Evaluating Supervised Machine Learning Models: Principles, Pitfalls, and Metric Selection

Evaluation in machine learning is typically treated as a neutral measurement process. However, in operational information systems, evaluation outcomes are often conditioned by the processes used to generate labels. This paper does not seek to improve classification performance. Instead, it examines the validity of performance measurement under differing label-authority regimes. This issue is particularly relevant in large-scale metadata-driven systems, where labels are often incomplete, inconsistent, or weakly supervised. We introduce evaluation sovereignty, defined as the degree to which performance metrics are independent of label authority and supervision regime, and propose a multi-track evaluation framework that systematically varies training and evaluation label sources. Using hierarchical multi-label classification on large-scale scientific metadata, we demonstrate that models exhibiting strong performance under operational ("silver") evaluation degrade substantially under independent ("gold") evaluation, particularly for fine-grained classification. For example, Micro-F1 decreases from approximately 0.54 to 0.03. Notably, ranking-based metrics remain above baseline, revealing a divergence between latent model signal and classification validity. These findings suggest that commonly reported performance metrics may reflect alignment with labeling processes rather than true predictive capability. We therefore reconceptualize evaluation validity as a system-level property shaped by label governance and provide a practical methodology for auditing intelligent systems operating under weak supervision.

Bias can be introduced in diverse ways in machine learning datasets, for example via selection or label bias. Although these bias types in themselves have an influence on important aspects of fair machine learning, their different impact has been understudied. In this work, we empirically analyze the effect of label bias and several subtypes of selection bias on the evaluation of classification models, on their performance, and on the effectiveness of bias mitigation methods. We also introduce a biasing and evaluation framework that allows to model fair worlds and their biased counterparts through the introduction of controlled bias in real-life datasets with low discrimination. Using our framework, we empirically analyze the impact of each bias type independently, while obtaining a more representative evaluation of models and mitigation methods than with the traditional use of a subset of biased data as test set. Our results highlight different factors that influence how impactful bias is on model performance. They also show an absence of trade-off between fairness and accuracy, and between individual and group fairness, when models are evaluated on a test set that does not exhibit unwanted bias. They furthermore indicate that the performance of bias mitigation methods is influenced by the type of bias present in the data. Our findings call for future work to develop more accurate evaluations of prediction models and fairness interventions, but also to better understand other types of bias, more complex scenarios involving the combination of different bias types, and other factors that impact the efficiency of the mitigation methods, such as dataset characteristics.

Evaluation harnesses are software systems that orchestrate model evaluation by managing model invocation, data loading, metric computation, and result reporting. Despite their critical role in machine learning infrastructure, their operational challenges and engineering concerns have received limited attention so far. We present an empirical study of 57 evaluation harnesses, deriving a five-stage harness model and classifying 16,560 issues by workflow stage and root cause. Most harness operational challenges concentrate in the Specification stage (41.4% of issues), where harnesses integrate external models, datasets, and scoring judges. The three most frequent root causes of operational challenges are unimplemented features (24.3%), documentation gaps (20.3%), and missing input validation (17.2%), which together account for 61.7% of classified issues, spanning both defects in existing functionality and capability gaps that block intended workflows. Root causes also vary by workflow stage: environment incompatibility and external dependency breakage account for 36.2% of provisioning issues, whereas algorithmic error (25.9%) and validation gap (22.5%) dominate assessment issues. Together, these contributions establish an empirical foundation for treating evaluation engineering as a distinct software engineering concern.