Graph Theory

We study an optimal intervention problem for linear threshold models. This is a popular class of dynamical network systems whereby a number of agents, identified with the nodes of a graph, strategically change their binary action (0 or 1) according to a threshold rule. Specifically, an agent adopts action 1 if and only if the fraction of its neighbors in the interaction graph that do so is greater than or equal to a prescribed threshold. Assuming that a planner can modify the agents' thresholds at a cost equal to the aggregate threshold increase, we study the minimum intervention cost needed to ensure global convergence to the all-1 configuration. Our main contribution is the introduction of a new graph-theoretic quantity, called oriented path number, that is the minimum number of disjoint paths needed to cover the graph that can be oriented to form a directed acyclic graph. When thresholds are all equal to 1/2, the optimal cost is shown to coincide with the oriented path number, whereas, in the general case, it turns out to be the main ingredient of a bound on the optimal intervention cost.

Whitney's theorem allows isomorphism testing for connected simple graphs, apart from $K_3$ and $K_{1,3}$, to be formulated as distinguishing their line graphs. However, the relation between fixed-dimensional Weisfeiler--Leman (WL) expressivity on line graphs and on their roots remains unresolved. We study this relation through Implicit Line-Graph WL (ILG-$k$-WL), which is exactly $k$-WL on $L(G)$, executed over the edges of $G$ with line-graph relations derived from endpoint incidence and without explicitly constructing $L(G)$. On the Whitney-general class, the relation between root-domain and line-graph WL depends on $k$. For $k=1,2$, ILG-$k$-WL adds no distinguishing power beyond root-domain $1$-WL and misses some pairs that $1$-WL separates. For $k=3$, we prove the backward containment $L(G)\equiv_{3\text{-WL}}L(H)\Rightarrow G\equiv_{3\text{-WL}}H$. Strongly regular witness pairs, including the Shrikhande/rook pair, show that ILG-$3$-WL is strictly more expressive than $3$-WL. The backward containment also extends to disconnected graphs with no isolated vertices when every connected component is Whitney-general. Deterministic ILG-$3$-WL separates all three substructure-counting witness pairs, all $105$ pairs in SR25, and $359$ of $400$ BREC pairs. An untrained dense ILG-$3$-GNN gives the same pairwise verdicts on these evaluations.

Graph Neural Networks (GNNs) have achieved remarkable success across diverse applications, yet they remain highly vulnerable to adversarial attacks that maliciously perturb graph structure. Existing defenses often lack rigorous theoretical grounding, rely on attack-specific heuristics, or require costly retraining procedures such as adversarial training. To address these limitations, we propose Kernel-Complexity Edge Sanitization (KCES), a training-free and model-agnostic framework for defending against structural attacks. KCES is built upon Graph Kernel Complexity (GKC), a principled metric derived from the graph Gram matrix that appears in a generalization upper bound on the GNN test error. From this bound, we define an edge-specific KC score that quantifies each edge's structural influence via its induced change in GKC. KCES then identifies and prunes high-KC edges, which are empirically enriched with adversarial perturbations under structural attacks, to mitigate their harmful impact. Computationally efficient and scalable, KCES operates as a lightweight preprocessing step without retraining and can be seamlessly integrated with existing defenses. Extensive experiments demonstrate that KCES consistently outperforms representative robust baselines across diverse attack settings and scales effectively to large graphs. Supported by theoretical analysis and extensive empirical validation, KCES provides a principled and efficient framework for securing GNNs. Our code is available at https://github.com/karpning/KCScore.

Parameterised graph theory studies how the complexity of graph-theoretic problems depends on structural parameters of the input graph. This perspective has proved useful in analysing tensor-network simulation (Markov and Shi, 2008). Its implications for tensor-network representations and tomography are less well understood. In particular, which graph parameters determine whether a tensor-network state (TNS) admits a tractable matrix product state (MPS) or tree tensor network (TTN) representation, and which control the complexity of learning the state? We address these questions using parameterised graph theory. First, we show that cutwidth and tree-cutwidth bound the bond dimension overhead required to represent a TNS as an MPS or TTN. In the TTN case, tree-cutwidth also bounds the local dimension of the grouped subsystems. The proofs are based on entanglement rerouting, a tensor-network analogue of rerouting information in a classical network. Second, we derive graph-dependent upper bounds on the sample and computational complexity of realisable TNS tomography, with exponents that depend on cutwidth, tree-cutwidth, and a new graph parameter, learning complexity, which we bound in terms of degree and treewidth. We obtain these results by extending the disentangling MPS learner of (Cramer et al., 2010), as analysed further in (Bakshi et al., 2025; Lin et al., 2025), to TTNs and to tensor networks on arbitrary known graphs. Finally, we extend the framework beyond the realisable setting. For an arbitrary input state, our agnostic learner outputs a pure state whose fidelity is within additive error $ε$ of the optimum over tensor-network states on the given graph with a given bond dimension, with explicit graph-dependent bounds on sample and computational complexity.

