Daily Papers

We investigate novel random graph embeddings that can be computed in expected polynomial time and that are able to distinguish all non-isomorphic graphs in expectation. Previous graph embeddings have limited expressiveness and either cannot distinguish all graphs or cannot be computed efficiently for every graph. To be able to approximate arbitrary functions on graphs, we are interested in efficient alternatives that become arbitrarily expressive with increasing resources. Our approach is based on Lov\'asz' characterisation of graph isomorphism through an infinite dimensional vector of homomorphism counts. Our empirical evaluation shows competitive results on several benchmark graph learning tasks.

This paper studies the problem of recovering cameras from a set of fundamental matrices. A set of fundamental matrices is said to be compatible if a set of cameras exists for which they are the fundamental matrices. We focus on the complete graph, where fundamental matrices for each pair of cameras are given. Previous work has established necessary and sufficient conditions for compatibility as rank and eigenvalue conditions on the n-view fundamental matrix obtained by concatenating the individual fundamental matrices. In this work, we show that the eigenvalue condition is redundant. We provide explicit homogeneous polynomials that describe necessary and sufficient conditions for compatibility in terms of the fundamental matrices and their epipoles. In this direction, we find that quadruple-wise compatibility is enough to ensure global compatibility for any number of cameras. We demonstrate that for four cameras, compatibility is generically described by triple-wise conditions and one additional equation involving all fundamental matrices.

We propose a graph clustering formulation based on multicut (a.k.a. weighted correlation clustering) on the complete graph. Our formulation does not need specification of the graph topology as in the original sparse formulation of multicut, making our approach simpler and potentially better performing. In contrast to unweighted correlation clustering we allow for a more expressive weighted cost structure. In dense multicut, the clustering objective is given in a factorized form as inner products of node feature vectors. This allows for an efficient formulation and inference in contrast to multicut/weighted correlation clustering, which has at least quadratic representation and computation complexity when working on the complete graph. We show how to rewrite classical greedy algorithms for multicut in our dense setting and how to modify them for greater efficiency and solution quality. In particular, our algorithms scale to graphs with tens of thousands of nodes. Empirical evidence on instance segmentation on Cityscapes and clustering of ImageNet datasets shows the merits of our approach.

Large language models (LLMs) have recently been applied to 3D vision-language (3D-VL) tasks, which require spatial reasoning to identify target objects relative to anchors. Scene graphs are commonly employed to represent such relations, but reasoning over complete graphs incurs high token costs and computational inefficiencies, motivating the need for pruning. Existing pruning methods primarily rely on spatial proximity and often remove task-relevant relations, thereby undermining reliable spatial reasoning. To address these limitations, we derive a key requirement for scene graph pruning: preserving spatial relations that are most pertinent to the specific 3D-VL task. Guided by this insight, we propose the Conceptual-Adjacent Scene Graph Pruner (CAPruner). CAPruner integrates fuzzy semantic relevance with spatial proximity to estimate the importance of relations, enabling the selection of critical relations in a task-specific context. Moreover, to avoid costly relation-level annotations, CAPruner is trained by supervising the aggregated scores of each node's incident edges. Extensive experiments demonstrate that CAPruner effectively preserves relations essential for spatial reasoning, leading to substantial performance improvements of LLMs on 3D-VL tasks. Code is available at https://github.com/fz-zsl/CAPruner.

Graph unlearning has emerged as a pivotal method to delete information from a pre-trained graph neural network (GNN). One may delete nodes, a class of nodes, edges, or a class of edges. An unlearning method enables the GNN model to comply with data protection regulations (i.e., the right to be forgotten), adapt to evolving data distributions, and reduce the GPU-hours carbon footprint by avoiding repetitive retraining. Existing partitioning and aggregation-based methods have limitations due to their poor handling of local graph dependencies and additional overhead costs. More recently, GNNDelete offered a model-agnostic approach that alleviates some of these issues. Our work takes a novel approach to address these challenges in graph unlearning through knowledge distillation, as it distills to delete in GNN (D2DGN). It is a model-agnostic distillation framework where the complete graph knowledge is divided and marked for retention and deletion. It performs distillation with response-based soft targets and feature-based node embedding while minimizing KL divergence. The unlearned model effectively removes the influence of deleted graph elements while preserving knowledge about the retained graph elements. D2DGN surpasses the performance of existing methods when evaluated on various real-world graph datasets by up to 43.1% (AUC) in edge and node unlearning tasks. Other notable advantages include better efficiency, better performance in removing target elements, preservation of performance for the retained elements, and zero overhead costs. Notably, our D2DGN surpasses the state-of-the-art GNNDelete in AUC by 2.4%, improves membership inference ratio by +1.3, requires 10.2times10^6 fewer FLOPs per forward pass and up to 3.2times faster.

