diff --git a/models/finetuned/bace/config.json b/models/finetuned/bace/config.json deleted file mode 100644 index 228d2b8873a018f2297c9a6e4c9ed365bed86152..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/config.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "_name_or_path": "data/epoch_267/hf", - "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, - "output_hidden_states": true, - "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/finetuning_optimized_config.json b/models/finetuned/bace/finetuning_optimized_config.json deleted file mode 100644 index 990f891548f7e8006ced416643b393abc97f1a79..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/classification/bace/bace.csv", - "dataset_embs_npz": "data/finetuning_datasets/classification/bace/bace_embs.npz", - "use_scaffold": 1, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "binary", - "label_column": "Class", - "num_labels": 2, - "batch_size": 16, - "max_len": 128, - "epochs": 25, - "backbone_lr": 5e-06, - "head_lr": 5e-05, - "weight_decay": 0.001, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": "data/models/finetuned/bace" -} diff --git a/models/finetuned/bace/merges.txt b/models/finetuned/bace/merges.txt deleted file mode 100644 index e630115f8c73e6a19033b40484129e4cd9e2e859..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/merges.txt +++ /dev/null @@ -1,162 +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 l -# C -/ C -N H1 -+ 1 -- 1 -= Ring1 -O -1 -N +1 -\ C -/ N -# N -= Ring2 -= S -=N +1 -N a -Na +1 -\ N -S +1 -/ O -\ S -\ O -Br -1 -I -1 -Cl -1 -/ C@H1 -Branch 3 -/ C@@H1 -= P -/ S -=N -1 -S i -K +1 -N -1 -S e -L i -Li +1 -+ 3 -Cl +3 -\ C@H1 -Ring 3 -\ C@@H1 -/ N+1 -/ P -\ F -P @ -2 H -P H1 -/ Br -N @ -P +1 -/ Cl -\ NH1 -\ Br -@ +1 -/ I -/ C@ -T e -\ N+1 -P@ @ -1 2 -5 I -\ O-1 -12 5I -/ F -# N+1 -\ Cl -N@ +1 -\ I -- / -/ C@@ -N@ @ -N@ @+1 --/ Ring2 -- \ -1 4 -B -1 -C -1 -S @+1 -14 C -H 2 -H 4 -I +1 -S -1 -\ P -=S +1 -=P @ -Si H4 -+ 2 -3 H -@ @+1 -A g -C +1 -S @@+1 -Cl +1 -=S e --\ Ring1 -H 0 -O H0 -1 1 -= Branch3 -= Te -M g -O +1 -Z n -\ C@ -\ S+1 -H1 -1 -Se H1 -P@ +1 --\ Ring2 -11 C -=Te +1 -Zn +2 -/ NH1 -1 8 -A s -B H2 -B H1-1 -C a -H 3 -O H1-1 -S H2 -=O +1 -Se +1 -Te H2 -125I H1 --/ Ring1 -14C H2 -Ag +1 -=Se +1 -Mg H2 -Mg +2 -11C H3 -18 F -BH2 -1 -Ca +2 diff --git a/models/finetuned/bace/model.pt b/models/finetuned/bace/model.pt deleted file mode 100644 index b899331cde40c9e7f760f7f8dd4af573845a8cde..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:f17ebde0f06fdca997a8be88bb399bd42ff14b293ddc28bd8223fcb9253dfb13 -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 - }, - "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/bace/tokenizer.json b/models/finetuned/bace/tokenizer.json deleted file mode 100644 index 352fe17863f4a3195683ccc43d7ad3fa2f7b339c..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/tokenizer.json +++ /dev/null @@ -1,473 +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, - 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89, - "/O": 90, - "\\S": 91, - "\\O": 92, - "Br-1": 93, - "I-1": 94, - "Cl-1": 95, - "/C@H1": 96, - "Branch3": 97, - "/C@@H1": 98, - "=P": 99, - "/S": 100, - "=N-1": 101, - "Si": 102, - "K+1": 103, - "N-1": 104, - "Se": 105, - "Li": 106, - "Li+1": 107, - "+3": 108, - "Cl+3": 109, - "\\C@H1": 110, - "Ring3": 111, - "\\C@@H1": 112, - "/N+1": 113, - "/P": 114, - "\\F": 115, - "P@": 116, - "2H": 117, - "PH1": 118, - "/Br": 119, - "N@": 120, - "P+1": 121, - "/Cl": 122, - "\\NH1": 123, - "\\Br": 124, - "@+1": 125, - "/I": 126, - "/C@": 127, - "Te": 128, - "\\N+1": 129, - "P@@": 130, - "12": 131, - "5I": 132, - "\\O-1": 133, - "125I": 134, - "/F": 135, - "#N+1": 136, - "\\Cl": 137, - "N@+1": 138, - "\\I": 139, - "-/": 140, - "/C@@": 141, - "N@@": 142, - "N@@+1": 143, - "-/Ring2": 144, - "-\\": 145, - "14": 146, - "B-1": 147, - "C-1": 148, - "S@+1": 149, - "14C": 150, - "H2": 151, - "H4": 152, - "I+1": 153, - "S-1": 