\ 125I
-=S @@
-\S -1
-6 Br
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
-11C H2
-14 C@@H1
-Te H2
-15 NH1
-Bi +3
-/ P+1
-/ 13C
-/ 13CH1
-0 B
-1 0B
-= Al
-= 18O
-B H0
-F -1
-N H3
-S -2
-Br +2
-Cl +2
-\S i
-/S -1
-=P H2
-14 C@H1
-NH3 +1
-# 14C
-# O+1
-- 3
-2 2
-4 H
-5 Se
-5 Sr+2
-7 5Se
-8 5Sr+2
-= B-1
-= 13C
-@ -1
-B e
-B @@
-B @-1
-C a
-C H1
-I +3
-K H1
-O H1+1
-R a+2
-S H1-1
-\ PH1
-\ 123I
-=C a
-\C H1-1
-=S @
-\S eH1
-/S eH1
-Se -1
-Li H1
-18F -1
-125I H1
-11C H1
-Te H1
-Zn +1
-Zn -2
-Al -3
-13C H3
-15 N
-Be +2
-B@@ -1
-# P
-# S
-- 4
-/ PH1
-/ P@@
-/ As
-/ 14C
-/ 14CH1
-2 K+1
-2 Rb+1
-3 Se
-3 Ra+2
-4 5
-4 7
-4 2K+1
-5 I-1
-7 3Se
-8 9
-8 2Rb+1
-= 32
-= 32P
-C H0
-C H2
-I +2
-N H0
-N H4
-O H1
-P H2+1
-S H0
-S H2
-\ 3H
-\ 11CH3
-\C -1
-\S e
-Si @
-Si -1
-Si H1-1
-Si H3-1
-/S e
-Se -2
-\NH1 -1
-18F H1
-12 5I-1
-11 C@@H1
-11 C-1
-As H1
-As -1
-14 C@@
-Te -1
-Mg +1
-123 I-1
-123 Te
-123I H1
-13 5I
-131 I-1
-Ag -4
-124 I-1
-76Br H1
-18O H1
-22 Na+1
-22 3Ra+2
-Ca H2
-45 Ca+2
-47 Ca+2
-89 Sr+2
-=32 PH1
-NH4 +1
diff --git a/models/finetuned/sider/model.pt b/models/finetuned/sider/model.pt
deleted file mode 100644
index d5262ada0a1773d2f5142c00c258de47e32fbb41..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:da1c7d30cd890211ba9b7db75d9c59a4b465aa3ca4e8de458cad8b54e2af215d
-size 1023174845
diff --git a/models/finetuned/sider/special_tokens_map.json b/models/finetuned/sider/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/sider/tokenizer.json b/models/finetuned/sider/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
- "Fixed": 128
- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 3,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 4,
- "content": "",
- "single_word": false,
- "lstrip": true,
- "rstrip": false,
- "normalized": true,
- "special": true
- }
- ],
- "normalizer": null,
- "pre_tokenizer": {
- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
- "type": "ByteLevel",
- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
- },
- "model": {
- "type": "BPE",
- "dropout": null,
- "unk_token": null,
- "continuing_subword_prefix": "",
- "end_of_word_suffix": "",
- "fuse_unk": false,
- "vocab": {
- "": 0,
- "": 1,
- "": 2,
- "": 3,
- "": 4,
- "\n": 5,
- "#": 6,
- "+": 7,
- "-": 8,
- ".": 9,
- "/": 10,
- "0": 11,
- "1": 12,
- "2": 13,
- "3": 14,
- "4": 15,
- "5": 16,
- "6": 17,
- "7": 18,
- "8": 19,
- "9": 20,
- "=": 21,
- "@": 22,
- "A": 23,
- "B": 24,
- "C": 25,
- "F": 26,
- "H": 27,
- "I": 28,
- "K": 29,
- "L": 30,
- "M": 31,
- "N": 32,
- "O": 33,
- "P": 34,
- "R": 35,
- "S": 36,
- "T": 37,
- "Z": 38,
- "\\": 39,
- "a": 40,
- "b": 41,
- "c": 42,
- "e": 43,
- "g": 44,
- "h": 45,
- "i": 46,
- "l": 47,
- "n": 48,
- "r": 49,
- "s": 50,
- "Br": 51,
- "an": 52,
- "ch": 53,
- "Bran": 54,
- "Branch": 55,
- "Branch1": 56,
- "=C": 57,
- "Ri": 58,
- "ng": 59,
- "Ring": 60,
- "Ring1": 61,
- "=Branch1": 62,
- "Branch2": 63,
- "=O": 64,
- "Ring2": 65,
- "H1": 66,
- "C@": 67,
- "=N": 68,
- "#Branch1": 69,
- "C@@": 70,
- "=Branch2": 71,
- "C@H1": 72,
- "C@@H1": 73,
- "#Branch2": 74,
- "#C": 75,
- "Cl": 76,
- "/C": 77,
- "NH1": 78,
- "=Ring1": 79,
- "+1": 80,
- "-1": 81,
- "O-1": 82,
- "N+1": 83,
- "\\C": 84,
- "#N": 85,
- "/N": 86,
- "=Ring2": 87,
- "=S": 88,
- "=N+1": 89,
- "\\N": 90,
- "Na": 91,
- "Na+1": 92,
- "/O": 93,
- "\\O": 94,
- "Br-1": 95,
- "Branch3": 96,
- "\\S": 97,
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- "I-1": 100,
- "/C@@H1": 101,
- "Si": 102,
- "/C@H1": 103,
- "/S": 104,
- "=N-1": 105,
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- "=P": 107,
- "N-1": 108,
- "Ring3": 109,
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- "K+1": 112,
- "\\C@@H1": 113,
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- "@@": 116,
- "C-1": 117,
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- "B-1": 119,
- "+3": 120,
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- "\\NH1": 122,
- "Li": 123,
- "Li+1": 124,
- "PH1": 125,
- "18": 126,
- "18F": 127,
