               Amino_acid       0.81      0.59      0.68       297
        Anatomical_system       0.70      0.78      0.74       297
                   Cancer       0.74      0.73      0.73      3490
                     Cell       0.72      0.87      0.79      1360
       Cellular_component       0.00      0.00      0.00        99

Developing_anatomical_structure 0.00 0.00 0.00 11 Gene_or_gene_product 0.67 0.25 0.37 174 Immaterial_anatomical_entity 0.52 0.76 0.62 432 Multi-tissue_structure 0.83 0.59 0.69 317 Organ 0.00 0.00 0.00 49 Organism 0.71 0.48 0.57 464 Organism_subdivision 0.70 0.72 0.71 678 Organism_substance 0.00 0.00 0.00 128 Pathological_formation 0.62 0.05 0.09 108 Simple_chemical 0.00 0.00 0.00 56 Tissue 0.80 0.85 0.82 1566

                  micro avg       0.73      0.71      0.72      9526
                  macro avg       0.49      0.42      0.43      9526
               weighted avg       0.71      0.71      0.70      9526

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	0.4681	precision recall f1-score support

                 Amino_acid       1.00      0.02      0.04       297
          Anatomical_system       0.44      0.68      0.54       297
                     Cancer       0.68      0.63      0.65      3490
                       Cell       0.59      0.85      0.70      1360
         Cellular_component       0.00      0.00      0.00        99

Developing_anatomical_structure 0.00 0.00 0.00 11 Gene_or_gene_product 0.00 0.00 0.00 174 Immaterial_anatomical_entity 0.40 0.60 0.48 432 Multi-tissue_structure 0.86 0.06 0.11 317 Organ 0.00 0.00 0.00 49 Organism 0.88 0.02 0.03 464 Organism_subdivision 0.62 0.54 0.58 678 Organism_substance 0.00 0.00 0.00 128 Pathological_formation 0.00 0.00 0.00 108 Simple_chemical 0.00 0.00 0.00 56 Tissue 0.70 0.84 0.76 1566

                  micro avg       0.63      0.58      0.60      9526
                  macro avg       0.39      0.27      0.24      9526
               weighted avg       0.63      0.58      0.55      9526

| | No log | 2.0 | 191 | 0.3526 | precision recall f1-score support

                 Amino_acid       0.81      0.52      0.63       297
          Anatomical_system       0.66      0.77      0.71       297
                     Cancer       0.74      0.73      0.73      3490
                       Cell       0.71      0.87      0.78      1360
         Cellular_component       0.00      0.00      0.00        99

Developing_anatomical_structure 0.00 0.00 0.00 11 Gene_or_gene_product 0.76 0.20 0.32 174 Immaterial_anatomical_entity 0.46 0.76 0.57 432 Multi-tissue_structure 0.83 0.57 0.68 317 Organ 0.00 0.00 0.00 49 Organism 0.68 0.44 0.54 464 Organism_subdivision 0.71 0.67 0.69 678 Organism_substance 0.00 0.00 0.00 128 Pathological_formation 1.00 0.01 0.02 108 Simple_chemical 0.00 0.00 0.00 56 Tissue 0.78 0.85 0.81 1566

                  micro avg       0.72      0.70      0.71      9526
                  macro avg       0.51      0.40      0.41      9526
               weighted avg       0.70      0.70      0.68      9526

| | No log | 2.98 | 285 | 0.3339 | precision recall f1-score support

                 Amino_acid       0.81      0.59      0.68       297
          Anatomical_system       0.70      0.78      0.74       297
                     Cancer       0.74      0.73      0.73      3490
                       Cell       0.72      0.87      0.79      1360
         Cellular_component       0.00      0.00      0.00        99

                  micro avg       0.73      0.71      0.72      9526
                  macro avg       0.49      0.42      0.43      9526
               weighted avg       0.71      0.71      0.70      9526

Framework versions

Transformers 4.35.2
Pytorch 2.1.0+cu121
Datasets 2.15.0
Tokenizers 0.15.0

judithrosell/BioNLP13CG_ClinicalBERT_NER

BioNLP13CG_ClinicalBERT_NER

Model description

Intended uses & limitations

Training and evaluation data

Training procedure

Training hyperparameters

Training results

Framework versions

judithrosell/
BioNLP13CG_ClinicalBERT_NER