Abstract：
BACKGROUND:Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel convolutional neural network (CNN) architecture that regards biomedical entity normalization as a ranking problem and benefits from semantic information of biomedical entities. RESULTS:The CNN-based ranking method first generates candidates using handcrafted rules, and then ranks the candidates according to their semantic information modeled by CNN as well as their morphological information. Experiments on two benchmark datasets for biomedical entity normalization show that our proposed CNN-based ranking method outperforms traditional rule-based method with state-of-the-art performance. CONCLUSIONS:We propose a CNN architecture that regards biomedical entity normalization as a ranking problem. Comparison results show that semantic information is beneficial to biomedical entity normalization and can be well combined with morphological information in our CNN architecture for further improvement.
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Li H,Chen Q,Tang B,Wang X,Xu H,Wang B,Huang Ddoi
10.1186/s12859-017-1805-7subject
Has Abstractpub_date
2017-10-03 00:00:00pages
385issue
Suppl 11issn
1471-2105pii
10.1186/s12859-017-1805-7journal_volume
18pub_type
杂志文章abstract：BACKGROUND:High-throughput measurement of transcript intensities using Affymetrix type oligonucleotide microarrays has produced a massive quantity of data during the last decade. Different preprocessing techniques exist to convert the raw signal intensities measured by these chips into gene expression estimates. Althou...
journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2010-11-11 00:00:00
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journal_title：BMC bioinformatics
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更新日期：2009-06-15 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2019-12-27 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2010-01-12 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2010-02-12 00:00:00
abstract：BACKGROUND:The Immunoglobulins (IG) and the T cell receptors (TR) play the key role in antigen recognition during the adaptive immune response. Recent progress in next-generation sequencing technologies has provided an opportunity for the deep T cell receptor repertoire profiling. However, a specialised software is req...
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更新日期：2015-05-28 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2016-12-13 00:00:00
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journal_title：BMC bioinformatics
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更新日期：2011-07-29 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-15-181
更新日期：2014-06-11 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2009-10-08 00:00:00
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pub_type： 杂志文章
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更新日期：2009-03-30 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/s12859-018-2102-9
更新日期：2018-04-11 00:00:00
abstract：BACKGROUND:Over the last two decades, an innovative technology called Tissue Microarray (TMA), which combines multi-tissue and DNA microarray concepts, has been widely used in the field of histology. It consists of a collection of several (up to 1000 or more) tissue samples that are assembled onto a single support - ty...
journal_title：BMC bioinformatics
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更新日期：2018-04-19 00:00:00
abstract：:The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites....
journal_title：BMC bioinformatics
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更新日期：2012-01-01 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-9-267
更新日期：2008-06-06 00:00:00
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pub_type： 杂志文章
doi：10.1186/s12859-015-0866-8
更新日期：2016-01-05 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-7-99
更新日期：2006-02-28 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
doi：10.1186/1471-2105-11-420
更新日期：2010-08-09 00:00:00
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更新日期：2013-07-24 00:00:00
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pub_type： 杂志文章
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更新日期：2004-07-13 00:00:00
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更新日期：2011-03-29 00:00:00
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更新日期：2017-12-01 00:00:00
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更新日期：2019-11-08 00:00:00
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更新日期：2018-12-17 00:00:00
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pub_type： 临床试验,杂志文章
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更新日期：2019-02-28 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2012-10-30 00:00:00
abstract：BACKGROUND:New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS:We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifica...
journal_title：BMC bioinformatics
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更新日期：2018-04-25 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2018-12-12 00:00:00
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journal_title：BMC bioinformatics
pub_type： 杂志文章
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更新日期：2002-04-23 00:00:00