- "@+1": 128,
- "3H": 129,
- "P@@": 130,
- "H0": 131,
- "OH0": 132,
- "12": 133,
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- "+2": 135,
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- "/Br": 138,
- "-/": 139,
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- "\\O-1": 142,
- "11": 143,
- "5I": 144,
- "125I": 145,
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- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
- "-\\Ring2": 159,
- "14C": 160,
- "\\F": 161,
- "/C@": 162,
- "Te": 163,
- "H2": 164,
- "H1-1": 165,
- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
- "a+2": 172,
- "/I": 173,
- "OH1-1": 174,
- "Ca+2": 175,
- "\\Br": 176,
- "Mg": 177,
- "Zn+2": 178,
- "Al": 179,
- "/F": 180,
- "Mg+2": 181,
- "123": 182,
- "123I": 183,
- "13": 184,
- "I+1": 185,
- "/O-1": 186,
- "-\\Ring1": 187,
- "BH2": 188,
- "BH2-1": 189,
- "\\I": 190,
- "/NH1": 191,
- "O+1": 192,
- "131": 193,
- "131I": 194,
- "=14C": 195,
- "/S+1": 196,
- "=Ring3": 197,
- "\\C@@": 198,
- "H2+1": 199,
- "\\C@": 200,
- "Ag": 201,
- "=As": 202,
- "=Se+1": 203,
- "NH2+1": 204,
- "SeH1": 205,
- "-/Ring1": 206,
- "=Te": 207,
- "Al+3": 208,
- "NaH1": 209,
- "=Te+1": 210,
- "NH1+1": 211,
- "Ag+1": 212,
- "H1+1": 213,
- "NH1-1": 214,
- "\\P": 215,
- "14CH2": 216,
- "13C": 217,
- "14CH1": 218,
- "=11C": 219,
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- "=P@@": 221,
- "SiH2": 222,
- "H3-1": 223,
- "14CH3": 224,
- "BH3-1": 225,
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- "=14CH1": 227,
- "=PH1": 228,
- "=P@": 229,
- "=NH1+1": 230,
- "\\S+1": 231,
- "124": 232,
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- "Sr": 234,
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- "#C-1": 238,
- "/C-1": 239,
- "N@": 240,
- "/N-1": 241,
- "13CH1": 242,
- "/B": 243,
- "19": 244,
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- "H4": 246,
- "SH1+1": 247,
- "Se+1": 248,
- "19F": 249,
- "/125I": 250,
- "P@+1": 251,
- "Rb": 252,
- "Cl+1": 253,
- "SiH4": 254,
- "Rb+1": 255,
- "=Branch3": 256,
- "N@@": 257,
- "As+1": 258,
- "/Si": 259,
- "BH1-1": 260,
- "SH1": 261,
- "/123I": 262,
- "32": 263,
- "=Mg": 264,
- "H+1": 265,
- "\\B": 266,
- "SiH1": 267,
- "P@@+1": 268,
- "-2": 269,
- "15": 270,
- "17": 271,
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- "=13CH1": 273,
- "Cs": 274,
- "=NH2+1": 275,
- "=SH1": 276,
- "MgH2": 277,
- "32P": 278,
- "17F": 279,
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- "Cs+1": 281,
- "#11C": 282,
- "/131I": 283,
- "Bi": 284,
- "\\125I": 285,
- "=S@@": 286,
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- "6Br": 288,
- "7I": 289,
- "76Br": 290,
- "=B": 291,
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- "18O": 294,
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- "14C@@H1": 297,
- "TeH2": 298,
- "15NH1": 299,
- "Bi+3": 300,
- "/P+1": 301,
- "/13C": 302,
- "/13CH1": 303,
- "0B": 304,
- "10B": 305,
- "=Al": 306,
- "=18O": 307,
- "BH0": 308,
- "F-1": 309,
- "NH3": 310,
- "S-2": 311,
- "Br+2": 312,
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- "\\Si": 314,
- "/S-1": 315,
- "=PH2": 316,
- "14C@H1": 317,
- "NH3+1": 318,
- "#14C": 319,
- "#O+1": 320,
- "-3": 321,
- "22": 322,
- "4H": 323,
- "5Se": 324,
- "5Sr+2": 325,
- "75Se": 326,
- "85Sr+2": 327,
- "=B-1": 328,
- "=13C": 329,
- "@-1": 330,
- "Be": 331,
- "B@@": 332,
- "B@-1": 333,
- "Ca": 334,
- "CH1": 335,
- "I+3": 336,
- "KH1": 337,
- "OH1+1": 338,
- "Ra+2": 339,
- "SH1-1": 340,
- "\\PH1": 341,
- "\\123I": 342,
- "=Ca": 343,
- "\\CH1-1": 344,
- "=S@": 345,
- "\\SeH1": 346,
- "/SeH1": 347,
- "Se-1": 348,
- "LiH1": 349,
- "18F-1": 350,
- "125IH1": 351,
- "11CH1": 352,
- "TeH1": 353,
- "Zn+1": 354,
- "Zn-2": 355,
- "Al-3": 356,
- "13CH3": 357,
- "15N": 358,
- "Be+2": 359,
- "B@@-1": 360,
- "#P": 361,
- "#S": 362,
- "-4": 363,
- "/PH1": 364,
- "/P@@": 365,
- "/As": 366,
- "/14C": 367,
- "/14CH1": 368,
- "2K+1": 369,
- "2Rb+1": 370,
- "3Se": 371,
- "3Ra+2": 372,
- "45": 373,
