Daily Papers

Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a complete hierarchy of SWL with strictly growing expressivity. Concretely, we prove that any node-based subgraph GNN falls into one of the six SWL equivalence classes, among which SSWL achieves the maximal expressive power. We also study how these equivalence classes differ in terms of their practical expressiveness such as encoding graph distance and biconnectivity. Furthermore, we give a tight expressivity upper bound of all SWL algorithms by establishing a close relation with localized versions of WL and Folklore WL (FWL) tests. Our results provide insights into the power of existing subgraph GNNs, guide the design of new architectures, and point out their limitations by revealing an inherent gap with the 2-FWL test. Finally, experiments demonstrate that SSWL-inspired subgraph GNNs can significantly outperform prior architectures on multiple benchmarks despite great simplicity.

Seminal research in the field of graph neural networks (GNNs) has revealed a direct correspondence between the expressive capabilities of GNNs and the k-dimensional Weisfeiler-Leman (kWL) test, a widely-recognized method for verifying graph isomorphism. This connection has reignited interest in comprehending the specific graph properties effectively distinguishable by the kWL test. A central focus of research in this field revolves around determining the least dimensionality k, for which kWL can discern graphs with different number of occurrences of a pattern graph P. We refer to such a least k as the WL-dimension of this pattern counting problem. This inquiry traditionally delves into two distinct counting problems related to patterns: subgraph counting and induced subgraph counting. Intriguingly, despite their initial appearance as separate challenges with seemingly divergent approaches, both of these problems are interconnected components of a more comprehensive problem: "graph motif parameters". In this paper, we provide a precise characterization of the WL-dimension of labeled graph motif parameters. As specific instances of this result, we obtain characterizations of the WL-dimension of the subgraph counting and induced subgraph counting problem for every labeled pattern P. We additionally demonstrate that in cases where the kWL test distinguishes between graphs with varying occurrences of a pattern P, the exact number of occurrences of P can be computed uniformly using only local information of the last layer of a corresponding GNN. We finally delve into the challenge of recognizing the WL-dimension of various graph parameters. We give a polynomial time algorithm for determining the WL-dimension of the subgraph counting problem for given pattern P, answering an open question from previous work.

Combinatorial complexes have unified set-based (e.g., graphs, hypergraphs) and part-whole (e.g., simplicial, cellular complexes) structures into a common topological framework. Existing topological neural networks and Weisfeiler-Lehman variants remain fragmented, lacking a unified theoretical foundation for topological deep learning. In this work, we introduce the Combinatorial Complex Weisfeiler-Lehman (CCWL) test, an axiomatic-style extension of the WL test to combinatorial complexes. CCWL formalizes topological message passing through four types of neighborhood relation and provides a unified perspective on the expressive power of higher-order variants. We further prove that upper and lower neighborhoods are sufficient among the four adjacent WL tests to reach the expressivity of the full CCWL framework across topological structures of combinatorial complexes. Building on this framework, we also propose the Combinatorial Complex Isomorphism Network (CCIN) and evaluate it on synthetic and real-world benchmarks. Experimental results indicate CCIN outperforms baseline methods and offers a generalized expressive framework for topological deep learning.

Graph Neural Networks (GNN) are inherently limited in their expressive power. Recent seminal works (Xu et al., 2019; Morris et al., 2019b) introduced the Weisfeiler-Lehman (WL) hierarchy as a measure of expressive power. Although this hierarchy has propelled significant advances in GNN analysis and architecture developments, it suffers from several significant limitations. These include a complex definition that lacks direct guidance for model improvement and a WL hierarchy that is too coarse to study current GNNs. This paper introduces an alternative expressive power hierarchy based on the ability of GNNs to calculate equivariant polynomials of a certain degree. As a first step, we provide a full characterization of all equivariant graph polynomials by introducing a concrete basis, significantly generalizing previous results. Each basis element corresponds to a specific multi-graph, and its computation over some graph data input corresponds to a tensor contraction problem. Second, we propose algorithmic tools for evaluating the expressiveness of GNNs using tensor contraction sequences, and calculate the expressive power of popular GNNs. Finally, we enhance the expressivity of common GNN architectures by adding polynomial features or additional operations / aggregations inspired by our theory. These enhanced GNNs demonstrate state-of-the-art results in experiments across multiple graph learning benchmarks.

The expressive power of Graph Neural Networks (GNNs) has been studied extensively through the Weisfeiler-Leman (WL) graph isomorphism test. However, standard GNNs and the WL framework are inapplicable for geometric graphs embedded in Euclidean space, such as biomolecules, materials, and other physical systems. In this work, we propose a geometric version of the WL test (GWL) for discriminating geometric graphs while respecting the underlying physical symmetries: permutations, rotation, reflection, and translation. We use GWL to characterise the expressive power of geometric GNNs that are invariant or equivariant to physical symmetries in terms of distinguishing geometric graphs. GWL unpacks how key design choices influence geometric GNN expressivity: (1) Invariant layers have limited expressivity as they cannot distinguish one-hop identical geometric graphs; (2) Equivariant layers distinguish a larger class of graphs by propagating geometric information beyond local neighbourhoods; (3) Higher order tensors and scalarisation enable maximally powerful geometric GNNs; and (4) GWL's discrimination-based perspective is equivalent to universal approximation. Synthetic experiments supplementing our results are available at https://github.com/chaitjo/geometric-gnn-dojo

Formulating optimization problems for industrial applications demands significant manual effort and domain expertise. While Large Language Models (LLMs) show promise in automating this process, evaluating their performance remains difficult due to the absence of robust metrics. Existing solver-based approaches often face inconsistency, infeasibility issues, and high computational costs. To address these issues, we propose ORGEval, a graph-theoretic evaluation framework for assessing LLMs' capabilities in formulating linear and mixed-integer linear programs. ORGEval represents optimization models as graphs, reducing equivalence detection to graph isomorphism testing. We identify and prove a sufficient condition, when the tested graphs are symmetric decomposable (SD), under which the Weisfeiler-Lehman (WL) test is guaranteed to correctly detect isomorphism. Building on this, ORGEval integrates a tailored variant of the WL-test with an SD detection algorithm to evaluate model equivalence. By focusing on structural equivalence rather than instance-level configurations, ORGEval is robust to numerical variations. Experimental results show that our method can successfully detect model equivalence and produce 100\% consistent results across random parameter configurations, while significantly outperforming solver-based methods in runtime, especially on difficult problems. Leveraging ORGEval, we construct the Bench4Opt dataset and benchmark state-of-the-art LLMs on optimization modeling. Our results reveal that although optimization modeling remains challenging for all LLMs, DeepSeek-V3 and Claude-Opus-4 achieve the highest accuracies under direct prompting, outperforming even leading reasoning models.

It has been shown that a message passing neural networks (MPNNs), a popular family of neural networks for graph-structured data, are at most as expressive as the first-order Weisfeiler-Leman (1-WL) graph isomorphism test, which has motivated the development of more expressive architectures. In this work, we analyze if the limited expressiveness is actually a limiting factor for MPNNs and other WL-based models in standard graph datasets. Interestingly, we find that the expressiveness of WL is sufficient to identify almost all graphs in most datasets. Moreover, we find that the classification accuracy upper bounds are often close to 100\%. Furthermore, we find that simple WL-based neural networks and several MPNNs can be fitted to several datasets. In sum, we conclude that the performance of WL/MPNNs is not limited by their expressiveness in practice.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

Relational pooling is a framework for building more expressive and permutation-invariant graph neural networks. However, there is limited understanding of the exact enhancement in the expressivity of RP and its connection with the Weisfeiler Lehman hierarchy. Starting from RP, we propose to explicitly assign labels to nodes as additional features to improve expressive power of message passing neural networks. The method is then extended to higher dimensional WL, leading to a novel k,l-WL algorithm, a more general framework than k-WL. Theoretically, we analyze the expressivity of k,l-WL with respect to k and l and unifies it with a great number of subgraph GNNs. Complexity reduction methods are also systematically discussed to build powerful and practical k,l-GNN instances. We theoretically and experimentally prove that our method is universally compatible and capable of improving the expressivity of any base GNN model. Our k,l-GNNs achieve superior performance on many synthetic and real-world datasets, which verifies the effectiveness of our framework.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

How might one test the hypothesis that networks were sampled from the same distribution? Here, we compare two statistical tests that use subgraph counts to address this question. The first uses the empirical subgraph densities themselves as estimates of those of the underlying distribution. The second test uses a new approach that converts these subgraph densities into estimates of the graph cumulants of the distribution (without any increase in computational complexity). We demonstrate -- via theory, simulation, and application to real data -- the superior statistical power of using graph cumulants. In summary, when analyzing data using subgraph/motif densities, we suggest using the corresponding graph cumulants instead.

Formal theorem proving, a field at the intersection of mathematics and computer science, has seen renewed interest with advancements in large language models (LLMs). This paper introduces SubgoalXL, a novel approach that synergizes subgoal-based proofs with expert learning to enhance LLMs' capabilities in formal theorem proving within the Isabelle environment. SubgoalXL addresses two critical challenges: the scarcity of specialized mathematics and theorem-proving data, and the need for improved multi-step reasoning abilities in LLMs. By optimizing data efficiency and employing subgoal-level supervision, SubgoalXL extracts richer information from limited human-generated proofs. The framework integrates subgoal-oriented proof strategies with an expert learning system, iteratively refining formal statement, proof, and subgoal generators. Leveraging the Isabelle environment's advantages in subgoal-based proofs, SubgoalXL achieves a new state-of-the-art performance of 56.1\% in Isabelle on the standard miniF2F dataset, marking an absolute improvement of 4.9\%. Notably, SubgoalXL successfully solves 41 AMC12, 9 AIME, and 3 IMO problems from miniF2F. These results underscore the effectiveness of maximizing limited data utility and employing targeted guidance for complex reasoning in formal theorem proving, contributing to the ongoing advancement of AI reasoning capabilities. The implementation is available at https://github.com/zhaoxlpku/SubgoalXL.