154, - "\\P": 155, - "=S+1": 156, - "=P@": 157, - "SiH4": 158, - "+2": 159, - "3H": 160, - "@@+1": 161, - "Ag": 162, - "C+1": 163, - "S@@+1": 164, - "Cl+1": 165, - "=Se": 166, - "-\\Ring1": 167, - "H0": 168, - "OH0": 169, - "11": 170, - "=Branch3": 171, - "=Te": 172, - "Mg": 173, - "O+1": 174, - "Zn": 175, - "\\C@": 176, - "\\S+1": 177, - "H1-1": 178, - "SeH1": 179, - "P@+1": 180, - "-\\Ring2": 181, - "11C": 182, - "=Te+1": 183, - "Zn+2": 184, - "/NH1": 185, - "18": 186, - "As": 187, - "BH2": 188, - "BH1-1": 189, - "Ca": 190, - "H3": 191, - "OH1-1": 192, - "SH2": 193, - "=O+1": 194, - "Se+1": 195, - "TeH2": 196, - "125IH1": 197, - "-/Ring1": 198, - "14CH2": 199, - "Ag+1": 200, - "=Se+1": 201, - "MgH2": 202, - "Mg+2": 203, - "11CH3": 204, - "18F": 205, - "BH2-1": 206, - "Ca+2": 207 - }, - "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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a/models/finetuned/bace/vocab.json b/models/finetuned/bace/vocab.json deleted file mode 100644 index daba22de60cb1e3d92619fc69f523dd7592bde00..0000000000000000000000000000000000000000 --- a/models/finetuned/bace/vocab.json +++ /dev/null @@ -1 +0,0 @@ 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\ 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 228d2b8873a018f2297c9a6e4c9ed365bed86152..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/config.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "_name_or_path": "data/epoch_267/hf", - "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, - "output_hidden_states": true, - "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/finetuning_optimized_config.json b/models/finetuned/bbbp/finetuning_optimized_config.json deleted file mode 100644 index 9d65735621e777148d8a4b6e0c463c340b841a0d..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/classification/bbbp/bbbp.csv", - "dataset_embs_npz": "data/finetuning_datasets/classification/bbbp/bbbp_embs.npz", - "use_scaffold": 1, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "binary", - "label_column": "p_np", - "num_labels": 2, - "batch_size": 32, - "max_len": 128, - "epochs": 25, - "backbone_lr": 5e-05, - "head_lr": 1e-05, - "weight_decay": 0.1, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": 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a/models/finetuned/bbbp/vocab.json b/models/finetuned/bbbp/vocab.json deleted file mode 100644 index daba22de60cb1e3d92619fc69f523dd7592bde00..0000000000000000000000000000000000000000 --- a/models/finetuned/bbbp/vocab.json +++ /dev/null @@ -1 +0,0 @@ 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-} diff --git a/models/finetuned/esol/finetuning_optimized_config.json b/models/finetuned/esol/finetuning_optimized_config.json deleted file mode 100644 index e7e6237919a5786da27257b0426e8e5cb1ec20bd..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/regression/esol/esol.csv", - "dataset_embs_npz": "data/finetuning_datasets/regression/esol/esol_embs.npz", - "use_scaffold": 0, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "regression", - "label_column": "measured log solubility in mols per litre", - "num_labels": 1, - "batch_size": 8, - "max_len": 128, - "epochs": 100, - "backbone_lr": 5e-05, - "head_lr": 5e-05, - "weight_decay": 0.1, - "checkpoint_every": 25, - 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a/models/finetuned/esol/vocab.json b/models/finetuned/esol/vocab.json deleted file mode 100644 index daba22de60cb1e3d92619fc69f523dd7592bde00..0000000000000000000000000000000000000000 --- a/models/finetuned/esol/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 228d2b8873a018f2297c9a6e4c9ed365bed86152..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/config.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "_name_or_path": "data/epoch_267/hf", - "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, - "output_hidden_states": true, - "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/finetuning_optimized_config.json b/models/finetuned/freesolv/finetuning_optimized_config.json deleted file mode 100644 index 016fb1d8c559c6f670e0c87129e63c68129e1678..