Graph Matching

Structure-mapping forms analogies by aligning systems of relationally connected elements based on shared structure instead of surface features. We introduce a new structure-mapping algorithm: Structure-Mapping with Tight Bounds (SMTB) that is 5--15x faster than the structure-mapping engine (SME) and about 50% better at finding mappings in large nested domains. SMTB is part of the broader Cognitive Rule Engine (CRE) project, a flexible multi-language-compatible framework with an accessible Python interface to state-of-the-art C++ implementations of core algorithms commonly used in cognitive systems such as pattern matching, planning, and structure-mapping. CRE and SMTB are designed to work with a wide range of representation choices. Unlike SME, which biases higher-order correspondences in tree-like predicate logic, SMTB maximizes relational connectivity without privileging higher-order relations. This allows SMTB to work just as well over arbitrary relational graphs as it does in tree-like domains of nested predicate logic. We discuss situations where privileging "higher-orderness" in structure-mapping can cause issues, and illustrate how SMTB avoids failure modes that SME would encounter in these situations. We also provide an evaluation comparing SMTB to SME v4 over 5845 domain pairs from the SME corpus.

Bayesian graph alignment estimates correspondence probabilities, but convergence of an alignment-score trace need not imply accurate correspondence marginals. We audit this gap on 240 new exact graph pairs from four source families, 240 larger pairs with 20-100 vertices, and a separate 60-case exact implementation check. Under an explicit edge-flip likelihood, we compare three samplers and score, marginal, indicator, categorical, and classifier-based diagnostics. Marginal disagreement improves error discrimination over score R-hat for the exact informed sampler, but its improvement for vanilla local sampling is uncertain. Assignment-based R* and short indicator panels are competitive; no diagnostic dominates across samplers and endpoints. At larger sizes, diagnostics predict subsequent marginal changes, not posterior error, and classification performance depends on the drift threshold. Disjoint-window and held-out-chain checks attenuate but preserve positive associations. Only 22 of 240 original reference sets pass an agreement screen. On forty failure-selected cases, eightfold SMC particle escalation does not resolve disagreement, whereas additional rejuvenation helps. Longer informed runs remain unstable. An elementary feasible-alignment bound demonstrates severely unrepresentative SMC and informed-chain scores in concentrated 100-vertex cases, independently of approximate reference consensus. We also exhibit common-start chains with near-zero disagreement despite exact marginal error near .967. These results support assignment-sensitive auditing while identifying limits of finite budgets, diagnostic rankings, and reference agreement as evidence of accuracy.

Recent advances in angiographic imaging have enabled longitudinal visualization of the microvasculature. Image processing pipelines based on vessel graphs are able to resolve subtle temporal changes at the level of individual blood vessels. However, current strategies for graph extraction, refinement, and matching are highly sensitive, with even minuscule differences in the underlying segmentation map resulting in substantially different vessel graphs. These artifacts severely inhibit the ability to accurately match sequential vessel graphs of the same subject over time. To address this problem, we propose a strategy that matches graphs before jointly refining them. Specifically, we perform an early matching after basic graph extraction before removing spurious bulges and merging junctions in both graphs using joint information. In experiments with complex retinal vessel graphs, we demonstrate that this strategy results in a higher matched area without graph fragmentation compared to separate or no refinement, respectively.

End-to-end Supervised Graph Prediction (SGP) requires a permutation-invariant loss to compare predicted and target graphs with arbitrary node orderings. Such losses typically involve a costly graph-matching problem. We first study three Optimal Transport relaxations of this problem and show, theoretically and empirically, that the Gromov-Wasserstein (GW) objective is the most suitable for SGP. Then, to avoid solving the resulting inner optimization for every training example, we propose to amortize the graph matching (node alignment) problem. For each training sample, the loss function leverages a transport plan provided by a parametric matcher based on the differentiable Sinkhorn algorithm applied on empirical node distributions. The graph prediction module and the matcher are jointly learned. We showcase the efficiency of this approach on toy and real world SGP problems of increasing complexity including a novel Mass-spectra to Scaffold task that we introduce.

