Extracting biomedical events from pairs of text entities

BMC Bioinformatics

Research

Xiao Liu¹  Yves Grandvalet¹  Antoine Bordes¹ 

[1] Sorbonne universités, Université de technologie de Compiègne, CNRS, Heudiasyc UMR 7253, 57 avenue de Landshut, CS 60319, 60203, Compiègne cedex, France;

关键词: Information Extraction;    Natural Language Processing;    Machine Learning;   

DOI  :  10.1186/1471-2105-16-S10-S8

来源: Springer

【 摘 要 】

BackgroundHuge amounts of electronic biomedical documents, such as molecular biology reports or genomic papers are generated daily. Nowadays, these documents are mainly available in the form of unstructured free texts, which require heavy processing for their registration into organized databases. This organization is instrumental for information retrieval, enabling to answer the advanced queries of researchers and practitioners in biology, medicine, and related fields. Hence, the massive data flow calls for efficient automatic methods of text-mining that extract high-level information, such as biomedical events, from biomedical text. The usual computational tools of Natural Language Processing cannot be readily applied to extract these biomedical events, due to the peculiarities of the domain. Indeed, biomedical documents contain highly domain-specific jargon and syntax. These documents also describe distinctive dependencies, making text-mining in molecular biology a specific discipline.ResultsWe address biomedical event extraction as the classification of pairs of text entities into the classes corresponding to event types. The candidate pairs of text entities are recursively provided to a multiclass classifier relying on Support Vector Machines. This recursive process extracts events involving other events as arguments. Compared to joint models based on Markov Random Fields, our model simplifies inference and hence requires shorter training and prediction times along with lower memory capacity. Compared to usual pipeline approaches, our model passes over a complex intermediate problem, while making a more extensive usage of sophisticated joint features between text entities. Our method focuses on the core event extraction of the Genia task of BioNLP challenges yielding the best result reported so far on the 2013 edition.

【 授权许可】

CC BY   
© Liu et al.; licensee BioMed Central Ltd. 2015