Upload 7 files
Browse files- added_tokens.json +1 -0
- config.json +124 -0
- special_tokens_map.json +1 -0
- tf_model.h5 +3 -0
- tokenizer.json +0 -0
- tokenizer_config.json +1 -0
- vocab.txt +0 -0
added_tokens.json
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{"@DiseaseSrc$": 28920, "@/DiseaseOrPhenotypicFeatureTgt$": 28900, "@GeneOrGeneProductTgt$": 28924, "@/DiseaseOrPhenotypicFeatureSrc$": 28899, "@CHEMICALSrc$": 28914, "@ChemicalSrc$": 28917, "@/ChemicalEntitySrc$": 28896, "@/GeneOrGeneProductTgt$": 28905, "@DiseaseOrPhenotypicFeatureSrc$": 28918, "@/drugTgt$": 28911, "@/GeneTgt$": 28907, "@/GeneSrc$": 28906, "@/ChemicalEntityTgt$": 28897, "@DiseaseTgt$": 28921, "@GeneSrc$": 28925, "@SequenceVariantSrc$": 28927, "@/SequenceVariantSrc$": 28908, "@/SequenceVariantTgt$": 28909, "@GeneTgt$": 28926, "@/proteinTgt$": 28913, "@GENETgt$": 28922, "@GeneOrGeneProductSrc$": 28923, "@/GENETgt$": 28903, "@proteinSrc$": 28931, "@/drugSrc$": 28910, "@SequenceVariantTgt$": 28928, "@DiseaseOrPhenotypicFeatureTgt$": 28919, "@ChemicalEntityTgt$": 28916, "@drugTgt$": 28930, "@/CHEMICALSrc$": 28895, "@/DiseaseSrc$": 28901, "@/GeneOrGeneProductSrc$": 28904, "@proteinTgt$": 28932, "@/DiseaseTgt$": 28902, "@drugSrc$": 28929, "@ChemicalEntitySrc$": 28915, "@/ChemicalSrc$": 28898, "@/proteinSrc$": 28912}
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config.json
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{
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"_name_or_path": "michiyasunaga/BioLinkBERT-base",
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"architectures": [
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"BertForSequenceClassification"
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],
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"attention_probs_dropout_prob": 0.1,
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"classifier_dropout": null,
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"finetuning_task": "text-classification",
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"gradient_checkpointing": false,
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"hidden_act": "gelu",
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"hidden_dropout_prob": 0.1,
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"hidden_size": 768,
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"id2label": {
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"0": "None",
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"1": "Association",
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"2": "Bind",
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"3": "Comparison",
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"4": "Conversion",
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"5": "Cotreatment",
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"6": "Drug_Interaction",
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"7": "Negative_Correlation",
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"8": "Positive_Correlation",
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"9": "None-CID",
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"10": "CID",
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"11": "None-PPIm",
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"12": "PPIm",
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"13": "None-AIMED",
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"14": "None-DDI",
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"15": "None-BC7",
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"16": "None-phargkb",
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"17": "None-GDA",
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"18": "None-DISGENET",
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"19": "None-EMU_BC",
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"20": "None-EMU_PC",
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"21": "None-HPRD50",
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"22": "None-PHARMGKB",
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"23": "ACTIVATOR",
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"24": "AGONIST",
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"25": "AGONIST-ACTIVATOR",
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"26": "AGONIST-INHIBITOR",
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"27": "ANTAGONIST",
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"28": "DIRECT-REGULATOR",
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"29": "INDIRECT-DOWNREGULATOR",
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"30": "INDIRECT-UPREGULATOR",
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"31": "INHIBITOR",
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"32": "PART-OF",
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"33": "PRODUCT-OF",
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"34": "SUBSTRATE",
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"35": "SUBSTRATE_PRODUCT-OF",
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"36": "mechanism",
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"37": "int",
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"38": "effect",
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"39": "advise",
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"40": "AIMED-Association",
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"41": "HPRD-Association",
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"42": "EUADR-Association",
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"43": "None-EUADR",
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"44": "Indirect_conversion",
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"45": "Non_conversion",
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"46": "None-Conversion"
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},
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"initializer_range": 0.02,
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"intermediate_size": 3072,
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"label2id": {
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"ACTIVATOR": 23,
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"AGONIST": 24,
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"AGONIST-ACTIVATOR": 25,
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"AGONIST-INHIBITOR": 26,
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"AIMED-Association": 40,
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"ANTAGONIST": 27,
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"Association": 1,