We study unsupervised hypergraph alignment, where the goal is to infer node correspondences between two hypergraphs using only structural information, without node features, labels, seed matches, or side information. Direct higher-order formulations can represent hyperedge interactions faithfully, but they can be computationally demanding and cumbersome for non-uniform hypergraphs. Graph-reduction approaches introduce a different challenge: clique expansions keep the alignment problem on the original node set but collapse all hyperedge evidence into one pairwise graph, whereas bipartite expansions preserve incidence structure but enlarge the problem from nodes to nodes plus hyperedges. We introduce FALCON (Filtration-based hypergrAph aLignment via Cross-scale Optimal traNsport), an unsupervised optimal-transport framework for hypergraph alignment. Instead of representing each hypergraph by a single collapsed clique graph, FALCON constructs a filtration-induced sequence of clique-based co-occurrence dissimilarity matrices and jointly aligns all levels through one shared multi-scale Gromov--Wasserstein (GW) objective. The shared transport plan enforces a globally consistent node correspondence across filtration levels while avoiding the auxiliary hyperedge nodes introduced by bipartite expansion. Experiments on perturbation benchmarks derived from real-world hypergraphs show that FALCON is robust to structural noise and in almost all cases outperforms strong graph- and hypergraph-alignment baselines.

In many applications of matching, the point clouds to be matched are not merely unstructured sets of points but rather samples from distributions with an intrinsic cluster structure. In such cases, as individual points are often interchangeable within a coherent region, finding a robust region-to-region alignment is more desirable than establishing a precise point-to-point correspondence. To this end, we propose a novel approach for cluster-aware matching based on Laplacian Optimal Transport (LapOT). The key idea is to regularize the optimal transport problem with quadratic Laplacian terms constructed from similarity graphs of the point clouds, which encourages the optimal coupling to respect the cluster structure of both point sets. We also introduce Refined Simultaneous Clustering (RSC), a method that leverages the cluster-aware coupling obtained from LapOT to produce consistent partitions across the point sets, which can overcome the limitations of independent clustering and yield more stable and interpretable results. We demonstrate the effectiveness of our approach through theoretical analysis and empirical experiments, showing that LapOT indeed produces cluster-aware matching that leads to more consistent and meaningful alignments between point clouds.

Network alignment identifies node correspondences across different networks and is a fundamental primitive in many data science applications, including social network analysis, fraud detection, and knowledge graph integration. However, state-of-the-art network alignment methods often achieve high accuracy by repeatedly constructing and updating dense matrices, sacrificing scalability in the process. To address this scalability limitation without compromising alignment accuracy, we present FastAlign, a scalable, sparsity-aware framework for optimal transport-based network alignment. Rather than introducing a new alignment model, FastAlign preserves the original OT formulation and reinterprets its computation as a set of recurring mixed sparse-dense operations. FastAlign combines sparsity-aware graph computation with domain-specific kernel fusion, including a custom SpMM kernel. Our results show that FastAlign achieves alignment quality comparable to state-of-the-art OT-based methods while substantially reducing end-to-end runtime up to 3.89x-9.45x on CPU and 2.24x-32.54x on GPU.

We present IsalHG, a method for representing the structure of any finite, connected hypergraph of bounded hyperedge arity as a string over a compact instruction alphabet $Σ_{\mathrm{HG}}$. The encoding is executed by a small virtual machine comprising a sparse hypergraph, a circular doubly-linked list (CDLL) of node references, and $k$ traversal pointers, where $k$ bounds the hyperedge arity. Instructions either move a pointer through the CDLL or insert a hyperedge, optionally together with new nodes, into the hypergraph. Every string over $Σ_{\mathrm{HG}}$ decodes to a valid hypergraph; the alphabet is closed. A greedy \emph{HypergraphToString} (h2s) algorithm encodes any connected hypergraph into a string; a backtracking variant seeded at nodes of lexicographically maximal structural tuple produces a \emph{canonical string} $w^{*}$, which we conjecture to be a complete isomorphism invariant. Canonical-string equality then decides hypergraph isomorphism natively, without the standard reduction to the Levi incidence graph followed by a graph-isomorphism engine. We verify the round-trip property $s2h(h2s(H)) \cong H$ on 150 connected random uniform hypergraphs and on named combinatorial designs, and we benchmark the canonical algorithm against the three practically available exact baselines -- nauty, Traces, and bliss operating on the 2-coloured Levi graph -- across a $(n, c)$ grid with ten seeds per cell. All four methods agree on every one of 600 isomorphism verdicts, consistent with the completeness conjecture. On wall-clock time the Levi baselines dominate every tested cell by three to five orders of magnitude (geometric-mean ratio $311\times$ to $117{,}672\times$), which we report as measured. We contribute the representation framework, a conjecture of canonical completeness, and the first native-versus-Levi benchmark for hypergraph isomorphism.

