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Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.

Abstract：

OBJECTIVE:Published clinical trials and high quality peer reviewed medical publications are considered as the main sources of evidence used for synthesizing systematic reviews or practicing Evidence Based Medicine (EBM). Finding all relevant published evidence for a particular medical case is a time and labour intensive task, given the breadth of the biomedical literature. Automatic quantification of conceptual relationships between key clinical evidence within and across publications, despite variations in the expression of clinically-relevant concepts, can help to facilitate synthesis of evidence. In this study, we aim to provide an approach towards expediting evidence synthesis by quantifying semantic similarity of key evidence as expressed in the form of individual sentences. Such semantic textual similarity can be applied as a key approach for supporting selection of related studies. MATERIAL AND METHODS:We propose a generalisable approach for quantifying semantic similarity of clinical evidence in the biomedical literature, specifically considering the similarity of sentences corresponding to a given type of evidence, such as clinical interventions, population information, clinical findings, etc. We develop three sets of generic, ontology-based, and vector-space models of similarity measures that make use of a variety of lexical, conceptual, and contextual information to quantify the similarity of full sentences containing clinical evidence. To understand the impact of different similarity measures on the overall evidence semantic similarity quantification, we provide a comparative analysis of these measures when used as input to an unsupervised linear interpolation and a supervised regression ensemble. In order to provide a reliable test-bed for this experiment, we generate a dataset of 1000 pairs of sentences from biomedical publications that are annotated by ten human experts. We also extend the experiments on an external dataset for further generalisability testing. RESULTS:The combination of all diverse similarity measures showed stronger correlations with the gold standard similarity scores in the dataset than any individual kind of measure. Our approach reached near 0.80 average Pearson correlation across different clinical evidence types using the devised similarity measures. Although they were more effective when combined together, individual generic and vector-space measures also resulted in strong similarity quantification when used in both unsupervised and supervised models. On the external dataset, our similarity measures were highly competitive with the state-of-the-art approaches developed and trained specifically on that dataset for predicting semantic similarity. CONCLUSION:Experimental results showed that the proposed semantic similarity quantification approach can effectively identify related clinical evidence that is reported in the literature. The comparison with a state-of-the-art method demonstrated the effectiveness of the approach, and experiments with an external dataset support its generalisability.

journal_name

J Biomed Inform

journal_title

Journal of biomedical informatics

authors

Hassanzadeh H,Nguyen A,Verspoor K

doi

10.1016/j.jbi.2019.103321

subject

Has Abstract

pub_date

2019-12-01 00:00:00

pages

103321

eissn

1532-0464

issn

1532-0480

pii

S1532-0464(19)30240-0

journal_volume

100

pub_type

杂志文章

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Quantifying semantic similarity of clinical evidence in the biomedical literature to facilitate related evidence synthesis.