Graph neural networks (GNNs) are a powerful architecture for tackling graph learning tasks, yet have been shown to be oblivious to eminent substructures such as cycles. We present TOGL, a novel layer that incorporates global topological information of a graph using persistent homology. TOGL can be easily integrated into any type of GNN and is strictly more expressive (in terms the Weisfeiler--Lehman graph isomorphism test) than message-passing GNNs. Augmenting GNNs with TOGL leads to improved predictive performance for graph and node classification tasks, both on synthetic data sets, which can be classified by humans using their topology but not by ordinary GNNs, and on real-world data.

Recently, many works studied the expressive power of graph neural networks (GNNs) by linking it to the 1-dimensional Weisfeiler--Leman algorithm (1-WL). Here, the 1-WL is a well-studied heuristic for the graph isomorphism problem, which iteratively colors or partitions a graph's vertex set. While this connection has led to significant advances in understanding and enhancing GNNs' expressive power, it does not provide insights into their generalization performance, i.e., their ability to make meaningful predictions beyond the training set. In this paper, we study GNNs' generalization ability through the lens of Vapnik--Chervonenkis (VC) dimension theory in two settings, focusing on graph-level predictions. First, when no upper bound on the graphs' order is known, we show that the bitlength of GNNs' weights tightly bounds their VC dimension. Further, we derive an upper bound for GNNs' VC dimension using the number of colors produced by the 1-WL. Secondly, when an upper bound on the graphs' order is known, we show a tight connection between the number of graphs distinguishable by the 1-WL and GNNs' VC dimension. Our empirical study confirms the validity of our theoretical findings.

Graph neural networks (GNNs) have recently become the standard approach for learning with graph-structured data. Prior work has shed light into their potential, but also their limitations. Unfortunately, it was shown that standard GNNs are limited in their expressive power. These models are no more powerful than the 1-dimensional Weisfeiler-Leman (1-WL) algorithm in terms of distinguishing non-isomorphic graphs. In this paper, we propose Path Neural Networks (PathNNs), a model that updates node representations by aggregating paths emanating from nodes. We derive three different variants of the PathNN model that aggregate single shortest paths, all shortest paths and all simple paths of length up to K. We prove that two of these variants are strictly more powerful than the 1-WL algorithm, and we experimentally validate our theoretical results. We find that PathNNs can distinguish pairs of non-isomorphic graphs that are indistinguishable by 1-WL, while our most expressive PathNN variant can even distinguish between 3-WL indistinguishable graphs. The different PathNN variants are also evaluated on graph classification and graph regression datasets, where in most cases, they outperform the baseline methods.

The problems of detecting and recovering planted structures/subgraphs in Erdős-Rényi random graphs, have received significant attention over the past three decades, leading to many exciting results and mathematical techniques. However, prior work has largely focused on specific ad hoc planted structures and inferential settings, while a general theory has remained elusive. In this paper, we bridge this gap by investigating the detection of an arbitrary planted subgraph Γ= Γ_n in an Erdős-Rényi random graph G(n, q_n), where the edge probability within Γ is p_n. We examine both the statistical and computational aspects of this problem and establish the following results. In the dense regime, where the edge probabilities p_n and q_n are fixed, we tightly characterize the information-theoretic and computational thresholds for detecting Γ, and provide conditions under which a computational-statistical gap arises. Most notably, these thresholds depend on Γ only through its number of edges, maximum degree, and maximum subgraph density. Our lower and upper bounds are general and apply to any value of p_n and q_n as functions of n. Accordingly, we also analyze the sparse regime where q_n = Θ(n^{-α}) and p_n-q_n =Θ(q_n), with αin[0,2], as well as the critical regime where p_n=1-o(1) and q_n = Θ(n^{-α}), both of which have been widely studied, for specific choices of Γ. For these regimes, we show that our bounds are tight for all planted subgraphs investigated in the literature thus farand many more. Finally, we identify conditions under which detection undergoes sharp phase transition, where the boundaries at which algorithms succeed or fail shift abruptly as a function of q_n.

When does an LLM controller outperform rule-based traversal for knowledge graph exploration? We study this question through RLM-on-KG, a retrieval system that treats an LLM as an autonomous navigator over an RDF-encoded mention graph for grounded question answering. Unlike GraphRAG pipelines that rely on offline LLM indexing, RLM-on-KG performs entity-first, multi-hop exploration at query time using deterministic graph construction and a fixed tool set. Our central finding is a conditional advantage: the value of LLM control depends on evidence scatter and tool-calling sophistication. The paper's core claim is LLM control versus heuristic traversal, not a generic win over GraphRAG. On GraphRAG-Bench Novel (519 questions), Gemini 2.0 Flash achieves +2.47 pp F1 over a rule-based heuristic baseline (p < 0.0001), but only +0.16 pp over a GraphRAG-local variant (not significant). With a stronger controller, Claude Haiku 4.5, the gain over heuristic grows to +4.37 pp (p < 0.001) and extends to a +2.42 pp significant improvement over GraphRAG-local (p < 0.001). The gain is largest when gold evidence is scattered across 6-10 chunks (+3.21 pp) and smallest for concentrated evidence (+1.85 pp). Cross-scale validation on MuSiQue confirms that the LLM-over-heuristic advantage transfers, with expected attenuation on smaller per-question graphs. The core architectural insight is the separation of candidate discovery from ranking: the LLM adds value through exploration breadth, while final evidence selection is best handled by pure vector re-ranking. Beyond retrieval, exploration traces provide a proposed stress-test harness for structured data quality, yielding diagnostics for coverage, connectivity, provenance, and queryability.

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.

Automating formal proofs of combinatorial identities is challenging for LLM-based provers, as long-horizon proof planning is required and unconstrained search quickly explodes. Symbolic methods such as the Wilf-Zeilberger (WZ) method can achieve a mechanized proof of combinatorial identities by constructing special auxiliary functions and demonstrating that they satisfy specific recurrence relations. We propose WZ-LLM, a neuro-symbolic framework that turns WZ proof plans into executable proof sketches in Lean 4 and uses an LLM-based prover to discharge the resulting machine-checkable subgoals. We also train a dedicated WZ-Prover via a Lean-kernel-verified bootstrapping loop with expert-verified iteration, followed by DAPO-based refinement. Experiments show that WZ-LLM achieves a 34% proof success rate on LCI-Test (100 classic combinatorial identities), outperforming strong baselines such as DeepSeek-V3 and Goedel-Prover-V2, and delivering consistent gains on CombiBench and PutnamBench-Comb. These results indicate that our framework provides two complementary strengths: improved direct proving for identities beyond the scope of WZ, and substantially higher end-to-end success when WZ sketches guide a specialized prover.

Money laundering detection faces challenges due to excessive false positives and inadequate adaptation to sophisticated multi-stage schemes that exploit modern financial networks. Graph analytics and AI are promising tools, but they struggle with the fuzziness of laundering patterns, which exhibit structural and temporal variations. Conventional data mining techniques require the detailed enumeration of pattern variants, which not only complicates the analyst's task to specify them, but also leads to large run-time overheads and difficulty training accurate AI models. The paper presents BlazingAML, a scalable AML system design that introduces: 1. A novel multi-stage framework for expressing fuzzy money laundering patterns 2. A domain-specific compiler that transforms high-level pattern descriptions into high-performance code for CPU and GPU back-ends The multi-stage abstraction decomposes complex laundering schemes into logical stages connected by graph operations, enabling diverse patterns to be expressed using unified primitives while capturing structural and temporal fuzziness. The compiler applies sophisticated optimizations, eliminating manual parallel programming requirements for financial analysts. Evaluation on IBM AML datasets shows BlazingAML achieves the same F1 score as state-of-the-art approaches while delivering 210x and 333x higher speedup on CPU and GPU respectively, with superior scalability.

Subgraph representation learning is a technique for analyzing local structures (or shapes) within complex networks. Enabled by recent developments in scalable Graph Neural Networks (GNNs), this approach encodes relational information at a subgroup level (multiple connected nodes) rather than at a node level of abstraction. We posit that certain domain applications, such as anti-money laundering (AML), are inherently subgraph problems and mainstream graph techniques have been operating at a suboptimal level of abstraction. This is due in part to the scarcity of annotated datasets of real-world size and complexity, as well as the lack of software tools for managing subgraph GNN workflows at scale. To enable work in fundamental algorithms as well as domain applications in AML and beyond, we introduce Elliptic2, a large graph dataset containing 122K labeled subgraphs of Bitcoin clusters within a background graph consisting of 49M node clusters and 196M edge transactions. The dataset provides subgraphs known to be linked to illicit activity for learning the set of "shapes" that money laundering exhibits in cryptocurrency and accurately classifying new criminal activity. Along with the dataset we share our graph techniques, software tooling, promising early experimental results, and new domain insights already gleaned from this approach. Taken together, we find immediate practical value in this approach and the potential for a new standard in anti-money laundering and forensic analytics in cryptocurrencies and other financial networks.