- "47": 374,
- "42K+1": 375,
- "5I-1": 376,
- "73Se": 377,
- "89": 378,
- "82Rb+1": 379,
- "=32": 380,
- "=32P": 381,
- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
- "SH0": 389,
- "SH2": 390,
- "\\3H": 391,
- "\\11CH3": 392,
- "\\C-1": 393,
- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
- "SiH3-1": 398,
- "/Se": 399,
- "Se-2": 400,
- "\\NH1-1": 401,
- "18FH1": 402,
- "125I-1": 403,
- "11C@@H1": 404,
- "11C-1": 405,
- "AsH1": 406,
- "As-1": 407,
- "14C@@": 408,
- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
- "Branch 1",
- "= C",
- "R i",
- "n g",
- "Ri ng",
- "Ring 1",
- "= Branch1",
- "Branch 2",
- "= O",
- "Ring 2",
- "H 1",
- "C @",
- "= N",
- "# Branch1",
- "C@ @",
- "= Branch2",
- "C@ H1",
- "C@@ H1",
- "# Branch2",
- "# C",
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- "/ C",
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- "= Ring1",
- "+ 1",
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- "= S",
- "=N +1",
- "\\ N",
- "N a",
- "Na +1",
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- "\\ O",
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- "Branch 3",
- "\\ S",
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- "Cl -1",
- "I -1",
- "/ C@@H1",
- "S i",
- "/ C@H1",
- "/ S",
- "=N -1",
- "S e",
- "= P",
- "N -1",
- "Ring 3",
- "2 H",
- "P +1",
- "K +1",
- "\\ C@@H1",
- "\\ C@H1",
- "/ N+1",
- "@ @",
- "C -1",
- "# N+1",
- "B -1",
- "+ 3",
- "Cl +3",
- "\\ NH1",
- "L i",
- "Li +1",
- "P H1",
- "1 8",
- "18 F",
- "@ +1",
- "3 H",
- "P @@",
- "H 0",
- "O H0",
- "1 2",
- "P @",
- "+ 2",
- "@@ +1",
- "S -1",
- "/ Br",
- "- /",
- "\\ Cl",
- "-/ Ring2",
- "\\ O-1",
- "1 1",
- "5 I",
- "12 5I",
- "11 C",
- "H 3",
- "\\ N+1",
- "- \\",
- "/ C@@",
- "S @+1",
- "A s",
- "/ Cl",
- "11C H3",
- "=S e",
- "S @@+1",
- "N @+1",
- "1 4",
- "-\\ Ring2",
- "14 C",
- "\\ F",
- "/ C@",
- "T e",
- "H 2",
- "H1 -1",
- "=O +1",
- "N @@+1",
- "C +1",
- "=S +1",
- "Z n",
- "/ P",
- "a +2",
- "/ I",
- "O H1-1",
- "C a+2",
- "\\ Br",
- "M g",
- "Zn +2",
- "A l",
- "/ F",
- "Mg +2",
- "12 3",
- "123 I",
- "1 3",
- "I +1",
- "/ O-1",
- "-\\ Ring1",
- "B H2",
- "BH2 -1",
- "\\ I",
- "/ NH1",
- "O +1",
- "13 1",
- "131 I",
- "= 14C",
- "/ S+1",
- "= Ring3",
- "\\ C@@",
- "H2 +1",
- "\\ C@",
- "A g",
- "= As",
- "=Se +1",
- "N H2+1",
- "Se H1",
- "-/ Ring1",
- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
- "=P @@",
- "Si H2",
- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
- "=N H1+1",
- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
- "#C -1",
- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
- "As +1",
- "/ Si",
- "B H1-1",
- "S H1",
- "/ 123I",
- "3 2",
- "= Mg",
- "H +1",
- "\\ B",
- "Si H1",
- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
- "O H1+1",
- "R a+2",
- "S H1-1",
- "\\ PH1",
- "\\ 123I",
- "=C a",
- "\\C H1-1",
- "=S @",
- "\\S eH1",
- "/S eH1",
- "Se -1",
- "Li H1",
- "18F -1",
- "125I H1",
- "11C H1",
- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/sider/tokenizer_config.json b/models/finetuned/sider/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/sider/train_stdout.log b/models/finetuned/sider/train_stdout.log
deleted file mode 100644
index a523764f132bdef6e1ba601f9f150225da05096f..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/train_stdout.log
+++ /dev/null
@@ -1,86 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=multilabel batch_size=16 max_len=128 backbone_lr=1e-05 head_lr=0.0005 weight_decay=0.001 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/sider/sider.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/sider/sider_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-[finetune] split sizes: train=1,141 val=143 test=143
-[finetune] train modality_non_empty: graph=1,040/1,141 text=922/1,141 kg=24/1,141
-[finetune] val modality_non_empty: graph=132/143 text=115/143 kg=2/143
-[finetune] test modality_non_empty: graph=127/143 text=114/143 kg=1/143
-[finetune] extracting labels...
