MOLIERE: Automatic Biomedical Hypothesis Generation System

Abstract

Hypothesis generation is becoming a crucial time-saving technique which allows biomedical researchers to quickly discover implicit connections between important concepts. Typically, these systems operate on domain-specific fractions of public medical data. MOLIERE, in contrast, utilizes information from over 24.5 million documents and does not limit the document vocabulary. At the heart of our approach lies a multi-modal and multi-relational network of biomedical objects extracted from several heterogeneous datasets from the National Center for Biotechnology Information (NCBI). These objects include but are not limited to scientific papers, keywords, genes, proteins, diseases, and diagnoses. We model hypotheses using Latent Dirichlet Allocation applied on abstracts found near shortest paths discovered within this network. We demonstrate the effectiveness of MOLIERE by performing hypothesis generation on historical data. Our network, implementation, and resulting data are all publicly available for the broad scientific community.

Publication
Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
Date

MOLIERE is a hypothesis generation system which is able to identify potential relationships from large text corpora. Our presented system was trained on the MEDLINE dataset, containing nearly 25 million documents dating back to the late 1800’s. We validate our system by predicting recent findings using only information present before 2010. These validations efforts are confirmed with the help of a domain expert.

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