Multi-hop reasoning over financial disclosures is often a retrieval problem before it becomes a reasoning or generation problem: relevant facts are dispersed across sections, filings, companies, and years, and LLMs often expend excessive tokens navigating noisy context. Without precise Knowledge Graph (KG)-guided selection of relevant context, even strong reasoning models either fail to answer or consume excessive tokens, whereas KG-linked evidence enables models to focus their reasoning on composing already retrieved facts. We present FinReflectKG - MultiHop, a benchmark built on FinReflectKG, a temporally indexed financial KG that links audited triples to source chunks from S&P 100 filings (2022-2024). Mining frequent 2-3 hop subgraph patterns across sectors (via GICS taxonomy), we generate financial analyst style questions with exact supporting evidence from the KG. A two-phase pipeline first creates QA pairs via pattern-specific prompts, followed by a multi-criteria quality control evaluation to ensure QA validity. We then evaluate three controlled retrieval scenarios: (S1) precise KG-linked paths; (S2) text-only page windows centered on relevant text spans; and (S3) relevant page windows with randomizations and distractors. Across both reasoning and non-reasoning models, KG-guided precise retrieval yields substantial gains on the FinReflectKG - MultiHop QA benchmark dataset, boosting correctness scores by approximately 24 percent while reducing token utilization by approximately 84.5 percent compared to the page window setting, which reflects the traditional vector retrieval paradigm. Spanning intra-document, inter-year, and cross-company scopes, our work underscores the pivotal role of knowledge graphs in efficiently connecting evidence for multi-hop financial QA. We also release a curated subset of the benchmark (555 QA Pairs) to catalyze further research.

The Large Language Model from Power Law Decoder Representations (PLDR-LLM) and its attention, Power Law Graph Attention (PLGA), replace the fixed bilinear form of scaled dot-product attention (SDPA) with a learned, input-generated bilinear operator G_{LM}, built from a positive tensor A_{LM} by elementwise power laws. The architecture is fully specified, verified against pinned reference releases; claims are labeled theorem, conditional theorem, measurement, or conjecture. Unconditionally: PLGA contains SDPA exactly at G_{LM}=I; A_{LM} and A_P are strictly entrywise positive, with Perron-Frobenius structure on A_{LM}; the DAG regularizer has the NOTEARS walk-counting form and positivity obstructs exact acyclicity; and, under nonresonance (satisfied by standard rotary frequencies), a commutant criterion identifies which operators preserve relative-position dependence. An inference-collapse theorem: exact input invariance of deductive outputs collapses inference to generalized SDPA with a constant operator. Measured invariance: relative fluctuations of 10^{-6} and below; perturbation bounds quantify but do not certify cached inference; the assembled proxy misses the decoding margin. A conditional three-stage mechanism (rotary twirl, concentration, row-map contraction) is measured on a released checkpoint. Blockwise training and scoring under the global Gram are stated with explicit target exposure; on tested samples, block and sequential scoring select identical answers and agree on the published TruthfulQA probability-mass metric within 5times 10^{-5} per item. Self-organized criticality enters as a phenomenological framework with an intrinsic order parameter; open claims become falsifiable conjectures. Selected proof cores are machine-checked in Lean 4.

Knowledge Graph-based Question Answering (KGQA) plays a pivotal role in complex reasoning tasks but remains constrained by two persistent challenges: the structural heterogeneity of Knowledge Graphs(KGs) often leads to semantic mismatch during retrieval, while existing reasoning path retrieval methods lack a global structural perspective. To address these issues, we propose Structure-Tracing Evidence Mining (STEM), a novel framework that reframes multi-hop reasoning as a schema-guided graph search task. First, we design a Semantic-to-Structural Projection pipeline that leverages KG structural priors to decompose queries into atomic relational assertions and construct an adaptive query schema graph. Subsequently, we execute globally-aware node anchoring and subgraph retrieval to obtain the final evidence reasoning graph from KG. To more effectively integrate global structural information during the graph construction process, we design a Triple-Dependent GNN (Triple-GNN) to generate a Global Guidance Subgraph (Guidance Graph) that guides the construction. STEM significantly improves both the accuracy and evidence completeness of multi-hop reasoning graph retrieval, and achieves State-of-the-Art performance on multiple multi-hop benchmarks.

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol documents, sensor streams, and existing biomedical ontologies. We present a repeatable structured expert elicitation methodology and federated Semantic Knowledge Graph (SKG) architecture for capturing and querying this knowledge, demonstrated through deployment at the Biochemical and Cellular Pharmacology Department of Genentech. Knowledge is elicited via the Protocol Intelligence Co-pilot, a purpose-built AI interview agent that applies structured elicitation lenses to surface tacit procedural knowledge with expert-assigned confidence scores, producing graph representations across three tiers: program-level decision milestones, assay protocol knowledge, and physical execution infrastructure. Separately constructed subgraphs, exemplified by immunoassay (ELISA), quantitative mass spectrometry (LC-MS/PRM), and laboratory automation, are aligned through a shared upper ontology and queried as a single federated graph. Evaluation demonstrates seven query types structurally unavailable from any individual data source, including a cross-subgraph traversal that identifies automation-masked silent failures -- conditions where execution logs report success while scientific validity is compromised. Critically, the MASKED_BY graph relationship encodes a class of laboratory risk invisible to current informatics platforms -- the structural gap that prevents existing systems from reasoning about scientific validity. This architecture provides the semantic world model that AI laboratory agents currently lack: a queryable representation of where workflows fail silently, where human judgment is irreplaceable, and which execution assets mask rather than detect failure.

Knowledge graphs (KGs) are increasingly used to support large lan guage model (LLM) reasoning, but standard triplet-based KGs treat each relation as globally valid. In many settings, whether a relation should count as evidence depends on the context. We therefore formulate triplet validity as a triplet-specific function of context and refer to this formulation as a Quantum Knowledge Graph (QKG). We instantiate QKG in medicine using a diabetes-centered PrimeKG subgraph, whose 68,651 context-sensitive relations are further annotated with patient-group-specific constraints. We evaluate it in a reasoner--validator pipeline for medical question answering on a KG-grounded subset of MedReason containing 2,788 questions. With Haiku-4.5 as both the Reasoner and the Validator, KG-backed validation significantly improves over a no-validator baseline (+0.61 pp), and QKG with context matching yields the largest gain, outperforming both KG validation without context matching (+0.79 pp) and the no-validator baseline (+1.40 pp; paired McNemar, all p<0.05). Under a stronger validator (Qwen-3.6-Plus), the raw QKG gain over the no-validator baseline grows from +1.40 pp to +5.96 pp; the context-matching gap is non-significant (p=0.73) on the raw set but becomes borderline significant (p=0.05) after adjustment for knowledge leakage and suspicious questions, consistent with a benchmark-gold ceiling rather than a QKG limitation. Taken together, the results support the view that the value of a KG in LLM-based clinical reasoning lies not merely in storing medically related facts, but in representing whether those facts are applicable to the specific patient context. For reproducibility and further research, we release the curated QKG datasets and source code.https://github.com/HKAI-Sci/QKG

Large Language Models (LLMs), with their exceptional ability to handle a wide range of tasks, have driven significant advancements in tackling reasoning and planning tasks, wherein decomposing complex problems into executable workflows is a crucial step in this process. Existing workflow evaluation frameworks either focus solely on holistic performance or suffer from limitations such as restricted scenario coverage, simplistic workflow structures, and lax evaluation standards. To this end, we introduce WorFBench, a unified workflow generation benchmark with multi-faceted scenarios and intricate graph workflow structures. Additionally, we present WorFEval, a systemic evaluation protocol utilizing subsequence and subgraph matching algorithms to accurately quantify the LLM agent's workflow generation capabilities. Through comprehensive evaluations across different types of LLMs, we discover distinct gaps between the sequence planning capabilities and graph planning capabilities of LLM agents, with even GPT-4 exhibiting a gap of around 15%. We also train two open-source models and evaluate their generalization abilities on held-out tasks. Furthermore, we observe that the generated workflows can enhance downstream tasks, enabling them to achieve superior performance with less time during inference. Code and dataset will be available at https://github.com/zjunlp/WorFBench.

Large language models have shown strong performance in natural language generation and downstream reasoning tasks, but they still struggle with logical consistency, factual grounding, and interpretability in complex multi-step reasoning. To address these limitations, this paper proposes SGR, a stepwise reasoning enhancement framework that integrates large language models with external knowledge graphs through query-relevant subgraph generation. Given an input question, SGR first extracts key entities, relations, and constraints to construct a structured schema, then retrieves compact subgraphs from a knowledge graph using schema-guided querying. The generated subgraphs provide explicit relational evidence that guides the language model through step-by-step reasoning. In addition, SGR combines direct Cypher-based reasoning with collaborative reasoning integration, allowing candidate answers from multiple reasoning paths to be validated and aggregated according to both model confidence and graph consistency. Experiments on benchmark datasets including CWQ, WebQSP, GrailQA, and KQA Pro demonstrate that SGR improves reasoning accuracy and Hits@1 performance over standard prompting and several knowledge-enhanced baselines. Ablation studies further show that schema guidance and Neo4j-based retrieval are both crucial to the effectiveness of the framework. These results indicate that dynamically generated external subgraphs can improve the accuracy, robustness, and interpretability of LLM-based reasoning.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

The remarkable progress of Multi-modal Large Language Models (MLLMs) has garnered unparalleled attention, due to their superior performance in visual contexts. However, their capabilities in visual math problem-solving remain insufficiently evaluated and understood. We investigate current benchmarks to incorporate excessive visual content within textual questions, which potentially assist MLLMs in deducing answers without truly interpreting the input diagrams. To this end, we introduce MathVerse, an all-around visual math benchmark designed for an equitable and in-depth evaluation of MLLMs. We meticulously collect 2,612 high-quality, multi-subject math problems with diagrams from publicly available sources. Each problem is then transformed by human annotators into six distinct versions, each offering varying degrees of information content in multi-modality, contributing to 15K test samples in total. This approach allows MathVerse to comprehensively assess whether and how much MLLMs can truly understand the visual diagrams for mathematical reasoning. In addition, we propose a Chain-of-Thought (CoT) evaluation strategy for a fine-grained assessment of the output answers. Rather than naively judging True or False, we employ GPT-4(V) to adaptively extract crucial reasoning steps, and then score each step with detailed error analysis, which can reveal the intermediate CoT reasoning quality by MLLMs. We hope the MathVerse benchmark may provide unique insights to guide the future development of MLLMs. Project page: https://mathverse-cuhk.github.io

