Position Spaces and Graphs

There are several methods for searching for graphs with prescribed properties, such as SAT solvers and specialized generators. These methods return the result as raw data: an adjacency matrix or a string encoding. The raw data certifies that the graph exists, but it does not reveal any structural properties of the graph. We ask whether one can automatically discover a short algebraic description if only this raw data is provided. We look for a description such as a Cayley graph $\mathrm{Cay}(Γ, S)$ or a lexicographic product $C_5[K_3]$. We address this question with a neurosymbolic approach. We propose an agent that runs on a general-purpose large language model with no fine-tuning or per-target training. The model interleaves reasoning with calls to the computer algebra system SageMath: it analyzes the target graph, proposes and tests candidate constructions, and revises them until the output matches the target. The agent communicates with SageMath through a Model Context Protocol (MCP) server, which we release as a general-purpose bridge. Whether a construction matches the target is checked by a single exact isomorphism test, and therefore rests on the symbolic side and not on the model. We test the approach on a benchmark of 100 highly symmetric graphs, namely two-orbit graphs on up to 25 vertices; the benchmark was fixed in advance. Our agent could find verified algebraic constructions for all of them, without falling back to raw encodings. A strong template-enumeration baseline reaches only about $20\%$, and a catalog lookup could not identify any of these graphs. However, construction quality declines when symmetry is removed. As a concrete application, we identify the smallest known counterexample to the Bernhart-Kainen dispersability conjecture, a $16$-vertex graph that enumeration found as raw data. For this graph, our agent found an explicit algebraic construction.

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.

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.