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Copula Based Fusion of Clinical and Genomic Machine Learning Risk Scores for Breast Cancer Risk Stratification
Aich, Agnideep, Hewage, Sameera, Murshed, Md Monzur
Clinical and genomic models are both used to predict breast cancer outcomes, but they are often combined using simple linear rules that do not account for how their risk scores relate, especially at the extremes. Using the METABRIC breast cancer cohort, we studied whether directly modeling the joint relationship between clinical and genomic machine learning risk scores could improve risk stratification for 5-year cancer-specific mortality. We created a binary 5-year cancer-death outcome and defined two sets of predictors: a clinical set (demographic, tumor, and treatment variables) and a genomic set (gene-expression $z$-scores). We trained several supervised classifiers, such as Random Forest and XGBoost, and used 5-fold cross-validated predicted probabilities as unbiased risk scores. These scores were converted to pseudo-observations on $(0,1)^2$ to fit Gaussian, Clayton, and Gumbel copulas. Clinical models showed good discrimination (AUC 0.783), while genomic models had moderate performance (AUC 0.681). The joint distribution was best captured by a Gaussian copula (bootstrap $p=0.997$), which suggests a symmetric, moderately strong positive relationship. When we grouped patients based on this relationship, Kaplan-Meier curves showed clear differences: patients who were high-risk in both clinical and genomic scores had much poorer survival than those high-risk in only one set. These results show that copula-based fusion works in real-world cohorts and that considering dependencies between scores can better identify patient subgroups with the worst prognosis.
Measuring Sample Quality with Copula Discrepancies
Aich, Agnideep, Aich, Ashit Baran, Wade, Bruce
The scalable Markov chain Monte Carlo (MCMC) algorithms that underpin modern Bayesian machine learning, such as Stochastic Gradient Langevin Dynamics (SGLD), sacrifice asymptotic exactness for computational speed, creating a critical diagnostic gap: traditional sample quality measures fail catastrophically when applied to biased samplers. While powerful Stein-based diagnostics can detect distributional mismatches, they provide no direct assessment of dependence structure, often the primary inferential target in multivariate problems. We introduce the Copula Discrepancy (CD), a principled and computationally efficient diagnostic that leverages Sklar's theorem to isolate and quantify the fidelity of a sample's dependence structure independent of its marginals. Our theoretical framework provides the first structure-aware diagnostic specifically designed for the era of approximate inference. Empirically, we demonstrate that a moment-based CD dramatically outperforms standard diagnostics like effective sample size for hyperparameter selection in biased MCMC, correctly identifying optimal configurations where traditional methods fail. Furthermore, our robust MLE-based variant can detect subtle but critical mismatches in tail dependence that remain invisible to rank correlation-based approaches, distinguishing between samples with identical Kendall's tau but fundamentally different extreme-event behavior. With computational overhead orders of magnitude lower than existing Stein discrepancies, the CD provides both immediate practical value for MCMC practitioners and a theoretical foundation for the next generation of structure-aware sample quality assessment.
From Sublinear to Linear: Fast Convergence in Deep Networks via Locally Polyak-Lojasiewicz Regions
Aich, Agnideep, Aich, Ashit Baran, Wade, Bruce
The convergence of gradient descent (GD) on the non-convex loss landscapes of deep neural networks (DNNs) presents a fundamental theoretical challenge. While recent work has established that GD converges to a stationary point at a sublinear rate within locally quasi-convex regions (LQCRs), this fails to explain the exponential convergence rates consistently observed in practice. In this paper, we resolve this discrepancy by proving that under a mild assumption on Neural Tangent Kernel (NTK) stability, these same regions satisfy a local Polyak-Lojasiewicz (PL) condition. We introduce the concept of a Locally Polyak-Lojasiewicz Region (LPLR), where the squared gradient norm lower-bounds the suboptimality gap, prove that properly initialized finite-width networks admit such regions around initialization, and establish that GD achieves linear convergence within an LPLR, providing the first finite-width guarantee that matches empirically observed rates. We validate our theory across diverse settings, from controlled experiments on fully-connected networks to modern ResNet architectures trained with stochastic methods, demonstrating that LPLR structure emerges robustly in practical deep learning scenarios. By rigorously connecting local landscape geometry to fast optimization through the NTK framework, our work provides a definitive theoretical explanation for the remarkable efficiency of gradient-based optimization in deep learning.
Bag of Coins: A Statistical Probe into Neural Confidence Structures
Aich, Agnideep, Aich, Ashit Baran, Murshed, Md Monzur, Hewage, Sameera, Wade, Bruce
Modern neural networks, despite their high accuracy, often produce poorly calibrated confidence scores, limiting their reliability in high-stakes applications. Existing calibration methods typically post-process model outputs without interrogating the internal consistency of the predictions themselves. In this work, we introduce a novel, non-parametric statistical probe, the Bag-of-Coins (BoC) test, that examines the internal consistency of a classifier's logits. The BoC test reframes confidence estimation as a frequentist hypothesis test: does the model's top-ranked class win 1-v-1 contests against random competitors at a rate consistent with its own stated softmax probability? When applied to modern deep learning architectures, this simple probe reveals a fundamental dichotomy. On Vision Transformers (ViTs), the BoC output serves as a state-of-the-art confidence score, achieving near-perfect calibration with an ECE of 0.0212, an 88% improvement over a temperature-scaled baseline. Conversely, on Convolutional Neural Networks (CNNs) like ResNet, the probe reveals a deep inconsistency between the model's predictions and its internal logit structure, a property missed by traditional metrics. We posit that BoC is not merely a calibration method, but a new diagnostic tool for understanding and exposing the differing ways that popular architectures represent uncertainty.
