MedType: Improving Medical Entity Linking with Semantic Type Prediction

Medical entity linking is the task of identifying and standardizing concepts referred in a scientific article or clinical record. Existing methods adopt a two-step approach of detecting mentions and identifying a list of candidate concepts for them. In this paper, we probe the impact of incorporating an entity disambiguation step in existing entity linkers. For this, we present MedType, a novel method that leverages the surrounding context to identify the semantic type of a mention and uses it for filtering out candidate concepts of the wrong types. We further present two novel largescale, automatically-created datasets of medical entity mentions: WIKIMED, a Wikipediabased dataset for cross-domain transfer learning, and PUBMEDDS, a distantly-supervised dataset of medical entity mentions in biomedical abstracts. Through extensive experiments across several datasets and methods, we demonstrate that MedType pre-trained on our proposed datasets substantially improve medical entity linking and gives state-of-the-art performance. We make our source code and datasets publicly available for medical entity linking research.