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

Anti-money laundering (AML) regulations mandate financial institutions to deploy AML systems based on a set of rules that, when triggered, form the basis of a suspicious alert to be assessed by human analysts. Reviewing these cases is a cumbersome and complex task that requires analysts to navigate a large network of financial interactions to validate suspicious movements. Furthermore, these systems have very high false positive rates (estimated to be over 95\%). The scarcity of labels hinders the use of alternative systems based on supervised learning, reducing their applicability in real-world applications. In this work we present LaundroGraph, a novel self-supervised graph representation learning approach to encode banking customers and financial transactions into meaningful representations. These representations are used to provide insights to assist the AML reviewing process, such as identifying anomalous movements for a given customer. LaundroGraph represents the underlying network of financial interactions as a customer-transaction bipartite graph and trains a graph neural network on a fully self-supervised link prediction task. We empirically demonstrate that our approach outperforms other strong baselines on self-supervised link prediction using a real-world dataset, improving the best non-graph baseline by 12 p.p. of AUC. The goal is to increase the efficiency of the reviewing process by supplying these AI-powered insights to the analysts upon review. To the best of our knowledge, this is the first fully self-supervised system within the context of AML detection.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

The Sliced-Wasserstein distance (SW) is a computationally efficient and theoretically grounded alternative to the Wasserstein distance. Yet, the literature on its statistical properties -- or, more accurately, its generalization properties -- with respect to the distribution of slices, beyond the uniform measure, is scarce. To bring new contributions to this line of research, we leverage the PAC-Bayesian theory and a central observation that SW may be interpreted as an average risk, the quantity PAC-Bayesian bounds have been designed to characterize. We provide three types of results: i) PAC-Bayesian generalization bounds that hold on what we refer as adaptive Sliced-Wasserstein distances, i.e. SW defined with respect to arbitrary distributions of slices (among which data-dependent distributions), ii) a principled procedure to learn the distribution of slices that yields maximally discriminative SW, by optimizing our theoretical bounds, and iii) empirical illustrations of our theoretical findings.

This paper presents a new state-of-the-art algorithm for exact 3times3 matrix multiplication over general non-commutative rings, achieving a rank-23 scheme with only 58 scalar additions. This improves the previous best additive complexity of 60 additions without a change of basis. The result was discovered through an automated search combining ternary-restricted flip-graph exploration with greedy intersection reduction for common subexpression elimination. The resulting scheme uses only coefficients from {-1, 0, 1}, ensuring both efficiency and portability across arbitrary fields. The total scalar operation count is reduced from 83 to 81.

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

Retrieving graphs from a large corpus, that contain a subgraph isomorphic to a given query graph, is a core operation in many real-world applications. While recent multi-vector graph representations and scores based on set alignment and containment can provide accurate subgraph isomorphism tests, their use in retrieval remains limited by their need to score corpus graphs exhaustively. We introduce CORGII (Contextual Representation of Graphs for Inverted Indexing), a graph indexing framework in which, starting with a contextual dense graph representation, a differentiable discretization module computes sparse binary codes over a learned latent vocabulary. This text document-like representation allows us to leverage classic, highly optimized inverted indices, while supporting soft (vector) set containment scores. Pushing this paradigm further, we replace the classical, fixed impact weight of a `token' on a graph (such as TFIDF or BM25) with a data-driven, trainable impact weight. Finally, we explore token expansion to support multi-probing the index for smoother accuracy-efficiency tradeoffs. To our knowledge, CORGII is the first indexer of dense graph representations using discrete tokens mapping to efficient inverted lists. Extensive experiments show that CORGII provides better trade-offs between accuracy and efficiency, compared to several baselines.

Subgraphs of a larger global graph may be distributed across multiple devices, and only locally accessible due to privacy restrictions, although there may be links between subgraphs. Recently proposed subgraph Federated Learning (FL) methods deal with those missing links across local subgraphs while distributively training Graph Neural Networks (GNNs) on them. However, they have overlooked the inevitable heterogeneity between subgraphs comprising different communities of a global graph, consequently collapsing the incompatible knowledge from local GNN models. To this end, we introduce a new subgraph FL problem, personalized subgraph FL, which focuses on the joint improvement of the interrelated local GNNs rather than learning a single global model, and propose a novel framework, FEDerated Personalized sUBgraph learning (FED-PUB), to tackle it. Since the server cannot access the subgraph in each client, FED-PUB utilizes functional embeddings of the local GNNs using random graphs as inputs to compute similarities between them, and use the similarities to perform weighted averaging for server-side aggregation. Further, it learns a personalized sparse mask at each client to select and update only the subgraph-relevant subset of the aggregated parameters. We validate our FED-PUB for its subgraph FL performance on six datasets, considering both non-overlapping and overlapping subgraphs, on which it significantly outperforms relevant baselines. Our code is available at https://github.com/JinheonBaek/FED-PUB.

Physics problem-solving is a challenging domain for large AI models, requiring integration of conceptual understanding, mathematical reasoning, and interpretation of physical diagrams. Current evaluation methodologies show notable limitations in capturing the breadth and complexity of undergraduate-level physics, underscoring the need for more rigorous assessments. To this end, we present PhysUniBench, a large-scale multimodal benchmark designed to evaluate and improve the reasoning capabilities of multimodal large language models (MLLMs) specifically on undergraduate-level physics problems. PhysUniBench consists of 3,304 physics questions spanning 8 major sub-disciplines of physics, each accompanied by one visual diagrams. The benchmark includes both open-ended and multiple-choice questions, systematically curated and difficulty-rated through an iterative model-in-the-loop process. The benchmark's construction involved a rigorous multi-stage process, including multiple roll-outs, expert-level evaluation, automated filtering of easily solved problems, and a nuanced difficulty grading system with five levels. Through extensive experiments, we observe that current state-of-the-art models encounter substantial challenges in physics reasoning. For example, GPT-4o mini achieves only about 34.2\% accuracy in the proposed PhysUniBench. These results highlight that current MLLMs struggle with advanced physics reasoning, especially on multi-step problems and those requiring precise diagram interpretation. By providing a broad and rigorous assessment tool, PhysUniBench aims to drive progress in AI for Science, encouraging the development of models with stronger physical reasoning, problem-solving skills, and multimodal understanding. The benchmark and evaluation scripts are available at https://prismax-team.github.io/PhysUniBenchmark/.

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

Graph-level anomaly detection has gained significant attention as it finds applications in various domains, such as cancer diagnosis and enzyme prediction. However, existing methods fail to capture the spectral properties of graph anomalies, resulting in unexplainable framework design and unsatisfying performance. In this paper, we re-investigate the spectral differences between anomalous and normal graphs. Our main observation shows a significant disparity in the accumulated spectral energy between these two classes. Moreover, we prove that the accumulated spectral energy of the graph signal can be represented by its Rayleigh Quotient, indicating that the Rayleigh Quotient is a driving factor behind the anomalous properties of graphs. Motivated by this, we propose Rayleigh Quotient Graph Neural Network (RQGNN), the first spectral GNN that explores the inherent spectral features of anomalous graphs for graph-level anomaly detection. Specifically, we introduce a novel framework with two components: the Rayleigh Quotient learning component (RQL) and Chebyshev Wavelet GNN with RQ-pooling (CWGNN-RQ). RQL explicitly captures the Rayleigh Quotient of graphs and CWGNN-RQ implicitly explores the spectral space of graphs. Extensive experiments on 10 real-world datasets show that RQGNN outperforms the best rival by 6.74% in Macro-F1 score and 1.44% in AUC, demonstrating the effectiveness of our framework. Our code is available at https://github.com/xydong127/RQGNN.

Hypergraphs offer a powerful framework for modeling higher-order interactions that traditional pairwise graphs cannot fully capture. However, practical constraints often lead to their simplification into projected graphs, resulting in substantial information loss and ambiguity in representing higher-order relationships. In this work, we propose MARIOH, a supervised approach for reconstructing the original hypergraph from its projected graph by leveraging edge multiplicity. To overcome the difficulties posed by the large search space, MARIOH integrates several key ideas: (a) identifying provable size-2 hyperedges, which reduces the candidate search space, (b) predicting the likelihood of candidates being hyperedges by utilizing both structural and multiplicity-related features, and (c) not only targeting promising hyperedge candidates but also examining less confident ones to explore alternative possibilities. Together, these ideas enable MARIOH to efficiently and effectively explore the search space. In our experiments using 10 real-world datasets, MARIOH achieves up to 74.51% higher reconstruction accuracy compared to state-of-the-art methods.

Given a signed bipartite graph (SBG) G with two disjoint node sets U and V, the goal of link sign prediction is to predict the signs of potential links connecting U and V based on known positive and negative edges in G. The majority of existing solutions towards link sign prediction mainly focus on unipartite signed graphs, which are sub-optimal due to the neglect of node heterogeneity and unique bipartite characteristics of SBGs. To this end, recent studies adapt graph neural networks to SBGs by introducing message-passing schemes for both inter-partition (UxV) and intra-partition (UxU or VxV) node pairs. However, the fundamental spectral convolutional operators were originally designed for positive links in unsigned graphs, and thus, are not optimal for inferring missing positive or negative links from known ones in SBGs. Motivated by this, this paper proposes GegenNet, a novel and effective spectral convolutional neural network model for link sign prediction in SBGs. In particular, GegenNet achieves enhanced model capacity and high predictive accuracy through three main technical contributions: (i) fast and theoretically grounded spectral decomposition techniques for node feature initialization; (ii) a new spectral graph filter based on the Gegenbauer polynomial basis; and (iii) multi-layer sign-aware spectral convolutional networks alternating Gegenbauer polynomial filters with positive and negative edges. Our extensive empirical studies reveal that GegenNet can achieve significantly superior performance (up to a gain of 4.28% in AUC and 11.69% in F1) in link sign prediction compared to 11 strong competitors over 6 benchmark SBG datasets.

