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Semi-Parametric Bayesian Additive Regression Trees for Risk Prediction with High-Dimensional Epigenetic Signatures and Low-Dimensional Covariates
Bhandari, Saurabh, Bhatti, Parveen, Chiu, Brian C. -H., Ji, Yuan
In the era of precision medicine, genome-wide epigenetic modifications offer rich data that could inform risk prediction. However, these data are high-dimensional and exhibit complex dependence structures, which makes it difficult to jointly model them with low-dimensional covariates when the goal is to obtain interpretable effect estimates for covariate adjustment. Standard Bayesian additive regression trees (BART) provide strong predictive performance but treat all predictors uniformly within the tree ensemble, obscuring the contributions of significant covariates and complicating variable selection in high-dimensional settings. We propose a semi-parametric BART model (spBART) that addresses this limitation by modeling low-dimensional covariates through a parametric component with interpretable coefficients, while capturing complex nonlinear associations among high-dimensional predictors through the tree ensemble. To perform stable variable selection, we develop a cross-validation-based procedure that aggregates posterior inclusion probabilities across folds and applies Bayesian false discovery rate control. We apply the proposed method to a pooled case--control analysis of high-dimensional genome-wide 5-hydroxymethylcytosine profiles derived from circulating cell-free DNA in two multiple myeloma studies ($N = 869$). The approach identifies a parsimonious set of candidate loci and achieves strong out-of-sample discrimination (AUC $= 0.96$) in a held-out validation set. Overall, spBART provides a unified framework for combining interpretable covariate inference with flexible modeling and variable selection in high-dimensional biomedical studies.
Symbolic Density Estimation for Discrete Distributions
Discrete probability laws underpin statistical modeling, yet the catalog of interpretable distributions has expanded only gradually through centuries of case-by-case mathematical derivations. We introduce symbolic density estimation (SDE), an unsupervised framework that automatically recovers closed-form probability mass functions by composing elementary analytic operations within a structured search space. Our method integrates domain-specific structural priors with evolutionary search and a validity-aware inference stage, and it extends to richer distribution families such as zero inflation and finite mixtures. To support systematic evaluation and future research, we contribute a benchmark dataset spanning a broad collection of commonly used discrete distributions. The proposed algorithm recovers all benchmark families with accurate parameter estimates. A real data application shows that it identifies concise and interpretable mixture models that improve goodness-of-fit over standard models.
Partial Fusion of Neural Networks: Efficient Tradeoffs Between Ensembles and Weight Aggregation
Morelli, Fabian, Eckstein, Stephan
Ensembles of neural networks typically outperform individual networks but incur large computational costs, whereas weight aggregation produces less costly, yet also less accurate, aggregate models. We introduce partial fusion of networks, which interpolates between ensembles and weight aggregation and thus allows for a flexible tradeoff between computational cost and performance. A direct way to achieve this is to extend existing weight aggregation methods based on neuron-level similarity between different networks, where partial fusion then only aggregates weights of neurons which are most similar. We showcase one particular method to jointly identify which neurons are most similar and match them via partial optimal transport. Further, we consider the more general perspective of weight aggregation and partial fusion as generalized pruning of ensemble models, where neurons cannot just be deleted, but also linearly combined. Finally, we show that generalized pruning applied to a single network yields similar benefits as partial fusion by allowing for a tradeoff between isolating, deleting, and linearly combining neurons based on similarity. Our code is available at https://github.com/Fabian-Mor/partial_fusion_nn.
Approximate Machine Unlearning through Manifold Representation Forgetting Guided by Self Mode Connectivity
Wang, Weiqi, Tian, Zhiyi, Zhang, Chenhan, Chen, Luoyu, Yu, Shui
Machine unlearning is a fundamental mechanism that enforces the right to be forgotten. Existing unlearning studies that rely on label manipulation or task-gradient reversal often deliver limited unlearning effectiveness. Moreover, they can undermine the original learning objective and typically do not guarantee equivalence to standard unlearning by retraining. In this paper, we propose \textbf{ManiF-SMC} (\textbf{Mani}fold \textbf{F}orgetting with \textbf{S}elf \textbf{M}ode \textbf{C}onnectivity), motivated by the observation that a model retrained on the remaining data tends to classify erased samples by their semantic similarity to the retained data. We begin with systematically recasting the approximate unlearning as pushing each erased sample away from its original learned manifold representation centroid toward its nearest semantic neighbors in the retained data. This reformulation aligns unlearning with retraining behavior and operates purely in representation space, reducing reliance on labels and task-specific gradients. To tackle the manifold representation-based unlearning problem, ManiF-SMC encapsulates the unlearning and representation preservation goals in a margin-based triplet loss. Because finding a suitable margin for unlearning is challenging, we propose a self-mode-connectivity module that rapidly reconstructs the local manifold to guide the adaptive margins generation for each unlearning case. Extensive experiments on four representative datasets show that ManiF-SMC achieves unlearning effectiveness comparable to state-of-the-art approximate methods while operating solely within the model's representation space.
