DeepVar: An end-to-end deep learning approach for genomic variant recognition in biomedical literature

Chaoran Cheng, Fei Tan, Zhi Wei

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We consider the problem of Named Entity Recognition (NER) on biomedical scientific literature, and more specifically the genomic variants recognition in this work. Significant success has been achieved for NER on canonical tasks in recent years where large data sets are generally available. However, it remains a challenging problem on many domain-specific areas, especially the domains where only small gold annotations can be obtained. In addition, genomic variant entities exhibit diverse linguistic heterogeneity, differing much from those that have been characterized in existing canonical NER tasks. The state-of-the-art machine learning approaches heavily rely on arduous feature engineering to characterize those unique patterns. In this work, we present the first successful end-to-end deep learning approach to bridge the gap between generic NER algorithms and low-resource applications through genomic variants recognition. Our proposed model can result in promising performance without any handcrafted features or post-processing rules. Our extensive experiments and results may shed light on other similar low-resource NER applications.

Original languageEnglish (US)
Title of host publicationAAAI 2020 - 34th AAAI Conference on Artificial Intelligence
PublisherAAAI press
Pages598-605
Number of pages8
ISBN (Electronic)9781577358350
StatePublished - 2020
Event34th AAAI Conference on Artificial Intelligence, AAAI 2020 - New York, United States
Duration: Feb 7 2020Feb 12 2020

Publication series

NameAAAI 2020 - 34th AAAI Conference on Artificial Intelligence

Conference

Conference34th AAAI Conference on Artificial Intelligence, AAAI 2020
Country/TerritoryUnited States
CityNew York
Period2/7/202/12/20

All Science Journal Classification (ASJC) codes

  • Artificial Intelligence

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