BioNLP13CG_SciBERT_NER

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BioNLP13CG_SciBERT_NER

This model is a fine-tuned version of allenai/scibert_scivocab_uncased on the None dataset. It achieves the following results on the evaluation set:

• Loss: 0.1817

• Seqeval classification report: precision recall f1-score support

                 Amino_acid       0.54      0.43      0.48        89
          Anatomical_system       0.00      0.00      0.00        41
                     Cancer       0.84      0.84      0.84      3620
                       Cell       0.00      0.00      0.00        11
         Cellular_component       0.00      0.00      0.00         7
  

Developing_anatomical_structure 0.00 0.00 0.00 37 Gene_or_gene_product 0.90 0.92 0.91 540 Immaterial_anatomical_entity 0.63 0.65 0.64 82 Multi-tissue_structure 0.63 0.71 0.67 144 Organ 0.00 0.00 0.00 56 Organism 0.86 0.17 0.28 36 Organism_subdivision 0.83 0.86 0.84 1086 Organism_substance 0.87 0.81 0.84 484 Pathological_formation 0.92 0.92 0.92 1430 Simple_chemical 0.58 0.72 0.64 304 Tissue 0.79 0.82 0.80 341

                  micro avg       0.84      0.82      0.83      8308
                  macro avg       0.52      0.49      0.49      8308
               weighted avg       0.82      0.82      0.82      8308

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       0.48      0.15      0.22        89
          Anatomical_system       0.00      0.00      0.00        41
                     Cancer       0.81      0.80      0.80      3620
                       Cell       0.00      0.00      0.00        11
         Cellular_component       0.00      0.00      0.00         7

Developing_anatomical_structure 0.00 0.00 0.00 37 Gene_or_gene_product 0.80 0.90 0.84 540 Immaterial_anatomical_entity 0.48 0.59 0.52 82 Multi-tissue_structure 0.62 0.45 0.52 144 Organ 0.00 0.00 0.00 56 Organism 0.00 0.00 0.00 36 Organism_subdivision 0.75 0.84 0.79 1086 Organism_substance 0.83 0.77 0.80 484 Pathological_formation 0.90 0.86 0.88 1430 Simple_chemical 0.53 0.69 0.60 304 Tissue 0.74 0.73 0.73 341

                  micro avg       0.79      0.78      0.78      8308
                  macro avg       0.43      0.42      0.42      8308
               weighted avg       0.77      0.78      0.77      8308

| | No log | 2.0 | 191 | 0.1850 | precision recall f1-score support

                 Amino_acid       0.52      0.40      0.46        89
          Anatomical_system       0.00      0.00      0.00        41
                     Cancer       0.83      0.84      0.84      3620
                       Cell       0.00      0.00      0.00        11
         Cellular_component       0.00      0.00      0.00         7

Developing_anatomical_structure 0.00 0.00 0.00 37 Gene_or_gene_product 0.89 0.92 0.90 540 Immaterial_anatomical_entity 0.56 0.65 0.60 82 Multi-tissue_structure 0.60 0.69 0.64 144 Organ 0.00 0.00 0.00 56 Organism 1.00 0.17 0.29 36 Organism_subdivision 0.80 0.87 0.83 1086 Organism_substance 0.87 0.79 0.83 484 Pathological_formation 0.91 0.93 0.92 1430 Simple_chemical 0.57 0.72 0.64 304 Tissue 0.77 0.79 0.78 341

                  micro avg       0.82      0.83      0.82      8308
                  macro avg       0.52      0.49      0.48      8308
               weighted avg       0.81      0.83      0.82      8308

| | No log | 2.98 | 285 | 0.1817 | precision recall f1-score support

                 Amino_acid       0.54      0.43      0.48        89
          Anatomical_system       0.00      0.00      0.00        41
                     Cancer       0.84      0.84      0.84      3620
                       Cell       0.00      0.00      0.00        11
         Cellular_component       0.00      0.00      0.00         7

Developing_anatomical_structure 0.00 0.00 0.00 37 Gene_or_gene_product 0.90 0.92 0.91 540 Immaterial_anatomical_entity 0.63 0.65 0.64 82 Multi-tissue_structure 0.63 0.71 0.67 144 Organ 0.00 0.00 0.00 56 Organism 0.86 0.17 0.28 36 Organism_subdivision 0.83 0.86 0.84 1086 Organism_substance 0.87 0.81 0.84 484 Pathological_formation 0.92 0.92 0.92 1430 Simple_chemical 0.58 0.72 0.64 304 Tissue 0.79 0.82 0.80 341

                  micro avg       0.84      0.82      0.83      8308
                  macro avg       0.52      0.49      0.49      8308
               weighted avg       0.82      0.82      0.82      8308

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Framework versions

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