Learning informative representations of phylogenetic tree structures is essential for analyzing evolutionary relationships. Classical distance-based methods have been widely used to project phylogenetic trees into Euclidean space, but they are often sensitive to the choice of distance metric and may lack sufficient resolution. In this paper, we introduce phylogenetic variational autoencoders (PhyloVAEs), an unsupervised learning framework designed for representation learning and generative modeling of tree topologies. Leveraging an efficient encoding mechanism inspired by autoregressive tree topology generation, we develop a deep latent-variable generative model that facilitates fast, parallelized topology generation. Phylo-VAE combines this generative model with a collaborative inference model based on learnable topological features, allowing for high-resolution representations of phylogenetic tree samples. Extensive experiments demonstrate PhyloVAE's robust representation learning capabilities and fast generation of phylogenetic tree topologies. Phylogenetic trees are the foundational structure for describing the evolutionary processes among individuals or groups of biological entities. Reconstructing these trees based on collected biological sequences (e.g., DNA, RNA, protein) from observed species, also known as phylogenetic inference (Felsenstein, 2004), is an essential discipline of computational biology (Fitch, 1971; Felsenstein, 1981; Yang & Rannala, 1997; Ronquist et al., 2012). Large collections of trees obtained from these approaches (e.g., posterior samples from MCMC runs (Ronquist et al., 2012)), however, are often difficult to summarize or visualize due to the discrete and non-Euclidean nature of the tree topology space The classical approach to visualize and analyze distributions of phylogenetic trees is to calculate pairwise distances between the trees and project them into a plane using multidimensional scaling (MDS) (Amenta & Klingner, 2002; Hillis et al., 2005; Jombart et al., 2017). However, these approaches have the shortcoming that one can not map an arbitrary point in the visualization to a tree, and therefore do not form an actual visualization of the relevant tree space.

Digital twins have been actively explored in many engineering applications, such as manufacturing and autonomous systems. However, model discrepancy is ubiquitous in most digital twin models and has significant impacts on the performance of using those models. In recent years, data-driven modeling techniques have been demonstrated promising in characterizing the model discrepancy in existing models, while the training data for the learning of model discrepancy is often obtained in an empirical way and an active approach of gathering informative data can potentially benefit the learning of model discrepancy. On the other hand, Bayesian experimental design (BED) provides a systematic approach to gathering the most informative data, but its performance is often negatively impacted by the model discrepancy. In this work, we build on sequential BED and propose an efficient approach to iteratively learn the model discrepancy based on the data from the BED. The performance of the proposed method is validated by a classical numerical example governed by a convection-diffusion equation, for which full BED is still feasible. The proposed method is then further studied in the same numerical example with a high-dimensional model discrepancy, which serves as a demonstration for the scenarios where full BED is not practical anymore. An ensemble-based approximation of information gain is further utilized to assess the data informativeness and to enhance learning model discrepancy. The results show that the proposed method is efficient and robust to the active learning of high-dimensional model discrepancy, using data suggested by the sequential BED. We also demonstrate that the proposed method is compatible with both classical numerical solvers and modern auto-differentiable solvers.

Rebuttal: thank you for your clarifications. I still think that learning kernel (parameters) from multiple realizations of a GP is not very novel in general, but sufficiently novel in your specific context to get discussed at NIPS. The authors use Gaussian processes to learn human function extrapolation behaviour from human sample data. After a comprehensive literature review, they introduce the main idea of the paper: learn the kernel parameters by maximizing the conditional probability of the extrapolation data given the training data. To allow for flexible kernel shapes, they use spectral mixture kernels.

The paper describes tricks to scale Bayesian network structure learning to thousands of variables. This is achieved by developing new heuristics for candidate parent set identification and the subsequent order based structure optimization. In general, the paper is clearly written and easy to read. There are issues in editing and style, but the problems do not affect readability (much). The suggested heuristics feel bit ad-hoc, thus the value of the work is eventually judged by empirical evaluation.

Summary and Contributions: The paper considers the problem of sampling from the posterior distribution in Bayesian inference. To be more precise, the paper approaches the question of stochastic sampling that relies only on minibatches of data at each iteration. To achieve rapid mixing between isolated modes, the authors consider parallel tempered chains and introduce replica-exchange steps into the stochastic Nose-Hoover Dynamics. The crux of this approach is the stochastic test for the replica-exchange step. To develop such a test, the authors follow the paper [An efficient minibatch acceptance test for metropolis-hastings], which introduces the concept of correction distribution.

