RECOGNITION OF GENE/PROTEIN NAMES USING CONDITIONAL RANDOM FIELDS

David Campos, Sérgio Matos, José Luis Oliveira

2010

Abstract

With the overwhelming amount of publicly available data in the biomedical field, traditional tasks performed by expert database annotators rapidly became hard and very expensive. This situation led to the development of computerized systems to extract information in a structured manner. The first step of such systems requires the identification of named entities (e.g. gene/protein names), a task called Named Entity Recognition (NER). Much of the current research to tackle this problem is based on Machine Learning (ML) techniques, which demand careful and sensitive definition of the several used methods. This article presents a NER system using Conditional Random Fields (CRFs) as the machine learning technique, combining the best techniques recently described in the literature. The proposed system uses biomedical knowledge and a large set of orthographic and morphological features. An F-measure of 0,7936 was obtained on the BioCreative II Gene Mention corpus, achieving a significantly better performance than similar baseline systems.

Paper Citation

in Harvard Style

Campos D., Matos S. and Oliveira J. (2010). RECOGNITION OF GENE/PROTEIN NAMES USING CONDITIONAL RANDOM FIELDS . In Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2010) ISBN 978-989-8425-28-7, pages 275-280. DOI: 10.5220/0003096902750280

in Bibtex Style

@conference{kdir10,
author={David Campos and Sérgio Matos and José Luis Oliveira},
title={RECOGNITION OF GENE/PROTEIN NAMES USING CONDITIONAL RANDOM FIELDS},
booktitle={Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2010)},
year={2010},
pages={275-280},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0003096902750280},
isbn={978-989-8425-28-7},
}

in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Knowledge Discovery and Information Retrieval - Volume 1: KDIR, (IC3K 2010)
TI - RECOGNITION OF GENE/PROTEIN NAMES USING CONDITIONAL RANDOM FIELDS
SN - 978-989-8425-28-7
AU - Campos D.
AU - Matos S.
AU - Oliveira J.
PY - 2010
SP - 275
EP - 280
DO - 10.5220/0003096902750280