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/regression/freesolv/freesolv.csv", - "dataset_embs_npz": "data/finetuning_datasets/regression/freesolv/freesolv_embs.npz", - "use_scaffold": 0, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "regression", - "label_column": "freesolv", - "num_labels": 1, - "batch_size": 4, - "max_len": 128, - "epochs": 25, - "backbone_lr": 5e-05, - "head_lr": 0.0002, - "weight_decay": 0.001, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": "data/models/finetuned/freesolv" -} diff --git a/models/finetuned/freesolv/merges.txt b/models/finetuned/freesolv/merges.txt deleted file mode 100644 index e630115f8c73e6a19033b40484129e4cd9e2e859..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/merges.txt +++ /dev/null @@ -1,162 +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 l -# C -/ C -N H1 -+ 1 -- 1 -= Ring1 -O -1 -N +1 -\ C -/ N -# N -= Ring2 -= S -=N +1 -N a -Na +1 -\ N -S +1 -/ O -\ S -\ O -Br -1 -I -1 -Cl -1 -/ C@H1 -Branch 3 -/ C@@H1 -= P -/ S -=N -1 -S i -K +1 -N -1 -S e -L i -Li +1 -+ 3 -Cl +3 -\ C@H1 -Ring 3 -\ C@@H1 -/ N+1 -/ P -\ F -P @ -2 H -P H1 -/ Br -N @ -P +1 -/ Cl -\ NH1 -\ Br -@ +1 -/ I -/ C@ -T e -\ N+1 -P@ @ -1 2 -5 I -\ O-1 -12 5I -/ F -# 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"unk_token": "" -} diff --git a/models/finetuned/freesolv/vocab.json b/models/finetuned/freesolv/vocab.json deleted file mode 100644 index daba22de60cb1e3d92619fc69f523dd7592bde00..0000000000000000000000000000000000000000 --- a/models/finetuned/freesolv/vocab.json +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file 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/finetuning_optimized_config.json b/models/finetuned/hiv/finetuning_optimized_config.json deleted file mode 100644 index c83842257d4c1e98018376ba0924df5ca5daa6d8..0000000000000000000000000000000000000000 --- a/models/finetuned/hiv/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/classification/hiv/hiv.csv", - "dataset_embs_npz": "data/finetuning_datasets/classification/hiv/hiv_embs.npz", - "use_scaffold": 1, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "binary", - "label_column": "HIV_active", - "num_labels": 2, - "batch_size": 16, - "max_len": 128, - "epochs": 50, - "backbone_lr": 5e-5, - "head_lr": 5e-5, - "weight_decay": 0.0, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": "data/models/finetuned/hiv" -} 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` -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/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": { - "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/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, - "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, 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"\\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", - 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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 228d2b8873a018f2297c9a6e4c9ed365bed86152..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/config.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "_name_or_path": "data/epoch_267/hf", - "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, - "output_hidden_states": true, - "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/finetuning_optimized_config.json b/models/finetuned/lipo/finetuning_optimized_config.json deleted file mode 100644 index c4a442aa42678be758db1c453dd4587895fb322c..