OTAR3088/CeLLaTe-ner-2class-pubmedbert-baseline

CeLLaTe-ner-pubmedbert-baseline

This model is a fine-tuned version of microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext on the OTAR3088/CeLLaTe_V3.2_contracted_ent_IOB dataset. It achieves the following results on the evaluation set:

• Loss: 0.0640
• Precision: 0.7746
• Recall: 0.7254
• F1: 0.7492
• Accuracy: 0.9839

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: 3407
• gradient_accumulation_steps: 2
• total_train_batch_size: 32
• optimizer: Use OptimizerNames.ADAMW_TORCH with betas=(0.9,0.999) and epsilon=1e-08 and optimizer_args=No additional optimizer arguments
• lr_scheduler_type: linear
• lr_scheduler_warmup_ratio: 0.01
• num_epochs: 20
• mixed_precision_training: Native AMP

Training results

Training Loss	Epoch	Step	Validation Loss	Precision	Recall	F1	Accuracy
0.2418	1.0	263	0.0612	0.6099	0.7212	0.6609	0.9794
0.0403	2.0	526	0.0520	0.7575	0.7224	0.7395	0.9834
0.0258	3.0	789	0.0613	0.7419	0.7401	0.7410	0.9829
0.0196	4.0	1052	0.0644	0.7746	0.7254	0.7492	0.9839
0.0145	5.0	1315	0.0683	0.7746	0.7047	0.7380	0.9831
0.011	6.0	1578	0.0768	0.7628	0.7084	0.7346	0.9831
0.0086	7.0	1841	0.0732	0.7468	0.7450	0.7459	0.9838

Framework versions

• Transformers 4.48.2
• Pytorch 2.4.1+cu121
• Datasets 3.0.2
• Tokenizers 0.21.0