A new evaluation methodology for literature-based discovery systems

Journal of Biomedical Informatics
Meliha Yetisgen-Yildiz, Wanda Pratt

Abstract

While medical researchers formulate new hypotheses to test, they need to identify connections to their work from other parts of the medical literature. However, the current volume of information has become a great barrier for this task. Recently, many literature-based discovery (LBD) systems have been developed to help researchers identify new knowledge that bridges gaps across distinct sections of the medical literature. Each LBD system uses different methods for mining the connections from text and ranking the identified connections, but none of the currently available LBD evaluation approaches can be used to compare the effectiveness of these methods. In this paper, we present an evaluation methodology for LBD systems that allows comparisons across different systems. We demonstrate the abilities of our evaluation methodology by using it to compare the performance of different correlation-mining and ranking approaches used by existing LBD systems. This evaluation methodology should help other researchers compare approaches, make informed algorithm choices, and ultimately help to improve the performance of LBD systems overall.

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Citations

Jun 17, 2011·Briefings in Bioinformatics·Alberto FaroConcetto Spampinato
Jul 27, 2012·Briefings in Bioinformatics·Udo HahnNigam H Shah
Jun 21, 2011·Bioinformatics·Yoshimasa TsuruokaSophia Ananiadou
Jul 22, 2014·Journal of Biomedical Informatics·Ning ShangTrevor Cohen
Jan 24, 2014·Applied Clinical Informatics·T Botsis, R Ball
Mar 30, 2010·Journal of Biomedical Informatics·Nancy C Baker, Bradley M Hemminger
Sep 19, 2009·Journal of Biomedical Informatics·Trevor CohenDominic Widdows
Feb 11, 2015·Journal of Biomedical Informatics·Delroy CameronOlivier Bodenreider
Jul 28, 2016·BMC Medical Informatics and Decision Making·Judita Preiss, Mark Stevenson
May 15, 2015·Journal of the American Medical Informatics Association : JAMIA·Judita PreissRobert Gaizauskas
Jan 23, 2018·Journal of Data and Information Science·Neil R Smalheiser
Oct 14, 2017·Bioinformatics·Jake LeverJonathan Wren
May 7, 2013·Journal of the American Medical Informatics Association : JAMIA·Diana Lynn MacLean, Jeffrey Heer
May 16, 2020·PloS One·Gamal CrichtonAnna Korhonen
Jun 8, 2018·Drug Safety : an International Journal of Medical Toxicology and Drug Experience·Mary K LaAlexander Tropsha
Dec 2, 2017·CPT: Pharmacometrics & Systems Pharmacology·Pengyue ZhangLang Li
May 30, 2019·BMC Bioinformatics·Judita Preiss
Oct 12, 2018·Bioinformatics·Sampo PyysaloAnna Korhonen
Aug 17, 2019·BMC Bioinformatics·Sam Henry, Bridget T McInnes
Jun 16, 2017·BMC Bioinformatics·Judita Preiss, Mark Stevenson
Dec 23, 2017·Frontiers in Research Metrics and Analytics·Yufang PengNeil R Smalheiser
Mar 13, 2019·Journal of Biomedical Informatics·Vishrawas GopalakrishnanAidong Zhang
Nov 18, 2019·PeerJ. Computer Science·Menasha ThilakaratneThushari Atapattu
Jul 13, 2021·Frontiers in Research Metrics and Analytics·Sam HenryBridget T McInnes

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