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judithrosell
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BioNLP13CG_bioBERT_NER

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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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+
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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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+
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+ # BioNLP13CG_bioBERT_NER
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+
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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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+
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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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+
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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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+
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+
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+ ## Model description
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+
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+ More information needed
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+
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+ ## Intended uses & limitations
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+
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+ More information needed
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+
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+ ## Training and evaluation data
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+
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+ More information needed
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+
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+ ## Training procedure
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+
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+ ### Training hyperparameters
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+
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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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+
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+ ### Training results
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+
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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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+
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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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+
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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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+ |
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+ | No log | 2.0 | 191 | 0.2053 | precision recall f1-score support
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+
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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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+
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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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+ |
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+ | No log | 2.98 | 285 | 0.1928 | precision recall f1-score support
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+
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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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+
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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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+ |
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+
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+
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+ ### Framework versions
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+
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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