Inspired by the human ability to learn and organize knowledge into hierarchical taxonomies with prototypes, this paper addresses key limitations in current deep hierarchical clustering methods. Existing methods often tie the structure to the number of classes and underutilize the rich prototype information available at intermediate hierarchical levels. We introduce deep taxonomic networks, a novel deep latent variable approach designed to bridge these gaps. Our method optimizes a large latent taxonomic hierarchy, specifically a complete binary tree structured mixture-of-Gaussian prior within a variational inference framework, to automatically discover taxonomic structures and associated prototype clusters directly from unlabeled data without assuming true label sizes. We analytically show that optimizing the ELBO of our method encourages the discovery of hierarchical relationships among prototypes. Empirically, our learned models demonstrate strong hierarchical clustering performance, outperforming baselines across diverse image classification datasets using our novel evaluation mechanism that leverages prototype clusters discovered at all hierarchical levels. Qualitative results further reveal that deep taxonomic networks discover rich and interpretable hierarchical taxonomies, capturing both coarse-grained semantic categories and fine-grained visual distinctions.

Longitudinal treatment decisions from multivariate time-series data require predicting potential outcomes under future treatment sequences in the presence of timevarying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically address this problem by training a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CAUSALLONGPFN), a prior-fitted network for time-series causal inference in longitudinal treatment-response data and zero-shot in-context counterfactual outcome prediction. To our knowledge, CAUSALLONGPFN is the first PFN-style model for history-conditional potential-outcome prediction under planned longitudinal treatment sequences, with systematic comparison against established longitudinal causal baselines on branchable counterfactual treatmentresponse benchmarks and factual real-world clinical data. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CAUSALLONGPFN remains frozen and is used zero-shot: it conditions on support trajectories, a query history, and a planned future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate the model on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CAUSALLONGPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a frozen, amortized alternative for zero-shot longitudinal treatment-response prediction when repeated domain-specific training is costly or impractical.

Electronic health records (EHR) pose large-scale multi-disease modeling problems in which many outcomes are rare and strongly influenced by shared risk factors. While modern approaches achieve strong predictive performance, they often treat diseases independently or rely on black-box architectures, offering limited insight into how risk factors organize disease risk and little principled uncertainty quantification. We introduce a Bayesian hypergraph inference framework that reframes multi-disease modeling around latent, risk-factor-modulated disease pathways. Risk factors act on hyperedges, latent disease subsets with shared risk patterns, allowing diseases to participate in multiple distinct pathways and enabling interpretable, higher-order structure beyond pairwise associations. A repulsion prior encourages parsimonious and identifiable structure, while posterior inference provides calibrated uncertainty over both disease groupings and risk-factor influence. To enable scalable inference on large EHR datasets, we develop a structured variational inference algorithm that preserves logical dependencies among hyperedge existence, disease membership, and pathway-level effects. Experiments on simulated data and UK Biobank demonstrate stable and interpretable disease pathway structure, well-calibrated uncertainty, improved estimation for rare diseases, and competitive predictive performance.

Undirected graphical models provide a fundamental framework for representing conditional independence structures among high-dimensional random variables. While undirected graphical model selection has become a central problem in high-dimensional statistics, most existing methods are restricted to parametric settings. In this paper, we develop a nonparametric approach to undirected graphical model selection based on diffusion models. Recent work has shown that diffusion models can adapt to the unknown graph structure of the underlying distribution, yet utilizing these models for explicit graph estimation remains unexplored. To bridge this gap, we introduce a novel diffusion-based method for nonparametric undirected graphical model selection. We establish the model selection consistency of the proposed method and demonstrate its empirical performance through extensive simulations and two real data analyses.

We study component recovery and mixing-matrix estimation from unlabeled finite mixtures whose observable distributions share the same latent components but have unknown mixing weights. The main identifying signal is marginal independence: each component is assumed to be independent on at least one coordinate pair, but no labels, clean component samples, or mixing weights are observed. We first prove a structural result for product components: under linear independence of the univariate marginals, any independent affine combination of the components must coincide with a single component. We then extend this principle to observable mixtures and show that, under full-rank and no-cancellation conditions, marginally independent affine combinations recover the corresponding latent components. When every component is independent on some coordinate pair, all components are identifiable, and the mixing matrix is recoverable under the stated completion conditions. Finally, we propose a Product-Marginal Maximum Mean Discrepancy (PM-MMD) estimator over affine combinations of the observable mixtures and prove uniform convergence and stability under approximate marginal independence. This framework also separates the empirical roles of the assumptions: irreducibility is, in general, not directly testable from the unlabeled mixtures alone, whereas marginal independence yields a candidate-level diagnostic through held-out PM-MMD. Controlled and flow-cytometry experiments show when marginal independence provides a useful recovery signal. In the reported multi-component comparisons, condition-aware representative selection stabilizes PM-MMD and improves recovery relative to clustering, factorization, and pairwise mixture-proportion baselines using the same unlabeled mixtures.