-[finetune] multilabel: num_labels_in_csv=28
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=72 val_steps=9 test_steps=9
-[finetune] overriding --num_labels=1 with num_labels_in_csv=28
-[finetune] initialized head: in_dim=3072 out=28
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=-2463.0879 val_loss=-8632.9700 time=19.9s tod=04:59
-[finetune] epoch 2/50: train_loss=-29240.3907 val_loss=-28515.0196 time=19.6s tod=04:59
-[finetune] epoch 3/50: train_loss=-56493.8012 val_loss=-42786.8129 time=19.4s tod=05:00
-[finetune] epoch 4/50: train_loss=-78403.9442 val_loss=-54933.7142 time=17.1s tod=05:00
-[finetune] epoch 5/50: train_loss=-98390.0560 val_loss=-61163.0579 time=13.3s tod=05:00
-[finetune] epoch 6/50: train_loss=-73340.5962 val_loss=-70785.7020 time=13.2s tod=05:01
-[finetune] epoch 7/50: train_loss=-102700.5125 val_loss=-16367.9551 time=16.9s tod=05:01
-[finetune] epoch 8/50: train_loss=-75565.5855 val_loss=-87597.7900 time=19.6s tod=05:01
-[finetune] epoch 9/50: train_loss=-101224.8124 val_loss=-56896.3166 time=19.6s tod=05:01
-[finetune] epoch 10/50: train_loss=-100191.3469 val_loss=-102080.0145 time=19.4s tod=05:02
-[finetune] epoch 11/50: train_loss=-141172.0164 val_loss=-109301.1324 time=19.6s tod=05:02
-[finetune] epoch 12/50: train_loss=-169078.9591 val_loss=-37835.9162 time=19.6s tod=05:02
-[finetune] epoch 13/50: train_loss=-96474.2053 val_loss=-30286.5900 time=19.5s tod=05:03
-[finetune] epoch 14/50: train_loss=-105256.3000 val_loss=-35972.5983 time=19.6s tod=05:03
-[finetune] epoch 15/50: train_loss=-178900.2351 val_loss=-37852.0637 time=19.7s tod=05:03
-[finetune] epoch 16/50: train_loss=-186680.4031 val_loss=-37577.4352 time=19.5s tod=05:04
-[finetune] epoch 17/50: train_loss=-195649.4959 val_loss=-90268.9497 time=19.5s tod=05:04
-[finetune] epoch 18/50: train_loss=-220532.2620 val_loss=-46100.1349 time=19.6s tod=05:04
-[finetune] epoch 19/50: train_loss=-246434.8544 val_loss=-46121.6348 time=19.6s tod=05:05
-[finetune] epoch 20/50: train_loss=-250533.9357 val_loss=-44846.5984 time=19.6s tod=05:05
-[finetune] epoch 21/50: train_loss=-269410.9093 val_loss=-48019.9503 time=19.6s tod=05:05
-[finetune] epoch 22/50: train_loss=-313211.1312 val_loss=-75566.5165 time=19.5s tod=05:06
-[finetune] epoch 23/50: train_loss=-327284.1272 val_loss=-58031.5497 time=19.5s tod=05:06
-[finetune] epoch 24/50: train_loss=-352373.0084 val_loss=-57549.3987 time=19.6s tod=05:06
-[finetune] epoch 25/50: train_loss=-364050.6847 val_loss=-54414.9680 time=18.6s tod=05:07
-[finetune] test_metrics: epoch=25 loss=-88607.4092 accuracy=0.7391 precision=0.7331 recall=0.8057 f1=0.7677 roc-auc=0.7350 prc-auc=0.7070
-[finetune] saved checkpoint (best roc-auc=0.7350): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/sider/ew0k1kqo/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=-385099.2705 val_loss=-54985.2346 time=19.4s tod=05:07
-[finetune] epoch 27/50: train_loss=-399822.8386 val_loss=-56467.5216 time=19.7s tod=05:07
-[finetune] epoch 28/50: train_loss=-415828.3384 val_loss=-52419.7444 time=19.5s tod=05:08
-[finetune] epoch 29/50: train_loss=-431865.9807 val_loss=-62103.1590 time=19.5s tod=05:08
-[finetune] epoch 30/50: train_loss=-447456.9427 val_loss=-56188.3156 time=19.6s tod=05:08
-[finetune] epoch 31/50: train_loss=-462273.6884 val_loss=-54661.3517 time=19.5s tod=05:09
-[finetune] epoch 32/50: train_loss=-508797.7937 val_loss=-60571.6111 time=18.8s tod=05:09
-[finetune] epoch 33/50: train_loss=-485794.6108 val_loss=-74456.0105 time=19.6s tod=05:09
-[finetune] epoch 34/50: train_loss=-497895.8270 val_loss=-72051.5103 time=19.5s tod=05:10
-[finetune] epoch 35/50: train_loss=-506471.9879 val_loss=-82966.3256 time=19.5s tod=05:10
-[finetune] epoch 36/50: train_loss=-516857.2304 val_loss=-65550.5172 time=19.6s tod=05:10
-[finetune] epoch 37/50: train_loss=-528256.5853 val_loss=-76332.1525 time=19.5s tod=05:11
-[finetune] epoch 38/50: train_loss=-536697.0948 val_loss=-67379.6054 time=19.6s tod=05:11
-[finetune] epoch 39/50: train_loss=-543221.3290 val_loss=-59524.8871 time=19.6s tod=05:11
-[finetune] epoch 40/50: train_loss=-560865.7400 val_loss=-71147.7508 time=19.5s tod=05:12
-[finetune] epoch 41/50: train_loss=-558859.0678 val_loss=-67798.4771 time=19.5s tod=05:12
-[finetune] epoch 42/50: train_loss=-564936.8555 val_loss=-82237.9927 time=19.5s tod=05:12
-[finetune] epoch 43/50: train_loss=-593958.3045 val_loss=-71737.9733 time=19.5s tod=05:13
-[finetune] epoch 44/50: train_loss=-649648.8877 val_loss=-73129.3121 time=19.6s tod=05:13
-[finetune] epoch 45/50: train_loss=-579354.1524 val_loss=-65233.4437 time=19.6s tod=05:13
-[finetune] epoch 46/50: train_loss=-583970.5857 val_loss=-69687.3034 time=19.5s tod=05:14
-[finetune] epoch 47/50: train_loss=-624626.7817 val_loss=-71989.2865 time=19.5s tod=05:14
-[finetune] epoch 48/50: train_loss=-586496.3253 val_loss=-69742.6843 time=19.6s tod=05:14
-[finetune] epoch 49/50: train_loss=-587622.2958 val_loss=-71131.1176 time=19.5s tod=05:15
-[finetune] epoch 50/50: train_loss=-616375.0225 val_loss=-70154.7495 time=19.5s tod=05:15
-[finetune] test_metrics: epoch=50 loss=-121892.1985 accuracy=0.7541 precision=0.7395 recall=0.8342 f1=0.7840 roc-auc=0.7490 prc-auc=0.7221
-[finetune] saved checkpoint (best roc-auc=0.7490): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/sider/ew0k1kqo/checkpoint_epoch_050
-[finetune] final evaluation on test split...
