Graph Neural Networks (GNNs) have achieved impressive results across diverse network modeling tasks, but accurately estimating uncertainty on graphs remains difficult--especially under distributional shifts. Unlike traditional uncertainty estimation, graph-based uncertainty must account for randomness arising from both the graph's structure and its label distribution, which adds complexity. In this paper, making an analogy between the evolution of a stochastic partial differential equation (SPDE) driven by Matérn Gaussian Process and message passing using GNN layers, we present a principled way to design a novel message passing scheme that incorporates spatial-temporal noises motivated by the Gaussian Process approach to SPDE. Our method simultaneously captures uncertainty across space and time and allows explicit control over the covariance kernel's smoothness, thereby enhancing uncertainty estimates on graphs with both low and high label informativeness. Our extensive experiments on Out-of-Distribution (OOD) detection on graph datasets with varying label informativeness demonstrate the soundness and superiority of our model to existing approaches.

Higher-order structures are powerful relational modeling tools, yet existing spectral operators decompose the topology into separate ranks, leaving practitioners to fuse the information back to vertices through ad hoc choices. We introduce Collapsed Effective Operators, which condense higher-order degrees of freedom into a single vertex-level operator via Schur complementation of a graded Laplacian. This yields a (generally dense) operator that encodes long-range interactions mediated by topology and is applicable to arbitrary higher-order constructs. We show it preserves positive semi-definiteness with a spectral upper bound relative to the rank-0 Hodge Laplacian, effectively lowering system energy under higher-order connectivity. Empirically, our operator improves spectral clustering, signal smoothing, and enables the inclusion of topological features in neural network architectures via positional encoding. The project page can be found http://circle-group.github.io/research/CollapsedEffectiveOperators

Graph Laplacians encode graph structures in matrix form, and thus facilitate the application of linear algebra to graph theory. In statistics, two related families of probabilistic graphical models can be parameterized by graph Laplacians. The first one is the Laplacian-constrained Gaussian graphical model (LCGGM), which imposes that the (pseudo-)inverse covariance matrix of a Gaussian random vector is a Laplacian matrix. Applications include graph signal processing and network topology learning. The second one is the Hüsler-Reiss graphical model, which is considered as an extremal analog of the Gaussian graphical model, and can be used in extremal dependence modeling of floods, heatwaves, and financial losses. For both models, the restriction to positive edge weights in the graph Laplacian gives rise to an approach for graph structure learning that does not require tuning parameters. While these approaches yield a strong model fit in many settings, the resulting graph estimates are typically much denser than the underlying ground truth, limiting interpretability and scalability. In order to improve the accuracy of Laplacian-constrained graph learning, we propose to use spectral graph sparsification as a post-estimation operation. To do so, we replace the original Laplacian estimate by a sparser Laplacian that is spectrally close, and re-fit the model on the resulting graph. We refer to the two resulting methods as Spectral-LCGGM and Spectral-HR. We investigate the properties of the proposed estimators and show several theoretical results on their performance. Furthermore, we demonstrate that the newly proposed methods perform well by running simulations on Erdős-Rényi and stochastic block model graphs, and we also showcase their applications to real data.

Smooth functions on graphs have wide applications in manifold and semi-supervised learning. In this paper, we study a bandit problem where the payoffs of arms are smooth on a graph. This framework is suitable for solving online learning problems that involve graphs, such as content-based recommendation. In this problem, each recommended item is a node and its expected rating is similar to its neighbors. The goal is to recommend items that have high expected ratings. We aim for the algorithms where the cumulative regret would not scale poorly with the number of nodes. In particular, we introduce the notion of an effective dimension, which is small in real-world graphs, and propose two algorithms for solving our problem that scale linearly in this dimension. Our experiments on real-world content recommendation problem show that a good estimator of user preferences for thousands of items can be learned from just tens nodes evaluations.

Gaussian process regression is widely used because of its ability to provide well-calibrated uncertainty estimates and handle small or sparse datasets. However, it struggles with high-dimensional data. One possible way to scale this technique to higher dimensions is to leverage the implicit low-dimensional manifold upon which the data actually lies, as postulated by the manifold hypothesis. Prior work ordinarily requires the manifold structure to be explicitly provided though, i.e. given by a mesh or be known to be one of the well-known manifolds like the sphere. In contrast, in this paper we propose a Gaussian process regression technique capable of inferring implicit structure directly from data (labeled and unlabeled) in a fully differentiable way. For the resulting model, we discuss its convergence to the Matérn Gaussian process on the assumed manifold. Our technique scales up to hundreds of thousands of data points, and improves the predictive performance and calibration of the standard Gaussian process regression in some high-dimensional settings.

Graph neural networks (GNNs) have achieved superior performance in various applications, but training dedicated GNNs can be costly for large-scale graphs. Some recent work started to study the pre-training of GNNs. However, none of them provide theoretical insights into the design of their frameworks, or clear requirements and guarantees towards their transferability. In this work, we establish a theoretically grounded and practically useful framework for the transfer learning of GNNs. Firstly, we propose a novel view towards the essential graph information and advocate the capturing of it as the goal of transferable GNN training, which motivates the design of EGI (Ego-Graph Information maximization) to analytically achieve this goal. Secondly, when node features are structure-relevant, we conduct an analysis of EGI transferability regarding the difference between the local graph Laplacians of the source and target graphs. We conduct controlled synthetic experiments to directly justify our theoretical conclusions. Comprehensive experiments on two real-world network datasets show consistent results in the analyzed setting of direct-transfering, while those on large-scale knowledge graphs show promising results in the more practical setting of transfering with fine-tuning.1

Scientific observations may consist of a large number of variables (features). Selecting a subset of meaningful features is often crucial for identifying patterns hidden in the ambient space. In this paper, we present a method for unsupervised feature selection, and we demonstrate its advantage in clustering, a common unsupervised task. We propose a differentiable loss that combines a graph Laplacian-based score that favors low-frequency features with a gating mechanism for removing nuisance features. Our method improves upon the naive graph Laplacian score by replacing it with a gated variant computed on a subset of low-frequency features. We identify this subset by learning the parameters of continuously relaxed Bernoulli variables, which gate the entire feature space. We mathematically motivate the proposed approach and demonstrate that it is crucial to compute the graph Laplacian on the gated inputs rather than on the full feature space in the high noise regime. Using several real-world examples, we demonstrate the efficacy and advantage of the proposed approach over leading baselines.

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

Smooth functions on graphs have wide applications in manifold and semi-supervised learning. In this paper, we study a bandit problem where the payoffs of arms are smooth on a graph. This framework is suitable for solving online learning problems that involve graphs, such as content-based recommendation. In this problem, each item we can recommend is a node and its expected rating is similar to its neighbors. The goal is to recommend items that have high expected ratings. We aim for the algorithms where the cumulative regret with respect to the optimal policy would not scale poorly with the number of nodes. In particular, we introduce the notion of an effective dimension, which is small in real-world graphs, and propose two algorithms for solving our problem that scale linearly and sublinearly in this dimension. Our experiments on real-world content recommendation problem show that a good estimator of user preferences for thousands of items can be learned from just tens of nodes evaluations.

Approximations of Laplace-Beltrami operators on manifolds through graph Laplacians have become popular tools in data analysis and machine learning. These discretized operators usually depend on bandwidth parameters whose tuning remains a theoretical and practical problem. In this paper, we address this problem for the unormalized graph Laplacian by establishing an oracle inequality that opens the door to a well-founded data-driven procedure for the bandwidth selection. Our approach relies on recent results by Lacour and Massart (2015) on the so-called Lepski's method.