In the one-time selling B2B context, the buying cycle may last months or even years. During the long process, targeting customers that have a high potential to make purchases and recommending personalized campaigns accordingly are important for effective marketing. For this goal, we study the following problems, B2B customer data aggregation, customer feature generation, and prediction of whether a B2B customer would show interest in making a purchase (i.e., prediction of conversion into sales funnel). We propose an algorithm to aggregate individual contacts to the B2B customer level based on multiple keys. For non-standardized keys such as company names, we propose a novel architecture to cluster them in a domain encompassing irregularities such as spelling mistakes and spelling variants. We then define and generate a set of features and apply the CatBoost model for customer conversion prediction. Our framework achieves 91% prediction accuracy. Based on the prediction results and analysis of the model, we then discuss personalized campaign recommendations to foster conversion.

Graph neural networks (GNN) based on message passing are provably no more powerful than the one-dimensional Weisfeiler--Leman colour-refinement test (1-WL): two graphs it cannot tell apart receive identical representations, however deep or wide the network. A common remedy augments node or edge features with precomputed structural descriptors, most often counts of a fixed small subgraph such as triangles or longer cycles, but such counts require committing in advance to the size of the substructure counted, a choice usually made blind to the data. We study a descriptor that avoids this choice. The edge-girth of an edge is the length of a shortest cycle through it, and its multiplicity is the number of such shortest cycles; together they form a per-edge invariant that reports cycles of arbitrary length, computable exactly by a single breadth-first search per edge. Injected into a gated message-passing architecture, EGAGNN, it reaches a test MAE a factor three below the closest gated comparator on the ZINC-12k regression benchmark at 104k parameters; against bounded cycle-counting descriptors under the same architecture, it matches only a dictionary counting cycles up to length eight, using twice as many channels, while a dictionary capped at length four performs no better than no structural information at all. On graph discrimination we prove a matching limitation: on graphs where every edge sees the same number of shortest cycles of the same length, the descriptor becomes constant and any model built on it collapses back to the 1-WL bound. This holds without exception across all 400 pairs of the BREC benchmark: not one of the 90 such pairs is distinguished.

Reliable uncertainty estimation is a crucial requirement for deploying large language models (LLMs) and vision-language models (VLMs) in safety-critical settings, especially when the model parameters are not accessible (black-box). We propose BiG-SURE, an uncertainty estimator based on cross-temperature semantic agreement. The method samples low-temperature responses as stable semantic anchors and high-temperature responses as probes under meaning-preserving input transformations. It then constructs an anchor-probe Bipartite Graph (BiG) using NLI-based entailment scores and defines confidence through the normalized squared spectral energy of this matrix, with uncertainty given by its complement. This bipartite graph-based Semantic Uncertainty and Reliability Estimation (SURE) score measures whether high-temperature probes remain semantically aligned with the model's stable low-temperature belief or not. We evaluate BiG-SURE on text QA, multilingual QA, and multimodal QA tasks across multiple model families. In these experiments, BiG-SURE improves average abstention AUROC over prior black-box uncertainty estimators, while remaining simple, unsupervised, and applicable to black-box model settings.

The purpose of this paper is to provide a general, comprehensive, theoretical framework that allows one to deal with fibrations on graphs labelled on a commutative monoid. This is a genuine extension of the theory of graph fibrations (as introduced in "Fibrations of Graphs" [Discrete Math., vol. 243, pp. 21-66, 2002]), that makes it possible to deal with weighted graphs, and also graphs labelled with other algebraic structures. The derived theory also lends itself naturally to consider approximate fibrations. As an example, we show how the derived theory can be applied to the reduction of weighted networks, providing a strong theoretical underpinning to recent empirical results.

The Zarankiewicz number Z(m,n,s,t) is the maximum number of edges in a bipartite graph with parts of orders m and n containing no copy of Ks,t. We give one combined, certificate-based computer-assisted proof for two finite slices and a corrected neighboring frontier: Z(12,n,3,3) = 6n (18 <= n <= 22), Z(13,22,3,3) = 137, Z(13, 18, 3, 3) = 116, Z(14, 18, 3, 3) = 124, Z(15,18,3,3) = 132, Z(14, 17, 3, 3) = 118, Z(15, 17, 3, 3) = 126, 132 <= Z(16,17,3,3) <= 133. The load-bearing new upper bounds are the exact 12 x 18 and 13 x 18 certificate packages. Their orbit certificates exclude every hypothetical matrix at the next edge count. Deletion lemmas and explicit witnesses close four neighboring cells, while the 16 x 17 entry is deliberately reported as an interval because only its 132-edge lower witness and the published 133 upper bound are certified here. Separately, the 13 x 22 proof excludes 138 ones by reducing to 83 degree profiles, rationally separating 77 of them, and eliminating the remaining six by marked-row congruences, leave enumeration, modular Gram tests, and exact Farkas certificates. All accepted claims are replayed by standard-library Python and exact integer/rational arithmetic; floating-point optimization is used only to discover certificates.

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.