Large Language Model (LLM) based multi-agent systems have shown remarkable performance in various tasks, especially when enhanced through collaborative communication. However, current methods often rely on a fixed number of agents and static communication structures, limiting their ability to adapt to varying task complexities. In this paper, we propose Adaptive Graph Pruning (AGP), a novel task-adaptive multi-agent collaboration framework that jointly optimizes agent quantity (hard-pruning) and communication topology (soft-pruning). Specifically, our method employs a two-stage training strategy: firstly, independently training soft-pruning networks for different agent quantities to determine optimal agent-quantity-specific complete graphs and positional masks across specific tasks; and then jointly optimizing hard-pruning and soft-pruning within a maximum complete graph to dynamically configure the number of agents and their communication topologies per task. Extensive experiments demonstrate that our approach is: (1) High-performing, achieving state-of-the-art results across six benchmarks and consistently generalizes across multiple mainstream LLM architectures, with a increase in performance of 2.58%sim 9.84%; (2) Task-adaptive, dynamically constructing optimized communication topologies tailored to specific tasks, with an extremely high performance in all three task categories (general reasoning, mathematical reasoning, and code generation); (3) Token-economical, having fewer training steps and token consumption at the same time, with a decrease in token consumption of 90%+; and (4) Training-efficient, achieving high performance with very few training steps compared with other methods. The performance will surpass the existing baselines after about ten steps of training under six benchmarks.

Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph Neural Networks (GNN) have shown great success in encoding graph structure, typical GNNs based on convolution or attention variants suffer from over-smoothing, noise, heterophily, are computationally expensive and typically require the complete graph being present. Instead, we propose Self-Supervised Contrastive Graph Clustering (SCGC), which imposes graph-structure via contrastive loss signals to learn discriminative node representations and iteratively refined soft cluster labels. We also propose SCGC*, with a more effective, novel, Influence Augmented Contrastive (IAC) loss to fuse richer structural information, and half the original model parameters. SCGC(*) is faster with simple linear units, completely eliminate convolutions and attention of traditional GNNs, yet efficiently incorporates structure. It is impervious to layer depth and robust to over-smoothing, incorrect edges and heterophily. It is scalable by batching, a limitation in many prior GNN models, and trivially parallelizable. We obtain significant improvements over state-of-the-art on a wide range of benchmark graph datasets, including images, sensor data, text, and citation networks efficiently. Specifically, 20% on ARI and 18% on NMI for DBLP; overall 55% reduction in training time and overall, 81% reduction on inference time. Our code is available at : https://github.com/gayanku/SCGC

Recent vision-language models have achieved tremendous advances. However, their computational costs are also escalating dramatically, making model acceleration exceedingly critical. To pursue more efficient vision-language Transformers, this paper introduces Cross-Guided Ensemble of Tokens (CrossGET), a general acceleration framework for vision-language Transformers. This framework adaptively combines tokens in real-time during inference, significantly reducing computational costs while maintaining high performance. CrossGET features two primary innovations: 1) Cross-Guided Matching and Ensemble. CrossGET leverages cross-modal guided token matching and ensemble to effectively utilize cross-modal information, achieving wider applicability across both modality-independent models, e.g., CLIP, and modality-dependent ones, e.g., BLIP2. 2) Complete-Graph Soft Matching. CrossGET introduces an algorithm for the token-matching mechanism, ensuring reliable matching results while facilitating parallelizability and high efficiency. Extensive experiments have been conducted on various vision-language tasks, such as image-text retrieval, visual reasoning, image captioning, and visual question answering. The performance on both classic multimodal architectures and emerging multimodal LLMs demonstrates the framework's effectiveness and versatility. The code is available at https://github.com/sdc17/CrossGET.

