Ontology-based protein-protein interactions extraction from literature using the hidden vector state model

Yulan He, Keiichi Nakata, Deyu Zhou

Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

Abstract

This paper proposes a novel framework of incorporating protein-protein interactions (PPI) ontology knowledge into PPI extraction from biomedical literature in order to address the emerging challenges of deep natural language understanding. It is built upon the existing work on relation extraction using the Hidden Vector State (HVS) model. The HVS model belongs to the category of statistical learning methods. It can be trained directly from un-annotated data in a constrained way whilst at the same time being able to capture the underlying named entity relationships. However, it is difficult to incorporate background knowledge or non-local information into the HVS model. This paper proposes to represent the HVS model as a conditionally trained undirected graphical model in which non-local features derived from PPI ontology through inference would be easily incorporated. The seamless fusion of ontology inference with statistical learning produces a new paradigm to information extraction.
Original languageEnglish
Title of host publication2008 IEEE international conference on data mining workshops
PublisherIEEE
Pages736-743
Number of pages8
ISBN (Electronic)978-0-7695-3503-6
DOIs
Publication statusPublished - 1 Jan 2008
EventIEEE international conference on data mining workshops - Pisa, Italy
Duration: 15 Dec 200819 Dec 2008

Conference

ConferenceIEEE international conference on data mining workshops
Abbreviated titleICDMW '08
CountryItaly
CityPisa
Period15/12/0819/12/08

Fingerprint

Ontology
Proteins
Fusion reactions

Bibliographical note

© 2008 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.

Keywords

  • hidden vector state model
  • PPI ontology
  • protein-protein interactions extraction
  • information extraction

Cite this

He, Y., Nakata, K., & Zhou, D. (2008). Ontology-based protein-protein interactions extraction from literature using the hidden vector state model. In 2008 IEEE international conference on data mining workshops (pp. 736-743). IEEE. https://doi.org/10.1109/ICDMW.2008.11
He, Yulan ; Nakata, Keiichi ; Zhou, Deyu. / Ontology-based protein-protein interactions extraction from literature using the hidden vector state model. 2008 IEEE international conference on data mining workshops. IEEE, 2008. pp. 736-743
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He, Y, Nakata, K & Zhou, D 2008, Ontology-based protein-protein interactions extraction from literature using the hidden vector state model. in 2008 IEEE international conference on data mining workshops. IEEE, pp. 736-743, IEEE international conference on data mining workshops, Pisa, Italy, 15/12/08. https://doi.org/10.1109/ICDMW.2008.11

Ontology-based protein-protein interactions extraction from literature using the hidden vector state model. / He, Yulan; Nakata, Keiichi; Zhou, Deyu.

2008 IEEE international conference on data mining workshops. IEEE, 2008. p. 736-743.

Research output: Chapter in Book/Report/Conference proceedingOther chapter contribution

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He Y, Nakata K, Zhou D. Ontology-based protein-protein interactions extraction from literature using the hidden vector state model. In 2008 IEEE international conference on data mining workshops. IEEE. 2008. p. 736-743 https://doi.org/10.1109/ICDMW.2008.11