Instructions to use judithrosell/PubMedBERT-ft-ner with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use judithrosell/PubMedBERT-ft-ner with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("token-classification", model="judithrosell/PubMedBERT-ft-ner")# Load model directly from transformers import AutoTokenizer, AutoModelForTokenClassification tokenizer = AutoTokenizer.from_pretrained("judithrosell/PubMedBERT-ft-ner") model = AutoModelForTokenClassification.from_pretrained("judithrosell/PubMedBERT-ft-ner") - Notebooks
- Google Colab
- Kaggle
| { | |
| "_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": "B-Organism_subdivision", | |
| "1": "I-Pathological_formation", | |
| "2": "I-Anatomical_system", | |
| "3": "B-Immaterial_anatomical_entity", | |
| "4": "I-GGP", | |
| "5": "I-Organism", | |
| "6": "I-CL", | |
| "7": "B-Organism", | |
| "8": "B-DNA", | |
| "9": "I-Gene_or_gene_product", | |
| "10": "I-Tissue", | |
| "11": "B-Developing_anatomical_structure", | |
| "12": "I-RNA", | |
| "13": "I-CHEBI", | |
| "14": "B-Multi-tissue_structure", | |
| "15": "I-DNA", | |
| "16": "B-GO", | |
| "17": "O", | |
| "18": "B-Cell", | |
| "19": "I-Multi-tissue_structure", | |
| "20": "B-cell_type", | |
| "21": "I-Immaterial_anatomical_entity", | |
| "22": "B-RNA", | |
| "23": "B-Cancer", | |
| "24": "I-Organism_subdivision", | |
| "25": "B-protein", | |
| "26": "B-Chemical", | |
| "27": "I-protein", | |
| "28": "I-Simple_chemical", | |
| "29": "I-Disease", | |
| "30": "I-Cellular_component", | |
| "31": "I-Chemical", | |
| "32": "B-Amino_acid", | |
| "33": "I-Organism_substance", | |
| "34": "I-Developing_anatomical_structure", | |
| "35": "I-SO", | |
| "36": "I-cell_type", | |
| "37": "B-Tissue", | |
| "38": "B-Organism_substance", | |
| "39": "B-GGP", | |
| "40": "B-cell_line", | |
| "41": "B-CHEBI", | |
| "42": "B-Organ", | |
| "43": "B-Gene_or_gene_product", | |
| "44": "I-Amino_acid", | |
| "45": "B-Taxon", | |
| "46": "I-GO", | |
| "47": "I-Organ", | |
| "48": "I-cell_line", | |
| "49": "I-Cancer", | |
| "50": "I-Cell", | |
| "51": "B-SO", | |
| "52": "B-Anatomical_system", | |
| "53": "B-CL", | |
| "54": "B-Simple_chemical", | |
| "55": "B-Disease", | |
| "56": "I-Taxon", | |
| "57": "B-Cellular_component", | |
| "58": "B-Pathological_formation" | |
| }, | |
| "initializer_range": 0.02, | |
| "intermediate_size": 3072, | |
| "label2id": { | |
| "B-Amino_acid": 32, | |
| "B-Anatomical_system": 52, | |
| "B-CHEBI": 41, | |
| "B-CL": 53, | |
| "B-Cancer": 23, | |
| "B-Cell": 18, | |
| "B-Cellular_component": 57, | |
| "B-Chemical": 26, | |
| "B-DNA": 8, | |
| "B-Developing_anatomical_structure": 11, | |
| "B-Disease": 55, | |
| "B-GGP": 39, | |
| "B-GO": 16, | |
| "B-Gene_or_gene_product": 43, | |
| "B-Immaterial_anatomical_entity": 3, | |
| "B-Multi-tissue_structure": 14, | |
| "B-Organ": 42, | |
| "B-Organism": 7, | |
| "B-Organism_subdivision": 0, | |
| "B-Organism_substance": 38, | |
| "B-Pathological_formation": 58, | |
| "B-RNA": 22, | |
| "B-SO": 51, | |
| "B-Simple_chemical": 54, | |
| "B-Taxon": 45, | |
| "B-Tissue": 37, | |
| "B-cell_line": 40, | |
| "B-cell_type": 20, | |
| "B-protein": 25, | |
| "I-Amino_acid": 44, | |
| "I-Anatomical_system": 2, | |
| "I-CHEBI": 13, | |
| "I-CL": 6, | |
| "I-Cancer": 49, | |
| "I-Cell": 50, | |
| "I-Cellular_component": 30, | |
| "I-Chemical": 31, | |
| "I-DNA": 15, | |
| "I-Developing_anatomical_structure": 34, | |
| "I-Disease": 29, | |
| "I-GGP": 4, | |
| "I-GO": 46, | |
| "I-Gene_or_gene_product": 9, | |
| "I-Immaterial_anatomical_entity": 21, | |
| "I-Multi-tissue_structure": 19, | |
| "I-Organ": 47, | |
| "I-Organism": 5, | |
| "I-Organism_subdivision": 24, | |
| "I-Organism_substance": 33, | |
| "I-Pathological_formation": 1, | |
| "I-RNA": 12, | |
| "I-SO": 35, | |
| "I-Simple_chemical": 28, | |
| "I-Taxon": 56, | |
| "I-Tissue": 10, | |
| "I-cell_line": 48, | |
| "I-cell_type": 36, | |
| "I-protein": 27, | |
| "O": 17 | |
| }, | |
| "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": "4.34.0", | |
| "type_vocab_size": 2, | |
| "use_cache": true, | |
| "vocab_size": 30522 | |
| } | |