We study the H-chromatic symmetric functions X_G^H (introduced in (arXiv:2011.06063) as a generalization of the chromatic symmetric function (CSF) X_G), which track homomorphisms from the graph G to the graph H. We focus first on the case of self-chromatic symmetric functions (self-CSFs) X_G^G, making some progress toward a conjecture from (arXiv:2011.06063) that the self-CSF, like the normal CSF, is always different for different trees. In particular, we show that the self-CSF distinguishes trees from non-trees with just one exception, we check using Sage that it distinguishes all trees on up to 12 vertices, and we show that it determines the number of legs of a spider and the degree sequence of a caterpillar given its spine length. We also show that the self-CSF detects the number of connected components of a forest, again with just one exception. Then we prove some results about the power sum expansions for H-CSFs when H is a complete bipartite graph, in particular proving that the conjecture from (arXiv:2011.06063) about p-monotonicity of ω(X_G^H) for H a star holds as long as H is sufficiently large compared to G. We also show that the self-CSFs of complete multipartite graphs form a basis for the ring Λ of symmetric functions, and we give some construction of bases for the vector space Λ^n of degree n symmetric functions using H-CSFs X_G^H where H is a fixed graph that is not a complete graph, answering a question from (arXiv:2011.06063) about whether such bases exist. However, we show that there generally do not exist such bases with G fixed, even with loops, answering another question from (arXiv:2011.06063). We also define the H-chromatic polynomial as an analogue of the chromatic polynomial, and ask when it is the same for different graphs.

The ZX-calculus is a universal graphical language for qubit quantum computation, meaning that every linear map between qubits can be expressed in the ZX-calculus. Furthermore, it is a complete graphical rewrite system: any equation involving linear maps that is derivable in the Hilbert space formalism for quantum theory can also be derived in the calculus by rewriting. It has widespread usage within quantum industry and academia for a variety of tasks such as quantum circuit optimisation, error-correction, and education. The ZW-calculus is an alternative universal graphical language that is also complete for qubit quantum computing. In fact, its completeness was used to prove that the ZX-calculus is universally complete. This calculus has advanced how quantum circuits are compiled into photonic hardware architectures in the industry. Recently, by combining these two calculi, a new calculus has emerged for qubit quantum computation, the ZXW-calculus. Using this calculus, graphical-differentiation, -integration, and -exponentiation were made possible, thus enabling the development of novel techniques in the domains of quantum machine learning and quantum chemistry. Here, we generalise the ZXW-calculus to arbitrary finite dimensions, that is, to qudits. Moreover, we prove that this graphical rewrite system is complete for any finite dimension. This is the first completeness result for any universal graphical language beyond qubits.

The higher-order correlation clustering problem is an expressive model, and recently, local search heuristics have been proposed for several applications. Certifying optimality, however, is NP-hard and practically hampered already by the complexity of the problem statement. Here, we focus on establishing partial optimality conditions for the special case of complete graphs and cubic objective functions. In addition, we define and implement algorithms for testing these conditions and examine their effect numerically, on two datasets.

We introduce fast algorithms for correlation clustering with respect to the Min Max objective that provide constant factor approximations on complete graphs. Our algorithms are the first purely combinatorial approximation algorithms for this problem. We construct a novel semi-metric on the set of vertices, which we call the correlation metric, that indicates to our clustering algorithms whether pairs of nodes should be in the same cluster. The paper demonstrates empirically that, compared to prior work, our algorithms sacrifice little in the objective quality to obtain significantly better run-time. Moreover, our algorithms scale to larger networks that are effectively intractable for known algorithms.

We propose Neural 3D Articulation Prior (NAP), the first 3D deep generative model to synthesize 3D articulated object models. Despite the extensive research on generating 3D objects, compositions, or scenes, there remains a lack of focus on capturing the distribution of articulated objects, a common object category for human and robot interaction. To generate articulated objects, we first design a novel articulation tree/graph parameterization and then apply a diffusion-denoising probabilistic model over this representation where articulated objects can be generated via denoising from random complete graphs. In order to capture both the geometry and the motion structure whose distribution will affect each other, we design a graph-attention denoising network for learning the reverse diffusion process. We propose a novel distance that adapts widely used 3D generation metrics to our novel task to evaluate generation quality, and experiments demonstrate our high performance in articulated object generation. We also demonstrate several conditioned generation applications, including Part2Motion, PartNet-Imagination, Motion2Part, and GAPart2Object.

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.