This paper introduces Diffusion Semi-Relaxed Fused Gromov-Wasserstein (DsrFGW), a novel method for graph comparison that unifies node features and structural connectivity through optimal transport. While traditional Gromov-Wasserstein and semi-relaxed variants (srGW, srFGW) capture graph structure, they often struggle with sparse, noisy, or partially observed graphs. Inspired by Graph Diffusion Distance, which posits graphs are similar if they enable similar information transmission patterns, DsrFGW incorporates diffusion processes allowing information propagation across nodes, capturing local and global structural patterns while reducing sensitivity to noise or missing edges. An extensive evaluation on 36 synthetic pairwise graph matching tasks (easy, medium, hard) demonstrates consistent superiority over srFGW, achieving accuracy improvements of 0-20 percentage points and dramatic Adjusted Rand Index (ARI) gains: in medium-difficulty scenarios, srFGW often achieves negative ARI (worse than random) while DsrFGW offers better performance in terms of both internal and external clustering quality measures (i.e., Adjusted Rank Index and Accuracy with respect to the true underlying clusters, respectively). Even under severe noise, DsrFGW improves clustering quality in 92% of the synthetic tasks with optimal diffusion scales adapting to problem difficulty, establishing DsrFGW as a robust framework for graph comparison under structural uncertainty.

Large language models (LLMs) are often asked to produce JSON conforming to a fixed schema, powering information extraction, tool calling, agentic planning, and knowledge-graph construction. Measuring how closely an output matches a gold reference is essential yet surprisingly hard: exact match is brittle, text similarity ignores structure, and an LLM judge is expensive, opaque, and non-deterministic. We address this with Object Aligner (OA), an open-source Python library that scores two JSON objects deterministically by recursively aligning their trees (the Hungarian algorithm for unordered collections, sequence alignment for ordered ones) and awarding partial credit at the granularity the schema declares. The Object Aligner is configured entirely through a set of JSON Schema extensions, so adapting it to a new task involves annotating a schema rather than writing code. Complex structured data, however, are rarely flat trees: records may form graphs or hypergraphs keyed by arbitrary identifiers, breaking the assumptions of prior similarity metrics. Our central contribution, referential alignment, closes this gap by inferring a bijection between gold and candidate identifiers and scoring every reference through it, so the score is invariant to relabeling. Since recovering this bijection exactly is graph isomorphism, the Object Aligner approximates it with Weisfeiler-Leman color refinement. An order-sensitive sequence regime targets ranking and planning. Since the same alignment localizes every mismatch, the Object Aligner emits ranked repair suggestions at no extra cost. Used as a reward inside the GEPA prompt optimizer, Object Aligner helps or stays neutral across all datasets.

Merging multiple 3D Gaussian Splatting (3DGS) scenes into a single unified Gaussian representation is essential for large-scale 3D mapping and long-term map management. Despite its importance, this area remains underexplored, and existing solutions exhibit several limitations. Learning-based methods attempt direct correspondence between Gaussian primitives and require training on large 3DGS datasets. Image-based optimization methods depend heavily on coarse initialization from generic foundation models and often incur expensive refinement. We present \ourmodel. Our method constructs a 3D scene graph from a 3DGS and its rendered images, \textit{reformulating 3DGS registration as a graph registration problem}. The proposed 3D scene graph represents each 3DGS at a higher-level representation, enabling a globally consistent understanding of semantic information and structural context for accurate registration. To further construct a seamless unified scene, we introduce a Self-Supervised Test-Time Optimization. Naively merging two 3D Gaussian scenes often suffers from occlusion artifacts such as hollows and floaters. To alleviate this issue, we refine the merged Gaussians to preserve visual consistency between the original scenes and the merged scene. We evaluate our method on real and synthetic benchmarks, demonstrating competitive registration accuracy and merged scene rendering quality.

