Evaluating Intersectional Fairness across Clinical Machine Learning Use Cases using Fairlogue and the All of Us Research Program

Objective: Algorithmic fairness is essential for equitable and trustworthy machine learning in healthcare. Most fairness tools emphasize single-axis demographic comparisons and may miss compounded disparities affecting intersectional populations. This study introduces Fairlogue, a toolkit designed to operationalize intersectional fairness assessment in observational and counterfactual contexts within clinical settings. Methods: Fairlogue is a Python-based toolkit composed of three components: 1) an observational framework extending demographic parity, equalized odds, and equal opportunity difference to intersectional populations; 2) a counterfactual framework evaluating fairness under treatment-based contexts; and 3) a generalized counterfactual framework assessing fairness under interventions on intersectional group membership. The toolkit was evaluated using electronic health record data from the All of Us Controlled Tier V8 dataset in a glaucoma surgery prediction task using logistic regression with race and gender as protected attributes. Results: Observational analysis identified substantial intersectional disparities despite moderate model performance (AUROC = 0.709; accuracy = 0.651). Intersectional evaluation revealed larger fairness gaps than single-axis analyses, including demographic parity differences of 0.20 and equalized odds true positive and false positive rate gaps of 0.33 and 0.15, respectively. Counterfactual analysis using permutation-based null distributions produced unfairness ("u-value") estimates near zero, suggesting observed disparities were consistent with chance after conditioning on covariates. Conclusion: Fairlogue provides a modular toolkit integrating observational and counterfactual methods for quantifying and evaluating intersectional bias in clinical machine learning workflows.

Algorithmic fairness methods are increasingly used to identify and mitigate bias in machine learning models, yet most approaches are evaluated in isolation and along single demographic axes. This limits practical guidance for selecting fairness strategies, where disparities may arise across intersectional subgroups and across multiple stages of the modeling lifecycle. This work presents FairSelect, a toolkit for systematically evaluating fairness mitigation strategies applied individually and in combination across preprocessing, inprocessing, and postprocessing stages. FairSelect supports multiple model architectures, intersectional subgroup evaluation, and comparison of fairness utility tradeoffs across baseline, single method, and multi level configurations. The framework was validated using synthetic clinical datasets designed to represent specific bias mechanisms and a real-world replication of two-year stroke risk prediction among patients with atrial fibrillation. Synthetic experiments showed that targeted fairness methods generally reduced intended subgroup disparities, while combined strategies produced larger average fairness improvements with modest utility tradeoffs. In the clinical prediction task, mitigation effects were highly variable, with some combinations improving both fairness and predictive performance while others were ineffective or counterproductive. These findings demonstrate that fairness interventions interact in nonadditive and context dependent ways. FairSelect provides a practical framework for systematically identifying fairness strategies that improve subgroup equity while preserving model performance in clinical machine learning.

The evaluation of fairness in machine learning systems has become a central concern in high-stakes applications, including biometric recognition, healthcare decision-making, and automated risk assessment. Existing approaches typically rely on a small number of fairness metrics to assess model behaviour across group partitions, implicitly assuming that these metrics provide consistent and reliable conclusions. However, different fairness metrics capture distinct statistical properties of model performance and may therefore produce conflicting assessments when applied to the same system. In this work, we investigate the consistency of fairness evaluation by conducting a systematic multi-metric analysis of demographic bias in machine learning models. Using face recognition as a controlled experimental setting, we evaluate model performance across multiple group partitions under a range of commonly used fairness metrics, including error-rate disparities and performance-based measures. Our results demonstrate that fairness assessments can vary significantly depending on the choice of metrics, leading to contradictory conclusions regarding model bias. To quantify this phenomenon, we introduce the Fairness Disagreement Index (FDI), a measure designed to capture the degree of inconsistency across fairness metrics. We further show that disagreement remains high across thresholds and model configurations. These findings highlight a critical limitation in current fairness evaluation practices and suggest that single-metric reporting is insufficient for reliable bias assessment.