Character-level neural network for biomedical named entity recognition

Journal of Biomedical Informatics
Mourad Gridach

Abstract

Biomedical named entity recognition (BNER), which extracts important named entities such as genes and proteins, is a challenging task in automated systems that mine knowledge in biomedical texts. The previous state-of-the-art systems required large amounts of task-specific knowledge in the form of feature engineering, lexicons and data pre-processing to achieve high performance. In this paper, we introduce a novel neural network architecture that benefits from both word- and character-level representations automatically, by using a combination of bidirectional long short-term memory (LSTM) and conditional random field (CRF) eliminating the need for most feature engineering tasks. We evaluate our system on two datasets: JNLPBA corpus and the BioCreAtIvE II Gene Mention (GM) corpus. We obtained state-of-the-art performance by outperforming the previous systems. To the best of our knowledge, we are the first to investigate the combination of deep neural networks, CRF, word embeddings and character-level representation in recognizing biomedical named entities.

Citations

Jan 1, 2019·Chemical Biology & Drug Design·Ranita PalPratim Kumar Chattaraj
Apr 17, 2020·International Journal of Environmental Research and Public Health·Xianglong ChenYi Bu
Dec 24, 2019·BMC Medical Informatics and Decision Making·Rebecka WeegarMaite Oronoz
Feb 1, 2020·Journal of Biomedical Informatics·Minsoo ChoSanghyun Park
May 14, 2019·Frontiers in Artificial Intelligence·Zihong LiangTianyong Hao
Mar 17, 2021·Journal of Ambient Intelligence and Humanized Computing·R Ramachandran, K Arutchelvan
Apr 12, 2021·Neural Networks : the Official Journal of the International Neural Network Society·Mourad Gridach
May 28, 2021·Journal of Biomedical Informatics·Yang YangShengping Liu
Jul 30, 2021·Frontiers in Research Metrics and Analytics·Darshini MahendranBridget T McInnes
Jul 27, 2021·Briefings in Bioinformatics·Bosheng SongXiangxiang Zeng
Aug 1, 2021·BMC Medical Informatics and Decision Making·Huanyao ZhangXudong Lu
Sep 30, 2020·Mathematical Biosciences and Engineering : MBE·Guang Xun SunZhan Gao
Dec 19, 2021·BMC Bioinformatics·Mayla R BoguslavLawrence E Hunter

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