Upload 7 files

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}

config.json

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+{
+  "_name_or_path": "michiyasunaga/BioLinkBERT-base",
+  "architectures": [
+    "BertForSequenceClassification"
+  ],
+  "attention_probs_dropout_prob": 0.1,
+  "classifier_dropout": null,
+  "finetuning_task": "text-classification",
+  "gradient_checkpointing": false,
+  "hidden_act": "gelu",
+  "hidden_dropout_prob": 0.1,
+  "hidden_size": 768,
+  "id2label": {
+    "0": "None",
+    "1": "Association",
+    "2": "Bind",
+    "3": "Comparison",
+    "4": "Conversion",
+    "5": "Cotreatment",
+    "6": "Drug_Interaction",
+    "7": "Negative_Correlation",
+    "8": "Positive_Correlation",
+    "9": "None-CID",
+    "10": "CID",
+    "11": "None-PPIm",
+    "12": "PPIm",
+    "13": "None-AIMED",
+    "14": "None-DDI",
+    "15": "None-BC7",
+    "16": "None-phargkb",
+    "17": "None-GDA",
+    "18": "None-DISGENET",
+    "19": "None-EMU_BC",
+    "20": "None-EMU_PC",
+    "21": "None-HPRD50",
+    "22": "None-PHARMGKB",
+    "23": "ACTIVATOR",
+    "24": "AGONIST",
+    "25": "AGONIST-ACTIVATOR",
+    "26": "AGONIST-INHIBITOR",
+    "27": "ANTAGONIST",
+    "28": "DIRECT-REGULATOR",
+    "29": "INDIRECT-DOWNREGULATOR",
+    "30": "INDIRECT-UPREGULATOR",
+    "31": "INHIBITOR",
+    "32": "PART-OF",
+    "33": "PRODUCT-OF",
+    "34": "SUBSTRATE",
+    "35": "SUBSTRATE_PRODUCT-OF",
+    "36": "mechanism",
+    "37": "int",
+    "38": "effect",
+    "39": "advise",
+    "40": "AIMED-Association",
+    "41": "HPRD-Association",
+    "42": "EUADR-Association",
+    "43": "None-EUADR",
+    "44": "Indirect_conversion",
+    "45": "Non_conversion",
+    "46": "None-Conversion"
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 3072,
+  "label2id": {
+    "ACTIVATOR": 23,
+    "AGONIST": 24,
+    "AGONIST-ACTIVATOR": 25,
+    "AGONIST-INHIBITOR": 26,
+    "AIMED-Association": 40,
+    "ANTAGONIST": 27,
+    "Association": 1,
+    "Bind": 2,
+    "CID": 10,
+    "Comparison": 3,
+    "Conversion": 4,
+    "Cotreatment": 5,
+    "DIRECT-REGULATOR": 28,
+    "Drug_Interaction": 6,
+    "EUADR-Association": 42,
+    "HPRD-Association": 41,
+    "INDIRECT-DOWNREGULATOR": 29,
+    "INDIRECT-UPREGULATOR": 30,
+    "INHIBITOR": 31,
+    "Indirect_conversion": 44,
+    "Negative_Correlation": 7,
+    "Non_conversion": 45,
+    "None": 0,
+    "None-AIMED": 13,
+    "None-BC7": 15,
+    "None-CID": 9,
+    "None-Conversion": 46,
+    "None-DDI": 14,
+    "None-DISGENET": 18,
+    "None-EMU_BC": 19,
+    "None-EMU_PC": 20,
+    "None-EUADR": 43,
+    "None-GDA": 17,
+    "None-HPRD50": 21,
+    "None-PHARMGKB": 22,
+    "None-PPIm": 11,
+    "None-phargkb": 16,
+    "PART-OF": 32,
+    "PPIm": 12,
+    "PRODUCT-OF": 33,
+    "Positive_Correlation": 8,
+    "SUBSTRATE": 34,
+    "SUBSTRATE_PRODUCT-OF": 35,
+    "advise": 39,
+    "effect": 38,
+    "int": 37,
+    "mechanism": 36
+  },
+  "layer_norm_eps": 1e-12,
+  "max_position_embeddings": 512,
+  "model_type": "bert",
+  "num_attention_heads": 12,
+  "num_hidden_layers": 12,
+  "pad_token_id": 0,
+  "position_embedding_type": "absolute",
+  "transformers_version": "4.18.0",
+  "type_vocab_size": 2,
+  "use_cache": true,
+  "vocab_size": 28933
+}

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$", "@proteinTgt$"]}

tf_model.h5

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+version https://git-lfs.github.com/spec/v1
+oid sha256:1e6ce8f1617635a12d3fa05442123529a01d445f4c2a2293bdea05907b011c9c
+size 522368624

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"}