Zihui Huang, Liqiang He, Yuhang Yang, Andi Li, Zhiwen Zhang, Siwei Wu, Yang Wang, Yan He, Xujie Liu
{"title":"将机器阅读理解技术应用于材料科学中的命名实体识别。","authors":"Zihui Huang, Liqiang He, Yuhang Yang, Andi Li, Zhiwen Zhang, Siwei Wu, Yang Wang, Yan He, Xujie Liu","doi":"10.1186/s13321-024-00874-5","DOIUrl":null,"url":null,"abstract":"<div><p>Materials science is an interdisciplinary field that studies the properties, structures, and behaviors of different materials. A large amount of scientific literature contains rich knowledge in the field of materials science, but manually analyzing these papers to find material-related data is a daunting task. In information processing, named entity recognition (NER) plays a crucial role as it can automatically extract entities in the field of materials science, which have significant value in tasks such as building knowledge graphs. The typically used sequence labeling methods for traditional named entity recognition in material science (MatNER) tasks often fail to fully utilize the semantic information in the dataset and cannot effectively extract nested entities. Herein, we proposed to convert the sequence labeling task into a machine reading comprehension (MRC) task. MRC method effectively can solve the challenge of extracting multiple overlapping entities by transforming it into the form of answering multiple independent questions. Moreover, the MRC framework allows for a more comprehensive understanding of the contextual information and semantic relationships within materials science literature, by integrating prior knowledge from queries. State-of-the-art (SOTA) performance was achieved on the Matscholar, BC4CHEMD, NLMChem, SOFC, and SOFC-Slot datasets, with F1-scores of 89.64%, 94.30%, 85.89%, 85.95%, and 71.73%, respectively in MRC approach. By effectively utilizing semantic information and extracting nested entities, this approach holds great significance for knowledge extraction and data analysis in the field of materials science, and thus accelerating the development of material science.</p><p><b>Scientific contribution</b></p><p>We have developed an innovative NER method that enhances the efficiency and accuracy of automatic entity extraction in the field of materials science by transforming the sequence labeling task into a MRC task, this approach provides robust support for constructing knowledge graphs and other data analysis tasks.</p></div>","PeriodicalId":617,"journal":{"name":"Journal of Cheminformatics","volume":"16 1","pages":""},"PeriodicalIF":7.1000,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00874-5","citationCount":"0","resultStr":"{\"title\":\"Application of machine reading comprehension techniques for named entity recognition in materials science\",\"authors\":\"Zihui Huang, Liqiang He, Yuhang Yang, Andi Li, Zhiwen Zhang, Siwei Wu, Yang Wang, Yan He, Xujie Liu\",\"doi\":\"10.1186/s13321-024-00874-5\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Materials science is an interdisciplinary field that studies the properties, structures, and behaviors of different materials. A large amount of scientific literature contains rich knowledge in the field of materials science, but manually analyzing these papers to find material-related data is a daunting task. In information processing, named entity recognition (NER) plays a crucial role as it can automatically extract entities in the field of materials science, which have significant value in tasks such as building knowledge graphs. The typically used sequence labeling methods for traditional named entity recognition in material science (MatNER) tasks often fail to fully utilize the semantic information in the dataset and cannot effectively extract nested entities. Herein, we proposed to convert the sequence labeling task into a machine reading comprehension (MRC) task. MRC method effectively can solve the challenge of extracting multiple overlapping entities by transforming it into the form of answering multiple independent questions. Moreover, the MRC framework allows for a more comprehensive understanding of the contextual information and semantic relationships within materials science literature, by integrating prior knowledge from queries. State-of-the-art (SOTA) performance was achieved on the Matscholar, BC4CHEMD, NLMChem, SOFC, and SOFC-Slot datasets, with F1-scores of 89.64%, 94.30%, 85.89%, 85.95%, and 71.73%, respectively in MRC approach. By effectively utilizing semantic information and extracting nested entities, this approach holds great significance for knowledge extraction and data analysis in the field of materials science, and thus accelerating the development of material science.</p><p><b>Scientific contribution</b></p><p>We have developed an innovative NER method that enhances the efficiency and accuracy of automatic entity extraction in the field of materials science by transforming the sequence labeling task into a MRC task, this approach provides robust support for constructing knowledge graphs and other data analysis tasks.</p></div>\",\"PeriodicalId\":617,\"journal\":{\"name\":\"Journal of Cheminformatics\",\"volume\":\"16 1\",\"pages\":\"\"},\"PeriodicalIF\":7.1000,\"publicationDate\":\"2024-07-02\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-024-00874-5\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Cheminformatics\",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://link.springer.com/article/10.1186/s13321-024-00874-5\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MULTIDISCIPLINARY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Cheminformatics","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1186/s13321-024-00874-5","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
Application of machine reading comprehension techniques for named entity recognition in materials science
Materials science is an interdisciplinary field that studies the properties, structures, and behaviors of different materials. A large amount of scientific literature contains rich knowledge in the field of materials science, but manually analyzing these papers to find material-related data is a daunting task. In information processing, named entity recognition (NER) plays a crucial role as it can automatically extract entities in the field of materials science, which have significant value in tasks such as building knowledge graphs. The typically used sequence labeling methods for traditional named entity recognition in material science (MatNER) tasks often fail to fully utilize the semantic information in the dataset and cannot effectively extract nested entities. Herein, we proposed to convert the sequence labeling task into a machine reading comprehension (MRC) task. MRC method effectively can solve the challenge of extracting multiple overlapping entities by transforming it into the form of answering multiple independent questions. Moreover, the MRC framework allows for a more comprehensive understanding of the contextual information and semantic relationships within materials science literature, by integrating prior knowledge from queries. State-of-the-art (SOTA) performance was achieved on the Matscholar, BC4CHEMD, NLMChem, SOFC, and SOFC-Slot datasets, with F1-scores of 89.64%, 94.30%, 85.89%, 85.95%, and 71.73%, respectively in MRC approach. By effectively utilizing semantic information and extracting nested entities, this approach holds great significance for knowledge extraction and data analysis in the field of materials science, and thus accelerating the development of material science.
Scientific contribution
We have developed an innovative NER method that enhances the efficiency and accuracy of automatic entity extraction in the field of materials science by transforming the sequence labeling task into a MRC task, this approach provides robust support for constructing knowledge graphs and other data analysis tasks.
期刊介绍:
Journal of Cheminformatics is an open access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling.
Coverage includes, but is not limited to:
chemical information systems, software and databases, and molecular modelling,
chemical structure representations and their use in structure, substructure, and similarity searching of chemical substance and chemical reaction databases,
computer and molecular graphics, computer-aided molecular design, expert systems, QSAR, and data mining techniques.