AI agents are vulnerable to prompt injection attacks, where malicious content hijacks agent behavior to steal credentials or cause financial loss. The only known robust defense is architectural isolation that strictly separates trusted task planning from untrusted environment observations. However, applying this design to Computer Use Agents (CUAs) -- systems that automate tasks by viewing screens and executing actions -- presents a fundamental challenge: current agents require continuous observation of UI state to determine each action, conflicting with the isolation required for security. We resolve this tension by demonstrating that UI workflows, while dynamic, are structurally predictable. We introduce Single-Shot Planning for CUAs, where a trusted planner generates a complete execution graph with conditional branches before any observation of potentially malicious content, providing provable control flow integrity guarantees against arbitrary instruction injections. Although this architectural isolation successfully prevents instruction injections, we show that additional measures are needed to prevent Branch Steering attacks, which manipulate UI elements to trigger unintended valid paths within the plan. We evaluate our design on OSWorld, and retain up to 57% of the performance of frontier models while improving performance for smaller open-source models by up to 19%, demonstrating that rigorous security and utility can coexist in CUAs.

Recent advances in multimodal pre-trained models have significantly improved information extraction from visually-rich documents (VrDs), in which named entity recognition (NER) is treated as a sequence-labeling task of predicting the BIO entity tags for tokens, following the typical setting of NLP. However, BIO-tagging scheme relies on the correct order of model inputs, which is not guaranteed in real-world NER on scanned VrDs where text are recognized and arranged by OCR systems. Such reading order issue hinders the accurate marking of entities by BIO-tagging scheme, making it impossible for sequence-labeling methods to predict correct named entities. To address the reading order issue, we introduce Token Path Prediction (TPP), a simple prediction head to predict entity mentions as token sequences within documents. Alternative to token classification, TPP models the document layout as a complete directed graph of tokens, and predicts token paths within the graph as entities. For better evaluation of VrD-NER systems, we also propose two revised benchmark datasets of NER on scanned documents which can reflect real-world scenarios. Experiment results demonstrate the effectiveness of our method, and suggest its potential to be a universal solution to various information extraction tasks on documents.

Let F be a graph, and let B_r(F) be the class of r-uniform Berge-F hypergraphs. In this paper, we establish a relationship between the spectral radius of the adjacency tensor of a uniform hypergraph and its local structure through walks. Based on the relationship, we give a spectral asymptotic bound for B_{r}(C_3)-free linear r-uniform hypergraphs and upper bounds for the spectral radii of B_{r}(K_{2,t})-free or {B_{r}(K_{s,t}),B_{r}(C_{3})}-free linear r-uniform hypergraphs, where C_{3} and K_{s,t} are respectively the triangle and the complete bipartite graph with one part having s vertices and the other part having t vertices. Our work implies an upper bound for the number of edges of {B_{r}(K_{s,t}),B_{r}(C_{3})}-free linear r-uniform hypergraphs and extends some of the existing research on (spectral) extremal problems of hypergraphs.

The original Grover's algorithm suffers from the souffle problem, which means that the success probability of quantum search decreases dramatically if the iteration time is too small or too large from the right time. To overcome the souffle problem, the fixed-point quantum search with an optimal number of queries was proposed [Phys. Rev. Lett. 113, 210501 (2014)], which always finds a marked state with a high probability when a lower bound of the proportion of marked states is given. The fixed-point quantum search relies on a key lemma regarding the explicit formula of recursive quasi-Chebyshev polynomials, but its proof is not given explicitly. In this work, we give a detailed proof of this lemma, thus providing a sound foundation for the correctness of the fixed-point quantum search. This lemma may be of independent interest as well, since it expands the mathematical form of the recursive relation of Chebyshev polynomials of the first kind, and it also constitutes a key component in overcoming the souffle problem of quantum walk-based search algorithms, for example, robust quantum walk search on complete bipartite graphs [Phys. Rev. A 106, 052207 (2022)]. Hopefully, more applications of the lemma will be found in the future.

Crystal structures are characterized by atomic bases within a primitive unit cell that repeats along a regular lattice throughout 3D space. The periodic and infinite nature of crystals poses unique challenges for geometric graph representation learning. Specifically, constructing graphs that effectively capture the complete geometric information of crystals and handle chiral crystals remains an unsolved and challenging problem. In this paper, we introduce a novel approach that utilizes the periodic patterns of unit cells to establish the lattice-based representation for each atom, enabling efficient and expressive graph representations of crystals. Furthermore, we propose ComFormer, a SE(3) transformer designed specifically for crystalline materials. ComFormer includes two variants; namely, iComFormer that employs invariant geometric descriptors of Euclidean distances and angles, and eComFormer that utilizes equivariant vector representations. Experimental results demonstrate the state-of-the-art predictive accuracy of ComFormer variants on various tasks across three widely-used crystal benchmarks. Our code is publicly available as part of the AIRS library (https://github.com/divelab/AIRS).

