A large number of embeddings trained on medical data have emerged, but it remains unclear how well they represent medical terminology, in particular whether the close relationship of semantically similar medical terms is encoded in these embeddings. To date, only small datasets for testing medical term similarity are available, not allowing to draw conclusions about the generalisability of embeddings to the enormous amount of medical terms used by doctors. We present multiple automatically created large-scale medical term similarity datasets and confirm their high quality in an annotation study with doctors. We evaluate state-of-the-art word and contextual embeddings on our new datasets, comparing multiple vector similarity metrics and word vector aggregation techniques. Our results show that current embeddings are limited in their ability to adequately encode medical terms. The novel datasets thus form a challenging new benchmark for the development of medical embeddings able to accurately represent the whole medical terminology.
Published Date: 2020-06-02
Registration: ISSN 2374-3468 (Online) ISSN 2159-5399 (Print) ISBN 978-1-57735-835-0 (10 issue set)
Copyright: Published by AAAI Press, Palo Alto, California USA Copyright © 2020, Association for the Advancement of Artificial Intelligence All Rights Reserved