Literature DB >> 19232399

Empirical distributional semantics: methods and biomedical applications.

Trevor Cohen1, Dominic Widdows.   

Abstract

Over the past 15 years, a range of methods have been developed that are able to learn human-like estimates of the semantic relatedness between terms from the way in which these terms are distributed in a corpus of unannotated natural language text. These methods have also been evaluated in a number of applications in the cognitive science, computational linguistics and the information retrieval literatures. In this paper, we review the available methodologies for derivation of semantic relatedness from free text, as well as their evaluation in a variety of biomedical and other applications. Recent methodological developments, and their applicability to several existing applications are also discussed.

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Year:  2009        PMID: 19232399      PMCID: PMC2750802          DOI: 10.1016/j.jbi.2009.02.002

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  33 in total

1.  The NLM Indexing Initiative.

Authors:  A R Aronson; O Bodenreider; H F Chang; S M Humphrey; J G Mork; S J Nelson; T C Rindflesch; W J Wilbur
Journal:  Proc AMIA Symp       Date:  2000

Review 2.  Consumer health information seeking on the Internet: the state of the art.

Authors:  R J Cline; K M Haynes
Journal:  Health Educ Res       Date:  2001-12

3.  GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Authors:  C Friedman; P Kra; H Yu; M Krauthammer; A Rzhetsky
Journal:  Bioinformatics       Date:  2001       Impact factor: 6.937

4.  Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.

Authors:  A R Aronson
Journal:  Proc AMIA Symp       Date:  2001

5.  Evaluation of the vector space representation in text-based gene clustering.

Authors:  P Glenisson; P Antal; J Mathys; Y Moreau; B De Moor
Journal:  Pac Symp Biocomput       Date:  2003

6.  Representations of health concepts: a cognitive perspective.

Authors:  Jiajie Zhang
Journal:  J Biomed Inform       Date:  2002-02       Impact factor: 6.317

7.  Semantic annotation for concept-based cross-language medical information retrieval.

Authors:  Martin Volk; Bärbel Ripplinger; Spela Vintar; Paul Buitelaar; Diana Raileanu; Bogdan Sacaleanu
Journal:  Int J Med Inform       Date:  2002-12-04       Impact factor: 4.046

8.  The structure of science information.

Authors:  Zellig S Harris
Journal:  J Biomed Inform       Date:  2002-08       Impact factor: 6.317

9.  The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text.

Authors:  Thomas C Rindflesch; Marcelo Fiszman
Journal:  J Biomed Inform       Date:  2003-12       Impact factor: 6.317

10.  Simulating expert clinical comprehension: adapting latent semantic analysis to accurately extract clinical concepts from psychiatric narrative.

Authors:  Trevor Cohen; Brett Blatter; Vimla Patel
Journal:  J Biomed Inform       Date:  2008-03-27       Impact factor: 6.317

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  55 in total

1.  Enhancing clinical concept extraction with distributional semantics.

Authors:  Siddhartha Jonnalagadda; Trevor Cohen; Stephen Wu; Graciela Gonzalez
Journal:  J Biomed Inform       Date:  2011-11-07       Impact factor: 6.317

2.  A hybrid knowledge-based and data-driven approach to identifying semantically similar concepts.

Authors:  Rimma Pivovarov; Noémie Elhadad
Journal:  J Biomed Inform       Date:  2012-01-25       Impact factor: 6.317

3.  Predication-based semantic indexing: permutations as a means to encode predications in semantic space.

Authors:  Trevor Cohen; Roger W Schvaneveldt; Thomas C Rindflesch
Journal:  AMIA Annu Symp Proc       Date:  2009-11-14

4.  Using text to build semantic networks for pharmacogenomics.

Authors:  Adrien Coulet; Nigam H Shah; Yael Garten; Mark Musen; Russ B Altman
Journal:  J Biomed Inform       Date:  2010-08-17       Impact factor: 6.317

5.  Characterizing the sublanguage of online breast cancer forums for medications, symptoms, and emotions.

Authors:  Noémie Elhadad; Shaodian Zhang; Patricia Driscoll; Samuel Brody
Journal:  AMIA Annu Symp Proc       Date:  2014-11-14

Review 6.  Recent progress in automatically extracting information from the pharmacogenomic literature.

Authors:  Yael Garten; Adrien Coulet; Russ B Altman
Journal:  Pharmacogenomics       Date:  2010-10       Impact factor: 2.533

7.  The Centroid Cannot Hold: Comparing Sequential and Global Estimates of Coherence as Indicators of Formal Thought Disorder.

Authors:  Weizhe Xu; Jake Portanova; Ayesha Chander; Dror Ben-Zeev; Trevor Cohen
Journal:  AMIA Annu Symp Proc       Date:  2021-01-25

8.  Feature extraction for phenotyping from semantic and knowledge resources.

Authors:  Wenxin Ning; Stephanie Chan; Andrew Beam; Ming Yu; Alon Geva; Katherine Liao; Mary Mullen; Kenneth D Mandl; Isaac Kohane; Tianxi Cai; Sheng Yu
Journal:  J Biomed Inform       Date:  2019-02-07       Impact factor: 6.317

9.  Discovering discovery patterns with Predication-based Semantic Indexing.

Authors:  Trevor Cohen; Dominic Widdows; Roger W Schvaneveldt; Peter Davies; Thomas C Rindflesch
Journal:  J Biomed Inform       Date:  2012-07-26       Impact factor: 6.317

10.  EpiphaNet: An Interactive Tool to Support Biomedical Discoveries.

Authors:  Trevor Cohen; G Kerr Whitfield; Roger W Schvaneveldt; Kavitha Mukund; Thomas Rindflesch
Journal:  J Biomed Discov Collab       Date:  2010-09-21
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