The information flow in the graph neural networks (GNNs) is fundamentally constrained by over-squashing, where structural bottlenecks impede long range information propagation. Graph-rewiring methods, which modify graph topology, have been extensively used to alleviate this. However, existing approaches often introduce prohibitive structural and computational bottlenecks, fail to preserve the critical properties of original graphs, and increase the edge counts massively. We introduce a novel method Schreier-Coset Graph Rewiring , a group-theoretic rewiring method that augments the input graph with a Schreier-Coset graph derived from a special linear group. Our method provides theoretical guarantees, a graph that exhibits spectral gap and a bounded effective resistance, creating a low-resistance bypass for long-range communication. Empirical evaluations demonstrate that SCGR reduces effective resistance by 5-40% across various learning tasks, effectively mitigating connectivity bottlenecks while maintaining competitive accuracy.

Razborov's flag algebra method is a powerful tool for proving asymptotic inequalities in extremal graph theory, often reducing the task to finding a finite certificate by semidefinite programming. We present a machine-checked formalization of the method for finite simple graphs, together with a certificate-to-proof compiler that turns externally generated certificate data into algebraic proofs checked by Lean. The formalization covers the foundations of the method: partially labeled graphs, their densities in large graphs, the quotient algebra of density expressions, graph-limit semantics through positive homomorphisms, and the downward operators used to average out labels. The compiler treats the external semidefinite programming output as candidate data rather than trusted input: Lean independently computes the required density and multiplication facts, verifies positive semidefiniteness exactly over $\mathbb{Q}$, and carries out the algebraic normalization steps of flag-algebra proofs. Our case studies yield formal proofs of seven Turán-type upper bounds, including Mantel's theorem and the Erdős pentagon theorem, a $C_4$-density bound for triangle-free graphs, and edge-density bounds for $K_4$-free, $K_5$-free, and $C_5$-free graphs. Independently of the compiler, we formalize the matching constructions that complete the exact Turán densities of Mantel's theorem and the Erdős pentagon theorem, and prove two inequalities of Goodman. Our constrained semantics also prompted a meta-theoretic comparison of two ways of imposing graph constraints: building a hereditary constraint into the flag algebra from the start, or testing inequalities afterward on constrained graph limits with labels chosen at random. We state the resulting root-plantability criterion characterizing when the two approaches agree; a forthcoming paper will present the complete account.

Indoor robots are increasingly employed for facility management tasks such as cleaning and inspection. These applications primarily rely on navigation and can be effectively supported by predefined routes or perception-driven Simultaneous Localization and Mapping (SLAM) techniques. However, more complex tasks, such as locating and repairing leaking pipes, require not only navigation but also access to building information, including the location, geometry, material, and operational attributes of components. Existing navigation approaches provide only limited environmental understanding and cannot readily supply such information. In contrast, Building Information Modeling (BIM) contains rich geometric, semantic, and operational information that remains largely underutilized in robotic applications. This study proposes a BIM-enabled, agent-based simulation platform for knowledge-driven indoor robot navigation and operation planning. Within the framework, indoor environments are discretized into grid cells that are mapped to graph nodes and classified as target, obstacle, or regular nodes according to their spatial relationships with building elements. Traversal costs are assigned to edges connecting neighboring nodes, enabling graph-theoretic algorithms to compute efficient and collision-free navigation paths while avoiding obstacles. Simulation results demonstrate that the proposed graph representation enables efficient and collision-free navigation. A key limitation associated with coarse discretization, namely overlap between target-occupied and obstacle-occupied cells, is identified and mitigated through grid refinement, improving spatial accuracy and path feasibility. The proposed platform supports virtual evaluation of robotic operations prior to deployment and provides a foundation for BIM-informed robotic systems in facility management.

Motivated by real-world scenarios where malicious entities tamper with existing networks, we define a model where an adversary seeks to hide a set of \emph{corrupted vertices} inside a graph $G^*$. To this end, the adversary can add edges between the corrupted vertices, as well as edges between the corrupted vertices and $G^*$, and its power is then measured by the size of the \emph{neighborhood} of the corrupted vertices in $G^*$. Our goal is to design an active learning algorithm that efficiently finds the subset of corrupted vertices using a small number of label queries. We devise an efficient algorithm that approximately recovers the corrupted vertices with a query complexity that depends polynomially on both the power of the adversary and the \emph{vertex expansion} of $G^*$, a fundamental measure of graph connectivity. At the heart of this result is a polynomial-time algorithm, obtained by carefully adapting sum-of-squares algorithms for approximating minimum expansion, that finds a set with small vertex expansion subject to cardinality constraints. To the best of our knowledge, this is the first time that the vertex expansion is shown to play a key role in determining the query complexity of active learning algorithms robust to structural adversarial attacks.