The dominant graph neural networks (GNNs) over-rely on the graph links, several serious performance problems with which have been witnessed already, e.g., suspended animation problem and over-smoothing problem. What's more, the inherently inter-connected nature precludes parallelization within the graph, which becomes critical for large-sized graph, as memory constraints limit batching across the nodes. In this paper, we will introduce a new graph neural network, namely GRAPH-BERT (Graph based BERT), solely based on the attention mechanism without any graph convolution or aggregation operators. Instead of feeding GRAPH-BERT with the complete large input graph, we propose to train GRAPH-BERT with sampled linkless subgraphs within their local contexts. GRAPH-BERT can be learned effectively in a standalone mode. Meanwhile, a pre-trained GRAPH-BERT can also be transferred to other application tasks directly or with necessary fine-tuning if any supervised label information or certain application oriented objective is available. We have tested the effectiveness of GRAPH-BERT on several graph benchmark datasets. Based the pre-trained GRAPH-BERT with the node attribute reconstruction and structure recovery tasks, we further fine-tune GRAPH-BERT on node classification and graph clustering tasks specifically. The experimental results have demonstrated that GRAPH-BERT can out-perform the existing GNNs in both the learning effectiveness and efficiency.

Graphic design is essential for visual communication with layouts being fundamental to composing attractive designs. Layout generation differs from pixel-level image synthesis and is unique in terms of the requirement of mutual relations among the desired components. We propose a method for design layout generation that can satisfy user-specified constraints. The proposed neural design network (NDN) consists of three modules. The first module predicts a graph with complete relations from a graph with user-specified relations. The second module generates a layout from the predicted graph. Finally, the third module fine-tunes the predicted layout. Quantitative and qualitative experiments demonstrate that the generated layouts are visually similar to real design layouts. We also construct real designs based on predicted layouts for a better understanding of the visual quality. Finally, we demonstrate a practical application on layout recommendation.

Since its 2009 genesis block, the Bitcoin network has processed >1.08 billion (B) transactions representing >8.72B BTC, offering rich potential for machine learning (ML); yet, its pseudonymity and obscured flow of funds inherent in its \utxo-based design, have rendered this data largely inaccessible for ML research. Addressing this gap, we present an ML-compatible graph modeling the Bitcoin's economic topology by reconstructing the flow of funds. This temporal, heterogeneous graph encompasses complete transaction history up to block \cutoffHeight, consisting of >2.4B nodes and >39.72B edges. Additionally, we provide custom sampling methods yielding node and edge feature vectors of sampled communities, tools to load and analyze the Bitcoin graph data within specialized graph databases, and ready-to-use database snapshots. This comprehensive dataset and toolkit empower the ML community to tackle Bitcoin's intricate ecosystem at scale, driving progress in applications such as anomaly detection, address classification, market analysis, and large-scale graph ML benchmarking. Dataset and code available at https://github.com/B1AAB/EBA{github.com/b1aab/eba}

We propose SAM-Road, an adaptation of the Segment Anything Model (SAM) for extracting large-scale, vectorized road network graphs from satellite imagery. To predict graph geometry, we formulate it as a dense semantic segmentation task, leveraging the inherent strengths of SAM. The image encoder of SAM is fine-tuned to produce probability masks for roads and intersections, from which the graph vertices are extracted via simple non-maximum suppression. To predict graph topology, we designed a lightweight transformer-based graph neural network, which leverages the SAM image embeddings to estimate the edge existence probabilities between vertices. Our approach directly predicts the graph vertices and edges for large regions without expensive and complex post-processing heuristics, and is capable of building complete road network graphs spanning multiple square kilometers in a matter of seconds. With its simple, straightforward, and minimalist design, SAM-Road achieves comparable accuracy with the state-of-the-art method RNGDet++, while being 40 times faster on the City-scale dataset. We thus demonstrate the power of a foundational vision model when applied to a graph learning task. The code is available at https://github.com/htcr/sam_road.

