CHEMNER: Fine-Grained Chemistry Named Entity Recognition with Ontology-Guided Distant Supervision

Xuan Wang, Vivian Hu, Xiangchen Song, Shweta Garg, Jinfeng Xiao, Jiawei Han

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

Abstract

Scientific literature analysis needs fine-grained named entity recognition (NER) to provide a wide range of information for scientific discovery. For example, chemistry research needs to study dozens to hundreds of distinct, fine-grained entity types, making consistent and accurate annotation difficult even for crowds of domain experts. On the other hand, domain-specific ontologies and knowledge bases (KBs) can be easily accessed, constructed, or integrated, which makes distant supervision realistic for fine-grained chemistry NER. In distant supervision, training labels are generated by matching mentions in a document with the concepts in the knowledge bases (KBs). However, this kind of KB-matching suffers from two major challenges: incomplete annotation and noisy annotation. We propose CHEMNER, an ontology-guided, distantly-supervised method for fine-grained chemistry NER to tackle these challenges. It leverages the chemistry type ontology structure to generate distant labels with novel methods of flexible KB-matching and ontology-guided multi-type disambiguation. It significantly improves the distant label generation for the subsequent sequence labeling model training. We also provide an expert-labeled, chemistry NER dataset with 62 fine-grained chemistry types (e.g., chemical compounds and chemical reactions). Experimental results show that CHEMNER is highly effective, outperforming substantially the state-of-the-art NER methods (with.25 absolute F1 score improvement).

Original languageEnglish (US)
Title of host publicationEMNLP 2021 - 2021 Conference on Empirical Methods in Natural Language Processing, Proceedings
PublisherAssociation for Computational Linguistics (ACL)
Pages5227-5240
Number of pages14
ISBN (Electronic)9781955917094
StatePublished - 2021
Externally publishedYes
Event2021 Conference on Empirical Methods in Natural Language Processing, EMNLP 2021 - Virtual, Punta Cana, Dominican Republic
Duration: Nov 7 2021Nov 11 2021

Publication series

NameEMNLP 2021 - 2021 Conference on Empirical Methods in Natural Language Processing, Proceedings

Conference

Conference2021 Conference on Empirical Methods in Natural Language Processing, EMNLP 2021
Country/TerritoryDominican Republic
CityVirtual, Punta Cana
Period11/7/2111/11/21

ASJC Scopus subject areas

  • Computational Theory and Mathematics
  • Computer Science Applications
  • Information Systems

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