BioNLP13CG_bioBERT_NER

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BioNLP13CG_bioBERT_NER

This model is a fine-tuned version of dmis-lab/biobert-v1.1 on the None dataset. It achieves the following results on the evaluation set:

• Loss: 0.1928

• Seqeval classification report: precision recall f1-score support

                 Amino_acid       0.89      0.88      0.88       576
          Anatomical_system       0.96      0.82      0.89       317
                     Cancer       0.92      0.91      0.91      1649
                       Cell       0.00      0.00      0.00        25
         Cellular_component       0.00      0.00      0.00        12
  

Developing_anatomical_structure 0.75 0.85 0.80 438 Gene_or_gene_product 0.87 0.18 0.29 74 Immaterial_anatomical_entity 0.84 0.84 0.84 4142 Multi-tissue_structure 0.85 0.84 0.84 451 Organ 0.51 0.23 0.31 80 Organism 0.52 0.66 0.58 182 Organism_subdivision 0.81 0.80 0.81 314 Organism_substance 0.73 0.66 0.69 96 Pathological_formation 0.75 0.68 0.71 262 Simple_chemical 0.55 0.44 0.49 112 Tissue 0.82 0.91 0.87 300

                  micro avg       0.84      0.82      0.83      9030
                  macro avg       0.67      0.60      0.62      9030
               weighted avg       0.84      0.82      0.83      9030

Model description

More information needed

Intended uses & limitations

More information needed

Training and evaluation data

More information needed

Training procedure

Training hyperparameters

The following hyperparameters were used during training:

• learning_rate: 2e-05
• train_batch_size: 16
• eval_batch_size: 16
• seed: 42
• gradient_accumulation_steps: 2
• total_train_batch_size: 32
• optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
• lr_scheduler_type: linear
• num_epochs: 3

Training results

                 Amino_acid       0.68      0.81      0.73       576
          Anatomical_system       0.93      0.74      0.82       317
                     Cancer       0.89      0.89      0.89      1649
                       Cell       0.00      0.00      0.00        25
         Cellular_component       0.00      0.00      0.00        12

Developing_anatomical_structure 0.56 0.79 0.65 438 Gene_or_gene_product 0.00 0.00 0.00 74 Immaterial_anatomical_entity 0.79 0.76 0.77 4142 Multi-tissue_structure 0.84 0.75 0.79 451 Organ 0.00 0.00 0.00 80 Organism 0.62 0.08 0.15 182 Organism_subdivision 0.64 0.78 0.70 314 Organism_substance 0.00 0.00 0.00 96 Pathological_formation 0.63 0.44 0.52 262 Simple_chemical 0.79 0.13 0.23 112 Tissue 0.82 0.45 0.58 300

                  micro avg       0.78      0.72      0.75      9030
                  macro avg       0.51      0.41      0.43      9030
               weighted avg       0.76      0.72      0.73      9030

| | No log | 2.0 | 191 | 0.2053 | precision recall f1-score support

                 Amino_acid       0.87      0.87      0.87       576
          Anatomical_system       0.98      0.80      0.88       317
                     Cancer       0.89      0.92      0.91      1649
                       Cell       0.00      0.00      0.00        25
         Cellular_component       0.00      0.00      0.00        12

Developing_anatomical_structure 0.74 0.84 0.79 438 Gene_or_gene_product 1.00 0.05 0.10 74 Immaterial_anatomical_entity 0.83 0.83 0.83 4142 Multi-tissue_structure 0.85 0.82 0.83 451 Organ 0.48 0.15 0.23 80 Organism 0.49 0.66 0.56 182 Organism_subdivision 0.79 0.80 0.80 314 Organism_substance 0.75 0.58 0.65 96 Pathological_formation 0.76 0.66 0.71 262 Simple_chemical 0.48 0.42 0.45 112 Tissue 0.80 0.90 0.85 300

                  micro avg       0.82      0.82      0.82      9030
                  macro avg       0.67      0.58      0.59      9030
               weighted avg       0.82      0.82      0.81      9030

| | No log | 2.98 | 285 | 0.1928 | precision recall f1-score support

                 Amino_acid       0.89      0.88      0.88       576
          Anatomical_system       0.96      0.82      0.89       317
                     Cancer       0.92      0.91      0.91      1649
                       Cell       0.00      0.00      0.00        25
         Cellular_component       0.00      0.00      0.00        12

Developing_anatomical_structure 0.75 0.85 0.80 438 Gene_or_gene_product 0.87 0.18 0.29 74 Immaterial_anatomical_entity 0.84 0.84 0.84 4142 Multi-tissue_structure 0.85 0.84 0.84 451 Organ 0.51 0.23 0.31 80 Organism 0.52 0.66 0.58 182 Organism_subdivision 0.81 0.80 0.81 314 Organism_substance 0.73 0.66 0.69 96 Pathological_formation 0.75 0.68 0.71 262 Simple_chemical 0.55 0.44 0.49 112 Tissue 0.82 0.91 0.87 300

                  micro avg       0.84      0.82      0.83      9030
                  macro avg       0.67      0.60      0.62      9030
               weighted avg       0.84      0.82      0.83      9030

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Framework versions

• Transformers 4.35.2
• Pytorch 2.1.0+cu121
• Datasets 2.15.0
• Tokenizers 0.15.0