End of training

README.md

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+---
+base_model: allenai/scibert_scivocab_uncased
+tags:
+- generated_from_trainer
+model-index:
+- name: BioNLP13CG_SciBERT_NER
+ results: []
+---
+
+<!-- This model card has been generated automatically according to the information the Trainer had access to. You
+should probably proofread and complete it, then remove this comment. -->
+
+# BioNLP13CG_SciBERT_NER
+
+This model is a fine-tuned version of [allenai/scibert_scivocab_uncased](https://huggingface.co/allenai/scibert_scivocab_uncased) on the None dataset.
+It achieves the following results on the evaluation set:
+- Loss: 0.1817
+- Seqeval classification report: precision recall f1-score support
+
+ Amino_acid 0.54 0.43 0.48 89
+ Anatomical_system 0.00 0.00 0.00 41
+ Cancer 0.84 0.84 0.84 3620
+ Cell 0.00 0.00 0.00 11
+ Cellular_component 0.00 0.00 0.00 7
+Developing_anatomical_structure 0.00 0.00 0.00 37
+ Gene_or_gene_product 0.90 0.92 0.91 540
+ Immaterial_anatomical_entity 0.63 0.65 0.64 82
+ Multi-tissue_structure 0.63 0.71 0.67 144
+ Organ 0.00 0.00 0.00 56
+ Organism 0.86 0.17 0.28 36
+ Organism_subdivision 0.83 0.86 0.84 1086
+ Organism_substance 0.87 0.81 0.84 484
+ Pathological_formation 0.92 0.92 0.92 1430
+ Simple_chemical 0.58 0.72 0.64 304
+ Tissue 0.79 0.82 0.80 341
+
+ micro avg 0.84 0.82 0.83 8308
+ macro avg 0.52 0.49 0.49 8308
+ weighted avg 0.82 0.82 0.82 8308
+
+
+## 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 | 0.2278 | precision recall f1-score support
+
+ Amino_acid 0.48 0.15 0.22 89
+ Anatomical_system 0.00 0.00 0.00 41
+ Cancer 0.81 0.80 0.80 3620
+ Cell 0.00 0.00 0.00 11
+ Cellular_component 0.00 0.00 0.00 7
+Developing_anatomical_structure 0.00 0.00 0.00 37
+ Gene_or_gene_product 0.80 0.90 0.84 540
+ Immaterial_anatomical_entity 0.48 0.59 0.52 82
+ Multi-tissue_structure 0.62 0.45 0.52 144
+ Organ 0.00 0.00 0.00 56
+ Organism 0.00 0.00 0.00 36
+ Organism_subdivision 0.75 0.84 0.79 1086
+ Organism_substance 0.83 0.77 0.80 484
+ Pathological_formation 0.90 0.86 0.88 1430
+ Simple_chemical 0.53 0.69 0.60 304
+ Tissue 0.74 0.73 0.73 341
+
+ micro avg 0.79 0.78 0.78 8308
+ macro avg 0.43 0.42 0.42 8308
+ weighted avg 0.77 0.78 0.77 8308
+ |
+| No log | 2.0 | 191 | 0.1850 | precision recall f1-score support
+
+ Amino_acid 0.52 0.40 0.46 89
+ Anatomical_system 0.00 0.00 0.00 41
+ Cancer 0.83 0.84 0.84 3620
+ Cell 0.00 0.00 0.00 11
+ Cellular_component 0.00 0.00 0.00 7
+Developing_anatomical_structure 0.00 0.00 0.00 37
+ Gene_or_gene_product 0.89 0.92 0.90 540
+ Immaterial_anatomical_entity 0.56 0.65 0.60 82
+ Multi-tissue_structure 0.60 0.69 0.64 144
+ Organ 0.00 0.00 0.00 56
+ Organism 1.00 0.17 0.29 36
+ Organism_subdivision 0.80 0.87 0.83 1086
+ Organism_substance 0.87 0.79 0.83 484
+ Pathological_formation 0.91 0.93 0.92 1430
+ Simple_chemical 0.57 0.72 0.64 304
+ Tissue 0.77 0.79 0.78 341
+
+ micro avg 0.82 0.83 0.82 8308
+ macro avg 0.52 0.49 0.48 8308
+ weighted avg 0.81 0.83 0.82 8308
+ |
+| No log | 2.98 | 285 | 0.1817 | precision recall f1-score support
+
+ Amino_acid 0.54 0.43 0.48 89
+ Anatomical_system 0.00 0.00 0.00 41
+ Cancer 0.84 0.84 0.84 3620
+ Cell 0.00 0.00 0.00 11
+ Cellular_component 0.00 0.00 0.00 7
+Developing_anatomical_structure 0.00 0.00 0.00 37
+ Gene_or_gene_product 0.90 0.92 0.91 540
+ Immaterial_anatomical_entity 0.63 0.65 0.64 82
+ Multi-tissue_structure 0.63 0.71 0.67 144
+ Organ 0.00 0.00 0.00 56
+ Organism 0.86 0.17 0.28 36
+ Organism_subdivision 0.83 0.86 0.84 1086
+ Organism_substance 0.87 0.81 0.84 484
+ Pathological_formation 0.92 0.92 0.92 1430
+ Simple_chemical 0.58 0.72 0.64 304
+ Tissue 0.79 0.82 0.80 341
+
+ micro avg 0.84 0.82 0.83 8308
+ macro avg 0.52 0.49 0.49 8308
+ weighted avg 0.82 0.82 0.82 8308
+ |
+
+
+### Framework versions
+
+- Transformers 4.35.2
+- Pytorch 2.1.0+cu121
+- Datasets 2.15.0
+- Tokenizers 0.15.0