Automatic Human-like Mining and Constructing Reliable Genetic Association Database with Deep Reinforcement Learning

Pac Symp Biocomput. 2019;24:112-123.


The increasing amount of scientific literature in biological and biomedical science research has created a challenge in continuous and reliable curation of the latest knowledge discovered, and automatic biomedical text-mining has been one of the answers to this challenge. In this paper, we aim to further improve the reliability of biomedical text-mining by training the system to directly simulate the human behaviors such as querying the PubMed, selecting articles from queried results, and reading selected articles for knowledge. We take advantage of the efficiency of biomedical text-mining, the exibility of deep reinforcement learning, and the massive amount of knowledge collected in UMLS into an integrative artificial intelligent reader that can automatically identify the authentic articles and effectively acquire the knowledge conveyed in the articles. We construct a system, whose current primary task is to build the genetic association database between genes and complex traits of human. Our contributions in this paper are three-fold: 1) We propose to improve the reliability of text-mining by building a system that can directly simulate the behavior of a researcher, and we develop corresponding methods, such as Bi-directional LSTM for text mining and Deep Q-Network for organizing behaviors. 2) We demonstrate the effectiveness of our system with an example in constructing a genetic association database. 3) We release our implementation as a generic framework for researchers in the community to conveniently construct other databases.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Computational Biology / methods
  • Data Mining / methods*
  • Databases, Genetic / statistics & numerical data*
  • Decision Support Techniques
  • Deep Learning*
  • Genetic Association Studies / statistics & numerical data*
  • Humans
  • Knowledge Bases
  • Markov Chains
  • PubMed
  • Reproducibility of Results
  • Unified Medical Language System