Graph Positional Encoding

Directed graphs naturally model many real-world systems in which interactions are asymmetric, such as citation networks, web graphs, and information-flow networks. However, graph learning methods commonly rely on message passing with symmetrized graph representations or positional encodings that only partially exploit edge directionality. We introduce PathLapPE, a novel spectral positional encoding (PE) derived from the path Laplacian on directed graphs. PathLapPE provides node- and edge-level features that encode directional higher-order structure and can be incorporated into standard graph learning architectures. Empirical results on node- and graph-level benchmark tasks show that PathLapPE yields consistent improvements across several architectures, especially when combined with direction-aware message passing. Compared with magnetic Laplacian positional encodings, a widely studied spectral positional encoding for directed graphs, PathLapPE does not require additional fine-tuning of directionality hyperparameters while offering competitive runtime and performance.

Many real-world systems exhibit higher-order interactions among groups of entities that cannot be captured by pairwise relationships alone. Graph Transformers and Graph Neural Networks increasingly rely on positional encodings to enrich graph representations, yet existing positional encodings are computed solely from the original graph and therefore cannot directly capture observed higher-order interactions. Topological Deep Learning addresses this limitation by lifting graphs to simplicial complexes, but typically requires performing message passing or attention on higher-order neural network representations. We introduce a representation learning paradigm that enriches graph representations with higher-order topology through positional encodings, enabling standard graph learning models to exploit lifted incidence structure without modifying the backbone. We derive a theoretical characterization of the expressivity of higher-order positional encodings, proving that node-level operators induced by higher-order lifts can mix graph Laplacian frequencies in ways that scalar graph spectral filters cannot. Guided by this theory, we instantiate higher-order positional encodings using Hodge Laplacians derived from clique complexes. Experiments with Graph Transformers on ZINC and controlled synthetic benchmarks demonstrate improvements in predictive performance, while a fixed-1-skeleton experiment shows that the pipeline can transmit higher-order information when cells are supplied independently of the graph. Together, our results establish higher-order positional encodings as a principled bridge between graph positional encodings and topological deep learning.

Cross-structural motion retargeting aims to transfer motion between different skeletal topologies. Despite recent progress, existing state-of-the-art models struggle with reliability in zero-shot settings, i.e. skeletons with different topologies which were unseen during training, and recent Transformer-based attempts have failed to outperform specialized geometric methods. We bridge this gap with a Transformer Autoencoder that learns a topology- and translation-invariant latent space. Our core contribution is a learnable flattening of skeletal graphs that captures both local dependencies and global structure. Unlike the standard transformer architecture, which adds positional information to token content, we integrate graph-based positional encodings multiplicatively, a design choice that follows directly from our flattening formulation. The resulting model handles diverse skeletal topologies within a single unified architecture and trains in a fully unsupervised manner, requiring no paired retargeting data. Ablation studies show, that the graph encodings, multiplicative formulation, and Transformer backbone is critical for the performance. In zero-shot evaluations, our method reduces global joint position error by $43-47\%$ over current benchmarks. A user study ($n = 37$), including expert animators, further ranks our approach highest in motion alignment and physical plausibility ($p < 0.05$). These results demonstrate that our model design is key to making transformer architectures effective for motion retargeting, outperforming existing approaches.

Rotary position encodings make attention sensitive to relative position, but extending them to graphs requires choosing how graph structure enters the rotation. Previous works assign each node a rotation from spectral coordinates, so the rotary factor between two nodes depends only on their endpoints and cannot distinguish the routes connecting them. We introduce Analytic-Walk Rotary Positional Encodings (AW-RoPE), which place the rotations on edges and sum the transported features over all walks, so contributions along different routes can reinforce or cancel. An exact variant evaluates the complete sum by a differentiable linear solve, and a sparse variant truncates it at a finite depth. We prove forward and parameter-derivative truncation bounds at fixed inputs and parameters. Both variants act on projected queries and keys, and the sparse recurrence also augments message-passing networks. Across five synthetic tasks both variants reduce nRMSE by $15$--$58\%$ relative to the strongest baseline, and on real superpixel, peptide and OGB benchmarks the sparse recurrence attains the best mean on every dataset with Performer kernels and on twelve of thirteen datasets with GIN. Analysis shows that AW-RoPE can distinguish routes whose only cue is how two endpoints are connected, while node-wise rotary encodings cannot.

Graph positional encodings are widely used in graph neural networks and graph Transformers, yet it remains unclear when the code itself can identify nodes. We study a hybrid distance-spectral encoding that combines anchor-distance profiles with quantized low-frequency Laplacian-energy coordinates. Treating the encoding as an observation map yields a simplex-refined converse, an exact collision factorization $κ_H=κ_Dκ_{S|D}$, and the collision information $I_H=-\logκ_D-\logκ_{S|D}$. On random regular graphs, the criterion is made explicit through a bounded-correlation Gaussian-wave surrogate; for actual Laplacian-energy coordinates, we give the distance-conditioned spectral collision condition sufficient for conditional actual-coordinate achievability. Experiments show that $I_H/\log n$ calibrates localization success, and PE-only structural task probes on Universal Dependencies trees show that hybrid encodings better recover syntactic-tree geometry than distance-only or spectral-only baselines.