Human-Centered Learning Mechanics: A Dynamical Framework for Entropy-Regulated Representation Learning
Deep learning is increasingly viewed as a dynamical process in parameter space, yet many existing theories still treat training as a closed optimization system. This view is limited for real-world AI, where models operate under uncertainty, resource constraints, distribution shift, downstream decision risks, and human feedback. We propose Human-Centered Learning Mechanics (HCLM), a dynamical and information-theoretic framework for open and controlled learning systems. The central idea is that entropy regularization is useful only when the chosen entropy surrogate generates a non-degenerate information force along the optimization trajectory. Otherwise, entropy terms may produce weak, unstable, or misaligned gradients, causing the dynamics to collapse toward ordinary loss minimization. We introduce the notion of effective entropy and study tractable geometric entropy surrogates, including variance-based and log-determinant covariance proxies. The paper makes three contributions. First, it formalizes entropy regularization through effective information force and characterizes degenerate entropy regimes. Second, it derives convergence, entropy-flow, Wasserstein-gradient-flow, and noisy-representation generalization results under explicit assumptions. Third, it offers a conditional dynamical interpretation of scaling-law-like behavior as a balance between information injection, entropy dissipation, and residual risk, without claiming an unconditional derivation of empirical neural scaling laws. Controlled representation-learning experiments support the hypothesis that geometric entropy surrogates, especially log-determinant covariance entropy, induce stronger and more stable information forces than softmax-normalized entropy.
Diffusion-based Denoising Beats Vanilla Score Matching in Parameter Estimation: A Theoretical Explanation
Schwienhorst, Benedikt Lรผtke, Klein, Nadja, Lederer, Johannes
Score matching is an alternative to maximum likelihood estimation when the normalizing constant is unknown or too costly to evaluate. However, vanilla score matching has shown to be inefficient relative to maximum likelihood estimation for multimodal distributions with well-separated modes, which are commonly encountered in practical applications. We compare a novel diffusion-based denoising score matching estimator (DDSME) to the vanilla score matching estimator (SME) in this scenario. In particular, we prove statistical guarantees for both estimators, showing that the error bound for the vanilla SME worsens when the separation between the modes increases, which can be avoided in case of the DDSME with suitable hyperparameter tuning. This provides a novel theoretical explanation for the superior behavior of diffusion-based score matching over the vanilla version.
Uncertainty-aware classification and triage of structural heart disease using electrocardiography and echocardiography metrics
Machine learning methods provide a methodological innovation that can help screen for cardiovascular disease through noninvasive and readily available measurement modalities. Recent investments in using electrocardiogram (ECG) data to screen for structural heart disease (SHD) are one example, where ECGs provide a low-cost, available modality for screening. This has led to the EchoNext dataset, a paired ECG-echocardiogram data repository for testing new methods of SHD detection. However, relatively few studies have investigated how more probabilistic classification through Bayesian inference may improve uncertainty quantification in this setting. Moreover, few studies have considered how triage systems can be developed to alleviate healthcare bottlenecks, such as the review of data from underserved, rural clinics by expert sonographers for SHD assessment. In this study, we leverage existing ECG-echocardiogram data to compare frequentist and Bayesian neural network classifiers. We show that the Bayesian approach is comparable or better than frequentist methods in SHD classification, and that they have a more robust uncertainty quantification attached to them. We provide an example of how this uncertainty-aware classification scheme can be used for screening SHD, providing a proof-of-concept for how machine learning can help with triage in getting individuals expert sonographer input when SHD is highly likely or measurements are highly uncertain.
HawkesLLM: Semantic Uncertainty Propagation in Agentic Text Simulation
Deng, Zewei, Ye, Tinghan, Xie, Liyan
Agentic text-simulation systems write in sequence, with each item becoming possible context for later steps. That makes uncertainty path-dependent: an early ambiguity can affect later outputs. This paper studies this problem with HawkesLLM, a framework that separates temporal influence modeling from text generation. We represent the cascade as a network whose nodes are text-generating agents. A multivariate Hawkes process models how these nodes activate over time and which earlier node outputs should influence later prompts. A language model then writes each new event from the compact memory selected by this temporal model. We evaluate the framework on a held-out Global Database of Events, Language, and Tone (GDELT) news-cascade case study. The diagnostics track semantic alignment with local held-out references and separate local drift from global drift. In this setting, HawkesLLM improves late-stage semantic alignment under a compact prompt-memory budget.
Anytime Training with Schedule-Free Spectral Optimization
Apte, Anuj, Deshpande, Pranav, Kumar, Niraj, Chakrabarti, Shouvanik, Kim, Junhyung Lyle
Standard neural network training relies on learning-rate schedules tied to a fixed horizon, leading to strong path dependence and costly re-tuning as data availability changes. Schedule-Free (SF) methods address this by removing explicit schedules, yet SF-AdamW, the current state-of-the-art anytime optimizer, consistently underperforms well-tuned AdamW baselines. We propose SF-NorMuon, a schedule-free spectral optimizer that closes this gap: with a single hyperparameter configuration, SF-NorMuon matches or exceeds tuned AdamW on 125M and 772M parameter language models across $1$--$8\times$ Chinchilla horizons. On the theoretical side, we prove a stationarity guarantee for schedule-free spectral dynamics and identify weight decay at the fast iterate as essential for long-horizon stability. SF-NorMuon enables practitioners to obtain high-quality checkpoints at any point during training without committing to a horizon in advance. By closing the performance gap with tuned baselines, SF-NorMuon makes horizon-free optimization more practical, taking a step towards truly open-ended, continual learning.
Mode-Shape Expansion Using Physics-Constrained Gaussian Process Regression
This paper addresses the challenge of reconstructing full-field structural mode shapes from sparse sensor data. While Gaussian Process Regression (GPR) offers a robust non-parametric framework for spatial interpolation and uncertainty quantification, standard formulations often yield physically inconsistent mode-shape reconstructions under sparse sensing conditions. A Physics-Constrained Single-Output Gaussian Process (CONS-SOGP) framework is derived that utilizes independent modal kernels while coupling the optimization via a mass-orthogonality penalty. The paper presents derivations for the marginal likelihood, hyperparameter gradients, and penalty coupling. Numerical verification on a multi-degree-of-freedom structure demonstrates that the proposed method overcomes existing limitations in GP-based prediction, providing more accurate and reliable expanded mode shapes.