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Ranking Interactions for a Curation Task


Clematide, S; Rinaldi, Fabio (2011). Ranking Interactions for a Curation Task. In: 10th International Conference on Machine Learning and Applications and Workshops, Honolulu, Hawaii USA, 18 December 2011 - 21 December 2011, 100-105.

Abstract

One of the key pieces of information which biomedical text mining systems are expected to extract from the literature are interactions among different types of biomedical entities (proteins, genes, diseases, drugs, etc.). Different types of entities might be considered, for example protein-protein interactions have been extensively studied as part of the Bio Creative competitive evaluations. However, more complex interactions such as those among genes, drugs, and diseases are increasingly of interest. Different databases have been used as reference for the evaluation of extraction and ranking techniques. The aim of this paper is to describe a machine-learning based reranking approach for candidate interactions extracted from the literature. The results are evaluated using data derived from the Pharm GKB database. The importance of a good ranking is particularly evident when the results are applied to support human curators.

Abstract

One of the key pieces of information which biomedical text mining systems are expected to extract from the literature are interactions among different types of biomedical entities (proteins, genes, diseases, drugs, etc.). Different types of entities might be considered, for example protein-protein interactions have been extensively studied as part of the Bio Creative competitive evaluations. However, more complex interactions such as those among genes, drugs, and diseases are increasingly of interest. Different databases have been used as reference for the evaluation of extraction and ranking techniques. The aim of this paper is to describe a machine-learning based reranking approach for candidate interactions extracted from the literature. The results are evaluated using data derived from the Pharm GKB database. The importance of a good ranking is particularly evident when the results are applied to support human curators.

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Additional indexing

Item Type:Conference or Workshop Item (Paper), refereed, original work
Communities & Collections:06 Faculty of Arts > Institute of Computational Linguistics
Dewey Decimal Classification:000 Computer science, knowledge & systems
410 Linguistics
Language:English
Event End Date:21 December 2011
Deposited On:06 Mar 2012 16:24
Last Modified:07 Dec 2017 12:18
Publisher:IEEE Computer Society
ISBN:978-0-7695-4607-0
Funders:Swiss National Science Foundation (grant 100014-118396/1)
Additional Information:© 2011 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.
Publisher DOI:https://doi.org/10.1109/ICMLA.2011.119
Related URLs:http://doi.ieeecomputersociety.org

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