Hierarchical Navigable Small World (HNSW) graphs serve as the industry standard due to their logarithmic complexity and strong empirical performance. However, HNSW relies on greedy graph traversal, a heuristic that provides no theoretical guarantees of correctness. In this paper, we propose a novel "Certify-then-Rectify" framework that bridges the gap between the speed of heuristic search and the rigor of exact retrieval. Rather than discarding HNSW, our approach first employs a distribution-free statistical certifier to dynamically evaluate the quality of a standard HNSW search with minimal overhead. If certification indicates that the retrieved neighbors are of low quality, the framework safely escalates to a rigorous exact recovery algorithm. To make this exact recovery computationally feasible, we reinterpret the HNSW graph as a geometric spanner and utilize Extreme Value Theory to stochastically estimate its maximum empirical stretch factor. This allows us to mathematically bound the maximum distance of true nearest neighbors. Extensive evaluations on benchmark datasets demonstrate that our tiered framework delivers the average-case speed of HNSW while ensuring the worst-case correctness of exact search and outperforming other applicable approaches.

We study a broad class of graphical models whose independencies correspond to vertex separation in mixed graphs with directed, undirected, and bidirected edges, that are capable of encoding independence structures arising from feedback, latent and selection mechanisms. In particular, we introduce separable graphs, in which each missing edge implies the existence of a separating set for its endpoints, and essentially separable graphs, those graphs separation equivalent to a separable graph. We show that these models include many existing graph families used to define graphical models an provide several characterizations of separable graphs and essentially separable graphs. We also provide multiple characterizations of separation equivalence for separable graphs. One is a graphical characterization in terms of ordinary graph properties, extending earlier results for specific subfamilies Another is a separational characterization depending only on graph separation properties. Finally, we provide a canonical representation for the equivalence classes of essentially separable graphs and develop an algorithm that, under suitable assumptions, identifies the equivalence class of any essentially separable graph.

Thin-structure segmentation--power lines, cracks, lane markings at 1-3 pixel width--requires preserving connectivity that standard representations preclude: patching severs continuous structures and conventional superpixels merge thin targets into background before classification. Topology-aware losses penalize connectivity breaks at the objective level but cannot recover what the representation has already destroyed. We propose SEMIR, a framework that replaces the pixel lattice with a parameterized graph minor whose contraction map preserves thin-structure connectivity under the contraction criterion. The minor collapses millions of pixels into tens or hundreds of boundary-aligned supernodes, enabling full-resolution inference without patching at scales demonstrated up to 21 MP in this paper; a lightweight GNN classifies the reduced graph and an exact map lifts predictions to pixel resolution. One pipeline--identical architecture, features, loss, and GNN hyperparameters across all dataset--matches or exceeds domain-specific baselines on TTPLA (power lines), CrackSeg9k (pavement cracks), and SkyScapes Lane (aerial markings) on Dice, IoU, and Boundary F1 while reducing mask fragmentation by at least 4.6x relative to SLIC at matched inference.

Verification of multi-agent systems requires the ability to check meticulous topological properties when it comes to agents that can move through space in continuous time. This demands a logic with sufficient expressiveness to capture these dynamics. MuTGL logic has interesting properties for expressing entangled space-time properties. However, this logic lacks the expressivity needed to analyse reachability within specific distance bounds, or to track the length or the cost of communication chains: these are fundamental for decentralized monitoring, or graph-theoretic analysis of distributed protocols, where algorithmic complexities often relates with the system's communication graph diameter. We then introduce an extension of muTGL, including a new operator called the space horizon. This addition allows us to bound the distance of communication chains, hence enhancing the logic's expressiveness. We show that this operator allows to encode modalities from other logics, such as reachability or escaping which were not available in vanilla muTGL, while allowing a deeper entanglement of spatial and temporal properties. We provide a centralized offline monitoring algorithm for this logic and illustrate it on several examples on simulations of Consensus-Based Bundle Algorithms, distributed protocols for task allocation.

Local search is a well-known heuristic method used in optimization. In this thesis, we explore its capabilities on the vertex coloring problem, an $NP$-hard problem with relevance in both theoretical analysis and practical application. To recognize limitations in the applicability of local search of the vertex coloring problem, we analyze local search landscapes on differently-structured bipartite graphs. We identify structures that ensure only global optima can exist as well as ones that enable the existence of non-global local optima, showing that on general bipartite graphs, it is possible for local search to return arbitrarily bad results. Further, we analyze the capabilities of local search on graphs where a local optimum can be found. To do so, we introduce a gray-box local search mutation operator that removes less frequent colors with higher probability and prove that it finds an optimal coloring on complete bipartite graphs in an expected run time of $Θ(n \log n)$. This is a drastic improvement to the exponential tun time of the black-box Random Local Search, showing that gray-box mutation operators can improve the run time of local search.

Gray-box optimization is an approach for making some problem-specific information available to the algorithm while still relying on fitness information as the main guide to an optimum. This approach was shown to be beneficial in various combinatorial optimization tasks and neatly captures the continuum between fully black-box algorithms and tailored algorithms. In this work, we discuss different flavors of gray-box algorithms. We show that RLS can find a proper $2$-coloring in a bipartite graph starting from a random $2$-coloring, in an expected time of $\mathcal{O}(n \log n)$. In contrast, when starting from a proper $n$-coloring, the (1+1) EA cannot find such a coloring except when offered additional guiding on plateaus of the search space. Finally, we show the run time for this setting can be much improved by using gray-box operators.