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/regression/lipo/lipo.csv", - "dataset_embs_npz": "data/finetuning_datasets/regression/lipo/lipo_embs.npz", - "use_scaffold": 0, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "regression", - "label_column": "lipo", - "num_labels": 1, - "batch_size": 32, - "max_len": 128, - "epochs": 100, - "backbone_lr": 5e-05, - "head_lr": 5e-06, - "weight_decay": 0.1, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": 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a/models/finetuned/lipo/vocab.json b/models/finetuned/lipo/vocab.json deleted file mode 100644 index daba22de60cb1e3d92619fc69f523dd7592bde00..0000000000000000000000000000000000000000 --- a/models/finetuned/lipo/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 228d2b8873a018f2297c9a6e4c9ed365bed86152..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/config.json +++ /dev/null @@ -1,28 +0,0 @@ -{ - "_name_or_path": "data/epoch_267/hf", - "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, - "output_hidden_states": true, - "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/finetuning_optimized_config.json b/models/finetuned/pdbbind_full/finetuning_optimized_config.json deleted file mode 100644 index fc22694722f7dd1fb9657adf0e0809b97708b4fb..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/finetuning_optimized_config.json +++ /dev/null @@ -1,24 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full.csv", - "dataset_embs_npz": "data/finetuning_datasets/regression/pdbbind_full/pdbbind_full_embs.npz", - "use_scaffold": 0, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "regression", - "label_column": "-logKd/Ki", - "num_labels": 1, - "batch_size": 32, - "max_len": 128, - "epochs": 75, - "backbone_lr": 5e-05, - "head_lr": 1e-06, - "weight_decay": 0.01, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": "data/models/finetuned/pdbbind_full" -} diff --git a/models/finetuned/pdbbind_full/merges.txt b/models/finetuned/pdbbind_full/merges.txt deleted file mode 100644 index e630115f8c73e6a19033b40484129e4cd9e2e859..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/merges.txt +++ /dev/null @@ -1,162 +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 l -# C -/ C -N H1 -+ 1 -- 1 -= Ring1 -O -1 -N +1 -\ C -/ N -# N -= Ring2 -= S -=N +1 -N a -Na +1 -\ N -S +1 -/ O -\ S -\ O -Br -1 -I -1 -Cl -1 -/ C@H1 -Branch 3 -/ C@@H1 -= P -/ S -=N -1 -S i -K +1 -N -1 -S e -L i -Li +1 -+ 3 -Cl +3 -\ C@H1 -Ring 3 -\ C@@H1 -/ N+1 -/ P -\ F -P @ -2 H -P H1 -/ Br -N @ -P +1 -/ Cl -\ NH1 -\ Br -@ +1 -/ I -/ C@ -T e -\ N+1 -P@ @ -1 2 -5 I -\ O-1 -12 5I -/ F -# N+1 -\ Cl -N@ +1 -\ I -- / -/ C@@ -N@ @ -N@ @+1 --/ Ring2 -- \ -1 4 -B -1 -C -1 -S @+1 -14 C -H 2 -H 4 -I +1 -S -1 -\ P -=S +1 -=P @ -Si H4 -+ 2 -3 H -@ @+1 -A g -C +1 -S @@+1 -Cl +1 -=S e --\ Ring1 -H 0 -O H0 -1 1 -= Branch3 -= Te -M g -O +1 -Z n -\ C@ -\ S+1 -H1 -1 -Se H1 -P@ +1 --\ Ring2 -11 C -=Te +1 -Zn +2 -/ NH1 -1 8 -A s -B H2 -B H1-1 -C a -H 3 -O H1-1 -S H2 -=O +1 -Se +1 -Te H2 -125I H1 --/ Ring1 -14C H2 -Ag +1 -=Se +1 -Mg H2 -Mg +2 -11C H3 -18 F -BH2 -1 -Ca +2 diff --git a/models/finetuned/pdbbind_full/model.pt b/models/finetuned/pdbbind_full/model.pt deleted file mode 100644 index db2db3cc556804a8b3f815d3d4b4b617f343f1ad..0000000000000000000000000000000000000000 --- a/models/finetuned/pdbbind_full/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:277b22d16091f3a608b0b34aa5783abfd80c773e6ea70788f13aa25ae5d35d42 -size 1022843005 diff --git 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800 -} diff --git a/models/finetuned/sider/finetuning_optimized_config.json b/models/finetuned/sider/finetuning_optimized_config.json deleted file mode 100644 index 039476500e2840173dc884b21a6563ab845a3f95..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/finetuning_optimized_config.json +++ /dev/null @@ -1,23 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/classification/sider/sider.csv", - "dataset_embs_npz": "data/finetuning_datasets/classification/sider/sider_embs.npz", - "use_scaffold": 0, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "multilabel", - "num_labels": 0, - "batch_size": 8, - "max_len": 128, - "epochs": 25, - "backbone_lr": 5e-05, - "head_lr": 5e-06, - "weight_decay": 0.001, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": "data/models/finetuned/sider" -} diff --git a/models/finetuned/sider/merges.txt b/models/finetuned/sider/merges.txt deleted file mode 100644 index e630115f8c73e6a19033b40484129e4cd9e2e859..