Hamada Ali Mohamed Ali Nayel
Lecturer
Improving Multi-Word Entity Recognition for Biomedical Texts
International Journal of Pure and Applied Mathematics • 2018
Publication Information
Authors
Hamada A Nayel, HL Shashirekha, Hiroyuki Shindo, Yuji Matsumoto
Keywords
Biomedical Text Mining, Segment Representations, Biomedical Named Entity Recognition, BiLSTM.
Journal
International Journal of Pure and Applied Mathematics
Publisher
Academic Publications Ltd.
Volume
118
Issue
16
Pages
301-319
publication.type
International
Paper Link
Open Link
Supplementary Materials
Not Available
Abstract
Biomedical Named Entity Recognition (BioNER) is a crucial step for analyzing Biomedical texts, which aims at extracting biomedical named entities from a given text. Different supervised machine learning algorithms have been applied for BioNER by various researchers. The main requirement of these approaches is an annotated dataset used for learning the parameters of machine learning algorithms. Segment Representation (SR) models comprise of different tag sets used for representing the annotated data, such as IOB2, IOE2 and IOBES. In this paper, we propose an extension of IOBES model to improve the performance of BioNER. The proposed SR model, FROBES, improves the representation of multi-word entities. We used Bidirectional Long Short-Term Memory (BiLSTM) network; an instance of Recurrent Neural Networks (RNN), to design a baseline system for BioNER and evaluated the new SR model on two datasets, i2b2/VA 2010 challenge dataset and JNLPBA 2004 shared task dataset. The proposed SR model outperforms other models for multi-word entities with length greater than two. Further, the outputs of different SR models have been combined using majority voting ensemble method which outperforms the baseline models performance.
