Towards self-learning based hypotheses generation in biomedical text domain

Vishrawas Gopalakrishnan; Kishlay Jha; Guangxu Xun; Hung Q. Ngo; Aidong Zhang

doi:10.1093/bioinformatics/btx837

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Towards self-learning based hypotheses generation in biomedical text domain

Journal article

Open access

Peer reviewed

Towards self-learning based hypotheses generation in biomedical text domain

Vishrawas Gopalakrishnan, Kishlay Jha, Guangxu Xun, Hung Q. Ngo and Aidong Zhang

BIOINFORMATICS, Vol.34(12), pp.2103-2115

06/15/2018

DOI: 10.1093/bioinformatics/btx837

PMID: 29293920

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Abstract

Motivation: The overwhelming amount of research articles in the domain of bio-medicine might cause important connections to remain unnoticed. Literature Based Discovery is a sub-field within biomedical text mining that peruses these articles to formulate high confident hypotheses on possible connections between medical concepts. Although many alternate methodologies have been proposed over the last decade, they still suffer from scalability issues. The primary reason, apart from the dense inter-connections between biological concepts, is the absence of information on the factors that lead to the edge-formation. In this work, we formulate this problem as a collaborative filtering task and leverage a relatively new concept of word-vectors to learn and mimic the implicit edge-formation process. Along with single-class classifier, we prune the search-space of redundant and irrelevant hypotheses to increase the efficiency of the system and at the same time maintaining and in some cases even boosting the overall accuracy. Results: We show that our proposed framework is able to prune up to 90% of the hypotheses while still retaining high recall in top-K results. This level of efficiency enables the discovery algorithm to look for higher-order hypotheses, something that was infeasible until now. Furthermore, the generic formulation allows our approach to be agile to perform both open and closed discovery. We also experimentally validate that the core data-structures upon which the system bases its decision has a high concordance with the opinion of the experts.This coupled with the ability to understand the edge formation process provides us with interpretable results without any manual intervention.

Biochemical Research Methods

Biochemistry & Molecular Biology

Biotechnology & Applied Microbiology

Computer Science

Computer Science, Interdisciplinary Applications

Life Sciences & Biomedicine

Mathematical & Computational Biology

Mathematics

Physical Sciences

Science & Technology

Statistics & Probability

Technology

Details

Title: Subtitle: Towards self-learning based hypotheses generation in biomedical text domain
Creators: Vishrawas Gopalakrishnan - University at Buffalo, State University of New York
Kishlay Jha - University at Buffalo, State University of New York
Guangxu Xun - University at Buffalo, State University of New York
Hung Q. Ngo - University at Buffalo, State University of New York
Aidong Zhang - University at Buffalo, State University of New York
Resource Type: Journal article
Publication Details: BIOINFORMATICS, Vol.34(12), pp.2103-2115
DOI: 10.1093/bioinformatics/btx837
PMID: 29293920
NLM abbreviation: Bioinformatics
ISSN: 1367-4803
eISSN: 1460-2059
Publisher: Oxford Univ Press
Number of pages: 13
Grant note: IIS-1218393; IIS-1514204 / National Science Foundation; National Science Foundation (NSF)
Language: English
Date published: 06/15/2018
Academic Unit: Electrical and Computer Engineering
Record Identifier: 9984294926102771

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