medical data scientists

Abstract: Individualized attribution estimates which functional networks drive a model prediction for a given subject and is often proposed as an interpretable resting-state fMRI (rs-fMRI) biomarker, but its test-retest reliability is rarely quantified. We evaluate per-subject network-ablation attribution for a frozen resting-state functional connectivity (FC) predictor (Schaefer-200 FC predicting MMSE/ADAS-Cog13) trained on N=875 subjects from the Alzheimer's Disease Neuroimaging Initiative (ADNI), using, and (iii) a subject-level permutation null. Split-half reliability is near-ceiling (Spearman p=0.948/0.950) but drops on scan-rescan (p=0.609/0.616). Under the mismatched-subject null, correlations remain substantial (p~0.46-0.47), indicating strong population-shared structure, yet matched pairs exceed this null (z~6.6-6.9, p<=10-4). Thus, in ADNI, individualized network attribution contains a modest but non-zero person-specific component atop a strong population-shared pattern. We recommend reporting scan-rescan reliability together with a permutation-null control, rather than within-session proxies alone, to avoid overstating individual specificity.

Abstract: Concept-based models (CMs) learn human-interpretable intermediate representations that enable users to understand the model's reasoning and steer its predictions through test-time concept interventions. However, in realistic settings, their performance can be limited by concept incompleteness, where the training concepts fail to capture all task-relevant information. Adding an unconstrained residual pathway to the model's predictive process can overcome the consequences of incompleteness. However, this introduces an inscrutable, leak-prone prediction pathway that may weaken concept interventions, as these often leave residual variables unchanged. To address this limitation, we introduce Residual Stochastic Concept Bottleneck Models (Res-SCBMs), a family of concept-based models that jointly model concept and residual variables through a multivariate Gaussian distribution. Res-SCBMs learn a covariance structure that explicitly captures dependencies between the known concepts and learnt residual variables, allowing interventions to propagate to statistically dependent residual variables through Gaussian conditioning. This extends the intervention capabilities of previous CMs without requiring concept completeness during training. Our results show that, across multiple concept-incomplete benchmarks, Res-SCBMs improve predictive performance over competing baselines while retaining effective test-time concept interventions.

Abstract: Estimating causal effects on right-censored time-to-event outcomes is challenging under unmeasured confounding. Proximal causal inference addresses unmeasured confounding through proxy variables, but existing proximal survival methods rely largely on restrictive parametric bridge models. We introduce Proximal Survival Bridge learning (PSB), a flexible doubly robust proximal framework for censored outcomes. Building on existing proximal identification of treatment-specific survival curves, the framework yields outcome-bridge (OB), treatment-bridge (TB), and doubly robust (DR) estimators, with two flexible bridge learners: PSB-K, a kernel estimator with a low-rank time decomposition, and PSB-N, a neural estimator trained by a projected maximum-moment-restriction loss. Unlike existing flexible proximal learners for scalar outcomes, PSB directly handles censoring and survival-curve targets. On a standard SEM benchmark, a proximal semi-synthetic ACTG study, and the real-world Framingham study, PSB-K performs strongest on SEM and ACTG, whereas PSB-N is the most stable on Framingham. Additional results with modern causal survival baselines, weakened or invalid proxies, and heavier censoring assess robustness across challenging settings.

Abstract: Deep learning models for multi-modal breast cancer diagnosis achieve high predictive accuracy but remain clinically unacceptable without actionable, counterfactual explanations. Attribution-based methods (LIME, SHAP) are categorically inapplicable to this purpose, as they generate no alternative instances and thus cannot be evaluated on counterfactual quality metrics. This investigation provides empirical evidence that FCA-Guided Counterfactual (FCA-CF) framework that uses a Formal Concept Analysis (FCA) concept lattice as a hard structural constraint on counterfactual search, operating over a multi-modal TCGA-BRCA dataset. We benchmark against four genuine counterfactual methods: Wachter-style CF, DiCE, FACE, and NICE, evaluated on 60 benign-predicted TCGA-BRCA instances. The FCA-CF framework achieves Validity = 1.0000 (100% of counterfactuals successfully flip the prediction), Sparsity = 2.37 features changed (best among all valid methods), and Proximity = 0.900 (normalised L2-based, matching NICE as joint best). The classifier achieves Accuracy = 0.980, F1 = 0.976, ROC-AUC = 0.9947. Ablation analysis confirms that the FCA lattice constraint is the primary sparsity driver (removing it increases sparsity by +40%, p < 0.001, Cohen's d = 0.78), while Phase C greedy refinement accounts for the largest individual contribution (+113% sparsity increase when disabled, p < 0.001, d = 5.01). FCA-guided counterfactual generation achieves a clinically important Pareto-dominant outcome; it is simultaneously the sparsest and among the most proximate of all valid methods, with perfect validity. The emergent sparsity property arising from lattice topology rather than numerical penalty terms constitutes a structurally novel contribution to the counterfactual explanation literature.