This paper presents the first numerical realization of Suzuki's Weil-Quadratic-Form operator, a candidate for the Hilbert--Pólya program linking spectral positivity to the Riemann Hypothesis (RH). Suzuki's 2026 construction was purely theoretical; here, the operator is instantiated via P1 finite-element discretization and Richardson extrapolation. Key results include: (R1) In the prime-free regime, the spectrum follows a closed Archimedean law A_k(a) = log(1/a) + log(k-2) + B_0 + O(a), with B_0 = log q - 2log 2, confirmed to 30-digit precision. (R2) A Mellin double-pole argument proves the head coefficient B(ν) and shows B_0 depends only on the conductor q, independent of the Archimedean parameter. (R2b) The degree d of an L-function appears directly as the logarithmic slope of the spectrum. (R3) Total spectral intensity follows the prime number theorem, S(a) sim (2a)^3/6. (R4) Nontrivial zeros are not eigenvalues but occur in the explicit-formula error term of the prime symbol. (R5) The best-match line σ^*(a) descends toward the critical line. (R6) Weil's positivity criterion is realized in operator form: bounded residual growth corresponds to all zeros on the line, while an injected off-line zero causes exponential blow-up. (R7) The lowest eigenvalue λ_1(a) is strictly positive, decays superexponentially, and passes smoothly through the first prime threshold. (R8) The characteristic function W(a,0;z) is computed for the first time, with all zeros confirmed real. (R9) Indirect traces of GUE statistics appear in the moment structure, even where direct detection is blocked. The authors emphasize that this work does not prove RH. All results are Archimedean and universal, with significance lying in the faithful numerical realization of classical identities rather than new arithmetic.

Large language models (LLMs) are increasingly adopted for a variety of tasks with implicit graphical structures, such as planning in robotics, multi-hop question answering or knowledge probing, structured commonsense reasoning, and more. While LLMs have advanced the state-of-the-art on these tasks with structure implications, whether LLMs could explicitly process textual descriptions of graphs and structures, map them to grounded conceptual spaces, and perform structured operations remains underexplored. To this end, we propose NLGraph (Natural Language Graph), a comprehensive benchmark of graph-based problem solving designed in natural language. NLGraph contains 29,370 problems, covering eight graph reasoning tasks with varying complexity from simple tasks such as connectivity and shortest path up to complex problems such as maximum flow and simulating graph neural networks. We evaluate LLMs (GPT-3/4) with various prompting approaches on the NLGraph benchmark and find that 1) language models do demonstrate preliminary graph reasoning abilities, 2) the benefit of advanced prompting and in-context learning diminishes on more complex graph problems, while 3) LLMs are also (un)surprisingly brittle in the face of spurious correlations in graph and problem settings. We then propose Build-a-Graph Prompting and Algorithmic Prompting, two instruction-based approaches to enhance LLMs in solving natural language graph problems. Build-a-Graph and Algorithmic prompting improve the performance of LLMs on NLGraph by 3.07% to 16.85% across multiple tasks and settings, while how to solve the most complicated graph reasoning tasks in our setup with language models remains an open research question. The NLGraph benchmark and evaluation code are available at https://github.com/Arthur-Heng/NLGraph.

Drug discovery is a complex and time-intensive process that requires identifying and validating new therapeutic candidates. Computational approaches using large-scale biomedical knowledge graphs (KGs) offer a promising solution to accelerate this process. However, extracting meaningful insights from large-scale KGs remains challenging due to the complexity of graph traversal. Existing subgraph-based methods are tailored to graph neural networks (GNNs), making them incompatible with other models, such as large language models (LLMs). We introduce K-Paths, a retrieval framework that extracts structured, diverse, and biologically meaningful paths from KGs. Integrating these paths enables LLMs and GNNs to effectively predict unobserved drug-drug and drug-disease interactions. Unlike traditional path-ranking approaches, K-Paths retrieves and transforms paths into a structured format that LLMs can directly process, facilitating explainable reasoning. K-Paths employs a diversity-aware adaptation of Yen's algorithm to retrieve the K shortest loopless paths between entities in an interaction query, prioritizing biologically relevant and diverse relationships. Our experiments on benchmark datasets show that K-Paths improves the zero-shot performance of Llama 8.1B's F1-score by 12.45 points on drug repurposing and 13.42 points on interaction severity prediction. We also show that Llama 70B achieves F1-score gains of 6.18 and 8.46 points, respectively. K-Paths also improves the supervised training efficiency of EmerGNN, a state-of-the-art GNN, by reducing KG size by 90% while maintaining strong predictive performance. Beyond its scalability and efficiency, K-Paths uniquely bridges the gap between KGs and LLMs, providing explainable rationales for predicted interactions. These capabilities show that K-Paths is a valuable tool for efficient data-driven drug discovery.

Information retrieval based knowledge base question answering (KBQA) first retrieves a subgraph to reduce search space, then reasons on the subgraph to select answer entities. Existing approaches have three issues that impede the retrieval of such subgraphs. Firstly, there is no off-the-shelf toolkit for semantic-relevant subgraph retrieval. Secondly, existing methods are knowledge-graph-dependent, resulting in outdated knowledge graphs used even in recent studies. Thirdly, previous solutions fail to incorporate the best available techniques for entity linking or path expansion. In this paper, we present SRTK, a user-friendly toolkit for semantic-relevant subgraph retrieval from large-scale knowledge graphs. SRTK is the first toolkit that streamlines the entire lifecycle of subgraph retrieval across multiple knowledge graphs. Additionally, it comes with state-of-the-art subgraph retrieval algorithms, guaranteeing an up-to-date solution set out of the box.

This paper analyses a set of simple adaptations that transform standard message-passing Graph Neural Networks (GNN) into provably powerful directed multigraph neural networks. The adaptations include multigraph port numbering, ego IDs, and reverse message passing. We prove that the combination of these theoretically enables the detection of any directed subgraph pattern. To validate the effectiveness of our proposed adaptations in practice, we conduct experiments on synthetic subgraph detection tasks, which demonstrate outstanding performance with almost perfect results. Moreover, we apply our proposed adaptations to two financial crime analysis tasks. We observe dramatic improvements in detecting money laundering transactions, improving the minority-class F1 score of a standard message-passing GNN by up to 30%, and closely matching or outperforming tree-based and GNN baselines. Similarly impressive results are observed on a real-world phishing detection dataset, boosting three standard GNNs' F1 scores by around 15% and outperforming all baselines.

Multi-hop retrieval is not a single-step relevance problem: later-hop evidence should be ranked by its utility conditioned on retrieved bridge evidence, not by similarity to the original query alone. We present BridgeRAG, a training-free, graph-free retrieval method for retrieval-augmented generation (RAG) over multi-hop questions that operationalizes this view with a tripartite scorer s(q,b,c) over (question, bridge, candidate). BridgeRAG separates coverage from scoring: dual-entity ANN expansion broadens the second-hop candidate pool, while a bridge-conditioned LLM judge identifies the active reasoning chain among competing candidates without any offline graph or proposition index. Across four controlled experiments we show that this conditioning signal is (i) selective: +2.55pp on parallel-chain queries (p<0.001) vs. ~0 on single-chain subtypes; (ii) irreplaceable: substituting the retrieved passage with generated SVO query text reduces R@5 by 2.1pp, performing worse than even the lowest-SVO-similarity pool passage; (iii) predictable: cos(b,g2) correlates with per-query gain (Spearman rho=0.104, p<0.001); and (iv) mechanistically precise: bridge conditioning causes productive re-rankings (18.7% flip-win rate on parallel-chain vs. 0.6% on single-chain), not merely more churn. Combined with lightweight coverage expansion and percentile-rank score fusion, BridgeRAG achieves the best published training-free R@5 under matched benchmark evaluation on all three standard MHQA benchmarks without a graph database or any training: 0.8146 on MuSiQue (+3.1pp vs. PropRAG, +6.8pp vs. HippoRAG2), 0.9527 on 2WikiMultiHopQA (+1.2pp vs. PropRAG), and 0.9875 on HotpotQA (+1.35pp vs. PropRAG).

DeepSWE is a benchmark of 113 original, long-horizon software engineering tasks for evaluating coding agents. Most public agentic coding benchmarks follow SWE-bench in mining merged fixes from public GitHub repositories, which creates two problems: the fixes and their discussion were likely seen during pretraining, so a high score can reflect recall rather than problem-solving; and each task is graded by the tests that shipped with its merged fix, which were written to confirm one specific fix rather than grade an arbitrary solution, so they can fail a correct alternative or pass an incomplete one. DeepSWE avoids both. Its tasks are written from scratch across 91 active open-source repositories and five languages and are never contributed back upstream, so their reference solutions stay out of the public record that model training scrapes; and each task is graded by a hand-written verifier that checks the requested functionality and accepts any implementation that provides it. When an independent LLM judge re-reviews graded runs, it disagrees with DeepSWE's verifier about an order of magnitude less often than with SWE-Bench Pro's inherited tests (1.4% versus 32.4%). Despite being about half the length of SWE-Bench Pro's prompts, DeepSWE's prompts describe tasks whose reference solutions touch 5.5x more code, and the benchmark separates frontier agents across a wider score band than the leaderboards on which they otherwise cluster. We release the benchmark, its verifiers, and the full record of evaluation trajectories.

