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--- |
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license: mit |
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base_model: microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext |
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tags: |
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- generated_from_trainer |
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model-index: |
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- name: BioNLP13CG_PubMedBERT_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_PubMedBERT_NER |
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This model is a fine-tuned version of [microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext](https://huggingface.co/microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract-fulltext) on the None dataset. |
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It achieves the following results on the evaluation set: |
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- Loss: 0.2066 |
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- Seqeval classification report: precision recall f1-score support |
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Amino_acid 0.78 0.81 0.79 301 |
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Anatomical_system 0.00 0.00 0.00 3 |
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Cancer 0.00 0.00 0.00 37 |
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Cell 0.79 0.85 0.82 446 |
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Cellular_component 0.00 0.00 0.00 19 |
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Developing_anatomical_structure 0.55 0.78 0.65 399 |
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Gene_or_gene_product 0.68 0.41 0.51 128 |
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Immaterial_anatomical_entity 0.00 0.00 0.00 45 |
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Multi-tissue_structure 0.25 0.02 0.04 98 |
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Organ 0.00 0.00 0.00 19 |
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Organism 0.90 0.93 0.92 1108 |
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Organism_subdivision 0.71 0.12 0.21 120 |
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Organism_substance 0.62 0.59 0.60 128 |
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Pathological_formation 0.00 0.00 0.00 41 |
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Simple_chemical 0.87 0.86 0.86 4397 |
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Tissue 0.90 0.93 0.91 1790 |
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micro avg 0.84 0.83 0.84 9079 |
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macro avg 0.44 0.39 0.39 9079 |
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weighted avg 0.83 0.83 0.82 9079 |
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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 | 0.3390 | precision recall f1-score support |
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Amino_acid 0.81 0.10 0.18 301 |
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Anatomical_system 0.00 0.00 0.00 3 |
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Cancer 0.00 0.00 0.00 37 |
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Cell 0.82 0.76 0.79 446 |
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Cellular_component 0.00 0.00 0.00 19 |
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Developing_anatomical_structure 0.90 0.07 0.13 399 |
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Gene_or_gene_product 0.00 0.00 0.00 128 |
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Immaterial_anatomical_entity 0.00 0.00 0.00 45 |
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Multi-tissue_structure 0.00 0.00 0.00 98 |
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Organ 0.00 0.00 0.00 19 |
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Organism 0.64 0.86 0.73 1108 |
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Organism_subdivision 0.00 0.00 0.00 120 |
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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 41 |
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Simple_chemical 0.83 0.79 0.81 4397 |
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Tissue 0.74 0.91 0.82 1790 |
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micro avg 0.77 0.71 0.74 9079 |
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macro avg 0.30 0.22 0.22 9079 |
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weighted avg 0.73 0.71 0.69 9079 |
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| No log | 2.0 | 191 | 0.2209 | precision recall f1-score support |
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Amino_acid 0.76 0.75 0.76 301 |
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Anatomical_system 0.00 0.00 0.00 3 |
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Cancer 0.00 0.00 0.00 37 |
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Cell 0.78 0.87 0.82 446 |
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Cellular_component 0.00 0.00 0.00 19 |
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Developing_anatomical_structure 0.52 0.75 0.61 399 |
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Gene_or_gene_product 0.65 0.24 0.35 128 |
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Immaterial_anatomical_entity 0.00 0.00 0.00 45 |
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Multi-tissue_structure 0.00 0.00 0.00 98 |
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Organ 0.00 0.00 0.00 19 |
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Organism 0.89 0.92 0.91 1108 |
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Organism_subdivision 0.50 0.05 0.09 120 |
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Organism_substance 0.61 0.52 0.56 128 |
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Pathological_formation 0.00 0.00 0.00 41 |
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Simple_chemical 0.86 0.86 0.86 4397 |
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Tissue 0.87 0.93 0.90 1790 |
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micro avg 0.83 0.82 0.83 9079 |
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macro avg 0.40 0.37 0.37 9079 |
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weighted avg 0.81 0.82 0.81 9079 |
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| No log | 2.98 | 285 | 0.2066 | precision recall f1-score support |
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Amino_acid 0.78 0.81 0.79 301 |
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Anatomical_system 0.00 0.00 0.00 3 |
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Cancer 0.00 0.00 0.00 37 |
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Cell 0.79 0.85 0.82 446 |
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Cellular_component 0.00 0.00 0.00 19 |
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Developing_anatomical_structure 0.55 0.78 0.65 399 |
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Gene_or_gene_product 0.68 0.41 0.51 128 |
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Immaterial_anatomical_entity 0.00 0.00 0.00 45 |
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Multi-tissue_structure 0.25 0.02 0.04 98 |
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Organ 0.00 0.00 0.00 19 |
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Organism 0.90 0.93 0.92 1108 |
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Organism_subdivision 0.71 0.12 0.21 120 |
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Organism_substance 0.62 0.59 0.60 128 |
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Pathological_formation 0.00 0.00 0.00 41 |
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Simple_chemical 0.87 0.86 0.86 4397 |
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Tissue 0.90 0.93 0.91 1790 |
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micro avg 0.84 0.83 0.84 9079 |
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macro avg 0.44 0.39 0.39 9079 |
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weighted avg 0.83 0.83 0.82 9079 |
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### Framework versions |
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- Transformers 4.35.2 |
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- Pytorch 2.1.0+cu118 |
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- Datasets 2.15.0 |
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- Tokenizers 0.15.0 |
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