Machine Learning Approach for Multi-Layered Detection of Chemical Named Entities in Text

Abstract

Identification of chemical named entities in text and subsequent linkage of information to biological events is of immense value to fulfill the knowledge needs of pharmaceutical and chemical R&D. A significant amount of investigation has been carried out since a decade for identifying chemical named entities at morphological level. However, a barrier still remains in terms of value proposition to scientists at chemistry level. Therefore, the work described here aims to circumvent the information barrier by adaptation of a Conditional Random Fields-based approach for identifying chemical named entities at various levels namely generic chemical level, morphological level, and chemistry level. Substantial effort has been invested on generation of suitable multi-level annotated corpora. Recommended machine learning practices such as active learning-based training corpus generation and feature optimization have been systematically performed. Evaluation of system performance and benchmarking against the other state-of-the-approaches showed improved results.