Statistics of grain sizes and orientations in metals correlate to the material's mechanical properties. Reproducing representative volume elements for further analysis of deformation and failure in metals, like 316L stainless steel, is particularly important due to their wide use in manufacturing goods today. Two approaches, initially created for video games, were considered for the procedural generation of representative grain microstructures. The first is the Wave Function Collapse (WFC) algorithm, and the second is constraint propagation and probabilistic inference through Markov Junior, a free and open-source software. This study aimed to investigate these two algorithms' effectiveness in using reference electron backscatter diffraction (EBSD) maps and recreating a statistically similar one that could be used in further research. It utilized two stainless steel EBSD maps as references to test both algorithms. First, the WFC algorithm was too constricting and, thus, incapable of producing images that resembled EBSDs. The second, MarkovJunior, was much more effective in creating a Voronoi tessellation that could be used to create an EBSD map in Python. When comparing the results between the reference and the generated EBSD, we discovered that the orientation and volume fractions were extremely similar. With the study, it was concluded that MarkovJunior is an effective machine learning tool that can reproduce representative grain microstructures.

This thesis is divided into three parts. The first part deals with cylindric plane partitions. The second with lambda-determinants and the third with commutators in semi-circular systems. For more detailed abstract please see inside. Cylindric plane partitions may be thought of as a natural generalization of reverse plane partitions. A generating series for the enumeration of cylindric plane partitions was recently given by Borodin. The first result of section one is a new bijective proof of Borodin's identity which makes use of Fomin's growth diagram framework for generalized RSK correspondences. The second result is a (q,t)-analog of Borodin's identity which extends previous work by Okada in the reverse plane partition case. The third result is an explicit combinatorial interpretation of the Macdonald weight occurring in the (q,t)-analog using the non-intersecting lattice path model for cylindric plane partitions. Alternating sign matrices were discovered by Robbins and Rumsey whilst studying λ-determinants. In the second part of this thesis we prove a multi-parameter generalization of the λ-determinant, generalizing a recent result by di Francesco. Like the original λ-determinant, our formula exhibits the Laurent phenomenon. Semicircular systems were first introduced by Voiculescu as a part of his study of von Neumann algebras. In the third part of this thesis we study certain commutator subalgebras of the semicircular system. We find a projection matrix with an interesting self-similar structure. Making use of our projection formula we given an alternative, elementary proof that the semicircular system is a factor.

The Honeymoon Oberwolfach Problem HOP(2m_1,2m_2,ldots,2m_t) asks the following question. Given n=m_1+m_2+ldots +m_t newlywed couples at a conference and t round tables of sizes 2m_1,2m_2,ldots,2m_t, is it possible to arrange the 2n participants at these tables for 2n-2 meals so that each participant sits next to their spouse at every meal, and sits next to every other participant exactly once? A solution to HOP(2m_1,2m_2,ldots,2m_t) is a decomposition of K_{2n}+(2n-3)I, the complete graph K_{2n} with 2n-3 additional copies of a fixed 1-factor I, into 2-factors, each consisting of disjoint I-alternating cycles of lengths 2m_1,2m_2,ldots,2m_t. The Honeymoon Oberwolfach Problem was introduced in a 2019 paper by Lepine and Sajna. The authors conjectured that HOP(2m_1,2m_2,ldots, 2m_t) has a solution whenever the obvious necessary conditions are satisfied, and proved the conjecture for several large cases, including the uniform cycle length case m_1=ldots=m_t, and the small cases with n le 9. In the present paper, we extend the latter result to all cases with n le 20 using a computer search.

Reasoning Large Language Models (RLLMs) have recently achieved remarkable progress on complex reasoning tasks, largely enabled by their long chain-of-thought (Long CoT) capabilities. However, developing these Long CoT behaviors relies heavily on post-training with high-quality datasets, which are typically costly and human-curated (e.g., mathematics and code), leaving scalable alternatives unexplored. In this work, we introduce NP-hard (NPH) graph problems as a novel synthetic training corpus, as they inherently require deep reasoning, extensive exploration, and reflective strategies, which are core characteristics of Long CoT reasoning. Building on this insight, we develop a two-stage post-training framework: (i) Long CoT Supervised Fine-Tuning (SFT) on rejection-sampled NPH graph instances, which substantially enhances reasoning depth, and (ii) Reinforcement Learning (RL) with a fine-grained reward design, which sharpens reasoning efficiency. Our flagship model, Graph-R1-7B, demonstrates strong generalization across mathematics, coding, STEM, and logic, and surpasses QwQ-32B on NPH graph problems in both accuracy and reasoning efficiency. These results position NPH graph problems as an effective and scalable resource for advancing Long CoT reasoning in LLMs, opening a new frontier for LLM post-training. Our implementation is available at https://github.com/Graph-Reasoner/Graph-R1, with models and datasets hosted in our Hugging Face collection HKUST-DSAIL/Graph-R1.

In many real-world settings, a centralized decision-maker must repeatedly allocate finite resources to a population over multiple time steps. Individuals who receive a resource derive some stochastic utility; to characterize the population-level effects of an allocation, the expected individual utilities are then aggregated using a social welfare function (SWF). We formalize this setting and present a general confidence sequence framework for SWF-based online learning and inference, valid for any monotonic, concave, and Lipschitz-continuous SWF. Our key insight is that monotonicity alone suffices to lift confidence sequences from individual utilities to anytime-valid bounds on optimal welfare. Building on this foundation, we propose SWF-UCB, a SWF-agnostic online learning algorithm that achieves near-optimal O(n+nkT) regret (for k resources distributed among n individuals at each of T time steps). We instantiate our framework on three normatively distinct SWF families: Weighted Power Mean, Kolm, and Gini, providing bespoke oracle algorithms for each. Experiments confirm T scaling and reveal rich interactions between k and SWF parameters. This framework naturally supports inference applications such as sequential hypothesis testing, optimal stopping, and policy evaluation.

Evaluating and enhancing the general capabilities of large language models (LLMs) has been an important research topic. Graph is a common data structure in the real world, and understanding graph data is a crucial part for advancing general intelligence. To evaluate and enhance the graph understanding abilities of LLMs, in this paper, we propose a benchmark named GraphInstruct, which comprehensively includes 21 classical graph reasoning tasks, providing diverse graph generation pipelines and detailed reasoning steps. Based on GraphInstruct, we further construct GraphLM through efficient instruction-tuning, which shows prominent graph understanding capability. In order to enhance the LLM with graph reasoning capability as well, we propose a step mask training strategy, and construct a model named GraphLM+. As one of the pioneering efforts to enhance the graph understanding and reasoning abilities of LLMs, extensive experiments have demonstrated the superiority of GraphLM and GraphLM+ over other LLMs. We look forward to more researchers exploring the potential of LLMs in the graph data mining domain through GraphInstruct. Our code for generating GraphInstruct is released publicly at: https://github.com/CGCL-codes/GraphInstruct.

Recent advancements in large language models (LLMs) have spurred growing interest in automatic theorem proving using Lean4, where effective tree search methods are crucial for navigating proof search spaces. While the existing approaches primarily rely on value functions and Monte Carlo Tree Search (MCTS), the potential of simpler methods like Best-First Search (BFS) remains underexplored. This paper investigates whether BFS can achieve competitive performance in large-scale theorem proving tasks. We present BFS-Prover, a scalable expert iteration framework, featuring three key innovations. First, we implement strategic data filtering at each expert iteration round, excluding problems solvable via beam search node expansion to focus on harder cases. Second, we improve the sample efficiency of BFS through Direct Preference Optimization (DPO) applied to state-tactic pairs automatically annotated with compiler error feedback, refining the LLM's policy to prioritize productive expansions. Third, we employ length normalization in BFS to encourage exploration of deeper proof paths. BFS-Prover achieves a score of 71.31 on the MiniF2F test set and therefore challenges the perceived necessity of complex tree search methods, demonstrating that BFS can achieve competitive performance when properly scaled.

Large reasoning models (LRMs) spend substantial test-time compute on long chain-of-thought (CoT) traces, but what *characterizes* an effective CoT remains unclear. While prior work reports gains from lengthening CoTs and increasing review (revisiting earlier steps) via appended *wait* tokens, recent studies suggest that shorter thinking can outperform longer traces. We therefore conduct a systematic evaluation across ten LRMs on math and scientific reasoning. Contrary to the "longer-is-better" narrative, we find that both naive CoT lengthening and increased review are associated with *lower* accuracy. As CoT unfolds step by step, token-level metrics can conflate verbosity with process quality. We introduce a graph view of CoT to extract structure and identify a single statistic-the *Failed-Step Fraction (FSF)*, the fraction of steps in abandoned branches-that consistently outpredicts length and review ratio for correctness across models. To probe causality, we design two interventions. First, we rank candidate CoTs by each metric at test time, where FSF yields the largest pass@1 gains; second, we edit CoTs to remove failed branches, which significantly improves accuracy, indicating that failed branches bias subsequent reasoning. Taken together, these results characterize effective CoTs as those that *fail less* and support *structure-aware* test-time scaling over indiscriminately generating long CoT.

Machine-assisted theorem proving refers to the process of conducting structured reasoning to automatically generate proofs for mathematical theorems. Recently, there has been a surge of interest in using machine learning models in conjunction with proof assistants to perform this task. In this paper, we introduce Pantograph, a tool that provides a versatile interface to the Lean 4 proof assistant and enables efficient proof search via powerful search algorithms such as Monte Carlo Tree Search. In addition, Pantograph enables high-level reasoning by enabling a more robust handling of Lean 4's inference steps. We provide an overview of Pantograph's architecture and features. We also report on an illustrative use case: using machine learning models and proof sketches to prove Lean 4 theorems. Pantograph's innovative features pave the way for more advanced machine learning models to perform complex proof searches and high-level reasoning, equipping future researchers to design more versatile and powerful theorem provers.

