CeLLaTe-ner-2class-pubmedbert-baseline

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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

Framework versions

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