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

He, Yulan, Nakata, Keiichi and Zhou, Deyu (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.

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.

Publication DOI: https://doi.org/10.1109/ICDMW.2008.11
Divisions: Engineering & Applied Sciences > Computer science
Engineering & Applied Sciences > Systems analytics research institute (SARI)
Engineering & Applied Sciences > Computer science research group
Additional Information: © 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.
Event Title: IEEE international conference on data mining workshops
Event Type: Other
Event Dates: 2008-12-15 - 2008-12-19
Uncontrolled Keywords: hidden vector state model,PPI ontology,protein-protein interactions extraction,information extraction
Full Text Link: http://ieeexplo ... rnumber=4734001
Related URLs: http://www.scop ... tnerID=8YFLogxK (Scopus URL)
Published Date: 2008-01-01
Authors: He, Yulan ( 0000-0003-3948-5845)
Nakata, Keiichi
Zhou, Deyu

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