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

Reliability and validity in comparative studies of software prediction models

Empirical studies on software prediction models do not converge with respect to the question "which prediction model is best?" The reason for this lack of convergence is poorly understood. In this simulation study, we have examined a frequently used research procedure comprising three main ingredients: a single data sample, an accuracy indicator, and cross validation. Typically, these empirical studies compare a machine learning model with a regression model. In our study, we use simulation and compare a machine learning and a regression model. The results suggest that it is the research procedure itself that is unreliable. This lack of reliability may strongly contribute to the lack of convergence. Our findings thus cast some doubt on the conclusions of any study of competing software prediction models that used this research procedure as a basis of model comparison. Thus, we need to develop more reliable research procedures before we can have confidence in the conclusions of comparative studies of software prediction models

Are Smell-Based Metrics Actually Useful in Effort-Aware Structural Change-Proneness Prediction? An Empirical Study

Bad code smells (also named as code smells) are symptoms of poor design choices in implementation. Existing studies empirically confirmed that the presence of code smells increases the likelihood of subsequent changes (i.e., change-proness). However, to the best of our knowledge, no prior studies have leveraged smell-based metrics to predict particular change type (i.e., structural changes). Moreover, when evaluating the effectiveness of smell-based metrics in structural change-proneness prediction, none of existing studies take into account of the effort inspecting those change-prone source code. In this paper, we consider five smell-based metrics for effort-aware structural change-proneness prediction and compare these metrics with a baseline of well-known CK metrics in predicting particular categories of change types. Specifically, we first employ univariate logistic regression to analyze the correlation between each smellbased metric and structural change-proneness. Then, we build multivariate prediction models to examine the effectiveness of smell-based metrics in effort-aware structural change-proneness prediction when used alone and used together with the baseline metrics, respectively. Our experiments are conducted on six Java open-source projects with up to 60 versions and results indicate that: (1) all smell-based metrics are significantly related to structural change-proneness, except metric ANS in hive and SCM in camel after removing confounding effect of file size; (2) in most cases, smell-based metrics outperform the baseline metrics in predicting structural change-proneness; and (3) when used together with the baseline metrics, the smell-based metrics are more effective to predict change-prone files with being aware of inspection effort