Neural Information Processing Systems http://nips.cc/

A cluster tree provides a highly-interpretable summary of a density function by representing the hierarchy of its high-density clusters. It is estimated using the empirical tree, which is the cluster tree constructed from a density estimator. This paper addresses the basic question of quantifying our uncertainty by assessing the statistical significance of topological features of an empirical cluster tree. We first study a variety of metrics that can be used to compare different trees, analyze their properties and assess their suitability for inference. We then propose methods to construct and summarize confidence sets for the unknown true cluster tree. We introduce a partial ordering on cluster trees which we use to prune some of the statistically insignificant features of the empirical tree, yielding interpretable and parsimonious cluster trees. Finally, we illustrate the proposed methods on a variety of synthetic examples and furthermore demonstrate their utility in the analysis of a Graft-versus-Host Disease (GvHD) data set.

Bayesian optimization is a prominent method for optimizing expensive-to-evaluate black-box functions that is widely applied to tuning the hyperparameters of machine learning algorithms. Despite its successes, the prototypical Bayesian optimization approach - using Gaussian process models - does not scale well to either many hyperparameters or many function evaluations. Attacking this lack of scalability and flexibility is thus one of the key challenges of the field. We present a general approach for using flexible parametric models (neural networks) for Bayesian optimization, staying as close to a truly Bayesian treatment as possible. We obtain scalability through stochastic gradient Hamiltonian Monte Carlo, whose robustness we improve via a scale adaptation.

Conformal prediction provides finite-sample, distribution-free coverage under exchangeability, but standard constructions may lack robustness in the presence of outliers or heavy tails. We propose a robust conformal method based on a non-conformity score defined as the half-mass radius around a point, equivalently the distance to its $(\lfloor n/2\rfloor+1)$-nearest neighbour. We show that the resulting conformal regions are marginally valid for any sample size and converge in probability to a robust population central set defined through a distance-to-a-measure functional. Under mild regularity conditions, we establish exponential concentration and tail bounds that quantify the deviation between the empirical conformal region and its population counterpart. These results provide a probabilistic justification for using robust geometric scores in conformal prediction, even for heavy-tailed or multi-modal distributions.

The inverse Potts problem for estimating evolutionary single-site fields and pairwise couplings in homologous protein sequences from their single-site and pairwise amino acid frequencies observed in their multiple sequence alignment would be still one of useful methods in the studies of protein structure and evolution. Since the reproducibility of fields and couplings are the most important, the Boltzmann machine method is employed here, although it is computationally intensive. In order to reduce computational time required for the Boltzmann machine, parallel, persistent Markov chain Monte Carlo method is employed to estimate the single-site and pairwise marginal distributions in each learning step. Also, stochastic gradient descent methods are used to reduce computational time for each learning. Another problem is how to adjust the values of hyperparameters; there are two regularization parameters for evolutionary fields and couplings. The precision of contact residue pair prediction is often used to adjust the hyperparameters. However, it is not sensitive to these regularization parameters. Here, they are adjusted for the fields and couplings to satisfy a specific condition that is appropriate for protein conformations. This method has been applied to eight protein families.

Predictions from machine learning algorithms can vary across random seeds, inducing instability in downstream debiased machine learning estimators. We formalize random seed stability via a concentration condition and prove that subbagging guarantees stability for any bounded-outcome regression algorithm. We introduce a new cross-fitting procedure, adaptive cross-bagging, which simultaneously eliminates seed dependence from both nuisance estimation and sample splitting in debiased machine learning. Numerical experiments confirm that the method achieves the targeted level of stability whereas alternatives do not. Our method incurs a small computational penalty relative to standard practice whereas alternative methods incur large penalties.

