Delete models/finetuned

models/finetuned/bace/checkpoint_epoch_025/config.json

@@ -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
-}

models/finetuned/bace/checkpoint_epoch_025/merges.txt

@@ -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
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-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
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-\ O
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-\ S
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-Cl -1
-I -1
-/ C@@H1
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-/ 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
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-=P H1
-=P @
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-\S +1
-12 4
-C H1-1
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-1 9
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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
-7 I
-7 6Br
-= B
-e H1
-\N -1
-18 O
-12 7I
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-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
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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
-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

models/finetuned/bace/checkpoint_epoch_025/model.pt

@@ -1,3 +0,0 @@
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models/finetuned/bace/checkpoint_epoch_025/special_tokens_map.json

@@ -1,51 +0,0 @@
-{
-  "bos_token": {
-    "content": "<s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
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-    "lstrip": false,
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-    "single_word": false
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-    "content": "</s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
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-  "mask_token": {
-    "content": "<mask>",
-    "lstrip": true,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
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-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "sep_token": {
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-    "rstrip": false,
-    "single_word": false
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-    "content": "<unk>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  }
-}

models/finetuned/bace/checkpoint_epoch_025/tokenizer.json

@@ -1,909 +0,0 @@
-{
-  "version": "1.0",
-  "truncation": {
-    "direction": "Right",
-    "max_length": 128,
-    "strategy": "LongestFirst",
-    "stride": 0
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models/finetuned/bace/checkpoint_epoch_025/tokenizer_config.json

@@ -1,65 +0,0 @@
-{
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models/finetuned/bace/checkpoint_epoch_025/vocab.json

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models/finetuned/bace/config.json

@@ -1,27 +0,0 @@
-{
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models/finetuned/bace/merges.txt

@@ -1,378 +0,0 @@
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-      "\\ 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"
-    ]
-  }
-}

models/finetuned/bace/tokenizer_config.json

@@ -1,65 +0,0 @@
-{
-  "add_prefix_space": false,
-  "bos_token": {
-    "__type": "AddedToken",
-    "content": "<s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "cls_token": {
-    "__type": "AddedToken",
-    "content": "<s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "eos_token": {
-    "__type": "AddedToken",
-    "content": "</s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "errors": "replace",
-  "mask_token": {
-    "__type": "AddedToken",
-    "content": "<mask>",
-    "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": "<pad>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "sep_token": {
-    "__type": "AddedToken",
-    "content": "</s>",
-    "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": "<unk>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  }
-}

models/finetuned/bace/train_stdout.log

@@ -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

models/finetuned/bace/vocab.json

@@ -1 +0,0 @@
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models/finetuned/bbbp/checkpoint_epoch_025/config.json

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-{
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-  "architectures": [
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-  "pad_token_id": 1,
-  "position_embedding_type": "absolute",
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-  "type_vocab_size": 1,
-  "use_cache": true,
-  "vocab_size": 800
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models/finetuned/bbbp/checkpoint_epoch_025/merges.txt

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models/finetuned/bbbp/checkpoint_epoch_025/model.pt

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models/finetuned/bbbp/checkpoint_epoch_025/special_tokens_map.json

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-{
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-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
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-    "rstrip": false,
-    "single_word": false
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-  "mask_token": {
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models/finetuned/bbbp/checkpoint_epoch_025/tokenizer.json

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-{
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-      "= 13C",
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-      "B @@",
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-      "11 C@@H1",
-      "11 C-1",
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-      "131 I-1",
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-      "45 Ca+2",
-      "47 Ca+2",
-      "89 Sr+2",
-      "=32 PH1",
-      "NH4 +1"
-    ]
-  }
-}

models/finetuned/bbbp/checkpoint_epoch_025/tokenizer_config.json

@@ -1,65 +0,0 @@
-{
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-  "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
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-    "content": "<unk>",
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-    "normalized": true,
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models/finetuned/bbbp/checkpoint_epoch_025/vocab.json

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models/finetuned/bbbp/checkpoint_epoch_050/config.json

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-{
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-  "pad_token_id": 1,
-  "position_embedding_type": "absolute",
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-  "use_cache": true,
-  "vocab_size": 800
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models/finetuned/bbbp/checkpoint_epoch_050/merges.txt

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models/finetuned/bbbp/checkpoint_epoch_050/model.pt

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models/finetuned/bbbp/checkpoint_epoch_050/special_tokens_map.json

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-{
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-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
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-  },
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-  "mask_token": {
-    "content": "<mask>",
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-    "normalized": true,
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models/finetuned/bbbp/checkpoint_epoch_050/tokenizer.json

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-{
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-    "strategy": "LongestFirst",
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-      "= 13C",
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-      "B @@",
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-      "11 C-1",
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-      "131 I-1",
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-      "45 Ca+2",
-      "47 Ca+2",
-      "89 Sr+2",
-      "=32 PH1",
-      "NH4 +1"
-    ]
-  }
-}

models/finetuned/bbbp/checkpoint_epoch_050/tokenizer_config.json

@@ -1,65 +0,0 @@
-{
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-  "name_or_path": "/home/erva/SELFormerMM/data/pretrained_multimodal_chembl36",
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-    "content": "<unk>",
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-    "normalized": true,
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models/finetuned/bbbp/checkpoint_epoch_050/vocab.json

@@ -1 +0,0 @@
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models/finetuned/bbbp/config.json