-[finetune] test_metrics: loss=-121892.1985 accuracy=0.7541 precision=0.7395 recall=0.8342 f1=0.7840 roc-auc=0.7490 prc-auc=0.7221
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/sider/ew0k1kqo
-[finetune] done in 971.3s
diff --git a/models/finetuned/sider/vocab.json b/models/finetuned/sider/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/sider/vocab.json
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diff --git a/models/finetuned/tox21/checkpoint_epoch_025/config.json b/models/finetuned/tox21/checkpoint_epoch_025/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/checkpoint_epoch_025/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
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- "RobertaForMaskedLM"
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- "model_type": "roberta",
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- "position_embedding_type": "absolute",
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- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
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diff --git a/models/finetuned/tox21/checkpoint_epoch_025/merges.txt b/models/finetuned/tox21/checkpoint_epoch_025/merges.txt
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--- a/models/finetuned/tox21/checkpoint_epoch_025/merges.txt
+++ /dev/null
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-#version: 0.2 - Trained by `huggingface/tokenizers`
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-=32 PH1
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diff --git a/models/finetuned/tox21/checkpoint_epoch_025/model.pt b/models/finetuned/tox21/checkpoint_epoch_025/model.pt
deleted file mode 100644
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--- a/models/finetuned/tox21/checkpoint_epoch_025/model.pt
+++ /dev/null
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-version https://git-lfs.github.com/spec/v1
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diff --git a/models/finetuned/tox21/checkpoint_epoch_025/special_tokens_map.json b/models/finetuned/tox21/checkpoint_epoch_025/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/checkpoint_epoch_025/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
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diff --git a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer.json b/models/finetuned/tox21/checkpoint_epoch_025/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
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- "Na H1",
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- "Ag +1",
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- "123 Te",
- "123I H1",
- "13 5I",
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- "Ag -4",
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- "18O H1",
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- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer_config.json b/models/finetuned/tox21/checkpoint_epoch_025/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/checkpoint_epoch_025/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/tox21/checkpoint_epoch_025/vocab.json b/models/finetuned/tox21/checkpoint_epoch_025/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/checkpoint_epoch_025/vocab.json
+++ /dev/null
@@ -1 +0,0 @@
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diff --git a/models/finetuned/tox21/config.json b/models/finetuned/tox21/config.json
deleted file mode 100644
index 3811e21539577b37e06313eab31ec11e53f0cbbc..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/config.json
+++ /dev/null
@@ -1,27 +0,0 @@
-{
- "_name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "architectures": [
- "RobertaForMaskedLM"
- ],
- "attention_probs_dropout_prob": 0.1,
- "bos_token_id": 0,
- "classifier_dropout": null,
- "eos_token_id": 2,
- "hidden_act": "gelu",
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- "hidden_size": 768,
- "initializer_range": 0.02,
- "intermediate_size": 3072,
- "layer_norm_eps": 1e-12,
- "max_position_embeddings": 514,
- "model_type": "roberta",
- "num_attention_heads": 4,
- "num_hidden_layers": 12,
- "pad_token_id": 1,
- "position_embedding_type": "absolute",
- "torch_dtype": "float32",
- "transformers_version": "4.26.1",
- "type_vocab_size": 1,
- "use_cache": true,
- "vocab_size": 800
-}
diff --git a/models/finetuned/tox21/merges.txt b/models/finetuned/tox21/merges.txt
deleted file mode 100644
index 7cd5ec62809503c23f18c80afc0ba3bdf9d253d0..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/merges.txt
+++ /dev/null
@@ -1,378 +0,0 @@
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diff --git a/models/finetuned/tox21/model.pt b/models/finetuned/tox21/model.pt
deleted file mode 100644
index 325f6ea1b1d99bc89c07b9206975695cac0ce067..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/model.pt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:c958fad0f8f2b485c9e2a8839f74fac88eb616d464b69d272613c564a27f2e8b
-size 1022990461
diff --git a/models/finetuned/tox21/special_tokens_map.json b/models/finetuned/tox21/special_tokens_map.json
deleted file mode 100644
index 06a55849fa69a91e7179d909e373179ff7467d8c..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/special_tokens_map.json
+++ /dev/null
@@ -1,51 +0,0 @@
-{
- "bos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "mask_token": {
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "pad_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "unk_token": {
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/tox21/tokenizer.json b/models/finetuned/tox21/tokenizer.json
deleted file mode 100644