Link prediction aims to identify potential or future connections within a given graph structure. Position information is essential for link prediction, as it distinguishes homogeneous nodes through their relative relationships, facilitating the accurate capture of structural patterns and implicit connections. Previous studies derive node positional information as distances to single-granularity landmarks, defined as the centers of homophilic regions, while neglecting the multi-granularity nature of homophilic structures and their hierarchical interrelations. We propose the Multi-Granularity Position Embedding of Graphs via Granular-Ball for Link Prediction (MGLP) method to obtain multi-granularity position embedding of graphs. Specifically, MGLP introduces an Adaptive Granular-Ball Graph Refinement mechanism to adaptively refine the graph into homophilic subdomains with optimal levels of granularity. The central nodes within subdomains are treated as landmarks, which form a Hierarchical Central Graph. Moreover, a novel Multi-granularity Hierarchical Distance encoding mechanism is proposed to capture both the homophilic structures within a graph and their hierarchical correlations, improving the discriminative power of nodes. Experimental results demonstrate that the multi-granularity position embedding generated by our method exhibits excellent performance and strong competitiveness compared to baseline algorithms for link prediction. Our codes are available in https://anonymous.4open.science/r/MGLP-D3C5/.

Spectral positional encodings (PEs) for directed graphs face two obstacles: magnetic Laplacians require an $O(n^3)$ Hermitian eigendecomposition per potential, and their complex eigenvectors are defined only up to unitary gauge, which prior work handles with basis-invariant architectures. We propose learnable spectral PEs of the form $h_θ(A_q)\,R$, where $A_q$ is a normalized magnetic operator, $h_θ$ a learnable scalar spectral response, and $R$ a block of random probes. Because the PE is a matrix function of the operator, it is gauge-invariant by construction. We compute it in a Hermitian block Krylov subspace from sparse matrix--vector products only, prove that $k = O(\log(1/\varepsilon))$ block steps suffice uniformly over heat--resolvent response families, and give a covering-number argument for why low-dimensional structured families generalize where free per-eigenvalue weights overfit. On a directed SBM whose symmetrization is uninformative by construction, direction-blind PEs stay at chance while magnetic Krylov PEs converge to the exact-eigendecomposition oracle as the depth grows. The same probes yield gauge-invariant pairwise features with $1/\sqrt{s}$ Monte-Carlo error, and the undirected $q{=}0$ case improves heterophilous benchmarks over no-PE and polynomial baselines.

Positional encodings (PEs) are essential for Transformers. Yet designing effective PEs for non-Euclidean graphs remains challenging. Such encodings should ideally induce an Attention-Compatible Geometry for self-attention: not merely describing graph structure, but defining a geometry whose inner products reflect meaningful structural relatedness. To realize this geometry, we propose Communicability-Inspired Positional Encoding (CIPE), built from communicability, a measure between pairs of nodes that aggregates contributions from paths of all lengths. By construction, CIPE inner products recover communicability, converting global multi-path connectivity into an attention-ready similarity geometry. For practical Transformer training, we introduce dimensionality alignment, mapping graph-size-dependent CIPE representations to prescribed dimensions while faithfully preserving the induced geometry. Empirically, CIPE improves structure-agnostic Transformers by 35.5% on average across seven benchmarks, outperforming representative PEs; it also consistently improves structure-biased graph Transformers, where competing PEs often yield only marginal benefits. These results position CIPE as a principled framework for attention-compatible graph positional encodings.

Positional encodings (PEs) enhance the power of graph neural networks (GNNs), both theoretically and empirically. Two of the most popular families of PEs - spectral (e.g., Laplacian eigenspaces, effective resistance) and walk-based (polynomials of the adjacency matrix) - are theoretically equivalent in expressive power, with expressivity between the 1-WL and 3-WL tests. However, this equivalence assumes the GNN uses the "complete" version of these PEs, which requires $O(n^3)$ time and space complexity. Instead, practitioners commonly use truncated variants of these encodings, such as the first $k$ eigenspaces or powers of the adjacency matrix. However, the theoretical properties of these truncated PEs are unknown. In this work, we initiate the study of these truncated PEs. Theoretically, we show that, under truncation, several families of PEs are fundamentally different in expressive power. As a corollary, we show that truncated spectral PEs are no longer stronger than the 1-WL test. We also study a family of spectral PEs, the $k$-harmonic distances, to highlight the differences in expressive power of even closely related truncated PEs. Finally, we experimentally show that a mix of truncated PEs is preferable to any single family on real-world datasets.

