| # BioBERT-NLI | |
| This is the model [BioBERT](https://github.com/dmis-lab/biobert) [1] fine-tuned on the [SNLI](https://nlp.stanford.edu/projects/snli/) and the [MultiNLI](https://www.nyu.edu/projects/bowman/multinli/) datasets using the [`sentence-transformers` library](https://github.com/UKPLab/sentence-transformers/) to produce universal sentence embeddings [2]. | |
| The model uses the original BERT wordpiece vocabulary and was trained using the **average pooling strategy** and a **softmax loss**. | |
| **Base model**: `monologg/biobert_v1.1_pubmed` from HuggingFace's `AutoModel`. | |
| **Training time**: ~6 hours on the NVIDIA Tesla P100 GPU provided in Kaggle Notebooks. | |
| **Parameters**: | |
| | Parameter | Value | | |
| |------------------|-------| | |
| | Batch size | 64 | | |
| | Training steps | 30000 | | |
| | Warmup steps | 1450 | | |
| | Lowercasing | False | | |
| | Max. Seq. Length | 128 | | |
| **Performances**: The performance was evaluated on the test portion of the [STS dataset](http://ixa2.si.ehu.es/stswiki/index.php/STSbenchmark) using Spearman rank correlation and compared to the performances of a general BERT base model obtained with the same procedure to verify their similarity. | |
| | Model | Score | | |
| |-------------------------------|-------------| | |
| | `biobert-nli` (this) | 73.40 | | |
| | `gsarti/scibert-nli` | 74.50 | | |
| | `bert-base-nli-mean-tokens`[3]| 77.12 | | |
| An example usage for similarity-based scientific paper retrieval is provided in the [Covid Papers Browser](https://github.com/gsarti/covid-papers-browser) repository. | |
| **References:** | |
| [1] J. Lee et al, [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://academic.oup.com/bioinformatics/article/36/4/1234/5566506) | |
| [2] A. Conneau et al., [Supervised Learning of Universal Sentence Representations from Natural Language Inference Data](https://www.aclweb.org/anthology/D17-1070/) | |
| [3] N. Reimers et I. Gurevych, [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://www.aclweb.org/anthology/D19-1410/) | |