index 3b64b273e6fa9799e2d8375722b9e815de9ebb8f..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/tokenizer.json
+++ /dev/null
@@ -1,909 +0,0 @@
-{
- "version": "1.0",
- "truncation": {
- "direction": "Right",
- "max_length": 128,
- "strategy": "LongestFirst",
- "stride": 0
- },
- "padding": {
- "strategy": {
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- },
- "direction": "Right",
- "pad_to_multiple_of": null,
- "pad_id": 3,
- "pad_type_id": 0,
- "pad_token": ""
- },
- "added_tokens": [
- {
- "id": 0,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
- },
- {
- "id": 1,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
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- "id": 2,
- "content": "",
- "single_word": false,
- "lstrip": false,
- "rstrip": false,
- "normalized": true,
- "special": true
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- "single_word": false,
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- "content": "",
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- "normalized": true,
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- "normalizer": null,
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- "type": "ByteLevel",
- "add_prefix_space": false,
- "trim_offsets": true,
- "use_regex": true
- },
- "post_processor": {
- "type": "RobertaProcessing",
- "sep": [
- "",
- 2
- ],
- "cls": [
- "",
- 1
- ],
- "trim_offsets": true,
- "add_prefix_space": false
- },
- "decoder": {
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- "add_prefix_space": true,
- "trim_offsets": true,
- "use_regex": true
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- "model": {
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- "end_of_word_suffix": "",
- "fuse_unk": false,
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- "11": 143,
- "5I": 144,
- "125I": 145,
- "11C": 146,
- "H3": 147,
- "\\N+1": 148,
- "-\\": 149,
- "/C@@": 150,
- "S@+1": 151,
- "As": 152,
- "/Cl": 153,
- "11CH3": 154,
- "=Se": 155,
- "S@@+1": 156,
- "N@+1": 157,
- "14": 158,
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- "14C": 160,
- "\\F": 161,
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- "Te": 163,
- "H2": 164,
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- "=O+1": 166,
- "N@@+1": 167,
- "C+1": 168,
- "=S+1": 169,
- "Zn": 170,
- "/P": 171,
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- "/I": 173,
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- "Al": 179,
- "/F": 180,
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- "13": 184,
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- "NaH1": 209,
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- "/125I": 250,
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- "2Rb+1": 370,
- "3Se": 371,
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- "45": 373,
- "47": 374,
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- "5I-1": 376,
- "73Se": 377,
- "89": 378,
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- "=32": 380,
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- "CH0": 382,
- "CH2": 383,
- "I+2": 384,
- "NH0": 385,
- "NH4": 386,
- "OH1": 387,
- "PH2+1": 388,
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- "\\3H": 391,
- "\\11CH3": 392,
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- "\\Se": 394,
- "Si@": 395,
- "Si-1": 396,
- "SiH1-1": 397,
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- "/Se": 399,
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- "\\NH1-1": 401,
- "18FH1": 402,
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- "11C-1": 405,
- "AsH1": 406,
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- "Te-1": 409,
- "Mg+1": 410,
- "123I-1": 411,
- "123Te": 412,
- "123IH1": 413,
- "135I": 414,
- "131I-1": 415,
- "Ag-4": 416,
- "124I-1": 417,
- "76BrH1": 418,
- "18OH1": 419,
- "22Na+1": 420,
- "223Ra+2": 421,
- "CaH2": 422,
- "45Ca+2": 423,
- "47Ca+2": 424,
- "89Sr+2": 425,
- "=32PH1": 426,
- "NH4+1": 427
- },
- "merges": [
- "B r",
- "a n",
- "c h",
- "Br an",
- "Bran ch",
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- "= C",
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- "Li +1",
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- "/ Br",
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- "12 3",
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- "1 3",
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- "BH2 -1",
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- "/ NH1",
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- "= 14C",
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- "\\ C@",
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- "= As",
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- "N H2+1",
- "Se H1",
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- "= Te",
- "Al +3",
- "Na H1",
- "=Te +1",
- "NH1 +1",
- "Ag +1",
- "H1 +1",
- "NH1 -1",
- "\\ P",
- "14C H2",
- "13 C",
- "14C H1",
- "= 11C",
- "S @@",
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- "H3 -1",
- "14C H3",
- "B H3-1",
- "S @",
- "=14C H1",
- "=P H1",
- "=P @",
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- "\\S +1",
- "12 4",
- "C H1-1",
- "S r",
- "=S i",
- "124 I",
- "Sr +2",
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- "/C -1",
- "N @",
- "/N -1",
- "13C H1",
- "/ B",
- "1 9",
- "B a+2",
- "H 4",
- "S H1+1",
- "Se +1",
- "19 F",
- "/ 125I",
- "P @+1",
- "R b",
- "Cl +1",
- "Si H4",
- "Rb +1",
- "= Branch3",
- "N @@",
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- "/ Si",
- "B H1-1",
- "S H1",
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- "= Mg",
- "H +1",
- "\\ B",
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- "P@@ +1",
- "- 2",
- "1 5",
- "1 7",