Multi-Agent Reinforcement Learning (MARL) is increasingly deployed in safety-critical domains, yet methods for interpretable failure detection and attribution remain underdeveloped. We introduce a two-stage gradient-based framework that provides interpretable diagnostics for three critical failure analysis tasks: (1) detecting the true initial failure source (Patient-0); (2) validating why non-attacked agents may be flagged first due to domino effects; and (3) tracing how failures propagate through learned coordination pathways. Stage 1 performs interpretable per-agent failure detection via Taylor-remainder analysis of policy-gradient costs, declaring an initial Patient-0 candidate at the first threshold crossing. Stage 2 provides validation through geometric analysis of critic derivatives-first-order sensitivity and directional second-order curvature aggregated over causal windows to construct interpretable contagion graphs. This approach explains "downstream-first" detection anomalies by revealing pathways that amplify upstream deviations. Evaluated across 500 episodes in Simple Spread (3 and 5 agents) and 100 episodes in StarCraft II using MADDPG and HATRPO, our method achieves 88.2-99.4% Patient-0 detection accuracy while providing interpretable geometric evidence for detection decisions. By moving beyond black-box detection to interpretable gradient-level forensics, this framework offers practical tools for diagnosing cascading failures in safety-critical MARL systems.

Graph-based retrieval-augmented generation (Graph-based RAG) has demonstrated significant potential in enhancing Large Language Models (LLMs) with structured knowledge. However, existing methods face three critical challenges: Inaccurate Graph Construction, caused by LLM hallucination; Poor Reasoning Ability, caused by failing to generate explicit reasons telling LLM why certain chunks were selected; and Inadequate Answering, which only partially answers the query due to the inadequate LLM reasoning, making their performance lag behind NaiveRAG on certain tasks. To address these issues, we propose AGRAG, an advanced graph-based retrieval-augmented generation framework. When constructing the graph, AGRAG substitutes the widely used LLM entity extraction method with a statistics-based method, avoiding hallucination and error propagation. When retrieval, AGRAG formulates the graph reasoning procedure as the Minimum Cost Maximum Influence (MCMI) subgraph generation problem, where we try to include more nodes with high influence score, but with less involving edge cost, to make the generated reasoning paths more comprehensive. We prove this problem to be NP-hard, and propose a greedy algorithm to solve it. The MCMI subgraph generated can serve as explicit reasoning paths to tell LLM why certain chunks were retrieved, thereby making the LLM better focus on the query-related part contents of the chunks, reducing the impact of noise, and improving AGRAG's reasoning ability. Furthermore, compared with the simple tree-structured reasoning paths, our MCMI subgraph can allow more complex graph structures, such as cycles, and improve the comprehensiveness of the generated reasoning paths.

We prove that the celebrated Planar Product Structure Theorem by Dujmovic et al, and also related graph product structure results, can be formulated with the induced subgraph containment relation. Precisely, we prove that if a graph G is a subgraph of the strong product of a graph Q of bounded maximum degree (such as a path) and a graph M of bounded tree-width, then G is an induced subgraph of the strong product of Q and a graph M' of bounded tree-width being at most exponential in the maximum degree of Q and the tree-width of M. In particular, if G is planar, we show that G is an induced subgraph of the strong product of a path and a graph of tree-width 39. In the course of proving this result, we introduce and study H-clique-width, a new single structural measure that captures a hereditary analogue of the traditional product structure (where, informally, the strong product has one factor from the graph class H and one factor of bounded clique-width).

We present Forge-UGC (FX Optimization and Register-Graph Engine for Universal Graph Compilation), a four-phase compiler for transformer deployment on heterogeneous accelerator hardware, validated on Intel AI Boost NPU. Existing frameworks such as OpenVINO and ONNX Runtime often use opaque compilation pipelines, limited pass-level visibility, and weak buffer management, which can lead to higher compilation cost and runtime overhead. Forge-UGC addresses this with a hardware-agnostic design that separates graph capture, optimization, intermediate representation lowering, and backend scheduling. Phase 1 captures graphs with torch.export at the ATen operator level, supporting modern transformer components such as rotary position embeddings, grouped-query attention, and SwiGLU without manual decomposition. Phase 2 applies six optimization passes: dead code elimination, common subexpression elimination, constant folding, attention fusion, operator fusion, and layout optimization, reducing graph node count by 14.2 to 21.9%. Phase 3 lowers the optimized graph into a typed intermediate representation with explicit virtual register assignments. Phase 4 performs liveness analysis, linear-scan buffer allocation, reducing peak buffer count by 30 to 48%, and device-affinity scheduling, reducing NPU-CPU transitions by 42 to 65%. Across six model families ranging from 125M to 8B parameters, evaluated on WikiText-103 and GLUE, Forge-UGC delivers 6.9 to 9.2x faster compilation than OpenVINO and ONNX Runtime, 18.2 to 35.7% lower inference latency, and 30.2 to 40.9% lower energy per inference. Fidelity is preserved, with max absolute logit differences below 2.1e-5 and KL divergence below 8.4e-9. We also introduce Fusion Gain Ratio, Compilation Efficiency Index, and per-pass execution profiling for systematic evaluation of NPU compilation pipelines.

Multimodal Large Language Models (MLLMs) excel at recognizing individual visual elements and reasoning over simple linear diagrams. However, when faced with complex topological structures involving branching paths, converging flows, and cyclic dependencies, their reasoning capabilities degrade sharply, even on tasks as basic as counting endpoints. Existing benchmarks fail to probe this gap, focusing on semantic comprehension rather than structural reasoning. We introduce ReactBench, a benchmark that reveals fundamental limitations in structural reasoning through chemical reaction diagrams. These real-world scientific diagrams offer an ideal testbed because they naturally span diverse structures from linear chains to cyclic graphs, while requiring both precise local recognition and coherent global reasoning. Our benchmark comprises 1,618 expert-annotated QA pairs across four hierarchical task dimensions. Extensive evaluation across 17 MLLMs reveals a significant performance gap exceeding 30% between anchor-based tasks and holistic structural reasoning tasks. Controlled ablations confirm this bottleneck lies in reasoning, not perception. These findings expose a fundamental deficit in structural understanding and establish directions for advancing visual reasoning.

Molecular relational learning, whose goal is to learn the interaction behavior between molecular pairs, got a surge of interest in molecular sciences due to its wide range of applications. Recently, graph neural networks have recently shown great success in molecular relational learning by modeling a molecule as a graph structure, and considering atom-level interactions between two molecules. Despite their success, existing molecular relational learning methods tend to overlook the nature of chemistry, i.e., a chemical compound is composed of multiple substructures such as functional groups that cause distinctive chemical reactions. In this work, we propose a novel relational learning framework, called CGIB, that predicts the interaction behavior between a pair of graphs by detecting core subgraphs therein. The main idea is, given a pair of graphs, to find a subgraph from a graph that contains the minimal sufficient information regarding the task at hand conditioned on the paired graph based on the principle of conditional graph information bottleneck. We argue that our proposed method mimics the nature of chemical reactions, i.e., the core substructure of a molecule varies depending on which other molecule it interacts with. Extensive experiments on various tasks with real-world datasets demonstrate the superiority of CGIB over state-of-the-art baselines. Our code is available at https://github.com/Namkyeong/CGIB.

Large Language Models (LLMs) have garnered considerable interest within both academic and industrial. Yet, the application of LLMs to graph data remains under-explored. In this study, we evaluate the capabilities of four LLMs in addressing several analytical problems with graph data. We employ four distinct evaluation metrics: Comprehension, Correctness, Fidelity, and Rectification. Our results show that: 1) LLMs effectively comprehend graph data in natural language and reason with graph topology. 2) GPT models can generate logical and coherent results, outperforming alternatives in correctness. 3) All examined LLMs face challenges in structural reasoning, with techniques like zero-shot chain-of-thought and few-shot prompting showing diminished efficacy. 4) GPT models often produce erroneous answers in multi-answer tasks, raising concerns in fidelity. 5) GPT models exhibit elevated confidence in their outputs, potentially hindering their rectification capacities. Notably, GPT-4 has demonstrated the capacity to rectify responses from GPT-3.5-turbo and its own previous iterations. The code is available at: https://github.com/Ayame1006/LLMtoGraph.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Message passing mechanism contributes to the success of GNNs in various applications, but also brings the oversquashing problem. Recent works combat oversquashing by improving the graph spectrums with rewiring techniques, disrupting the structural bias in graphs, and having limited improvement on oversquashing in terms of oversquashing measure. Motivated by unitary RNN, we propose Graph Unitary Message Passing (GUMP) to alleviate oversquashing in GNNs by applying unitary adjacency matrix for message passing. To design GUMP, a transformation is first proposed to make general graphs have unitary adjacency matrix and keep its structural bias. Then, unitary adjacency matrix is obtained with a unitary projection algorithm, which is implemented by utilizing the intrinsic structure of unitary adjacency matrix and allows GUMP to be permutation-equivariant. Experimental results show the effectiveness of GUMP in improving the performance on various graph learning tasks.