Large language models (LLMs) are increasingly used as self-study assistants in technical disciplines, yet their reliability as mathematical reasoning assistants remains poorly understood. We introduce GTBench, a curriculum-grounded benchmark for evaluating LLMs as mathematical research assistants in graph theory, comprising 63 problems organized into three groups of increasing difficulty: undergraduate definitions and basic properties (Group 1), algorithm tracing and structural reasoning (Group 2), and graduate-level proof construction (Group 3). Problems are sourced from verified academic materials including Diestel's Graph Theory. We evaluate five frontier models -- GPT-5, Claude Sonnet 4.6, Gemini 2.5 Flash-Lite, Llama 3.3 70B, and Mistral Large 3 -- under zero-shot and chain-of-thought prompting, using exact-match and LLM-as-judge evaluation for Groups 1 and 2, and a hybrid human expert and LLM-as-judge protocol for Group 3. Our results reveal a pronounced performance hierarchy: GPT-5 approaches ceiling on Group 1 (95.8% zero-shot) and maintains meaningful accuracy on graduate proofs (82%), while all other models degrade substantially with difficulty, with Llama achieving 0% under human evaluation on Group 3 zero-shot. Failure mode analysis shows that correct algorithm, wrong execution errors dominate Groups 1 and 2, while Group 3 additionally surfaces incomplete reasoning failures and reveals systematic disagreement between human evaluators and the automated judge, particularly on verbose or near-complete proofs (kappa = 0.48-0.83 across human pairs). GTBench provides the first curriculum-grounded evaluation framework for graph-theoretic reasoning in LLMs, with direct implications for the governance of AI tools in mathematical education and scientific research.

This work investigates theoretically the interplay between interpolation and aggregation in regression. We establish that the $γ$-graph dimension characterizes learnability for a broad class of natural aggregation procedures. Furthermore, we prove that an extremely simple aggregation procedure, combining three interpolating hypotheses via the median, is optimal among all these aggregation procedures, and is strictly more powerful than proper learning. Finally, we show that some hypothesis classes are learnable only by aggregating infinitely many hypotheses or by using non-interpolating aggregation rules (which may predict outside the range of their inputs), and any finite interpolating aggregation fails to achieve even trivial performance.

Exploiting the indistinguishability of objects in a probabilistic graphical model such as a factor graph is key to lifted probabilistic inference algorithms and allows for tractable probabilistic inference problems with respect to domain sizes. A central building block for the exploitation of indistinguishable objects in factor graphs is the identification of commutative factors, i.e., factors whose output values are invariant under permutations of input values assigned to a subset of their arguments. In this paper, we revisit the theoretical foundations underlying the state-of-the-art algorithm to detect commutative factors. Specifically, we show that in its current form, the state-of-the-art algorithm relies on a central theorem that is mistakenly regarded as a sufficient condition to identify commutative factors, while it actually only implies necessary condition. Consequently, the state of the art might, as we show in this paper, deliver incorrect results. To fix the flaws currently present in the state of the art, we prove a slightly modified version of the aforementioned theorem, which serves as a necessary condition to identify commutative factors. Moreover, we present a corrected version of the state-of-the-art algorithm, which keeps its efficiency while ensuring correctness and introduce a complementary algorithm with tighter worst-case bounds.

Graphs with a simple spectrum admit cubic-time isomorphism testing, yet we prove that for every natural number $k$, the $k$-Weisfeiler-Leman ($k$-WL) test cannot distinguish all non-isomorphic graphs with a simple spectrum. As the WL hierarchy upper-bounds the distinguishing power of widely-used Graph Neural Networks (GNNs), this incompleteness applies to all such GNNs, ruling out completeness for every $k$-WL-aligned GNN family. To close this gap, we introduce PRiSM (Partition, Refine, Solve, Match), the first provably complete canonicalization of simple-spectrum eigendecompositions. PRiSM obtains the completeness guarantee that prior canonicalizations provably lack, and resolves the open problem of achieving complete expressivity on simple-spectrum graphs. When composed with DeepSets or a Transformer, PRiSM achieves universal approximation on simple-spectrum graphs, justifying the use of canonicalized Laplacian positional encodings. Empirically, PRiSM performs comparably to or outperforms existing spectral canonicalizations on graph regression, classification, and expressivity

We study the contradiction graphs associated with binary concept classes. For a class $H \subseteq \{0,1\}^X$, the order-$m$ contradiction graph $G_m(H)$ has as vertices the $H$-realizable labeled sequences of length $m$, with two vertices adjacent when the two sequences assign opposite labels to some common domain point. Our main result is that the single graph $G_m(H)$ determines the threshold predicate $\mathrm{VCdim}(H)\ge m$. Consequently, the full sequence $(G_m(H))_{m \ge 1}$ determines the exact VC dimension and, in particular, detects finite versus infinite VC dimension, answering a question posed by Alon et al. (2024).