- "3 5",
- "= 13CH1",
- "C s",
- "=N H2+1",
- "=S H1",
- "Mg H2",
- "32 P",
- "17 F",
- "35 S",
- "Cs +1",
- "# 11C",
- "/ 131I",
- "B i",
- "\\ 125I",
- "=S @@",
- "\\S -1",
- "6 Br",
- "7 I",
- "7 6Br",
- "= B",
- "e H1",
- "\\N -1",
- "18 O",
- "12 7I",
- "11C H2",
- "14 C@@H1",
- "Te H2",
- "15 NH1",
- "Bi +3",
- "/ P+1",
- "/ 13C",
- "/ 13CH1",
- "0 B",
- "1 0B",
- "= Al",
- "= 18O",
- "B H0",
- "F -1",
- "N H3",
- "S -2",
- "Br +2",
- "Cl +2",
- "\\S i",
- "/S -1",
- "=P H2",
- "14 C@H1",
- "NH3 +1",
- "# 14C",
- "# O+1",
- "- 3",
- "2 2",
- "4 H",
- "5 Se",
- "5 Sr+2",
- "7 5Se",
- "8 5Sr+2",
- "= B-1",
- "= 13C",
- "@ -1",
- "B e",
- "B @@",
- "B @-1",
- "C a",
- "C H1",
- "I +3",
- "K H1",
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- "R a+2",
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- "=C a",
- "\\C H1-1",
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- "Se -1",
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- "Te H1",
- "Zn +1",
- "Zn -2",
- "Al -3",
- "13C H3",
- "15 N",
- "Be +2",
- "B@@ -1",
- "# P",
- "# S",
- "- 4",
- "/ PH1",
- "/ P@@",
- "/ As",
- "/ 14C",
- "/ 14CH1",
- "2 K+1",
- "2 Rb+1",
- "3 Se",
- "3 Ra+2",
- "4 5",
- "4 7",
- "4 2K+1",
- "5 I-1",
- "7 3Se",
- "8 9",
- "8 2Rb+1",
- "= 32",
- "= 32P",
- "C H0",
- "C H2",
- "I +2",
- "N H0",
- "N H4",
- "O H1",
- "P H2+1",
- "S H0",
- "S H2",
- "\\ 3H",
- "\\ 11CH3",
- "\\C -1",
- "\\S e",
- "Si @",
- "Si -1",
- "Si H1-1",
- "Si H3-1",
- "/S e",
- "Se -2",
- "\\NH1 -1",
- "18F H1",
- "12 5I-1",
- "11 C@@H1",
- "11 C-1",
- "As H1",
- "As -1",
- "14 C@@",
- "Te -1",
- "Mg +1",
- "123 I-1",
- "123 Te",
- "123I H1",
- "13 5I",
- "131 I-1",
- "Ag -4",
- "124 I-1",
- "76Br H1",
- "18O H1",
- "22 Na+1",
- "22 3Ra+2",
- "Ca H2",
- "45 Ca+2",
- "47 Ca+2",
- "89 Sr+2",
- "=32 PH1",
- "NH4 +1"
- ]
- }
-}
\ No newline at end of file
diff --git a/models/finetuned/tox21/tokenizer_config.json b/models/finetuned/tox21/tokenizer_config.json
deleted file mode 100644
index 08860954acd34fad07fd77f7635298fa565f3149..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/tokenizer_config.json
+++ /dev/null
@@ -1,65 +0,0 @@
-{
- "add_prefix_space": false,
- "bos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "cls_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "eos_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "errors": "replace",
- "mask_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": true,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "model_max_length": 1000000000000000019884624838656,
- "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
- "pad_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "sep_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- },
- "special_tokens_map_file": null,
- "tokenizer_class": "RobertaTokenizer",
- "trim_offsets": true,
- "unk_token": {
- "__type": "AddedToken",
- "content": "",
- "lstrip": false,
- "normalized": true,
- "rstrip": false,
- "single_word": false
- }
-}
diff --git a/models/finetuned/tox21/train_stdout.log b/models/finetuned/tox21/train_stdout.log
deleted file mode 100644
index 3360f20215181e93710f5f5cf87e7964fe267b0f..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/train_stdout.log
+++ /dev/null
@@ -1,92 +0,0 @@
-[finetune] starting
-[finetune] device=cuda task_type=multilabel batch_size=8 max_len=128 backbone_lr=1e-05 head_lr=0.0005 weight_decay=0.001 epochs=50
-[finetune] dataset_meta_csv=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/tox21/tox21.csv
-[finetune] dataset_embs_npz=/home/erva/SELFormerMM/data/new_finetuning_datasets/classification/tox21/tox21_embs.npz
-[finetune] model_path=HUBioDataLab/SELFormer tokenizer_path=HUBioDataLab/SELFormer
-[finetune] pretrained_multimodal_dir=/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36
-[finetune] use_scaffold=False seed=42 fracs=(0.8,0.1,0.1)
-[finetune] loading dataset bundle (meta csv + embs npz) ...
-[finetune] splitting dataset...
-[finetune] split sizes: train=6,264 val=783 test=784
-[finetune] train modality_non_empty: graph=6,258/6,264 text=4,796/6,264 kg=298/6,264
-[finetune] val modality_non_empty: graph=782/783 text=623/783 kg=25/783
-[finetune] test modality_non_empty: graph=783/784 text=592/784 kg=38/784
-[finetune] extracting labels...
-[finetune] multilabel: num_labels_in_csv=13
-[finetune] loading config/tokenizer/backbone...
-[finetune] initializing multimodal model...
-[finetune] loading multimodal pretrained weights: /home/erva/SELFormerMM/data/pretrained_multimodal_chembl36/pytorch_model.bin
-[finetune] freezing roberta layers (trainable: encoder.layer.9-11)...
-[finetune] backbone trainable params: 181,443,072/246,245,376
-[finetune] building datasets/dataloaders...
-[finetune] train_steps_per_epoch=783 val_steps=98 test_steps=98
-[finetune] overriding --num_labels=1 with num_labels_in_csv=13
-[finetune] initialized head: in_dim=3072 out=13
-[finetune] initializing optimizer/scheduler/finetuner...
-[finetune] optimizer groups: backbone_decay=45 backbone_nodecay=57 head_decay=2 head_nodecay=2
-[finetune] training loop...
-[finetune] epoch 1/50: train_loss=-216193.6333 val_loss=-113671.4013 time=54.7s tod=16:14
-[finetune] epoch 2/50: train_loss=-412453.9276 val_loss=-440000.0230 time=54.0s tod=16:15
-[finetune] epoch 3/50: train_loss=-887676.8236 val_loss=-952418.1257 time=54.5s tod=16:16
-[finetune] epoch 4/50: train_loss=-1524831.5284 val_loss=-1035367.8295 time=53.7s tod=16:17
-[finetune] epoch 5/50: train_loss=-2351748.6775 val_loss=-1452939.0927 time=54.0s tod=16:17
-[finetune] epoch 6/50: train_loss=-3184443.9216 val_loss=-1768902.9329 time=53.7s tod=16:18
