We introduce ChemDisGene, a new dataset for training and evaluating multi-class multi-label biomedical relation extraction models. Our dataset contains 80k biomedical research abstracts labeled with mentions of chemicals, diseases, and genes, portions of which human experts labeled with 18 types of biomedical relationships between these entities (intended for evaluation), and the remainder of which (intended for training) has been distantly labeled via the CTD database with approximately 78% accuracy. In comparison to similar preexisting datasets, ours is both substantially larger and cleaner; it also includes annotations linking mentions to their entities. We also provide three baseline deep neural network relation extraction models trained and evaluated on our new dataset.

Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using learned representations of entities. Previous approaches link each mention independently, ignoring the relationships within and across documents between the entity mentions. These relations can be very useful for linking mentions in biomedical text where linking decisions are often difficult due mentions having a generic or a highly specialized form. In this paper, we introduce a model in which linking decisions can be made not merely by linking to a knowledge base entity but also by grouping multiple mentions together via clustering and jointly making linking predictions. In experiments on the largest publicly available biomedical dataset, we improve the best independent prediction for entity linking by 3.0 points of accuracy, and our clustering-based inference model further improves entity linking by 2.3 points.

We describe a Deep Learning approach to modeling the relevance of a document’s text to a query, applied to biomedical literature. Instead of mapping each document and query to a common semantic space, we compute a variable-length difference vector between the query and document which is then passed through a deep convolution stage followed by a deep regression network to produce the estimated probability of the document’s relevance to the query. Despite the small amount of training data, this approach produces a more robust predictor than computing similarities between semantic vector representations of the query and document, and also results in significant improvements over traditional IR text factors. In the future, we plan to explore its application in improving PubMed search.