12,085 research outputs found
Essential guidelines for computational method benchmarking
In computational biology and other sciences, researchers are frequently faced
with a choice between several computational methods for performing data
analyses. Benchmarking studies aim to rigorously compare the performance of
different methods using well-characterized benchmark datasets, to determine the
strengths of each method or to provide recommendations regarding suitable
choices of methods for an analysis. However, benchmarking studies must be
carefully designed and implemented to provide accurate, unbiased, and
informative results. Here, we summarize key practical guidelines and
recommendations for performing high-quality benchmarking analyses, based on our
experiences in computational biology.Comment: Minor update
Improving transparency and scientific rigor in academic publishing.
Progress in basic and clinical research is slowed when researchers fail to provide a complete and accurate report of how a study was designed, executed, and the results analyzed. Publishing rigorous scientific research involves a full description of the methods, materials, procedures, and outcomes. Investigators may fail to provide a complete description of how their study was designed and executed because they may not know how to accurately report the information or the mechanisms are not in place to facilitate transparent reporting. Here, we provide an overview of how authors can write manuscripts in a transparent and thorough manner. We introduce a set of reporting criteria that can be used for publishing, including recommendations on reporting the experimental design and statistical approaches. We also discuss how to accurately visualize the results and provide recommendations for peer reviewers to enhance rigor and transparency. Incorporating transparency practices into research manuscripts will significantly improve the reproducibility of the results by independent laboratories
Essential guidelines for computational method benchmarking
In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology
Evolution of statistical analysis in empirical software engineering research: Current state and steps forward
Software engineering research is evolving and papers are increasingly based
on empirical data from a multitude of sources, using statistical tests to
determine if and to what degree empirical evidence supports their hypotheses.
To investigate the practices and trends of statistical analysis in empirical
software engineering (ESE), this paper presents a review of a large pool of
papers from top-ranked software engineering journals. First, we manually
reviewed 161 papers and in the second phase of our method, we conducted a more
extensive semi-automatic classification of papers spanning the years 2001--2015
and 5,196 papers. Results from both review steps was used to: i) identify and
analyze the predominant practices in ESE (e.g., using t-test or ANOVA), as well
as relevant trends in usage of specific statistical methods (e.g.,
nonparametric tests and effect size measures) and, ii) develop a conceptual
model for a statistical analysis workflow with suggestions on how to apply
different statistical methods as well as guidelines to avoid pitfalls. Lastly,
we confirm existing claims that current ESE practices lack a standard to report
practical significance of results. We illustrate how practical significance can
be discussed in terms of both the statistical analysis and in the
practitioner's context.Comment: journal submission, 34 pages, 8 figure
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