IGNIS: A Robust Neural Network Framework for Constrained Parameter Estimation in Archimedean Copulas
Classical estimators, the cornerstones of statistical inference, face insurmountable challenges when applied to important emerging classes of Archimedean copulas. These models exhibit pathological properties, including numerically unstable densities, non-monotonic parameter-to-dependence mappings, and vanishingly small likelihood gradients, rendering methods like Maximum Likelihood (MLE) and Method of Moments (MoM) inconsistent or computationally infeasible. We introduce IGNIS, a unified neural estimation framework that sidesteps these barriers by learning a direct, robust mapping from data-driven dependency measures to the underlying copula parameter theta. IGNIS utilizes a multi-input architecture and a theory-guided output layer (softplus(z) + 1) to automatically enforce the domain constraint theta_hat >= 1. Trained and validated on four families (Gumbel, Joe, and the numerically challenging A1/A2), IGNIS delivers accurate and stable estimates for real-world financial and health datasets, demonstrating its necessity for reliable inference in modern, complex dependence models where traditional methods fail.
Temporal Conformal Prediction (TCP): A Distribution-Free Statistical and Machine Learning Framework for Adaptive Risk Forecasting
Aich, Agnideep, Aich, Ashit Baran, Jain, Dipak C.
We propose Temporal Conformal Prediction (TCP), a principled framework for constructing well-calibrated prediction intervals for non-stationary time series. TCP integrates a machine learning-based quantile forecaster with an online conformal calibration layer. This layer's thresholds are updated via a modified Robbins-Monro scheme, allowing the model to dynamically adapt to volatility clustering and regime shifts without rigid parametric assumptions. We benchmark TCP against GARCH, Historical Simulation, and static Quantile Regression across diverse financial assets. Our empirical results reveal a critical flaw in static methods: while sharp, Quantile Regression is poorly calibrated, systematically over-covering the nominal 95% target. In contrast, TCP's adaptive mechanism actively works to achieve the correct coverage level, successfully navigating the coverage-sharpness tradeoff. Visualizations during the 2020 market crash confirm TCP's superior adaptive response, and a comprehensive sensitivity analysis demonstrates the framework's robustness to hyperparameter choices. Overall, TCP offers a practical and theoretically-grounded solution to the central challenge of calibrated uncertainty quantification for time series under distribution shift, advancing the interface between statistical inference and machine learning.
CopulaSMOTE: A Copula-Based Oversampling Approach for Imbalanced Classification in Diabetes Prediction
Aich, Agnideep, Murshed, Md Monzur, Hewage, Sameera, Mayeaux, Amanda
Diabetes mellitus poses a significant health risk, as nearly 1 in 9 people are affected by it. Early detection can significantly lower this risk. Despite significant advancements in machine learning for identifying diabetic cases, results can still be influenced by the imbalanced nature of the data. To address this challenge, our study considered copula-based data augmentation, which preserves the dependency structure when generating data for the minority class and integrates it with machine learning (ML) techniques. We selected the Pima Indian dataset and generated data using A2 copula, then applied four machine learning algorithms: logistic regression, random forest, gradient boosting, and extreme gradient boosting. Our findings indicate that XGBoost combined with A2 copula oversampling achieved the best performance improving accuracy by 4.6%, precision by 15.6%, recall by 20.4%, F1-score by 18.2% and AUC by 25.5% compared to the standard SMOTE method. Furthermore, we statistically validated our results using the McNemar test. This research represents the first known use of A2 copulas for data augmentation and serves as an alternative to the SMOTE technique, highlighting the efficacy of copulas as a statistical method in machine learning applications.
Theoretical Foundations of the Deep Copula Classifier: A Generative Approach to Modeling Dependent Features
Aich, Agnideep, Aich, Ashit Baran, Wade, Bruce
Traditional classifiers often assume feature independence or rely on overly simplistic relationships, leading to poor performance in settings where real-world dependencies matter. We introduce the Deep Copula Classifier (DCC), a generative model that separates the learning of each feature's marginal distribution from the modeling of their joint dependence structure via neural network-parameterized copulas. For each class, lightweight neural networks are used to flexibly and adaptively capture feature interactions, making DCC particularly effective when classification is driven by complex dependencies. We establish that DCC converges to the Bayes-optimal classifier under standard conditions and provide explicit convergence rates of O(n^{-r/(2r + d)}) for r-smooth copula densities. Beyond theoretical guarantees, we outline several practical extensions, including high-dimensional scalability through vine and factor copula architectures, semi-supervised learning via entropy regularization, and online adaptation using streaming gradient methods. By unifying statistical rigor with the representational power of neural networks, DCC offers a mathematically grounded and interpretable framework for dependency-aware classification.
A2 Copula-Driven Spatial Bayesian Neural Network For Modeling Non-Gaussian Dependence: A Simulation Study
Aich, Agnideep, Hewage, Sameera, Murshed, Md Monzur, Aich, Ashit Baran, Mayeaux, Amanda, Dey, Asim K., Das, Kumer P., Wade, Bruce
In this paper, we introduce the A2 Copula Spatial Bayesian Neural Network (A2-SBNN), a predictive spatial model designed to map coordinates to continuous fields while capturing both typical spatial patterns and extreme dependencies. By embedding the dual-tail novel Archimedean copula viz. A2 directly into the network's weight initialization, A2-SBNN naturally models complex spatial relationships, including rare co-movements in the data. The model is trained through a calibration-driven process combining Wasserstein loss, moment matching, and correlation penalties to refine predictions and manage uncertainty. Simulation results show that A2-SBNN consistently delivers high accuracy across a wide range of dependency strengths, offering a new, effective solution for spatial data modeling beyond traditional Gaussian-based approaches.