EasyClassifier: Honest, Reproducible Machine-Learning Classification for Researchers Who Do Not Program

Data leakage remains a recurrent source of optimistic bias in biomedical machine learning studies. Standard row-wise cross-validation and globally estimated preprocessing steps are often inappropriate for data with repeated measurements, study-level heterogeneity, batch effects, or temporal dependencies. This paper describes bioLeak, an R package for constructing leakage-aware resampling workflows and for auditing fitted models for common leakage mechanisms. The package provides leakage-aware split construction, train-fold-only preprocessing, cross-validated model fitting, nested hyperparameter tuning, post hoc leakage audits, and HTML reporting. The implementation supports binary classification, multiclass classification, regression, and survival analysis, with task-specific metrics and S4 containers for splits, fits, audits, and inflation summaries. The simulation artifacts show how apparent performance changes under controlled leakage mechanisms, and the case study illustrates how guarded and leaky pipelines can yield materially different conclusions on multi-study transcriptomic data. The emphasis throughout is on software design, reproducible workflows, and interpretation of diagnostic output.

Researchers increasingly use text classification--supervised models or large language models--to measure constructs from natural language, providing metrics such as recall and precision as evidence of their validity. Yet, though these metrics are point estimates subject to sampling variation, measures of uncertainty are inconsistently reported alongside them. Further, when they are reported, they are often estimated with methods that are not appropriate when relevant labelled datasets are small or performance is high. To increase and improve confidence interval reporting in the field, this paper evaluates confidence interval methods for performance metrics under conditions typical of social science text classification: small to moderate sample sizes, infrequent constructs, and texts nested within individuals. Across simulations, default methods such as the Wald interval and the basic percentile bootstrap are the least accurate, with coverage sometimes far below the nominal 95% level. Accuracy is improved with the use of Agresti-Coull, Wilson, Clopper-Pearson, and a novel pseudo-count regularized bootstrap (which is particularly relevant to the calculation of F1). When texts are nested within individuals, we demonstrate that adjustment for both effective N and the appropriate degrees of freedom is necessary for producing accurate analytic intervals. Among bootstrap intervals, the hierarchical bootstrap is more accurate than the cluster bootstrap when individuals produce a moderate number of texts but overly conservative when individuals produce only a few. By providing guidance to the field on appropriate interval estimation, we aim to improve the transparency of machine learning applications, and to encourage greater attention to the validation sample size at the design stage.

Small-to-medium scientific datasets place machine learning pipelines under two compounding pressures. Single-run feature selection produces feature sets that change substantially under small perturbations of the training data, and any procedure that uses the same data for selection, tuning, and evaluation produces optimistically biased performance estimates. The two failure modes are routinely treated as separable, but in the regimes where scientific data live, they interact: an unstable selection inflates the variance of an already-optimistic score, and standard remedies for one rarely address the other. RobustModelMaker is a Python framework that couples bootstrap stability selection with strict nested cross-validation, performs all preprocessing and selection inside each fold, and produces a stability-tested feature subset together with a leakage-safe performance estimate. The framework supports nine algorithms across binary classification, multiclass classification, and regression. Behaviour is verified by a deterministic test suite spanning unit, performance, and reproducibility checks on three real scientific datasets comparing to three alternative selectors (ANOVA F-test, recursive feature elimination with cross-validation, and Boruta) on both predictive score and a Jaccard measure of selection stability. RobustModelMaker is competitive in score with the best alternative selector on each dataset, and occupies a position on the joint score-stability frontier that none of the alternatives match across all three task types. Two example applications, ovarian cancer biomarker discovery from the PLCO Trial and critical-temperature regression on the UCI Superconductivity Data, illustrate how the framework is used in practice and what trade-offs become visible when stability is treated as a first-class deliverable rather than an emergent property.