Extraction of Gene-Environment Interaction from the Biomedical Literature

Jinseon You, Jin-Woo Chung, Wonsuk Yang, Jong C. Park


Abstract
Genetic information in the literature has been extensively looked into for the purpose of discovering the etiology of a disease. As the gene-disease relation is sensitive to external factors, their identification is important to study a disease. Environmental influences, which are usually called Gene-Environment interaction (GxE), have been considered as important factors and have extensively been researched in biology. Nevertheless, there is still a lack of systems for automatic GxE extraction from the biomedical literature due to new challenges: (1) there are no preprocessing tools and corpora for GxE, (2) expressions of GxE are often quite implicit, and (3) document-level comprehension is usually required. We propose to overcome these challenges with neural network models and show that a modified sequence-to-sequence model with a static RNN decoder produces a good performance in GxE recognition.
Anthology ID:
I17-1087
Volume:
Proceedings of the Eighth International Joint Conference on Natural Language Processing (Volume 1: Long Papers)
Month:
November
Year:
2017
Address:
Taipei, Taiwan
Venue:
IJCNLP
SIG:
Publisher:
Asian Federation of Natural Language Processing
Note:
Pages:
865–874
Language:
URL:
https://www.aclweb.org/anthology/I17-1087
DOI:
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PDF:
http://aclanthology.lst.uni-saarland.de/I17-1087.pdf