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--- |
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base_model: medicalai/ClinicalBERT |
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tags: |
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- generated_from_trainer |
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model-index: |
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- name: BioNLP13CG_ClinicalBERT_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_ClinicalBERT_NER |
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This model is a fine-tuned version of [medicalai/ClinicalBERT](https://huggingface.co/medicalai/ClinicalBERT) on the None dataset. |
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It achieves the following results on the evaluation set: |
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- Loss: 0.3339 |
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- Seqeval classification report: precision recall f1-score support |
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Amino_acid 0.81 0.59 0.68 297 |
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Anatomical_system 0.70 0.78 0.74 297 |
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Cancer 0.74 0.73 0.73 3490 |
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Cell 0.72 0.87 0.79 1360 |
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Cellular_component 0.00 0.00 0.00 99 |
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Developing_anatomical_structure 0.00 0.00 0.00 11 |
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Gene_or_gene_product 0.67 0.25 0.37 174 |
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Immaterial_anatomical_entity 0.52 0.76 0.62 432 |
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Multi-tissue_structure 0.83 0.59 0.69 317 |
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Organ 0.00 0.00 0.00 49 |
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Organism 0.71 0.48 0.57 464 |
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Organism_subdivision 0.70 0.72 0.71 678 |
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Organism_substance 0.00 0.00 0.00 128 |
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Pathological_formation 0.62 0.05 0.09 108 |
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Simple_chemical 0.00 0.00 0.00 56 |
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Tissue 0.80 0.85 0.82 1566 |
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micro avg 0.73 0.71 0.72 9526 |
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macro avg 0.49 0.42 0.43 9526 |
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weighted avg 0.71 0.71 0.70 9526 |
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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 | 0.4681 | precision recall f1-score support |
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Amino_acid 1.00 0.02 0.04 297 |
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Anatomical_system 0.44 0.68 0.54 297 |
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Cancer 0.68 0.63 0.65 3490 |
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Cell 0.59 0.85 0.70 1360 |
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Cellular_component 0.00 0.00 0.00 99 |
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Developing_anatomical_structure 0.00 0.00 0.00 11 |
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Gene_or_gene_product 0.00 0.00 0.00 174 |
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Immaterial_anatomical_entity 0.40 0.60 0.48 432 |
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Multi-tissue_structure 0.86 0.06 0.11 317 |
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Organ 0.00 0.00 0.00 49 |
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Organism 0.88 0.02 0.03 464 |
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Organism_subdivision 0.62 0.54 0.58 678 |
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Organism_substance 0.00 0.00 0.00 128 |
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Pathological_formation 0.00 0.00 0.00 108 |
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Simple_chemical 0.00 0.00 0.00 56 |
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Tissue 0.70 0.84 0.76 1566 |
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micro avg 0.63 0.58 0.60 9526 |
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macro avg 0.39 0.27 0.24 9526 |
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weighted avg 0.63 0.58 0.55 9526 |
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| No log | 2.0 | 191 | 0.3526 | precision recall f1-score support |
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Amino_acid 0.81 0.52 0.63 297 |
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Anatomical_system 0.66 0.77 0.71 297 |
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Cancer 0.74 0.73 0.73 3490 |
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Cell 0.71 0.87 0.78 1360 |
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Cellular_component 0.00 0.00 0.00 99 |
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Developing_anatomical_structure 0.00 0.00 0.00 11 |
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Gene_or_gene_product 0.76 0.20 0.32 174 |
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Immaterial_anatomical_entity 0.46 0.76 0.57 432 |
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Multi-tissue_structure 0.83 0.57 0.68 317 |
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Organ 0.00 0.00 0.00 49 |
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Organism 0.68 0.44 0.54 464 |
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Organism_subdivision 0.71 0.67 0.69 678 |
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Organism_substance 0.00 0.00 0.00 128 |
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Pathological_formation 1.00 0.01 0.02 108 |
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Simple_chemical 0.00 0.00 0.00 56 |
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Tissue 0.78 0.85 0.81 1566 |
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micro avg 0.72 0.70 0.71 9526 |
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macro avg 0.51 0.40 0.41 9526 |
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weighted avg 0.70 0.70 0.68 9526 |
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| No log | 2.98 | 285 | 0.3339 | precision recall f1-score support |
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Amino_acid 0.81 0.59 0.68 297 |
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Anatomical_system 0.70 0.78 0.74 297 |
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Cancer 0.74 0.73 0.73 3490 |
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Cell 0.72 0.87 0.79 1360 |
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Cellular_component 0.00 0.00 0.00 99 |
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Developing_anatomical_structure 0.00 0.00 0.00 11 |
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Gene_or_gene_product 0.67 0.25 0.37 174 |
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Immaterial_anatomical_entity 0.52 0.76 0.62 432 |
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Multi-tissue_structure 0.83 0.59 0.69 317 |
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Organ 0.00 0.00 0.00 49 |
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Organism 0.71 0.48 0.57 464 |
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Organism_subdivision 0.70 0.72 0.71 678 |
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Organism_substance 0.00 0.00 0.00 128 |
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Pathological_formation 0.62 0.05 0.09 108 |
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Simple_chemical 0.00 0.00 0.00 56 |
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Tissue 0.80 0.85 0.82 1566 |
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micro avg 0.73 0.71 0.72 9526 |
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macro avg 0.49 0.42 0.43 9526 |
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weighted avg 0.71 0.71 0.70 9526 |
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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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