Scientific discovery via symbolic regression is often viewed as statistically and computationally intractable because the hypothesis space of expressions grows combinatorially with depth. This paper revisits the statistical side through the lens of PAC learning, focusing on compositional function trees built from a finite vocabulary of smooth operators (e.g., {+,times,sin,exp} and affine maps). We prove that the relevant generalization quantity, Rademacher complexity, hence the excess risk, does not necessarily blow up exponentially with the number of distinct symbolic structures, but is controlled by (i) the depth d and (ii) the Lipschitz constants of the base operators along the composed computation graph. Concretely, under mild Lipschitz conditions on operators and bounded affine leaves, a finite-union bound over a vocabulary of size K=|H_{base}| together with Maurer-type vector contraction yields R_n(H_{comp}^{d}) leq (Kb2L)^{d-1}R_n(H_{comp}^{1}) with arity bound b; corresponding high-probability risk bounds scale as O(L^{d}/n) when K,b=O(1) and R_n(H_{comp}^{1})=O(n^{-1/2}). We complement the theory with a modular codebase that trains differentiable operator trees (not MLPs) on synthetic "physics-like" targets of controlled depth and shows that the empirical generalization gap correlates positively with the predicted complexity term (L^{d})/n.

We study one-sided and α-correct sequential hypothesis testing for data generated by an ergodic, finite-state Markov chain. The null hypothesis is that the unknown transition matrix belongs to a prescribed set P of stochastic matrices, and the alternative corresponds to a disjoint set Q. We establish a non-asymptotic instance-dependent lower bound on the expected stopping time of any valid sequential test under the alternative, which is asymptotically tight. Our novel analysis improves the existing lower bounds, which are either asymptotic or provably sub-optimal in this setting. Our lower bound incorporates both the stationary distribution and the transition structure induced by the unknown Markov chain. We further propose an optimal test whose expected stopping time matches this lower bound asymptotically as αto 0. We illustrate the usefulness of our framework through applications to sequential detection of model misspecification in Markov Chain Monte Carlo and to testing structural properties, such as the linearity of transition dynamics, in Markov decision processes. Our findings yield a sharp and general characterization of optimal sequential testing procedures under Markovian dependence.

Detecting fraudulent transactions is an essential component to control risk in e-commerce marketplaces. Apart from rule-based and machine learning filters that are already deployed in production, we want to enable efficient real-time inference with graph neural networks (GNNs), which is useful to catch multihop risk propagation in a transaction graph. However, two challenges arise in the implementation of GNNs in production. First, future information in a dynamic graph should not be considered in message passing to predict the past. Second, the latency of graph query and GNN model inference is usually up to hundreds of milliseconds, which is costly for some critical online services. To tackle these challenges, we propose a Batch and Real-time Inception GrapH Topology (BRIGHT) framework to conduct an end-to-end GNN learning that allows efficient online real-time inference. BRIGHT framework consists of a graph transformation module (Two-Stage Directed Graph) and a corresponding GNN architecture (Lambda Neural Network). The Two-Stage Directed Graph guarantees that the information passed through neighbors is only from the historical payment transactions. It consists of two subgraphs representing historical relationships and real-time links, respectively. The Lambda Neural Network decouples inference into two stages: batch inference of entity embeddings and real-time inference of transaction prediction. Our experiments show that BRIGHT outperforms the baseline models by >2\% in average w.r.t.~precision. Furthermore, BRIGHT is computationally efficient for real-time fraud detection. Regarding end-to-end performance (including neighbor query and inference), BRIGHT can reduce the P99 latency by >75\%. For the inference stage, our speedup is on average 7.8times compared to the traditional GNN.

As multi-modal large language models (MLLMs) frequently exhibit errors when solving scientific problems, evaluating the validity of their reasoning processes is critical for ensuring reliability and uncovering fine-grained model weaknesses. Since human evaluation is laborious and costly, prompting MLLMs as automated process judges has become a common practice. However, the reliability of these model-based judges remains uncertain. To address this, we introduce ProJudgeBench, the first comprehensive benchmark specifically designed for evaluating abilities of MLLM-based process judges. ProJudgeBench comprises 2,400 test cases and 50,118 step-level labels, spanning four scientific disciplines with diverse difficulty levels and multi-modal content. In ProJudgeBench, each step is meticulously annotated by human experts for correctness, error type, and explanation, enabling a systematic evaluation of judges' capabilities to detect, classify and diagnose errors. Evaluation on ProJudgeBench reveals a significant performance gap between open-source and proprietary models. To bridge this gap, we further propose ProJudge-173k, a large-scale instruction-tuning dataset, and a Dynamic Dual-Phase fine-tuning strategy that encourages models to explicitly reason through problem-solving before assessing solutions. Both contributions significantly enhance the process evaluation capabilities of open-source models. All the resources will be released to foster future research of reliable multi-modal process evaluation.

Charts are ubiquitous in scientific and financial literature for presenting structured data. However, chart reasoning remains challenging for multimodal large language models (MLLMs) due to the lack of high-quality training data, as well as the need for fine-grained visual grounding and precise numerical computation. To address these challenges, we first propose DuoChart, a scalable dual-source data pipeline that combines synthesized charts with real-world charts to construct diverse, high-quality chart training data. We then introduce CharTool, which equips MLLMs with external tools, including image cropping for localized visual perception and code-based computation for accurate numerical reasoning. Through agentic reinforcement learning on DuoChart, CharTool learns tool-integrated reasoning grounded in chart content. Extensive experiments on six chart benchmarks show that our method consistently improves over strong MLLM baselines across model scales. Notably, CharTool-7B outperforms the base model by **+8.0%** on CharXiv (Reasoning) and **+9.78%** on ChartQAPro, while achieving competitive performance with substantially larger or proprietary models. Moreover, CharTool demonstrates positive generalization to out-of-domain visual math reasoning benchmarks.

Topological deep learning has emerged for modeling higher-order relational structures beyond pairwise interactions that standard graph neural networks fail to capture. Although combinatorial complexes offer a unified topological framework, most existing topological deep learning methods rely on local message passing via attention mechanisms, which incur quadratic complexity and remain low-dimensional, limiting scalability and rank-aware information aggregation in higher-order complexes.We propose Combinatorial Complex Mamba (CCMamba), the first unified mamba-based neural framework for learning on combinatorial complexes. CCMamba reformulates message passing as a selective state-space modeling problem by organizing multi-rank incidence relations into structured sequences processed by rank-aware state-space models. This enables adaptive, directional, and long range information propagation in linear time without self attention. We further establish the theoretical analysis that the expressive power upper-bound of CCMamba message passing is the 1-Weisfeiler-Lehman test. Experiments on graph, hypergraph, and simplicial benchmarks demonstrate that CCMamba consistently outperforms existing methods while exhibiting improved scalability and robustness to depth.

World foundation models, which simulate the physical world by predicting future states from current observations and inputs, have become central to many applications in physical intelligence, including autonomous driving and robotics. However, these models require substantial computational resources for pretraining and are further constrained by available data during post-training. As such, scaling computation at test time emerges as both a critical and practical alternative to traditional model enlargement or re-training. In this work, we introduce SWIFT, a test-time scaling framework tailored for WFMs. SWIFT integrates our extensible WFM evaluation toolkit with process-level inference strategies, including fast tokenization, probability-based Top-K pruning, and efficient beam search. Empirical results on the COSMOS model demonstrate that test-time scaling exists even in a compute-optimal way. Our findings reveal that test-time scaling laws hold for WFMs and that SWIFT provides a scalable and effective pathway for improving WFM inference without retraining or increasing model size. The code is available at https://github.com/Mia-Cong/SWIFT.git.

Graph databases are gaining momentum thanks to the flexibility and expressiveness of their data models and query languages. A standardization activity driven by the ISO/IEC standardization body is also ongoing and has already conducted to the specification of the first versions of two standard graph query languages, namely SQL/PGQ and GQL, respectively in 2023 and 2024. Apart from the standards, there exists a panoply of concrete graph query languages provided by current graph database systems, each offering different query features. A common limitation of current graph query engines is the absence of an algebraic approach for evaluating path queries. To address this, we introduce an abstract algebra for evaluating path queries, allowing paths to be treated as first-class entities within the query processing pipeline. We demonstrate that our algebra can express a core fragment of path queries defined in GQL and SQL/PGQ, thereby serving as a formal framework for studying both standards and supporting their implementation in current graph database systems. We also show that evaluation trees for path algebra expressions can function as logical plans for evaluating path queries and enable the application of query optimization techniques. Our algebraic framework has the potential to act as a lingua franca for path query evaluation, enabling different implementations to be expressed and compared.

We show that a Borel graph generated by finitely many bounded-to-1 commuting functions is hyperfinite. This recovers a theorem in the forthcoming paper by Naryshkin, Shinko, Weilacher and Yu.

Multi-modal large language models (MLLMs) have demonstrated promising capabilities across various tasks by integrating textual and visual information to achieve visual understanding in complex scenarios. Despite the availability of several benchmarks aims to evaluating MLLMs in tasks from visual question answering to complex problem-solving, most focus predominantly on mathematics or general visual understanding tasks. This reveals a critical gap in current benchmarks, which often overlook the inclusion of other key scientific disciplines such as physics and chemistry. To address this gap, we meticulously construct a comprehensive benchmark, named VisScience, which is utilized to assess the multi-modal scientific reasoning across the three disciplines of mathematics, physics, and chemistry. This benchmark comprises 3,000 questions drawn from K12 education - spanning elementary school through high school - equally distributed across three disciplines, with 1,000 questions per discipline. The questions within VisScience span 21 distinct subjects and are categorized into five difficulty levels, offering a broad spectrum of topics within each discipline. With VisScience, we present a detailed evaluation of the performance of 25 representative MLLMs in scientific reasoning. Experimental results demonstrate that closed-source MLLMs generally outperform open-source models. The best performance observed include a 53.4\% accuracy in mathematics by Claude3.5-Sonnet, 38.2\% in physics by GPT-4o, and 47.0\% in chemistry by Gemini-1.5-Pro. These results underscore the strengths and limitations of MLLMs, suggesting areas for future improvement and highlighting the importance of developing models that can effectively handle the diverse demands of multi-modal scientific reasoning.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.