Literature DB >> 27597572

Automated learning of domain taxonomies from text using background knowledge.

Julia Hoxha1, Guoqian Jiang2, Chunhua Weng3.   

Abstract

In this paper, we present an automated method for taxonomy learning, focusing on concept formation and hierarchical relation learning. To infer such relations, we partition the extracted concepts and group them into closely-related clusters using Hierarchical Agglomerative Clustering, informed by syntactic matching and semantic relatedness functions. We introduce a novel, unsupervised method for cluster detection based on automated dendrogram pruning, which is dynamic to each partition. We evaluate our approach with two different types of textual corpora, clinical trials descriptions and MEDLINE publication abstracts. The results of several experiments indicate that our method is superior to existing dynamic pruning and the state-of-art taxonomy learning methods. It yields higher concept coverage (95.75%) and higher accuracy of learned taxonomic relations (up to 0.71 average precision and 0.96 average recall).
Copyright © 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Concept discovery; Ontology learning; Semantic relation acquisition; Taxonomy extraction from text; Term recognition

Mesh:

Year:  2016        PMID: 27597572      PMCID: PMC5077645          DOI: 10.1016/j.jbi.2016.09.002

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


  8 in total

1.  A semantic lexicon for medical language processing.

Authors:  S B Johnson
Journal:  J Am Med Inform Assoc       Date:  1999 May-Jun       Impact factor: 4.497

Review 2.  Natural Language Processing methods and systems for biomedical ontology learning.

Authors:  Kaihong Liu; William R Hogan; Rebecca S Crowley
Journal:  J Biomed Inform       Date:  2010-07-18       Impact factor: 6.317

3.  Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R.

Authors:  Peter Langfelder; Bin Zhang; Steve Horvath
Journal:  Bioinformatics       Date:  2007-11-16       Impact factor: 6.937

4.  Semantic classification of biomedical concepts using distributional similarity.

Authors:  Jung-Wei Fan; Carol Friedman
Journal:  J Am Med Inform Assoc       Date:  2007-04-25       Impact factor: 4.497

5.  MedEx: a medication information extraction system for clinical narratives.

Authors:  Hua Xu; Shane P Stenner; Son Doan; Kevin B Johnson; Lemuel R Waitman; Joshua C Denny
Journal:  J Am Med Inform Assoc       Date:  2010 Jan-Feb       Impact factor: 4.497

6.  EliXR: an approach to eligibility criteria extraction and representation.

Authors:  Chunhua Weng; Xiaoying Wu; Zhihui Luo; Mary Regina Boland; Dimitri Theodoratos; Stephen B Johnson
Journal:  J Am Med Inform Assoc       Date:  2011-07-31       Impact factor: 4.497

7.  Toward high-throughput phenotyping: unbiased automated feature extraction and selection from knowledge sources.

Authors:  Sheng Yu; Katherine P Liao; Stanley Y Shaw; Vivian S Gainer; Susanne E Churchill; Peter Szolovits; Shawn N Murphy; Isaac S Kohane; Tianxi Cai
Journal:  J Am Med Inform Assoc       Date:  2015-04-29       Impact factor: 4.497

8.  Corpus-based Approach to Creating a Semantic Lexicon for Clinical Research Eligibility Criteria from UMLS.

Authors:  Zhihui Luo; Robert Duffy; Stephen Johnson; Chunhua Weng
Journal:  Summit Transl Bioinform       Date:  2010-03-01
  8 in total
  4 in total

1.  Validating UMLS Semantic Type Assignments Using SNOMED CT Semantic Tags.

Authors:  Huanying Gu; Zhe He; Duo Wei; Gai Elhanan; Yan Chen
Journal:  Methods Inf Med       Date:  2018-04-05       Impact factor: 2.176

2.  Extended Analysis of Topological-Pattern-Based Ontology Enrichment.

Authors:  Zhe He; Vipina Kuttichi Keloth; Yan Chen; James Geller
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2019-01-24

3.  Enriching consumer health vocabulary through mining a social Q&A site: A similarity-based approach.

Authors:  Zhe He; Zhiwei Chen; Sanghee Oh; Jinghui Hou; Jiang Bian
Journal:  J Biomed Inform       Date:  2017-03-27       Impact factor: 6.317

4.  Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.

Authors:  Zhe He; Yehoshua Perl; Gai Elhanan; Yan Chen; James Geller; Jiang Bian
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2017-12-18
  4 in total

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