Online inspection images of final optics in high-power laser facilities contain pseudo-damage sites that closely resemble true damage sites. Determining the authenticity of online-detected sites is therefore difficult and requires accurate matching to offline ground-truth sites. However, this matching remains highly challenging due to limited match-discriminative features, local geometric distortions, and numerous distractor sites. Existing matching models mainly suppress distractors implicitly through loss-function supervision. We propose a confidence-feedback-weighted graph matching network that requires only damage-site centroid coordinates as input. It estimates node matchability confidence from each round of matching scores and feeds it back as a reliability weight to guide subsequent edge-feature aggregation, thereby suppressing distractor propagation and enhancing cross-graph discriminability. Within this framework, a geometric consistency constraint calibrates spurious high-confidence matchability estimates, while a hard-example mining loss improves discrimination between structurally similar sites. Experiments on our Complex-Scene dataset show that the proposed method achieves a matching F1-score of 96.36$\%$ with robust and efficient performance.

Spatial pattern matching is the process of matching query entities and constraints with database entities and relations. It has many applications, including similar region search, housing market search, landmark search, and road network matching. To our knowledge, all existing spatial pattern matching approaches frame the problem in a 2 dimensional space, where entities lie in a cartesian plane and relationships defined between them are contained in 2 dimensions. However, this problem framing has significant limitations when searching for real world entities that have height in addition to position. To address this limitation, we extend spatial pattern matching to 3 dimensions and provide a generalized definition of the problem. We describe a subgraph matching algorithm capable of resolving 3D spatial patterns over distance relations and release two 3D spatial pattern matching datasets, one synthetic and one containing real 3D building data from the city of Hamburg, Germany. We test our subgraph matching algorithm on both datasets and present results as a baseline for future methods to build upon.

Spectral filtering recently delivered substantial pruning for \emph{static} subgraph matching: Laplacian interlacing rejects candidates whose neighborhoods cannot host the query. We study whether such aggregate structural tests can accelerate \emph{continuous} subgraph matching (CSM) over dynamic graphs, and answer in three parts. First, lazily maintained spectral bounds are infeasible exactly where spectral pruning has value: we characterize the tightest safe rule over a formalized perturbation relaxation and show that even it loses essentially all pruning power within four touching updates. Second, exact maintenance is affordable when selective: pruning utility and recomputation cost are anti-correlated across vertices -- hubs provably never prune -- so recomputing small-neighborhood spectra on touch sustains exact local spectra at microseconds per update, complete by construction. Third, integrated into a decoupled CSM benchmark against an identical-minus-spectra control, the tests remove up to $51\%$ of candidates or safely skip up to $47\%$ of update enumerations, yet enumeration intermediates remain unchanged -- beyond the gates' skipped first-level bindings, typically zero -- across two engines, four real graphs, two stream types, and $77$ solved queries; a constructed radius-stratified workload confirms the instrument detects the exception when one exists ($-99.9\%$ intermediates, $748\times$ faster). Aggregate tests accelerate what scales with candidate sets -- construction, list scans -- never adjacency-guided exploration. We distill an intermediate-invariance methodology for evaluating CSM filters and release a reusable dynamic local-spectra index.

Medical image re-identification (MedReID) enables longitudinal patient linkage but remains vulnerable to shortcut learning and often produces decisions that clinicians cannot audit against named anatomy. We propose Graph-of-Differences (GoD), which grounds identity comparisons in explicit anatomical structure. Each image is represented as an anatomy graph whose nodes correspond to named anatomical regions; given an image pair, soft node correspondence is established, and differences are computed over matched anatomy. A graph-level difference alignment objective ties these anatomy-matched differences to the global backbone difference, ensuring the retrieval signal is anchored in homologous structures rather than arbitrary spatial tokens. Explanations are defined over named graph nodes and quantitatively audited via node insertion/deletion tests, replacing unstable pixel heatmaps with verifiable structure-level evidence. On internal benchmarks, GoD improves Rank-1 by +7.1 pp on fundus and +3.1 pp on CXR over a strong frozen-backbone baseline, with further gains on zero-shot external transfers confirming that anatomy grounding improves both accuracy and generalization. Code is available at https://github.com/GenMI-Lab/GoD.git.