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/merges.txt +++ /dev/null @@ -1,162 +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 l -# C -/ C -N H1 -+ 1 -- 1 -= Ring1 -O -1 -N +1 -\ C -/ N -# N -= Ring2 -= S -=N +1 -N a -Na +1 -\ N -S +1 -/ O -\ S -\ O -Br -1 -I -1 -Cl -1 -/ C@H1 -Branch 3 -/ C@@H1 -= P -/ S -=N -1 -S i -K +1 -N -1 -S e -L i -Li +1 -+ 3 -Cl +3 -\ C@H1 -Ring 3 -\ C@@H1 -/ N+1 -/ P -\ F -P @ -2 H -P H1 -/ Br -N @ -P +1 -/ Cl -\ NH1 -\ Br -@ +1 -/ I -/ C@ -T e -\ N+1 -P@ @ -1 2 -5 I -\ O-1 -12 5I -/ F -# N+1 -\ Cl -N@ +1 -\ I -- / -/ C@@ -N@ @ -N@ @+1 --/ Ring2 -- \ -1 4 -B -1 -C -1 -S @+1 -14 C -H 2 -H 4 -I +1 -S -1 -\ P -=S +1 -=P @ -Si H4 -+ 2 -3 H -@ @+1 -A g -C +1 -S @@+1 -Cl +1 -=S e --\ Ring1 -H 0 -O H0 -1 1 -= Branch3 -= Te -M g -O +1 -Z n -\ C@ -\ S+1 -H1 -1 -Se H1 -P@ +1 --\ Ring2 -11 C -=Te +1 -Zn +2 -/ NH1 -1 8 -A s -B H2 -B H1-1 -C a -H 3 -O H1-1 -S H2 -=O +1 -Se +1 -Te H2 -125I H1 --/ Ring1 -14C H2 -Ag +1 -=Se +1 -Mg H2 -Mg +2 -11C H3 -18 F -BH2 -1 -Ca +2 diff --git a/models/finetuned/sider/model.pt b/models/finetuned/sider/model.pt deleted file mode 100644 index 56e71b846b3bb896ae3c0bdba2311015805ea384..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/model.pt +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:dd89653008c78dcd0f09b46c16d389153df6d9a0afb37069163ca270e2e6bf00 -size 1023162557 diff --git a/models/finetuned/sider/special_tokens_map.json b/models/finetuned/sider/special_tokens_map.json deleted file mode 100644 index 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a/models/finetuned/sider/vocab.json b/models/finetuned/sider/vocab.json deleted file mode 100644 index daba22de60cb1e3d92619fc69f523dd7592bde00..0000000000000000000000000000000000000000 --- a/models/finetuned/sider/vocab.json +++ /dev/null @@ -1 +0,0 @@ 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800 -} diff --git a/models/finetuned/tox21/finetuning_optimized_config.json b/models/finetuned/tox21/finetuning_optimized_config.json deleted file mode 100644 index 12bef724d38f154a8bbd9c20dd2a46b726d2118a..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/finetuning_optimized_config.json +++ /dev/null @@ -1,23 +0,0 @@ -{ - "dataset_meta_csv": "data/finetuning_datasets/classification/tox21/tox21.csv", - "dataset_embs_npz": "data/finetuning_datasets/classification/tox21/tox21_embs.npz", - "use_scaffold": 0, - "seed": 42, - "train_frac": 0.8, - "val_frac": 0.1, - "test_frac": 0.1, - "model_path": "HUBioDataLab/SELFormer", - "tokenizer_path": "HUBioDataLab/SELFormer", - "pretrained_multimodal_dir": "data/models/SELFormerMM", - "task_type": "multilabel", - "num_labels": 0, - "batch_size": 4, - "max_len": 128, - "epochs": 25, - "backbone_lr": 1e-05, - "head_lr": 0.0001, - "weight_decay": 0.01, - "checkpoint_every": 25, - "test_eval_every": 0, - "save_dir": "data/models/finetuned/tox21" -} diff --git a/models/finetuned/tox21/merges.txt b/models/finetuned/tox21/merges.txt deleted file mode 100644 index e630115f8c73e6a19033b40484129e4cd9e2e859..0000000000000000000000000000000000000000 --- a/models/finetuned/tox21/merges.txt +++ /dev/null @@ -1,162 +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 l -# C -/ C -N H1 -+ 1 -- 1 -= Ring1 -O -1 -N +1 -\ C -/ N -# N -= Ring2 -= S -=N +1 -N a -Na +1 -\ N -S +1 -/ O -\ S -\ O -Br -1 -I -1 -Cl -1 -/ C@H1 -Branch 3 -/ C@@H1 -= P -/ S -=N -1 -S i -K +1 -N -1 -S e -L i -Li +1 -+ 3 -Cl +3 -\ C@H1 -Ring 3 -\ C@@H1 -/ N+1 -/ P -\ F -P @ -2 H -P H1 -/ Br -N @ -P +1 -/ Cl -\ NH1 -\ Br -@ +1 -/ I -/ C@ -T e -\ N+1 -P@ @ -1 2 -5 I -\ O-1 -12 5I -/ F -# N+1 -\ Cl -N@ +1 -\ I -- / -/ C@@ -N@ @ -N@ @+1 --/ Ring2 -- \ -1 4 -B -1 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