Learning Bayesian network using parse trees for extraction of protein-protein interaction

Pedro Nelson Shiguihara-Juárez, Alneu De Andrade Lopes

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

6 Scopus citations

Abstract

Extraction of protein-protein interactions from scientific papers is a relevant task in the biomedical field. Machine learning-based methods such as kernel-based represent the state-of-the-art in this task. Many efforts have focused on obtaining new types of kernels in order to employ syntactic information, such as parse trees, to extract interactions from sentences. These methods have reached the best performances on this task. Nevertheless, parse trees were not exploited by other machine learning-based methods such as Bayesian networks. The advantage of using Bayesian networks is that we can exploit the structure of the parse trees to learn the Bayesian network structure, i.e., the parse trees provide the random variables and also possible relations among them. Here we use syntactic relation as a causal dependence between variables. Hence, our proposed method learns a Bayesian network from parse trees. The evaluation was carried out over five protein-protein interaction benchmark corpora. Results show that our method is competitive in comparison with state-of-the-art methods.

Original languageEnglish
Title of host publicationComputational Linguistics and Intelligent Text Processing - 14th International Conference, CICLing 2013, Proceedings
Pages347-358
Number of pages12
EditionPART 2
DOIs
StatePublished - 2013
Externally publishedYes
Event14th Annual Conference on Intelligent Text Processing and Computational Linguistics, CICLing 2013 - Samos, Greece
Duration: 24 Mar 201330 Mar 2013

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
NumberPART 2
Volume7817 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference14th Annual Conference on Intelligent Text Processing and Computational Linguistics, CICLing 2013
Country/TerritoryGreece
CitySamos
Period24/03/1330/03/13

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