               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

Training Loss	Epoch	Step	Validation Loss	Seqeval classification report
No log	0.99	95	0.2929	precision recall f1-score support

                 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

                  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

Framework versions

Transformers 4.35.2
Pytorch 2.1.0+cu121
Datasets 2.15.0
Tokenizers 0.15.0

judithrosell/BioNLP13CG_bioBERT_NER

BioNLP13CG_bioBERT_NER

Model description

Intended uses & limitations

Training and evaluation data

Training procedure

Training hyperparameters

Training results

Framework versions

judithrosell/
BioNLP13CG_bioBERT_NER