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-{
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-  "architectures": [
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-  "layer_norm_eps": 1e-12,
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-  "model_type": "roberta",
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-  "num_hidden_layers": 12,
-  "pad_token_id": 1,
-  "position_embedding_type": "absolute",
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-  "transformers_version": "4.26.1",
-  "type_vocab_size": 1,
-  "use_cache": true,
-  "vocab_size": 800
-}

models/finetuned/bbbp/merges.txt

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models/finetuned/bbbp/model.pt

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models/finetuned/bbbp/special_tokens_map.json

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-{
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-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
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-    "normalized": true,
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-    "single_word": false
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-    "lstrip": false,
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models/finetuned/bbbp/tokenizer.json

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-{
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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,
-      "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,
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-      "SeH1": 205,
-      "-/Ring1": 206,
-      "=Te": 207,
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-      "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,
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-      "124": 232,
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-      "Sr": 234,
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-      "Sr+2": 237,
-      "#C-1": 238,
-      "/C-1": 239,
-      "N@": 240,
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-      "13CH1": 242,
-      "/B": 243,
-      "19": 244,
-      "Ba+2": 245,
-      "H4": 246,
-      "SH1+1": 247,
-      "Se+1": 248,
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-      "/125I": 250,
-      "P@+1": 251,
-      "Rb": 252,
-      "Cl+1": 253,
-      "SiH4": 254,
-      "Rb+1": 255,
-      "=Branch3": 256,
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-      "/131I": 283,
-      "Bi": 284,
-      "\\125I": 285,
-      "=S@@": 286,
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-      "6Br": 288,
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-      "76Br": 290,
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-      "eH1": 292,
-      "\\N-1": 293,
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-      "/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,
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-      "14C@H1": 317,
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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,
-      "KH1": 337,
-      "OH1+1": 338,
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-      "\\123I": 342,
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-      "18F-1": 350,
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-      "TeH1": 353,
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-      "15N": 358,
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-      "82Rb+1": 379,
-      "=32": 380,
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-      "I+2": 384,
-      "NH0": 385,
-      "NH4": 386,
-      "OH1": 387,
-      "PH2+1": 388,
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-      "SH2": 390,
-      "\\3H": 391,
-      "\\11CH3": 392,
-      "\\C-1": 393,
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-      "Si@": 395,
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-      "SiH1-1": 397,
-      "SiH3-1": 398,
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-      "Se-2": 400,
-      "\\NH1-1": 401,
-      "18FH1": 402,
-      "125I-1": 403,
-      "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
-    },
-    "merges": [
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-      "a n",
-      "c h",
-      "Br an",
-      "Bran ch",
-      "Branch 1",
-      "= C",
-      "R i",
-      "n g",
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-      "Ring 1",
-      "= Branch1",
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-      "= O",
-      "Ring 2",
-      "H 1",
-      "C @",
-      "= N",
-      "# Branch1",
-      "C@ @",
-      "= Branch2",
-      "C@ H1",
-      "C@@ H1",
-      "# Branch2",
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-      "O -1",
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-      "= S",
-      "=N +1",
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-      "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",
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-      "C -1",
-      "# N+1",
-      "B -1",
-      "+ 3",
-      "Cl +3",
-      "\\ NH1",
-      "L i",
-      "Li +1",
-      "P H1",
-      "1 8",
-      "18 F",
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-      "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"
-    ]
-  }
-}

models/finetuned/bbbp/tokenizer_config.json

@@ -1,65 +0,0 @@
-{
-  "add_prefix_space": false,
-  "bos_token": {
-    "__type": "AddedToken",
-    "content": "<s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "cls_token": {
-    "__type": "AddedToken",
-    "content": "<s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "eos_token": {
-    "__type": "AddedToken",
-    "content": "</s>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "errors": "replace",
-  "mask_token": {
-    "__type": "AddedToken",
-    "content": "<mask>",
-    "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": "<pad>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  },
-  "sep_token": {
-    "__type": "AddedToken",
-    "content": "</s>",
-    "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": "<unk>",
-    "lstrip": false,
-    "normalized": true,
-    "rstrip": false,
-    "single_word": false
-  }
-}

models/finetuned/bbbp/train_stdout.log

@@ -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

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models/finetuned/esol/checkpoint_epoch_025/config.json

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-{
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-  "position_embedding_type": "absolute",
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models/finetuned/esol/checkpoint_epoch_025/model.pt

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models/finetuned/esol/checkpoint_epoch_025/special_tokens_map.json

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-{
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models/finetuned/esol/checkpoint_epoch_025/tokenizer.json

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-{
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-      "B @@",
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-      "C H1",
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models/finetuned/esol/checkpoint_epoch_025/tokenizer_config.json

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models/finetuned/esol/checkpoint_epoch_025/vocab.json

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models/finetuned/esol/checkpoint_epoch_050/config.json

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-{
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models/finetuned/esol/checkpoint_epoch_050/merges.txt

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-      "= 13C",
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-      "B e",
-      "B @@",
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-      "Si H1-1",
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-      "131 I-1",
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-      "45 Ca+2",
-      "47 Ca+2",
-      "89 Sr+2",
-      "=32 PH1",
-      "NH4 +1"
-    ]
-  }
-}

models/finetuned/esol/checkpoint_epoch_050/tokenizer_config.json

@@ -1,65 +0,0 @@
-{
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