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BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1

Token Classification
Transformers
PyTorch
English
bert
biology
protein structure
token classification
Eval Results
Inference Endpoints
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BiomedNLP-PubMedBERT-ProteinStructure-NER-v3.1
File size: 2,848 Bytes 
ab43145
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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{
  "_name_or_path": "microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext",
  "architectures": [
    "BertForTokenClassification"
  ],
  "attention_probs_dropout_prob": 0.1,
  "classifier_dropout": null,
  "hidden_act": "gelu",
  "hidden_dropout_prob": 0.1,
  "hidden_size": 768,
  "id2label": {
    "0": "O",
    "1": "B-chemical",
    "2": "B-species",
    "3": "B-gene",
    "4": "I-gene",
    "5": "B-taxonomy_domain",
    "6": "I-chemical",
    "7": "B-protein_type",
    "8": "B-experimental_method",
    "9": "I-experimental_method",
    "10": "I-protein_type",
    "11": "I-species",
    "12": "B-evidence",
    "13": "I-evidence",
    "14": "B-protein",
    "15": "I-protein",
    "16": "B-protein_state",
    "17": "B-site",
    "18": "I-site",
    "19": "B-structure_element",
    "20": "I-structure_element",
    "21": "B-complex_assembly",
    "22": "I-protein_state",
    "23": "I-complex_assembly",
    "24": "B-ptm",
    "25": "B-mutant",
    "26": "I-mutant",
    "27": "B-oligomeric_state",
    "28": "B-residue_name_number",
    "29": "B-bond_interaction",
    "30": "I-bond_interaction",
    "31": "B-residue_range",
    "32": "I-residue_range",
    "33": "B-residue_name",
    "34": "B-residue_number",
    "35": "I-ptm",
    "36": "I-taxonomy_domain",
    "37": "I-oligomeric_state",
    "38": "I-residue_name_number",
    "39": "I-residue_name",
    "40": "I-residue_number"
  },
  "initializer_range": 0.02,
  "intermediate_size": 3072,
  "label2id": {
    "B-bond_interaction": 29,
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    "B-complex_assembly": 21,
    "B-evidence": 12,
    "B-experimental_method": 8,
    "B-gene": 3,
    "B-mutant": 25,
    "B-oligomeric_state": 27,
    "B-protein": 14,
    "B-protein_state": 16,
    "B-protein_type": 7,
    "B-ptm": 24,
    "B-residue_name": 33,
    "B-residue_name_number": 28,
    "B-residue_number": 34,
    "B-residue_range": 31,
    "B-site": 17,
    "B-species": 2,
    "B-structure_element": 19,
    "B-taxonomy_domain": 5,
    "I-bond_interaction": 30,
    "I-chemical": 6,
    "I-complex_assembly": 23,
    "I-evidence": 13,
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    "I-gene": 4,
    "I-mutant": 26,
    "I-oligomeric_state": 37,
    "I-protein": 15,
    "I-protein_state": 22,
    "I-protein_type": 10,
    "I-ptm": 35,
    "I-residue_name": 39,
    "I-residue_name_number": 38,
    "I-residue_number": 40,
    "I-residue_range": 32,
    "I-site": 18,
    "I-species": 11,
    "I-structure_element": 20,
    "I-taxonomy_domain": 36,
    "O": 0
  },
  "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",
  "torch_dtype": "float32",
  "transformers_version": "4.28.0",
  "type_vocab_size": 2,
  "use_cache": true,
  "vocab_size": 30522
}