Saama Research at MEDIQA 2019: Pre-trained BioBERT with Attention Visualisation for Medical Natural Language Inference

AbstractNatural Language inference is the task of identifying relation between two sentences as entailment, contradiction or neutrality. MedNLI is a biomedical flavour of NLI for clinical domain. This paper explores the use of Bidirectional Encoder Representation from Transformer (BERT) for solving MedNLI. The proposed model, BERT pre-trained on PMC, PubMed and fine-tuned on MIMICIII v1.4, achieves state of the art results on MedNLI (83.45%) and an accuracy of 78.5% in MEDIQA challenge. The authors present an analysis of the attention patterns that emerged as a result of training BERT on MedNLI using a visualization tool, bertviz.