-[finetune] epoch 7/50: train_loss=-4038405.9811 val_loss=-2172572.4858 time=53.4s tod=16:19
-[finetune] epoch 8/50: train_loss=-4937786.7989 val_loss=-2350164.7637 time=53.8s tod=16:20
-[finetune] epoch 9/50: train_loss=-5681205.7596 val_loss=-2605011.2469 time=54.0s tod=16:21
-[finetune] epoch 10/50: train_loss=-6567555.5207 val_loss=-2593369.0649 time=53.4s tod=16:22
-[finetune] epoch 11/50: train_loss=-7387322.5679 val_loss=-3612002.6768 time=54.1s tod=16:23
-[finetune] epoch 12/50: train_loss=-8185306.1467 val_loss=-2633102.3551 time=53.6s tod=16:24
-[finetune] epoch 13/50: train_loss=-8990810.3031 val_loss=-3891463.0388 time=53.9s tod=16:25
-[finetune] epoch 14/50: train_loss=-9759411.5767 val_loss=-4663161.3781 time=53.8s tod=16:25
-[finetune] epoch 15/50: train_loss=-10479519.1598 val_loss=-4013720.2909 time=53.3s tod=16:26
-[finetune] epoch 16/50: train_loss=-11349079.8151 val_loss=-3809875.2072 time=53.8s tod=16:27
-[finetune] epoch 17/50: train_loss=-12140997.0294 val_loss=-4012518.1141 time=53.9s tod=16:28
-[finetune] epoch 18/50: train_loss=-12888118.4571 val_loss=-4380830.4794 time=53.4s tod=16:29
-[finetune] epoch 19/50: train_loss=-13520204.9583 val_loss=-4382646.9831 time=54.1s tod=16:30
-[finetune] epoch 20/50: train_loss=-14241493.7080 val_loss=-5114424.9447 time=54.3s tod=16:31
-[finetune] epoch 21/50: train_loss=-14975536.1623 val_loss=-5732739.2004 time=53.6s tod=16:32
-[finetune] epoch 22/50: train_loss=-15634874.3266 val_loss=-5503666.0586 time=53.5s tod=16:33
-[finetune] epoch 23/50: train_loss=-16297291.1342 val_loss=-5298696.2058 time=54.2s tod=16:34
-[finetune] epoch 24/50: train_loss=-17026477.4266 val_loss=-4584186.9219 time=53.5s tod=16:34
-[finetune] epoch 25/50: train_loss=-17412736.1286 val_loss=-6193778.4885 time=54.4s tod=16:35
-/home/erva/SELFormerMM/train_finetuning.py:155: RuntimeWarning: overflow encountered in exp
- return 1.0 / (1.0 + np.exp(-x))
-[finetune] test_metrics: epoch=25 loss=-10717827.3358 accuracy=0.9269 precision=0.3792 recall=0.2921 f1=0.3300 roc-auc=0.6336 prc-auc=0.1858
-[finetune] saved checkpoint (best roc-auc=0.6336): /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/tox21/xyrw6rkc/checkpoint_epoch_025
-[finetune] epoch 26/50: train_loss=-18012359.0458 val_loss=-5623670.3106 time=54.0s tod=16:36
-[finetune] epoch 27/50: train_loss=-18672690.9479 val_loss=-6479933.9914 time=53.3s tod=16:37
-[finetune] epoch 28/50: train_loss=-19280746.8376 val_loss=-5831075.7259 time=54.2s tod=16:38
-[finetune] epoch 29/50: train_loss=-19729831.8720 val_loss=-7317136.4007 time=54.1s tod=16:39
-[finetune] epoch 30/50: train_loss=-20169510.6495 val_loss=-6095962.3972 time=53.9s tod=16:40
-[finetune] epoch 31/50: train_loss=-20712630.3428 val_loss=-6431097.9831 time=53.3s tod=16:41
-[finetune] epoch 32/50: train_loss=-21138979.2127 val_loss=-6581554.7533 time=53.1s tod=16:42
-[finetune] epoch 33/50: train_loss=-21585666.2917 val_loss=-6187379.4101 time=53.4s tod=16:43
-[finetune] epoch 34/50: train_loss=-21839427.5970 val_loss=-6638206.6535 time=53.3s tod=16:43
-[finetune] epoch 35/50: train_loss=-22323325.7181 val_loss=-7626298.3497 time=53.7s tod=16:44
-[finetune] epoch 36/50: train_loss=-22618891.8809 val_loss=-7537031.2214 time=52.6s tod=16:45
-[finetune] epoch 37/50: train_loss=-22912492.7341 val_loss=-6675574.5707 time=53.0s tod=16:46
-[finetune] epoch 38/50: train_loss=-23171182.0316 val_loss=-7554391.4859 time=53.0s tod=16:47
-[finetune] epoch 39/50: train_loss=-23530399.3391 val_loss=-7706676.0849 time=53.2s tod=16:48
-[finetune] epoch 40/50: train_loss=-23791565.5375 val_loss=-7679242.5749 time=54.1s tod=16:49
-[finetune] epoch 41/50: train_loss=-23953559.3519 val_loss=-7454979.6627 time=53.9s tod=16:50
-[finetune] epoch 42/50: train_loss=-24229901.7895 val_loss=-7261276.1295 time=53.6s tod=16:51
-[finetune] epoch 43/50: train_loss=-24433469.5779 val_loss=-7703355.7898 time=51.6s tod=16:51
-[finetune] epoch 44/50: train_loss=-24593268.4133 val_loss=-7843873.5753 time=54.6s tod=16:52
-[finetune] epoch 45/50: train_loss=-24648599.9635 val_loss=-8010940.1643 time=52.9s tod=16:53
-[finetune] epoch 46/50: train_loss=-24824771.2119 val_loss=-7650992.9769 time=54.5s tod=16:54
-[finetune] epoch 47/50: train_loss=-24919698.8539 val_loss=-7686188.3593 time=53.5s tod=16:55
-[finetune] epoch 48/50: train_loss=-24983982.4635 val_loss=-7849183.9679 time=53.2s tod=16:56
-[finetune] epoch 49/50: train_loss=-25026115.0519 val_loss=-8320514.8827 time=53.4s tod=16:57
-[finetune] epoch 50/50: train_loss=-25057941.0290 val_loss=-8258987.8504 time=52.9s tod=16:58
-/home/erva/SELFormerMM/train_finetuning.py:155: RuntimeWarning: overflow encountered in exp
- return 1.0 / (1.0 + np.exp(-x))
-[finetune] test_metrics: epoch=50 loss=-13557626.8894 accuracy=0.9364 precision=0.4714 recall=0.2648 f1=0.3392 roc-auc=0.6260 prc-auc=0.2032
-[finetune] checkpoint skipped (current roc-auc=0.6260 vs best=0.6336 at epoch 25)
-[finetune] final evaluation on test split...
-/home/erva/SELFormerMM/train_finetuning.py:155: RuntimeWarning: overflow encountered in exp
- return 1.0 / (1.0 + np.exp(-x))
-[finetune] test_metrics: loss=-13557626.8894 accuracy=0.9364 precision=0.4714 recall=0.2648 f1=0.3392 roc-auc=0.6260 prc-auc=0.2032
-[finetune] saving model...
-[finetune] saved finetuned model to: /media/ubuntu/8TB/erva/selformer-mm/output/new_finetune_sweeps/tox21/xyrw6rkc
-[finetune] done in 2697.0s
diff --git a/models/finetuned/tox21/vocab.json b/models/finetuned/tox21/vocab.json
deleted file mode 100644
index f7e4cc22809f4e9035cc450ef189c8a7da8fd03e..0000000000000000000000000000000000000000
--- a/models/finetuned/tox21/vocab.json
+++ /dev/null
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