For minimally rigid graphs, the same edge-length data can admit multiple realizations (up to translations and rotations). Finding graphs with exceptionally many realizations is an extremal problem in rigidity theory, but exhaustive search quickly becomes infeasible due to the super-exponential growth of the number of candidate graphs and the high cost of realization-count evaluation. We propose a reinforcement-learning approach that constructs minimally rigid graphs via 0- and 1-extensions, also known as Henneberg moves. We optimize realization-count invariants using the Deep Cross-Entropy Method with a policy parameterized by a Graph Isomorphism Network encoder and a permutation-equivariant extension-level action head. Empirically, our method matches the known optima for planar realization counts and improves the best known bounds for spherical realization counts, yielding new record graphs.

Graph Anomaly Detection (GAD) is a critical task in graph machine learning with vital applications in financial fraud detection and social platform governance. However, existing GAD benchmarks are often restricted to small-scale, curated graphs with relatively balanced anomaly ratios, leaving a substantial gap between academic evaluation and real-world deployment. To bridge this gap, we present a multi-dimensional benchmark that systematically evaluates GAD models under three deployment-relevant challenges: million-scale graphs, extreme anomaly scarcity, and missing node attributes. We derive a family of controlled benchmark variants from five diverse graphs, including two native industrial-scale datasets with over 3.7 million nodes. Our extensive evaluation of nine representative GAD models reveals three major limitations: (1) most GNN-based methods fail to scale to million-node graphs due to prohibitive memory requirements; (2) detection performance drops sharply under realistic anomaly ratios (e.g., 0.1%), often resulting in zero recall; and (3) reconstruction-based models are highly sensitive to attribute imputation strategies. Our findings suggest that strong performance in laboratory settings does not guarantee robustness in production environments. We release this benchmark and empirical evaluation as a diagnostic testbed to promote the development of robust and scalable GAD systems for large-scale, imperfect graphs encountered in practice. Code is available at https://anonymous.4open.science/r/Benchmark_GAD-E7A3.

Progress on graph foundation models is hindered by benchmark practices that conflate the contributions of node features and graph structure, making it hard to tell whether a model actually learns from connectivity, or whether it even needs to. We propose addressing this using graph invariants, i.e., permutation-invariant, task-agnostic structural descriptors that serve as a diagnostic framework for graph benchmarks. We show that (i) invariants are more expressive than standard GNNs, (ii) invariants characterize structural heterogeneity within and across benchmark datasets, (iii) invariants predict multi-task performance, and (iv) simple invariant-based models are competitive with, and sometimes exceed, transformer and message-passing baselines across 26 datasets. Our results suggest that expressivity is not the main driver of predictive performance, and that on tasks where structure matters, a non-trainable structural proxy often matches trained message-passing models. We thus posit that invariant baselines should become a standard for evaluating whether structure is required for a task and whether a model picks up on it, serving as a stepping stone towards graph foundation models.

The Weisfeiler--Lehman (WL) test and its simplicial extension (SWL) characterize the combinatorial expressivity of message passing networks, but they are blind to geometry, i.e., meshes with identical connectivity but different embeddings are indistinguishable. We introduce the Geometric Simplicial Weisfeiler--Lehman (GSWL) test, which incorporates vertex coordinates into color refinement for geometric simplicial complexes. In addition, we show that (i) the expressivity of geometry-aware simplicial message passing schemes is bounded above by GSWL, and (ii) that there exist parameters such that the discriminating power of GSWL is matched by these schemes on any fixed finite family of geometric simplicial complexes. Combined with the Euler Characteristic Transform (ECT), a complete invariant for geometric simplicial complexes, this yields a geometric expressivity characterization together with an approximation framework. Experiments on synthetic and mesh datasets serve to validate our theory, showing a clear hierarchy from combinatorial to geometry-aware models.

Understanding how biological and artificial neural networks implement computation from connectivity is a central problem in neuroscience and machine learning. In neural systems, structural and functional connectivity are known to diverge, motivating approaches that move beyond direct connections alone. Here, we show that the spatial and temporal function of recurrent neural networks (RNNs) trained on hierarchically modular tasks can be recovered by modelling the network as a graph and analysing the multi-hop pathways between input and output units. In particular, decomposing these pathways by hop length reveals how the network temporally routes information. This perspective reframes regularisation: if function is implemented through multi-hop communication, then standard penalties such as L1 regularisation, which act only on individual weights, constrain single-hop structure rather than the multi-hop pathways that support computation. Motivated by this view, we introduce resolvent-RNNs (R-RNNs), which constrain multi-hop pathways and thereby induce temporal sparsity beyond that achieved by standard L1 regularisation. Compared with L1 regularisation, R-RNNs achieve improved performance by inducing temporal sparsity that matches the task structure, even when the task signal is sparse. Moreover, R-RNNs exhibit stronger sparsity-function alignment, reflected in their increased robustness under strong regularisation. Together, our results identify multi-hop communication as a key principle linking structure to function in recurrent networks, and suggest that sparsity should be defined over functional pathways rather than individual parameters.