We study the graph alignment problem for correlated Gaussian Orthogonal Ensemble (GOE) matrices, where the goal is to recover a hidden vertex permutation given two correlated symmetric Gaussian matrices $(A, B)$ with correlation $1/\sqrt{1+σ^2}$. While the maximum likelihood estimator is information-theoretically optimal, its computation, which reduces to a quadratic assignment problem, is intractable. Motivated by this, we analyze convex relaxations based on minimizing $\|AX - XB\|_F$ over the set of doubly stochastic matrices and the unit hypercube. We show that when the correlation parameter satisfies $σ= o(n^{-1/2}/\log^4 n)$, the solution of either relaxation $(X^\star)$ concentrates around the ground-truth permutation matrix $(Π^\star)$, i.e., $\|X^\star-Π^\star\|_F^2 = o(n)$, implying recovery of all but a vanishing fraction of vertices after simple post-processing. Combined with existing lower bounds, our results precisely characterize that $\|X^\star-Π^\star\|_F^2$ transitions from $o(n)$ for $σ= \tilde{o}(n^{-1/2})$ to $Ω(n)$ for $σ= \tildeΩ(n^{-1/2})$. In doing so, our analysis significantly tightens prior results and extends them beyond doubly stochastic relaxations.

Precise rover localization is a prerequisite for autonomous lunar exploration, yet the absence of Global Navigation Satellite System (GNSS) signals and the cumulative drift of local localization methods severely constrain long-range missions. Cross-view localization provides a promising drift-free global solution by matching rover-view and satellite-view imagery. However, the lunar environment poses unique challenges for correspondence alignment, including inter-entity entanglement, inter-viewpoint divergence, and simulation-to-real domain shift. To address these challenges, we propose Warped Alignment of Reprojected Graphs (WARG), a framework that leverages unified graph learning and reprojected graph matching for robust cross-view alignment. Pretrained on the synthetic LuSNAR dataset, WARG achieves an average test error of 0.32 m and demonstrates robust zero-shot generalization to the synthetic lunar south pole region with an error of 3.63 m. More importantly, when validated on real-world data from the YuTu-2 rover, WARG achieves a localization error of 1.68 m within a 100 m x 100 m search area, corresponding to nearly one-pixel precision in low-resolution satellite imagery with a spatial resolution of 1.40 m/pixel. Beyond accuracy, WARG is computationally efficient, containing only 1.56M parameters, corresponding to 16.12% of previous lightweight models, and operating at 5.49 Hz on an NVIDIA RTX A6000 GPU, approaching GNSS-level update frequency. Finally, we observe that WARG naturally develops low-level spatial awareness, including semantic segmentation and structural reasoning, through cross-view localization learning, highlighting its potential as a promising paradigm for spatial intelligence with minimal annotation cost. The source code is available at https://github.com/maochen-casia/warg.

Subgraph detection seeks to identify whether and where instances of query patterns occur within a larger graph. This problem is fundamental across scientific domains and is closely related to subgraph isomorphism, which is NP-complete, limiting combinatorial approaches to small patterns or moderately sized graphs. We introduce GraphDETR, a deep learning framework that formulates subgraph detection as a set prediction problem, analogous to DETR in object detection. GraphDETR encodes the target graph with a graph neural network, and employs a fixed set of learnable query vectors, decoded via a transformer decoder, to predict all pattern occurrences jointly in a single forward pass. This is enabled by training the model end-to-end with bipartite matching. Unlike traditional combinatorial methods that only solve exact structural matching, GraphDETR naturally extends to approximate matching, enabling detection beyond exact pattern correspondence. Empirically, we show that GraphDETR can detect diverse patterns, such as molecular structures, cycles, cliques, and fuzzy patterns of up to 50 nodes, in target graphs with up to 1000 nodes. We further evaluate on molecular functional group detection over the ChEMBL dataset, where GraphDETR predicts the complete set of functional groups per molecule, achieving a strong performance of $\text{AP}_{100} = 91.2$.

