Martin Burke


2023

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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
Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing: System Demonstrations

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 workflow: 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.