Fine-Grained Chemical Entity Typing with Multimodal Knowledge Representation

Chenkai Sun, Weijiang Li, Jinfeng Xiao, Nikolaus Nova Parulian, Chengxiang Zhai, Heng Ji

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

Abstract

Automated knowledge discovery from trending chemical literature is essential for more efficient biomedical research. How to extract detailed knowledge about chemical reactions from the core chemistry literature is a new emerging challenge that has not been well studied. In this paper, we study the new problem of fine-grained chemical entity typing, which poses interesting new challenges especially because of the complex name mentions frequently occurring in chemistry literature and graphic representation of entities. We introduce a new benchmark data set (CHEMET) to facilitate the study of the new task and propose a novel multi-modal representation learning framework to solve the problem of fine-grained chemical entity typing by leveraging external resources with chemical structures and using cross-modal attention to learn effective representation of text in the chemistry domain. Experiment results show that the proposed framework outperforms multiple state-of-the-art methods.

Original languageEnglish (US)
Title of host publicationProceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021
EditorsYufei Huang, Lukasz Kurgan, Feng Luo, Xiaohua Tony Hu, Yidong Chen, Edward Dougherty, Andrzej Kloczkowski, Yaohang Li
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages1984-1991
Number of pages8
ISBN (Electronic)9781665401265
DOIs
StatePublished - 2021
Externally publishedYes
Event2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 - Virtual, Online, United States
Duration: Dec 9 2021Dec 12 2021

Publication series

NameProceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

Conference

Conference2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021
Country/TerritoryUnited States
CityVirtual, Online
Period12/9/2112/12/21

Keywords

  • Chemistry
  • Deep Learning
  • Fine-Grained Entity Typing
  • Information Extraction
  • Multimodal Representation

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Science Applications
  • Biomedical Engineering
  • Health Informatics
  • Information Systems and Management

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