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Reproducibility of Studies on Text Mining for Citation Screening in Systematic Reviews: Evaluation and Checklist

Reproducibility of Studies on Text Mining for Citation Screening in Systematic Reviews: Evaluation and Checklist Thumbnail


Abstract

CONTEXT:
Independent validation of published scientific results through study replication is a pre-condition for accepting the validity of such results. In computation research, full replication is often unrealistic for independent results validation, therefore, study reproduction has been justified as the minimum acceptable standard to evaluate the validity of scientific claims. The application of text mining techniques to citation screening in the context of systematic literature reviews is a relatively young and growing computational field with high relevance for software engineering, medical research and other fields. However, there is little work so far on reproduction studies in the field.

OBJECTIVE:
In this paper, we investigate the reproducibility of studies in this area based on information contained in published articles and we propose reporting guidelines that could improve reproducibility.

METHODS:
The study was approached in two ways. Initially we attempted to reproduce results from six studies, which were based on the same raw dataset. Then, based on this experience, we identified steps considered essential to successful reproduction of text mining experiments and characterized them to measure how reproducible is a study given the information provided on these steps. 33 articles were systematically assessed for reproducibility using this approach.

RESULTS:
Our work revealed that it is currently difficult if not impossible to independently reproduce the results published in any of the studies investigated. The lack of information about the datasets used limits reproducibility of about 80% of the studies assessed. Also, information about the machine learning algorithms is inadequate in about 27% of the papers. On the plus side, the third party software tools used are mostly free and available.

CONCLUSIONS:
The reproducibility potential of most of the studies can be significantly improved if more attention is paid to information provided on the datasets used, how they were partitioned and utilized, and how any randomization was controlled. We introduce a checklist of information that needs to be provided in order to ensure that a published study can be reproduced.

Acceptance Date Jul 10, 2017
Publication Date Sep 1, 2018
Journal Journal of Biomedical Informatics
Print ISSN 1532-0464
Publisher Elsevier
Pages 1-13
DOI https://doi.org/10.1016/j.jbi.2017.07.010
Keywords Citation screening; Systematic review; Reproducibility; Text mining; Reproducible research
Publisher URL http://www.sciencedirect.com/science/article/pii/S1532046417301661http://www.sciencedirect.com/science/article/pii/S1532046417301661

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