REACTION MINER: An Integrated System for Chemical Reaction Extraction from Textual Data

Ming Zhong, Siru Ouyang, Yizhu Jiao, Priyanka Kargupta, Leo Luo, Yanzhen Shen, Bobby Zhou, Xianrui Zhong, Xuan Liu, Hongxiang Li, Jinfeng Xiao, Minhao Jiang, Vivian Hu, Xuan Wang, Heng Ji, Martin Burke, Huimin Zhao, Jiawei Han

Research output: Contribution to conferencePaperpeer-review

Abstract

Chemical reactions, as a core entity in the realm of chemistry, hold crucial implications in diverse areas ranging from hands-on laboratory research to advanced computational drug design. Despite a burgeoning interest in employing NLP techniques to extract these reactions, aligning this task with the real-world requirements of chemistry practitioners remains an ongoing challenge. In this paper, we present REACTION MINER, a system specifically designed to interact with raw scientific literature, delivering precise and more informative chemical reactions. Going beyond mere extraction, REACTION MINER integrates a holistic work-flow: it accepts PDF files as input, bypassing the need for pre-processing and bolstering user accessibility. Subsequently, a text segmentation module ensures that the refined text encapsulates complete chemical reactions, augmenting the accuracy of extraction. Moreover, REACTION MINER broadens the scope of existing pre-defined reaction roles, including vital attributes previously neglected, thereby offering a more comprehensive depiction of chemical reactions. Evaluations conducted by chemistry domain users highlight the efficacy of each module in our system, demonstrating REACTION MINER as a powerful tool in this field.

Original languageEnglish (US)
Pages389-402
Number of pages14
StatePublished - 2023
Event2023 Conference on Empirical Methods in Natural Language Processing, EMNLP 2023 - Hybrid, Singapore, Singapore
Duration: Dec 6 2023Dec 10 2023

Conference

Conference2023 Conference on Empirical Methods in Natural Language Processing, EMNLP 2023
Country/TerritorySingapore
CityHybrid, Singapore
Period12/6/2312/10/23

ASJC Scopus subject areas

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

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