using workflows to explore and optimise named entity recognition for chemistry使用工作流来探索和优化化学命名实体识别.pdfVIP

Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry 1 2 2 1 1 BalaKrishna Kolluru *, Lezan Hawizy , Peter Murray-Rust , Junichi Tsujii , Sophia Ananiadou 1 National Centre for Text Mining, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom, 2 Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, United Kingdom Abstract Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U- Compare. These workflows can be altered using the drag--drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, loweri