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"Bind": 2,
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"CID": 10,
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"Comparison": 3,
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"Conversion": 4,
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"Cotreatment": 5,
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"DIRECT-REGULATOR": 28,
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"Drug_Interaction": 6,
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"EUADR-Association": 42,
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"HPRD-Association": 41,
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"INDIRECT-DOWNREGULATOR": 29,
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"INDIRECT-UPREGULATOR": 30,
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"INHIBITOR": 31,
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"Indirect_conversion": 44,
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"Negative_Correlation": 7,
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"Non_conversion": 45,
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"None": 0,
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"None-AIMED": 13,
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"None-BC7": 15,
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"None-CID": 9,
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"None-Conversion": 46,
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"None-DDI": 14,
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"None-DISGENET": 18,
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"None-EMU_BC": 19,
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"None-EMU_PC": 20,
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"None-EUADR": 43,
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"None-GDA": 17,
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"None-HPRD50": 21,
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"None-PHARMGKB": 22,
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"None-PPIm": 11,
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"None-phargkb": 16,
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"PART-OF": 32,
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"PPIm": 12,
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"PRODUCT-OF": 33,
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"Positive_Correlation": 8,
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"SUBSTRATE": 34,
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"SUBSTRATE_PRODUCT-OF": 35,
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"advise": 39,
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"effect": 38,
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"int": 37,
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"mechanism": 36
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},
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"layer_norm_eps": 1e-12,
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"max_position_embeddings": 512,
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"model_type": "bert",
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"num_attention_heads": 12,
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"num_hidden_layers": 12,
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"pad_token_id": 0,
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"position_embedding_type": "absolute",
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"transformers_version": "4.18.0",
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"type_vocab_size": 2,
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"use_cache": true,
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"vocab_size": 28933
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}
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special_tokens_map.json
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{"unk_token": "[UNK]", "sep_token": "[SEP]", "pad_token": "[PAD]", "cls_token": "[CLS]", "mask_token": "[MASK]", "additional_special_tokens": ["@/CHEMICALSrc$", "@/ChemicalEntitySrc$", "@/ChemicalEntityTgt$", "@/ChemicalSrc$", "@/DiseaseOrPhenotypicFeatureSrc$", "@/DiseaseOrPhenotypicFeatureTgt$", "@/DiseaseSrc$", "@/DiseaseTgt$", "@/GENETgt$", "@/GeneOrGeneProductSrc$", "@/GeneOrGeneProductTgt$", "@/GeneSrc$", "@/GeneTgt$", "@/SequenceVariantSrc$", "@/SequenceVariantTgt$", "@/drugSrc$", "@/drugTgt$", "@/proteinSrc$", "@/proteinTgt$", "@CHEMICALSrc$", "@ChemicalEntitySrc$", "@ChemicalEntityTgt$", "@ChemicalSrc$", "@DiseaseOrPhenotypicFeatureSrc$", "@DiseaseOrPhenotypicFeatureTgt$", "@DiseaseSrc$", "@DiseaseTgt$", "@GENETgt$", "@GeneOrGeneProductSrc$", "@GeneOrGeneProductTgt$", "@GeneSrc$", "@GeneTgt$", "@SequenceVariantSrc$", "@SequenceVariantTgt$", "@drugSrc$", "@drugTgt$", "@proteinSrc$", "@proteinTgt$"]}
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tf_model.h5
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version https://git-lfs.github.com/spec/v1
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oid sha256:1e6ce8f1617635a12d3fa05442123529a01d445f4c2a2293bdea05907b011c9c
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size 522368624
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tokenizer.json
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tokenizer_config.json
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{"do_lower_case": true, "unk_token": "[UNK]", "sep_token": "[SEP]", "pad_token": "[PAD]", "cls_token": "[CLS]", "mask_token": "[MASK]", "tokenize_chinese_chars": true, "strip_accents": null, "special_tokens_map_file": null, "name_or_path": "michiyasunaga/BioLinkBERT-base", "do_basic_tokenize": true, "never_split": null, "additional_special_tokens": ["@/CHEMICALSrc$", "@/ChemicalEntitySrc$", "@/ChemicalEntityTgt$", "@/ChemicalSrc$", "@/DiseaseOrPhenotypicFeatureSrc$", "@/DiseaseOrPhenotypicFeatureTgt$", "@/DiseaseSrc$", "@/DiseaseTgt$", "@/GENETgt$", "@/GeneOrGeneProductSrc$", "@/GeneOrGeneProductTgt$", "@/GeneSrc$", "@/GeneTgt$", "@/SequenceVariantSrc$", "@/SequenceVariantTgt$", "@/drugSrc$", "@/drugTgt$", "@/proteinSrc$", "@/proteinTgt$", "@CHEMICALSrc$", "@ChemicalEntitySrc$", "@ChemicalEntityTgt$", "@ChemicalSrc$", "@DiseaseOrPhenotypicFeatureSrc$", "@DiseaseOrPhenotypicFeatureTgt$", "@DiseaseSrc$", "@DiseaseTgt$", "@GENETgt$", "@GeneOrGeneProductSrc$", "@GeneOrGeneProductTgt$", "@GeneSrc$", "@GeneTgt$", "@SequenceVariantSrc$", "@SequenceVariantTgt$", "@drugSrc$", "@drugTgt$", "@proteinSrc$", "@proteinTgt$"], "tokenizer_class": "BertTokenizer"}
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vocab.txt
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