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--- |
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base_model: dmis-lab/biobert-v1.1 |
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tags: |
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- generated_from_trainer |
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model-index: |
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- name: BioNLP13CG_bioBERT_NER |
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results: [] |
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--- |
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<!-- This model card has been generated automatically according to the information the Trainer had access to. You |
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should probably proofread and complete it, then remove this comment. --> |
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# BioNLP13CG_bioBERT_NER |
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This model is a fine-tuned version of [dmis-lab/biobert-v1.1](https://huggingface.co/dmis-lab/biobert-v1.1) on the None dataset. |
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It achieves the following results on the evaluation set: |
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- Loss: 0.1928 |
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- Seqeval classification report: precision recall f1-score support |
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Amino_acid 0.89 0.88 0.88 576 |
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Anatomical_system 0.96 0.82 0.89 317 |
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Cancer 0.92 0.91 0.91 1649 |
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Cell 0.00 0.00 0.00 25 |
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Cellular_component 0.00 0.00 0.00 12 |
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Developing_anatomical_structure 0.75 0.85 0.80 438 |
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Gene_or_gene_product 0.87 0.18 0.29 74 |
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Immaterial_anatomical_entity 0.84 0.84 0.84 4142 |
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Multi-tissue_structure 0.85 0.84 0.84 451 |
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Organ 0.51 0.23 0.31 80 |
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Organism 0.52 0.66 0.58 182 |
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Organism_subdivision 0.81 0.80 0.81 314 |
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Organism_substance 0.73 0.66 0.69 96 |
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Pathological_formation 0.75 0.68 0.71 262 |
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Simple_chemical 0.55 0.44 0.49 112 |
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Tissue 0.82 0.91 0.87 300 |
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micro avg 0.84 0.82 0.83 9030 |
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macro avg 0.67 0.60 0.62 9030 |
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weighted avg 0.84 0.82 0.83 9030 |
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## Model description |
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More information needed |
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## Intended uses & limitations |
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More information needed |
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## Training and evaluation data |
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More information needed |
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## Training procedure |
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### Training hyperparameters |
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The following hyperparameters were used during training: |
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- learning_rate: 2e-05 |
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- train_batch_size: 16 |
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- eval_batch_size: 16 |
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- seed: 42 |
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- gradient_accumulation_steps: 2 |
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- total_train_batch_size: 32 |
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- optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08 |
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- lr_scheduler_type: linear |
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- num_epochs: 3 |
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### Training results |
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| Training Loss | Epoch | Step | Validation Loss | Seqeval classification report | |
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|:-------------:|:-----:|:----:|:---------------:|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------:| |
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| No log | 0.99 | 95 | 0.2929 | precision recall f1-score support |
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Amino_acid 0.68 0.81 0.73 576 |
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Anatomical_system 0.93 0.74 0.82 317 |
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Cancer 0.89 0.89 0.89 1649 |
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Cell 0.00 0.00 0.00 25 |
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Cellular_component 0.00 0.00 0.00 12 |
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Developing_anatomical_structure 0.56 0.79 0.65 438 |
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Gene_or_gene_product 0.00 0.00 0.00 74 |
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Immaterial_anatomical_entity 0.79 0.76 0.77 4142 |
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Multi-tissue_structure 0.84 0.75 0.79 451 |
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Organ 0.00 0.00 0.00 80 |
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Organism 0.62 0.08 0.15 182 |
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Organism_subdivision 0.64 0.78 0.70 314 |
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Organism_substance 0.00 0.00 0.00 96 |
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Pathological_formation 0.63 0.44 0.52 262 |
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Simple_chemical 0.79 0.13 0.23 112 |
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Tissue 0.82 0.45 0.58 300 |
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micro avg 0.78 0.72 0.75 9030 |
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macro avg 0.51 0.41 0.43 9030 |
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weighted avg 0.76 0.72 0.73 9030 |
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| No log | 2.0 | 191 | 0.2053 | precision recall f1-score support |
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Amino_acid 0.87 0.87 0.87 576 |
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Anatomical_system 0.98 0.80 0.88 317 |
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Cancer 0.89 0.92 0.91 1649 |
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Cell 0.00 0.00 0.00 25 |
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Cellular_component 0.00 0.00 0.00 12 |
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Developing_anatomical_structure 0.74 0.84 0.79 438 |
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Gene_or_gene_product 1.00 0.05 0.10 74 |
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Immaterial_anatomical_entity 0.83 0.83 0.83 4142 |
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Multi-tissue_structure 0.85 0.82 0.83 451 |
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Organ 0.48 0.15 0.23 80 |
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Organism 0.49 0.66 0.56 182 |
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Organism_subdivision 0.79 0.80 0.80 314 |
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Organism_substance 0.75 0.58 0.65 96 |
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Pathological_formation 0.76 0.66 0.71 262 |
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Simple_chemical 0.48 0.42 0.45 112 |
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Tissue 0.80 0.90 0.85 300 |
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micro avg 0.82 0.82 0.82 9030 |
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macro avg 0.67 0.58 0.59 9030 |
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weighted avg 0.82 0.82 0.81 9030 |
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| No log | 2.98 | 285 | 0.1928 | precision recall f1-score support |
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Amino_acid 0.89 0.88 0.88 576 |
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Anatomical_system 0.96 0.82 0.89 317 |
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Cancer 0.92 0.91 0.91 1649 |
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Cell 0.00 0.00 0.00 25 |
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Cellular_component 0.00 0.00 0.00 12 |
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Developing_anatomical_structure 0.75 0.85 0.80 438 |
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Gene_or_gene_product 0.87 0.18 0.29 74 |
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Immaterial_anatomical_entity 0.84 0.84 0.84 4142 |
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Multi-tissue_structure 0.85 0.84 0.84 451 |
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Organ 0.51 0.23 0.31 80 |
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Organism 0.52 0.66 0.58 182 |
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Organism_subdivision 0.81 0.80 0.81 314 |
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Organism_substance 0.73 0.66 0.69 96 |
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Pathological_formation 0.75 0.68 0.71 262 |
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Simple_chemical 0.55 0.44 0.49 112 |
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Tissue 0.82 0.91 0.87 300 |
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micro avg 0.84 0.82 0.83 9030 |
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macro avg 0.67 0.60 0.62 9030 |
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weighted avg 0.84 0.82 0.83 9030 |
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### Framework versions |
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- Transformers 4.35.2 |
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- Pytorch 2.1.0+cu121 |
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- Datasets 2.15.0 |
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- Tokenizers 0.15.0 |
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