The paper proposes a novel MCMC-type algorithm to perform Bayesian inference on large datasets. The paper is a mixture of replica exchange, Nose-Hoover dynamics and non-standard acceptance criterion to deal with mini-batches. All the reviewers participated actively to the discussion after the rebuttal was made available. Although all the ingredients of the proposed method do exist, their combination is original and potentially useful for the ML literature as pointed out by most reviewers. Theorem 2 is also neat and proposes a nice way to propose swaps between replicas using mini-batches.

The asymptotic properties of Bayesian Neural Networks (BNNs) have been extensively studied, particularly regarding their approximations by Gaussian processes in the infinite-width limit. We extend these results by showing that posterior BNNs can be approximated by Student-t processes, which offer greater flexibility in modeling uncertainty. Specifically, we show that, if the parameters of a BNN follow a Gaussian prior distribution, and the variance of both the last hidden layer and the Gaussian likelihood function follows an Inverse-Gamma prior distribution, then the resulting posterior BNN converges to a Student-t process in the infinite-width limit. Our proof leverages the Wasserstein metric to establish control over the convergence rate of the Student-t process approximation.

Synthetic data generation for tabular datasets must balance fidelity, efficiency, and versatility to meet the demands of real-world applications. We introduce the Tabular Auto-Regressive Generative Network (TabularARGN), a flexible framework designed to handle mixed-type, multivariate, and sequential datasets. By training on all possible conditional probabilities, TabularARGN supports advanced features such as fairness-aware generation, imputation, and conditional generation on any subset of columns. The framework achieves state-of-the-art synthetic data quality while significantly reducing training and inference times, making it ideal for large-scale datasets with diverse structures. Evaluated across established benchmarks, including realistic datasets with complex relationships, TabularARGN demonstrates its capability to synthesize high-quality data efficiently. By unifying flexibility and performance, this framework paves the way for practical synthetic data generation across industries.

Availability of datasets is a strong driver for research on 3D semantic understanding, and whilst obtaining unlabeled 3D point cloud data is straightforward, manually annotating this data with semantic labels is time-consuming and costly. Recently, Vision Foundation Models (VFMs) enable open-set semantic segmentation on camera images, potentially aiding automatic labeling. However,VFMs for 3D data have been limited to adaptations of 2D models, which can introduce inconsistencies to 3D labels. This work introduces Label Any Pointcloud (LeAP), leveraging 2D VFMs to automatically label 3D data with any set of classes in any kind of application whilst ensuring label consistency. Using a Bayesian update, point labels are combined into voxels to improve spatio-temporal consistency. A novel 3D Consistency Network (3D-CN) exploits 3D information to further improve label quality. Through various experiments, we show that our method can generate high-quality 3D semantic labels across diverse fields without any manual labeling. Further, models adapted to new domains using our labels show up to a 34.2 mIoU increase in semantic segmentation tasks.

The estimation of uncertainties associated with predictions from quantitative structure-activity relationship (QSAR) models can accelerate the drug discovery process by identifying promising experiments and allowing an efficient allocation of resources. Several computational tools exist that estimate the predictive uncertainty in machine learning models. However, deviations from the i.i.d. setting have been shown to impair the performance of these uncertainty quantification methods. We use a real-world pharmaceutical dataset to address the pressing need for a comprehensive, large-scale evaluation of uncertainty estimation methods in the context of realistic distribution shifts over time. We investigate the performance of several uncertainty estimation methods, including ensemble-based and Bayesian approaches. Furthermore, we use this real-world setting to systematically assess the distribution shifts in label and descriptor space and their impact on the capability of the uncertainty estimation methods. Our study reveals significant shifts over time in both label and descriptor space and a clear connection between the magnitude of the shift and the nature of the assay. Moreover, we show that pronounced distribution shifts impair the performance of popular uncertainty estimation methods used in QSAR models. This work highlights the challenges of identifying uncertainty quantification methods that remain reliable under distribution shifts introduced by real-world data.