Recommender systems are essential components of modern online platforms which presents personalized content in various domain. The traditional collaborative filtering methods depends on static user-item interaction graphs and a limited subset of similarity measures which fail to capture the changing nature of preferences of an individual. Recent graph neural network (GNN) based approaches focus on user-item bipartite graphs which do not use explicit user-user relational modelling and dynamic graph evolution during training. To address these limitations, this paper proposes a Dynamic Graph SimilarityAware Attention Graph Neural Network (DG-SA-GNN) framework that integrates dynamic user similarity graph construction with multi-similarity propagation and attention-based aggregation. The proposed architecture constructs four parallel user similarity graphs using Cosine, Jaccard, Discounted Pearson Correlation Coefficient (Discount PCC), and IPIJ similarity functions, each processed by a dedicated UserGNN module. A Graph Transformer fuses the four graph views, and a CrossAttention module refines user embeddings through interaction with item embeddings. Crucially, the graphs are reconstructed at scheduled epochs during training, enabling the model to adapt to the learned embedding space constituting the dynamic graph component. Mini-batch training with hard negative sampling improves scalability and convergence. Experiments on the MovieLens100K benchmark demonstrate that DG-SA-GNN achieves a Recall@20 of 0.162 and NDCG@20 of 0.065 which is better than the LightGCN baseline in recall. The results validate that dynamic multi-similarity graph construction coupled with attention-based fusion which produce recommendation performance

The Zarankiewicz number $\textbf{Z}(m, n, s, t)$ is the maximum number of edges in a bipartite graph $G_{m, n}$ such that there is no complete $K_{s, t}$ bipartite subgraph. We determine for the first time the exact values of three Zarankiewicz numbers: $\textbf{Z}(11, 21, 3, 3)=116$, $\textbf{Z}(11, 22, 3, 3)=121$, and $\textbf{Z}(12, 22, 3, 3)=132$. We further establish lower bounds for 41 more Zarankiewicz numbers, including several that are within one edge of the best known upper bound, and we match the established value in four more closed cases. Our results are obtained using OpenEvolve, an open-source evolutionary algorithm based on Large Language Models (LLMs) that iteratively improves algorithms for generating mathematical constructions by optimizing a reward signal which we tailored for this specific problem. These findings provide new extremal graph constructions and demonstrate the potential of LLM-guided evolutionary search to contribute to mathematical research. In addition to presenting the resulting constructions, we report the generation algorithms produced, describe the relevant implementation details, and provide our computational costs. Our costs are remarkably low, at less than $30 for each Zarankiewicz parameter combination, showing that LLM-guided evolutionary search can be an inexpensive, reproducible, and accessible tool for discovering new combinatorial constructions.

We present \textit{CluProp}, a novel framework that reimagines varied-density clustering in high-dimensional spaces as a label propagation process over neighborhood graphs. Our approach formally bridges the gap between density-based clustering and graph connectivity, leveraging efficient propagation mechanisms from network science to mitigate the parameter sensitivity inherent in traditional density-based methods. Specifically, we introduce a deterministic density-based propagation strategy to ensure scalable neighborhood identification. The framework is agnostic to the choice of distance metric and exhibits superior performance on large-scale data, processing millions of points in minutes while consistently outperforming existing baselines in accuracy.

This paper proposes a novel algorithm for semisupervised learning. This algorithm learns graph cuts that maximize the margin with respect to the labels induced by the harmonic function solution. We motivate the approach, compare it to existing work, and prove a bound on its generalization error. The quality of our solutions is evaluated on a synthetic problem and three UCI ML repository datasets. In most cases, we outperform manifold regularization of support vector machines, which is a state-of-the-art approach to semi-supervised max-margin learning.

This book presents a comprehensive and systematic survey of graph theory under uncertainty, with particular emphasis on the unifying role of the uncertain graph framework. It reviews fundamental concepts, structural properties, graph classes, and graph parameters within fuzzy, neutrosophic, and related models, while also introducing a wide range of extensions such as uncertain digraphs, hypergraphs, superhypergraphs, and dynamic graphs. In addition to theoretical developments, the book explores practical applications, including uncertain molecular graphs, decision-making systems, graph neural networks, knowledge graphs, and cognitive maps. By organizing diverse uncertainty-aware graph models within a common perspective, this work provides a coherent framework for understanding their relationships, capabilities, and applications in complex systems.

Ramsey-good graphs are graphs that contain neither a clique of size $s$ nor an independent set of size $t$. We study doubly saturated Ramsey-good graphs, defined as Ramsey-good graphs in which the addition or removal of any edge necessarily creates an $s$-clique or a $t$-independent set. We present a method combining SAT solving with bespoke LLM-generated code to discover infinite families of such graphs, answering a question of Grinstead and Roberts from 1982. In addition, we use LLMs to generate and formalize correctness proofs in Lean. This case study highlights the potential of integrating automated reasoning, large language models, and formal verification to accelerate mathematical discovery. We argue that such tool-driven workflows will play an increasingly central role in experimental mathematics.

