bert-paper-classifier

This model is a fine-tuned version of microsoft/BiomedNLP-PubMedBERT-base-uncased-abstract on the dataset from González-Márquez et al., 2023.

Intended uses & limitations

This model is intended to predict the category given the paper title (and optionally its abstract) — for the biomedical papers. For example, it is likely to predict virology as a category for the paper with a title containing COVID-19.

So far only a subset of the PubMed dataset has been used for training. Future improvements to this model can come with using the full dataset with a combination of titles and abstracts for the fine-tuning as well as extending the training set to the preprints from bioRxiv and/or arXiv.

Training procedure

The code for the model fine-tuning can be found in the respective notebook.

Training hyperparameters

The following hyperparameters were used during training:

• learning_rate: 5e-05
• train_batch_size: 128
• eval_batch_size: 32
• seed: 42
• optimizer: Adam with betas=(0.9,0.999) and epsilon=1e-08
• lr_scheduler_type: linear
• num_epochs: 3

Framework versions

• Transformers 4.28.1
• Pytorch 2.0.0+cu117
• Datasets 2.11.0
• Tokenizers 0.13.3