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2015 ; 2015
(ä): 258-267
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Convolutional Neural Networks for Biomedical Text Classification: Application in
Indexing Biomedical Articles
#MMPMID28736769
Rios A
; Kavuluru R
ACM BCB
2015[Sep]; 2015
(ä): 258-267
PMID28736769
show ga
Building high accuracy text classifiers is an important task in biomedicine given
the wealth of information hidden in unstructured narratives such as research
articles and clinical documents. Due to large feature spaces, traditionally,
discriminative approaches such as logistic regression and support vector machines
with n-gram and semantic features (e.g., named entities) have been used for text
classification where additional performance gains are typically made through
feature selection and ensemble approaches. In this paper, we demonstrate that a
more direct approach using convolutional neural networks (CNNs) outperforms
several traditional approaches in biomedical text classification with the
specific use-case of assigning medical subject headings (or MeSH terms) to
biomedical articles. Trained annotators at the national library of medicine (NLM)
assign on an average 13 codes to each biomedical article, thus semantically
indexing scientific literature to support NLM's PubMed search system. Recent
evidence suggests that effective automated efforts for MeSH term assignment start
with binary classifiers for each term. In this paper, we use CNNs to build binary
text classifiers and achieve an absolute improvement of over 3% in macro F-score
over a set of selected hard-to-classify MeSH terms when compared with the best
prior results on a public dataset. Additional experiments on 50 high frequency
terms in the dataset also show improvements with CNNs. Our results indicate the
strong potential of CNNs in biomedical text classification tasks.