Bayesian experimental design (BED) for complex physical systems is often limited by the nested inference required to estimate the expected information gain (EIG) or its gradients. Each outer sample induces a different posterior, creating a large and heterogeneous set of inference targets. Existing methods have to sacrifice either accuracy or efficiency: they either perform per-outer-sample posterior inference, which yields higher fidelity but at prohibitive computational cost, or amortize the inner inference across all outer samples for computational reuse, at the risk of degraded accuracy under posterior heterogeneity. To improve accuracy and maintain cost at the amortized level, we propose a grouped geometric pooled posterior framework that partitions outer samples into groups and constructs a pooled proposal for each group. While such grouping strategy would normally require generating separate proposal samples for different groups, our tailored ensemble Kalman inversion (EKI) formulation generates these samples without extra forward-model evaluation cost. We also introduce a conservative diagnostic to assess importance-sampling quality to guide grouping. This grouping strategy improves within-group proposal-target alignment, yielding more accurate and stable estimators while keeping the cost comparable to amortized approaches. We evaluate the performance of our method on both Gaussian-linear and high-dimensional network-based model discrepancy calibration problems.

This paper investigates the off-policy evaluation (OPE) problem from a distributional perspective. Rather than focusing solely on the expectation of the total return, as in most existing OPE methods, we aim to estimate the entire return distribution. To this end, we introduce a quantile-based approach for OPE using deep quantile process regression, presenting a novel algorithm called Deep Quantile Process regression-based Off-Policy Evaluation (DQPOPE). We provide new theoretical insights into the deep quantile process regression technique, extending existing approaches that estimate discrete quantiles to estimate a continuous quantile function. A key contribution of our work is the rigorous sample complexity analysis for distributional OPE with deep neural networks, bridging theoretical analysis with practical algorithmic implementations. We show that DQPOPE achieves statistical advantages by estimating the full return distribution using the same sample size required to estimate a single policy value using conventional methods. Empirical studies further show that DQPOPE provides significantly more precise and robust policy value estimates than standard methods, thereby enhancing the practical applicability and effectiveness of distributional reinforcement learning approaches.

Conformal prediction (CP) has attracted broad attention as a simple and flexible framework for uncertainty quantification through prediction sets. In this work, we study how to deploy CP under differential privacy (DP) in a statistically efficient manner. We first introduce differential CP, a non-splitting conformal procedure that avoids the efficiency loss caused by data splitting and serves as a bridge between oracle CP and private conformal inference. By exploiting the stability properties of DP mechanisms, differential CP establishes a direct connection to oracle CP and inherits corresponding validity behavior. Building on this idea, we develop Differentially Private Conformal Prediction (DPCP), a fully private procedure that combines DP model training with a private quantile mechanism for calibration. We establish the end-to-end privacy guarantee of DPCP and investigate its coverage properties under additional regularity conditions. We further study the efficiency of both differential CP and DPCP under empirical risk minimization and general regression models, showing that DPCP can produce tighter prediction sets than existing private split conformal approaches under the same privacy budget. Numerical experiments on synthetic and real datasets demonstrate the practical effectiveness of the proposed methods.

The low-degree polynomial framework has emerged as a powerful tool for providing evidence of statistical-computational gaps in high-dimensional inference. For detection problems, the standard approach bounds the low-degree advantage through an explicit orthonormal basis. However, this method does not extend naturally to estimation tasks, and thus fails to capture the \emph{detection-recovery gap phenomenon} that arises in many high-dimensional problems. Although several important advances have been made to overcome this limitation \cite{SW22, SW25, CGGV25+}, the existing approaches often rely on delicate, model-specific combinatorial arguments. In this work, we develop a general approach for obtaining \emph{conditional computational lower bounds} for recovery problems from mild bounds on low-degree testing advantage. Our method combines the notion of algorithmic contiguity in \cite{Li25} with a cross-validation reduction in \cite{DHSS25} that converts successful recovery into a hypothesis test with lopsided success probabilities. In contrast to prior unconditional lower bounds, our argument is conceptually simple, flexible, and largely model-independent. We apply this framework to several canonical inference problems, including planted submatrix, planted dense subgraph, stochastic block model, multi-frequency angular synchronization, orthogonal group synchronization, and multi-layer stochastic block model. In the first three settings, our method recovers existing low-degree lower bounds for recovery in \cite{SW22, SW25} via a substantially simpler argument. In the latter three, it gives new evidence for conjectured computational thresholds including the persistence of detection-recovery gaps. Together, these results suggest that mild control of low-degree advantage is often sufficient to explain computational barriers for recovery in high-dimensional statistical models.