We define an information-complexity property for aggregation functions, capturing a vast range of practical aggregations, and prove that any Message-Passing Graph Neural Network (MP-GNN) model with such aggregations induces only a polynomial number of equivalence classes on all graphs - while the number of non-isomorphic graphs is super-exponential (in number of vertices). Adding a familiar perspective, we observe that merely 2 iterations of Color Refinement (CR) induce at least an exponential number of equivalence classes, making the aforementioned MP-GNNs relatively infinitely weaker. Previous studies state that sum-aggregation MP-GNNs match full CR however they consider a weak, 'non-uniform', notion of distinguishing-power where each graph size may require a different MP-GNN to distinguish graphs up to that size. Our results concern both distinguishing between non-equivariant vertices and distinguishing between non-isomorphic graphs.

Estimating causal quantities traditionally relies on bespoke estimators tailored to specific assumptions. Recently proposed Causal Foundation Models (CFMs) promise a more unified approach by amortising causal discovery and inference in a single step. However, in their current state, they do not allow for the incorporation of any domain knowledge, which can lead to suboptimal predictions. We bridge this gap by introducing methods to condition CFMs on causal information, such as the causal graph or more readily available ancestral information. When access to complete causal graph information is too strict a requirement, our approach also effectively leverages partial causal information. We systematically evaluate conditioning strategies and find that injecting learnable biases into the attention mechanism, together with a graph-convolutional encoder, is a highly effective method to utilise full and partial causal information. Our experiments show that this conditioning allows a general-purpose CFM to match the performance of specialised models trained on specific causal structures. Overall, our approach addresses a central hurdle on the path towards all-in-one causal foundation models: the capability to answer causal queries in a data-driven manner while effectively leveraging any amount of domain expertise.

Predictive machine learning models generally excel on in-distribution data, but their performance degrades on out-of-distribution (OOD) inputs. Reliable deployment therefore requires robust OOD detection, yet this is particularly challenging for irregular 3D graphs that combine continuous geometry with categorical identities and are unordered by construction. Here, we present a probabilistic OOD detection framework for complex 3D graph data built on a diffusion model that learns a density of the training distribution in a fully unsupervised manner. A key ingredient we introduce is a unified continuous diffusion over both 3D coordinates and discrete features: categorical identities are embedded in a continuous space and trained with cross-entropy, while the corresponding diffusion score is obtained analytically via posterior-mean interpolation from predicted class probabilities. This yields a single self-consistent probability-flow ODE (PF-ODE) that produces per-sample log-likelihoods, providing a principled typicality score for distribution shift. We validate the approach on protein-ligand complexes and construct strict OOD datasets by withholding entire protein families from training. PF-ODE likelihoods identify held-out families as OOD and correlate strongly with prediction errors of an independent binding-affinity model (GEMS), enabling a priori reliability estimates on new complexes. Beyond scalar likelihoods, we show that multi-scale PF-ODE trajectory statistics - including path tortuosity, flow stiffness, and vector-field instability - provide complementary OOD information. Modeling the joint distribution of these trajectory features yields a practical, high-sensitivity detector that improves separation over likelihood-only baselines, offering a label-free OOD quantification workflow for geometric deep learning.

Inspired by graph-based methodologies, we introduce a novel graph-spanning algorithm designed to identify changes in both offline and online data across low to high dimensions. This versatile approach is applicable to Euclidean and graph-structured data with unknown distributions, while maintaining control over error probabilities. Theoretically, we demonstrate that the algorithm achieves high detection power when the magnitude of the change surpasses the lower bound of the minimax separation rate, which scales on the order of $\sqrt{nd}$. Our method outperforms other techniques in terms of accuracy for both Gaussian and non-Gaussian data. Notably, it maintains strong detection power even with small observation windows, making it particularly effective for online environments where timely and precise change detection is critical.

We study the propagation of outliers in cyclic causal graphs with linear structural equations, tracing them back to one or several "root cause" nodes. We show that it is possible to identify a short list of potential root causes provided that the perturbation is sufficiently strong and propagates according to the same structural equations as in the normal mode. This shortlist consists of the true root causes together with those of its parents lying on a cycle with the root cause. Notably, our method does not require prior knowledge of the causal graph and yields encouraging results on simulated data and real data from biology and cloud computing.

We study the problem of restricting a Markov equivalence class of maximal ancestral graphs (MAGs) to only those MAGs that contain certain edge marks, which we refer to as expert or orientation knowledge. Such a restriction of the Markov equivalence class can be uniquely represented by a restricted essential ancestral graph. Our contributions are several-fold. First, we prove certain properties for the entire Markov equivalence class including a conjecture from Ali et al. (2009). Second, we present several new sound graphical orientation rules for adding orientation knowledge to an essential ancestral graph. We also show that some orientation rules of Zhang (2008b) are not needed for restricting the Markov equivalence class with orientation knowledge. Third, we provide an algorithm for including this orientation knowledge and show that in certain settings the output of our algorithm is a restricted essential ancestral graph. Finally, outside of the specified settings, we provide an algorithm for checking whether a graph is a restricted essential graph and discuss its runtime. This work can be seen as a generalization of Meek (1995) to settings which allow for latent confounding.