In regression modelling, the primary objective is to approximate the true conditional mean of a response given a set of features. To this end, various statistical models are used to fit a regression function that provides a mean estimate for each single set of features. This function is said to be calibrated if the resulting mean estimates match the true conditional means for almost all features. Aiming for calibration seems not achievable in practice as models are fitted on finite samples of noisy observations. A weaker notion of calibration is auto-calibration (sometimes also called mean-calibration or well-calibration); see, for example, Kr uger-Ziegel [22] and Denuit et al. [7]. This notion goes back to earlier works on the reliability of probabilistic forecasts in meteorology; we refer to Bross [2], Sanders [26] and Murphy-Winkler [23]. It means that when responses are grouped according to their mean estimates, the average of the responses within each group matches this estimate. This property is important in various applications where sums of mean estimates have to match sums of responses at a global and local level. This is, for example, the case in insurance pricing as an auto-calibrated pricing system avoids systematic cross-subsidy between different price cohorts; we refer the reader to Pohle [24], Denuit et al. [6], Fissler et al. [9] and W uthrich-Merz [30].

Externally controlled survival trials are increasingly used when concurrent randomized controls are infeasible, particularly in oncology and rare-disease settings with time-to-event endpoints. We target an average-treatment-effect-on-the-treated (ATT)-type marginal hazard-ratio estimand, comparing treatment with counterfactual control in the treated trial population, and estimate it using inverse-probability-weighted (IPW) Cox regression. Valid inference is challenging because IPW Cox regression depends on the weights through both event contributions and risk-set averages, making flexible machine-learning nuisance estimation difficult to incorporate directly. Building on machine-learning-assisted generalized entropy calibration (MEC) by Lee and Kim (2026), we propose MEC-Cox for ATT-weighted IPW Cox regression. The method begins with normalized source-propensity-score odds weights for external controls and then applies Bregman calibration to balance cross-fitted prognostic summaries between external controls and treated trial patients. The calibration basis may include control-survival predictions, Cox linear predictors, penalized-survival-model predictions, or other prognostic-score summaries. MEC-updated weights therefore play a dual role as source-transport and prognostic-score balancing weights. We establish consistency, characterize a calibration-induced efficiency gain, and develop a stacked sandwich variance estimator. Simulations show that MEC-Cox can reduce bias, increase efficiency, and improve coverage through flexible machine-learning-assisted adjustment.

Black-box variational inference (BBVI) is a methodology for posterior approximation that relies on stochastic optimization. In practice, the stochastic optimizers underpinning BBVI generally require extensive problem-specific tuning, which undermines its promise as a truly "black box" inference algorithm. However, over the past decade, many new adaptive stochastic optimization algorithms have been developed that reduce or remove entirely the need for tuning. In this work, we investigate this new collection of adaptive methods in the context of BBVI, with the goal of establishing the current state of the art in tuning-free optimization-based inference. In particular, we present a large-scale empirical evaluation of 56 stochastic gradient-based optimization algorithms applied to 1092 Bayesian inference optimization problems, involving over 550,000 individual optimization runs and 15 core-years of compute. The optimization algorithms we evaluate are chosen to represent a wide spectrum of recent approaches and the benchmark problems are chosen to span a range of difficulty, with posterior target dimension 1-10^4, condition number 1-10^8, and a range of variational families. Our results show that no single method dominates, but running a selection of 5 algorithms suffices to reliably get close to the best-possible observed performance. We thus provide a strong baseline for applications where expert tuning is not possible and for comparison when developing new stochastic optimization algorithms.

Data-adaptive two-sample testing assesses if two samples come from the same distribution, using a discrepancy learned from the data (e.g., via kernel-based feature representations). Such methods typically rely on data splitting to decouple learning from testing and control type I error. However, this paradigm is ill-suited to few-shot settings with severe sample-size imbalance: abundant reference samples are available, while only a handful of query samples arrive. In this paper, we show how this imbalance can be leveraged constructively. Using abundant reference data, we learn reference-dependent representations that summarize salient structure of the reference distribution and provide informative signals for detecting departures. We incorporate a collection of representation families that capture both global and local structure, and adaptively weight them using only reference samples via an uncertainty-guided principle. Theoretically, we establish permutation-based type I error control and show consistency of the aggregated test: as the sample sizes grow, the test power converges to one whenever the representation set contains at least one consistent representation. Empirically, our aggregation achieves strong performance across a range of benchmarks while retaining type I error control.

We adopt the canonical polyadic (CP) decomposition to model high-dimensional tensor time series. Our primary goal is to identify and estimate the factor loadings in the CP decomposition. We propose a one-pass estimation procedure through standard eigen-analysis for a matrix constructed based on the serial dependence structure of the data. The asymptotic properties of the proposed estimator are established under a general setting as long as the factor loading vectors are linearly independent, allowing the factors to be correlated and the factor loading vectors to be not nearly orthogonal. The procedure adapts to the sparsity of the factor loading vectors, accommodates weak factors, and demonstrates strong performance across a wide range of scenarios. To further reduce estimation errors, we also introduce an iterative algorithm based on a novel double projection approach. We theoretically justify the improved convergence rate of the iterative estimator, and derive the associated limiting distribution. A consistent estimator of the asymptotic variance is also provided, which plays a key role in the related inference problems. All results are validated through extensive simulations and two real data applications.