Graph foundation models (GFMs) aim to reuse a single backbone across diverse graph domains, yet their transfer is often uneven and can exhibit negative transfer. While most prior work improves transfer through architectural or adaptation choices, we ask a data-centric question: which properties of two graph domains determine how much a fixed representation model changes its outputs? Using a graphon-based continuous limit for dense graphs, we show that for both set-based and message-passing tokenizations, any Lipschitz backbone admits an explicit decomposition of cross-domain output shift into (i) graph-specific finite-sample approximation terms and (ii) an intrinsic, relabeling-invariant domain discrepancy capturing structural mismatch. A key ingredient is positional-encoding (PE) stability: we establish stability guarantees for spectral PEs and highlight contrasting behaviors of eigenvector- versus subspace-based PEs. Experiments on synthetic and real graphs validate the theory and translate the decomposition into guidance for data curation in GFM transfer.

Graph convolutional networks (GCNs) are widely used for 3D hand pose estimation, where the hand skeleton is encoded as a fixed adjacency graph. We revisit whether this is the most effective way to incorporate hand topology in 2D-to-3D lifting. In this paper, we perform controlled, parameter-matched ablations on the FPHA benchmark and show that standard multi-head self-attention consistently outperforms GCN baselines. Even when the GCN is strengthened with multi-hop adjacency and matched parameter count, self-attention reduces MPJPE from 12.36 mm to 10.09 mm. A skeleton-constrained graph attention network recovers most of this gap, indicating that input-dependent aggregation is a major source of improvement, while fully connected attention yields additional gains. We further show that hand topology is most effective when introduced as a soft structural prior through graph-distance positional encoding, rather than as a hard adjacency constraint. These results suggest that, for hand pose lifting, adaptive spatial attention is a more effective inductive bias than fixed graph convolution.

Transformer-based models have become the dominant paradigm for neural combinatorial optimization (NCO) of vehicle routing problems (VRPs), yet the role of positional encoding (PE) in these architectures remains largely unexplored. Unlike natural language, where tokens are uniformly spaced on a line, routing solutions exhibit several properties that render standard NLP positional encodings inadequate. In this work, we formalize three such structural properties that a routing-aware PE should respect, namely anisometric node distances, cyclic and direction-aware topology, and hierarchical depot-anchored global multi-route structure, combining them with a unifying design principle of geometric grounding. Guided by these criteria, we analyze and compare PE methods spanning NLP, graph-transformer, and routing-specific families, and propose a hierarchical anisometric PE that combines a distance-indexed, circularly consistent in-route encoding with a depot-anchored angular cross-route encoding. Extensive experiments across diverse VRP variants demonstrate that geometry-grounded PE consistently outperforms index-based alternatives, with gains that transfer across problem variants, model architectures, and distribution shifts.

Transformers have achieved remarkable success across domains, motivating the rise of Graph Transformers (GTs) as attention-based architectures for graph-structured data. A key design choice in GTs is the use of Graph Neural Network (GNN)-based positional encodings to incorporate structural information. In this work, we study GTs through the lens of manifold limit models for graph sequences and establish a theoretical connection between GTs with GNN positional encodings and Manifold Neural Networks (MNNs). Building on transferability results for GNNs under manifold convergence, we show that GTs inherit transferability guarantees from their positional encodings. In particular, GTs trained on small graphs provably generalize to larger graphs under mild assumptions. We complement our theory with extensive experiments on standard graph benchmarks, demonstrating that GTs exhibit scalable behavior on par with GNNs. To further show the efficiency in a real-world scenario, we implement GTs for shortest path distance estimation over terrains to better illustrate the efficiency of the transferable GTs. Our results provide new insights into the understanding of GTs and suggest practical directions for efficient training of GTs in large-scale settings.

We study the extent to which rotary position encodings (RoPE), a recent transformer position encoding algorithm broadly adopted in large language models (LLMs) and vision transformers (ViTs), can be applied to graph-structured data. We find that rotating tokens depending on the spectrum of the graph Laplacian efficiently injects structural information into the attention mechanism, boosting performance in synthetic and real-world graph learning tasks. This approach, coined Wave-Induced Rotary Encodings (WIRE), enjoys intriguing theoretical properties: it recovers regular RoPE on grids, and depends asymptotically on the graph effective resistance. Unlike bias-based relative position encodings, WIRE is compatible with linear attention.

We study the challenging problem for inference tasks on large-scale graph datasets of Graph Neural Networks: huge time and memory consumption, and try to overcome it by reducing reliance on graph structure. Even though distilling graph knowledge to student MLP is an excellent idea, it faces two major problems of positional information loss and low generalization. To solve the problems, we propose a new three-stage multitask distillation framework. In detail, we use Positional Encoding to capture positional information. Also, we introduce Neural Heat Kernels responsible for graph data processing in GNN and utilize hidden layer outputs matching for better performance of student MLP's hidden layers. To the best of our knowledge, it is the first work to include hidden layer distillation for student MLP on graphs and to combine graph Positional Encoding with MLP. We test its performance and robustness with several settings and draw the conclusion that our work can outperform well with good stability. Code implementation is in https://github.com/lijunxian111/KMP.