BioNLP13CG_PubMedBERT_NER

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BioNLP13CG_PubMedBERT_NER

This model is a fine-tuned version of microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext on the None dataset. It achieves the following results on the evaluation set:

• Loss: 0.2066

• Seqeval classification report: precision recall f1-score support

                 Amino_acid       0.78      0.81      0.79       301
          Anatomical_system       0.00      0.00      0.00         3
                     Cancer       0.00      0.00      0.00        37
                       Cell       0.79      0.85      0.82       446
         Cellular_component       0.00      0.00      0.00        19
  

Developing_anatomical_structure 0.55 0.78 0.65 399 Gene_or_gene_product 0.68 0.41 0.51 128 Immaterial_anatomical_entity 0.00 0.00 0.00 45 Multi-tissue_structure 0.25 0.02 0.04 98 Organ 0.00 0.00 0.00 19 Organism 0.90 0.93 0.92 1108 Organism_subdivision 0.71 0.12 0.21 120 Organism_substance 0.62 0.59 0.60 128 Pathological_formation 0.00 0.00 0.00 41 Simple_chemical 0.87 0.86 0.86 4397 Tissue 0.90 0.93 0.91 1790

                  micro avg       0.84      0.83      0.84      9079
                  macro avg       0.44      0.39      0.39      9079
               weighted avg       0.83      0.83      0.82      9079

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       0.81      0.10      0.18       301
          Anatomical_system       0.00      0.00      0.00         3
                     Cancer       0.00      0.00      0.00        37
                       Cell       0.82      0.76      0.79       446
         Cellular_component       0.00      0.00      0.00        19

Developing_anatomical_structure 0.90 0.07 0.13 399 Gene_or_gene_product 0.00 0.00 0.00 128 Immaterial_anatomical_entity 0.00 0.00 0.00 45 Multi-tissue_structure 0.00 0.00 0.00 98 Organ 0.00 0.00 0.00 19 Organism 0.64 0.86 0.73 1108 Organism_subdivision 0.00 0.00 0.00 120 Organism_substance 0.00 0.00 0.00 128 Pathological_formation 0.00 0.00 0.00 41 Simple_chemical 0.83 0.79 0.81 4397 Tissue 0.74 0.91 0.82 1790

                  micro avg       0.77      0.71      0.74      9079
                  macro avg       0.30      0.22      0.22      9079
               weighted avg       0.73      0.71      0.69      9079

| | No log | 2.0 | 191 | 0.2209 | precision recall f1-score support

                 Amino_acid       0.76      0.75      0.76       301
          Anatomical_system       0.00      0.00      0.00         3
                     Cancer       0.00      0.00      0.00        37
                       Cell       0.78      0.87      0.82       446
         Cellular_component       0.00      0.00      0.00        19

Developing_anatomical_structure 0.52 0.75 0.61 399 Gene_or_gene_product 0.65 0.24 0.35 128 Immaterial_anatomical_entity 0.00 0.00 0.00 45 Multi-tissue_structure 0.00 0.00 0.00 98 Organ 0.00 0.00 0.00 19 Organism 0.89 0.92 0.91 1108 Organism_subdivision 0.50 0.05 0.09 120 Organism_substance 0.61 0.52 0.56 128 Pathological_formation 0.00 0.00 0.00 41 Simple_chemical 0.86 0.86 0.86 4397 Tissue 0.87 0.93 0.90 1790

                  micro avg       0.83      0.82      0.83      9079
                  macro avg       0.40      0.37      0.37      9079
               weighted avg       0.81      0.82      0.81      9079

| | No log | 2.98 | 285 | 0.2066 | precision recall f1-score support

                 Amino_acid       0.78      0.81      0.79       301
          Anatomical_system       0.00      0.00      0.00         3
                     Cancer       0.00      0.00      0.00        37
                       Cell       0.79      0.85      0.82       446
         Cellular_component       0.00      0.00      0.00        19

Developing_anatomical_structure 0.55 0.78 0.65 399 Gene_or_gene_product 0.68 0.41 0.51 128 Immaterial_anatomical_entity 0.00 0.00 0.00 45 Multi-tissue_structure 0.25 0.02 0.04 98 Organ 0.00 0.00 0.00 19 Organism 0.90 0.93 0.92 1108 Organism_subdivision 0.71 0.12 0.21 120 Organism_substance 0.62 0.59 0.60 128 Pathological_formation 0.00 0.00 0.00 41 Simple_chemical 0.87 0.86 0.86 4397 Tissue 0.90 0.93 0.91 1790

                  micro avg       0.84      0.83      0.84      9079
                  macro avg       0.44      0.39      0.39      9079
               weighted avg       0.83      0.83      0.82      9079

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Framework versions

• Transformers 4.35.2
• Pytorch 2.1.0+cu118
• Datasets 2.15.0
• Tokenizers 0.15.0