Graph Edit Distance (GED) is a fundamental, albeit NP-hard, metric for structural graph similarity. Recent neural graph matching architectures approximate GED by first encoding graphs with a Graph Neural Network (GNN) and then applying either a graph-level regression head or a matching-based alignment module. Despite substantial architectural progress, the role of encoder geometry in neural GED estimation remains poorly understood. In this paper, we develop a theoretical framework that connects encoder geometry to GED estimation quality for two broad classes of neural GED estimators: graph similarity predictors and alignment-based methods. On fixed graph collections, where the doubly-stochastic metric $d_{\mathrm{DS}}$ is comparable to GED, we show that graph-level bi-Lipschitz encoders yield controlled GED surrogates and improved ranking stability; for matching-based estimators, node-level bi-Lipschitz geometry propagates to encoder-induced alignment costs and the resulting optimized alignment objective. We instantiate this perspective using FSW-GNN, a bi-Lipschitz WL-equivalent encoder, as a drop-in replacement in representative neural GED architectures. Across representative baselines and benchmark datasets, the resulting geometry-aware variants significantly improve GED prediction and ranking metrics. A faithfulness case study of untrained encoders, together with ablations and transfer experiments, supports the view that these gains arise from improved representation geometry, positioning encoder geometry as a useful design principle for neural graph matching.

Accurate localization is a fundamental requirement for autonomous robots operating in indoor environments. Scene graphs encode the spatial structure of an environment as a hierarchy of semantic entities and their relationships, and can be constructed both online from robot sensor data and offline from architectural priors such as Building Information Models (BIM). Matching these two complementary representations enables drift correction in SLAM by grounding robot observations against a known structural prior. However, establishing reliable node-to-node correspondences between them remains an open challenge: existing combinatorial methods are prohibitively expensive at scale, and prior learned approaches address only flat graph matching, ignoring the multi-level semantic structure present in both representations. Here we present a learned, end-to-end differentiable pipeline that augments both graphs with semantically motivated edge types encoding intra- and inter- level relationships, explicitly exploiting this hierarchy to enable simultaneous matching from high-level room concepts down to low-level wall surfaces. Trained exclusively on floor plans, the proposed method outperforms the combinatorial baseline in F1 on real LiDAR environments while running an order of magnitude faster, demonstrating viable zero-shot generalization for BIM-assisted robot localization.

Graph-based representations such as Scene Graphs enable localization in structured indoor environments by matching a locally observed graph, constructed from sensor data, to a prior map. This process is particularly challenging in environments with repetitive or symmetric layouts, where structural cues alone are often insufficient to resolve ambiguities. We propose a semantic-enhanced graph matching approach that explicitly models relations between detected objects and structural elements, such as rooms and wall planes. Objects are detected from RGB-D data and integrated into the graph, and their relations to structural elements are exploited to filter candidate correspondences prior to geometric verification, significantly reducing ambiguity and search complexity. The proposed method is integrated within the iS-Graphs framework and evaluated in synthetic and simulated environments. Results show that semantic relations significantly reduce the number of candidate matches, improve computational efficiency, and enable faster convergence, particularly in symmetric scenarios where purely geometric approaches fail.

We propose a novel benchmarking methodology for graph neural networks (GNNs) based on the graph alignment problem, a combinatorial optimization task that generalizes graph isomorphism by aligning two unlabeled graphs to maximize overlapping edges. We frame this problem as a self-supervised learning task and present several methods to generate graph alignment datasets using synthetic random graphs and real-world graph datasets from multiple domains. For a given graph dataset, we generate a family of graph alignment datasets with increasing difficulty, allowing us to rank the performance of various architectures. Our experiments prove that there is an optimal task difficulty for having a statistically relevant ranking of different models and that, even on a structure-only task, anisotropic models perform better compared to isotropic ones. To further prove that our synthetic task capture meaningful information, we show its effectiveness for self-supervised GNN pre-training: the learned node embeddings can be leveraged as positional encodings by transformers for graph regression or can be used to reconstruct the full structure of the graph with $98\%$ accuracy. To support reproducibility and further research, we provide an open-source Python package to generate graph alignment datasets and benchmark new GNN architectures. The source code is available at https://github.com/adrien-lagesse/graph-alignment-benchmark.