Graph kernels have emerged as a fundamental and widely adopted technique in graph machine learning. However, most existing graph kernel methods rely on fixed graph similarity estimation that cannot be directly optimized for task-specific objectives, leading to sub-optimal performance. To address this limitation, we propose a kernel-based learning framework called Hierarchical Shortest-Path Graph Kernel Network (HSP-GKN), which seamlessly integrates graph similarity estimation with downstream tasks within a unified optimization framework. Specifically, we design a hierarchical shortest-path graph kernel that efficiently preserves both the semantic and structural information of a given graph by transforming it into hierarchical features used for subsequent neural network learning. Building upon this kernel, we develop a novel end-to-end learning framework that matches hierarchical graph features with learnable hidden graph features to produce a similarity vector. This similarity vector subsequently serves as the graph embedding for endto-end training, enabling the neural network to learn task-specific representations. Extensive experimental results demonstrate the effectiveness and superiority of the designed kernel and its corresponding learning framework compared to current competitors.

A.1 Dataset Examples450 In this section of the appendix, we present a detailed overview of several representative tasks from451 each category included in REASONINGGYM. For each task, we describe its structure, complexity452 parameters, and provide examples.453 A.1.1 complex_arithmetic(Algebra)454 Find the solution of an arithmetic operation involving complex numbers.455 The spiral order is clockwise, starting from the top-left corner. Predict the corresponding output grid by applying the rule you found.

What is the shortest path between two data points lying in a high-dimensional space? While the answer is trivial in Euclidean geometry, it becomes significantly more complex when the data lies on a curved manifold--requiring a Riemannian metric to describe the space's local curvature. Estimating such a metric, however, remains a major challenge in high dimensions. In this work, we propose a method for deriving Riemannian metrics directly from pretrained Energy-Based Models (EBMs)--a class of generative models that assign low energy to high-density regions. These metrics define spatially varying distances, enabling the computation of geodesics--shortest paths that follow the data manifold's intrinsic geometry. We introduce two novel metrics derived from EBMs and show that they produce geodesics that remain closer to the data manifold and exhibit lower curvature distortion, as measured by alignment with ground-truth trajectories. We evaluate our approach on increasingly complex datasets: synthetic datasets with known data density, rotated character images with interpretable geometry, and high-resolution natural images embedded in a pretrained VAE latent space. Our results show that EBM-derived metrics consistently outperform established baselines, especially in high-dimensional settings. Our work is the first to derive Riemannian metrics from EBMs, enabling data-aware geodesics and unlocking scalable, geometry-driven learning for generative modeling and simulation.

The metric backbone of a weighted graph is the union of all-pairs shortest paths. It is obtained by removing all edges $(u,v)$ that are not the shortest path between $u$ and $v$. In networks with well-separated communities, the metric backbone tends to preserve many inter-community edges, because these edges serve as bridges connecting two communities, but tends to delete many intra-community edges because the communities are dense. This suggests that the metric backbone would dilute or destroy the community structure of the network. However, this is not borne out by prior empirical work, which instead showed that the metric backbone of real networks preserves the community structure of the original network well. In this work, we analyze the metric backbone of a broad class of weighted random graphs with communities, and we formally prove the robustness of the community structure with respect to the deletion of all the edges that are not in the metric backbone. An empirical comparison of several graph sparsification techniques confirms our theoretical finding and shows that the metric backbone is an efficient sparsifier in the presence of communities.

In this paper, we present a novel learning framework for finding shortest paths in graphs utilizing Generative Flow Networks (GFlowNets). First, we examine theoretical properties of GFlowNets in non-acyclic environments in relation to shortest paths. We prove that, if the total flow is minimized, forward and backward policies traverse the environment graph exclusively along shortest paths between the initial and terminal states. Building on this result, we show that the pathfinding problem in an arbitrary graph can be solved by training a non-acyclic GFlowNet with flow regularization. We experimentally demonstrate the performance of our method in pathfinding in permutation environments and in solving Rubik's Cubes. For the latter problem, our approach shows competitive results with state-of-the-art machine learning approaches designed specifically for this task in terms of the solution length, while requiring smaller search budget at test-time.

Which transformer scaling regimes are able to perfectly solve different classes of algorithmic problems?