Essential guidelines for computational method benchmarking

12/03/2018

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by   Lukas M. Weber, et al.

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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 the best choice of method for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate and unbiased results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our own experiences in computational biology.