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drugprot-scibert-ner-rel

Token Classification
Safetensors
English
biomedical
relation-extraction
named-entity-recognition
drugprot
scibert
Model card Files
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drugprot-scibert-ner-rel
File size: 2,820 Bytes
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{
 "bert_config": {
  "transformers_version": "5.22.2",
  "architectures": null,
  "output_hidden_states": false,
  "return_dict": true,
  "dtype": null,
  "chunk_size_feed_forward": 0,
  "is_encoder_decoder": false,
  "id2label": {
   "0": "LABEL_0",
   "1": "LABEL_1"
  },
  "label2id": {
   "LABEL_0": 0,
   "LABEL_1": 1
  },
  "problem_type": null,
  "vocab_size": 31116,
  "hidden_size": 768,
  "num_hidden_layers": 12,
  "num_attention_heads": 12,
  "intermediate_size": 3072,
  "hidden_act": "gelu",
  "hidden_dropout_prob": 0.1,
  "attention_probs_dropout_prob": 0.1,
  "max_position_embeddings": 512,
  "type_vocab_size": 2,
  "initializer_range": 0.02,
  "layer_norm_eps": 1e-12,
  "pad_token_id": 0,
  "use_cache": true,
  "classifier_dropout": null,
  "is_decoder": false,
  "add_cross_attention": false,
  "bos_token_id": null,
  "eos_token_id": null,
  "tie_word_embeddings": true,
  "_name_or_path": "",
  "model_type": "bert",
  "output_attentions": false
 },
 "max_span_width": 24,
 "head_hidden_size": 512,
 "dropout": 0.2,
 "relation_input": "markers",
 "relation_objective": "sigmoid",
 "relation_threshold": 0.5,
 "relation_markers": {
  "chemical_start": [
   5699,
   1360,
   3556,
   1360
  ],
  "chemical_end": [
   5699
  ],
  "gene_start": [
   3057,
   7691,
   1086,
   7691
  ],
  "gene_end": [
   3057
  ]
 },
 "ner_labels": [
  "None",
  "CHEMICAL",
  "GENE"
 ],
 "relation_labels": [
  "No_relation",
  "ACTIVATOR",
  "AGONIST",
  "AGONIST-ACTIVATOR",
  "AGONIST-INHIBITOR",
  "ANTAGONIST",
  "DIRECT-REGULATOR",
  "INDIRECT-DOWNREGULATOR",
  "INDIRECT-UPREGULATOR",
  "INHIBITOR",
  "PART-OF",
  "PRODUCT-OF",
  "SUBSTRATE",
  "SUBSTRATE_PRODUCT-OF"
 ],
 "checkpoint": "best",
 "epoch": 6,
 "step": 13895,
 "train_config": {
  "max_seq_len": 256,
  "max_span_width": 24,
  "head_hidden_size": 512,
  "dropout": 0.2,
  "relation_input": "markers",
  "relation_objective": "sigmoid",
  "relation_threshold": 0.5,
  "mode": "joint",
  "lambda_rel": 1.0,
  "max_pairs_per_step": 128,
  "epochs": 8,
  "max_steps": null,
  "batch_size": 16,
  "encoder_lr": 3e-05,
  "head_lr": 0.001,
  "weight_decay": 0.01,
  "warmup_proportion": 0.1,
  "grad_clip": 1.0,
  "bf16": false,
  "early_stopping_patience": 3,
  "eval_every_epochs": 1,
  "seed": 42
 },
 "provenance": {
  "corpus": "DrugProt (BioCreative VII Track 1) v1.2: training set minus 350 abstracts held out for model selection",
  "initialised_from": "allenai/scibert_scivocab_cased; NER and relation heads randomly initialised",
  "tokenizer": "allenai/scibert_scivocab_cased (cased, do_lower_case=False)",
  "mode": "joint",
  "lambda_rel": 1.0,
  "relation_input": "markers",
  "relation_objective": "sigmoid",
  "optimizer": "AdamW + linear warm-up/decay, global gradient-norm clipping",
  "seed": 42,
  "torch": "2.14.1+cu126"
 }
}