NER Models Using Pre-training and Transfer Learning for Healthcare

10/23/2019 ∙ by Amogh Kamat Tarcar, et al. ∙ 0

In this paper, we present our approach to extract structured information from unstructured Electronic Health Records (EHR) [2] to study adverse drug reactions on patients, due to chemicals in their products. Our solution uses a combination of Natural Language Processing (NLP) techniques and a web-based annotation tool to optimize the performance of a custom Named Entity Recognition (NER) [1] model trained on a limited amount of EHR training data. We showcase a combination of tools and techniques leveraging the recent advancements in NLP aimed at targeting domain shifts by applying transfer learning and language model pre-training techniques [3]. We present a comparison of our technique to the base models available and show the effective increase in performance of the NER model and the reduction in time to annotate data. A key observation of the results presented is that the F1 score of model (0.734) trained with our approach with just 50 outperforms the F1 score of the blank spaCy model (0.704) trained with 100 the available training data. We also demonstrate an annotation tool to minimize domain expert time and the manual effort required to generate such a training dataset. Further, we plan to release the annotated dataset as well as the pre-trained model to the community to further research in medical health records.

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