Spherical equivariant graph neural networks (EGNNs) provide a principled framework for learning on three-dimensional molecular and biomolecular systems, where predictions must respect the rotational symmetries inherent in physics. These models extend traditional message-passing GNNs and Transformers by representing node and edge features as spherical tensors that transform under irreducible representations of the rotation group SO(3), ensuring that predictions change in physically meaningful ways under rotations of the input. This guide develops a complete, intuitive foundation for spherical equivariant modeling - from group representations and spherical harmonics, to tensor products, Clebsch-Gordan decomposition, and the construction of SO(3)-equivariant kernels. Building on this foundation, we construct the Tensor Field Network and SE(3)-Transformer architectures and explain how they perform equivariant message-passing and attention on geometric graphs. Through clear mathematical derivations and annotated code excerpts, this guide serves as a self-contained introduction for researchers and learners seeking to understand or implement spherical EGNNs for applications in chemistry, molecular property prediction, protein structure modeling, and generative modeling.

Real-world tasks consist of multiple inter-dependent subtasks (e.g., a dirty pan needs to be washed before it can be used for cooking). In this work, we aim to model the causal dependencies between such subtasks from instructional videos describing the task. This is a challenging problem since complete information about the world is often inaccessible from videos, which demands robust learning mechanisms to understand the causal structure of events. We present Multimodal Subtask Graph Generation (MSG2), an approach that constructs a Subtask Graph defining the dependency between a task's subtasks relevant to a task from noisy web videos. Graphs generated by our multimodal approach are closer to human-annotated graphs compared to prior approaches. MSG2 further performs the downstream task of next subtask prediction 85% and 30% more accurately than recent video transformer models in the ProceL and CrossTask datasets, respectively.

Graph Convolutional Networks (GCNs) are powerful models for learning representations of attributed graphs. To scale GCNs to large graphs, state-of-the-art methods use various layer sampling techniques to alleviate the "neighbor explosion" problem during minibatch training. We propose GraphSAINT, a graph sampling based inductive learning method that improves training efficiency and accuracy in a fundamentally different way. By changing perspective, GraphSAINT constructs minibatches by sampling the training graph, rather than the nodes or edges across GCN layers. Each iteration, a complete GCN is built from the properly sampled subgraph. Thus, we ensure fixed number of well-connected nodes in all layers. We further propose normalization technique to eliminate bias, and sampling algorithms for variance reduction. Importantly, we can decouple the sampling from the forward and backward propagation, and extend GraphSAINT with many architecture variants (e.g., graph attention, jumping connection). GraphSAINT demonstrates superior performance in both accuracy and training time on five large graphs, and achieves new state-of-the-art F1 scores for PPI (0.995) and Reddit (0.970).

Large language models excel at function- and file-level code generation, yet generating complete repositories from scratch remains a fundamental challenge. This process demands coherent and reliable planning across proposal- and implementation-level stages, while natural language, due to its ambiguity and verbosity, is ill-suited for faithfully representing complex software structures. To address this, we introduce the Repository Planning Graph (RPG), a persistent representation that unifies proposal- and implementation-level planning by encoding capabilities, file structures, data flows, and functions in one graph. RPG replaces ambiguous natural language with an explicit blueprint, enabling long-horizon planning and scalable repository generation. Building on RPG, we develop ZeroRepo, a graph-driven framework for repository generation from scratch. It operates in three stages: proposal-level planning and implementation-level refinement to construct the graph, followed by graph-guided code generation with test validation. To evaluate this setting, we construct RepoCraft, a benchmark of six real-world projects with 1,052 tasks. On RepoCraft, ZeroRepo produces repositories averaging nearly 36K LOC, roughly 3.9times the strongest baseline (Claude Code) and about 64times other baselines. It attains 81.5% functional coverage and a 69.7% pass rate, exceeding Claude Code by 27.3 and 35.8 percentage points, respectively. Further analysis shows that RPG models complex dependencies, enables progressively more sophisticated planning through near-linear scaling, and enhances LLM understanding of repositories, thereby accelerating agent localization.

We propose a fully spectral, neuro\-symbolic reasoning architecture that leverages Graph Signal Processing (GSP) as the primary computational backbone for integrating symbolic logic and neural inference. Unlike conventional reasoning models that treat spectral graph methods as peripheral components, our approach formulates the entire reasoning pipeline in the graph spectral domain. Logical entities and relationships are encoded as graph signals, processed via learnable spectral filters that control multi-scale information propagation, and mapped into symbolic predicates for rule-based inference. We present a complete mathematical framework for spectral reasoning, including graph Fourier transforms, band-selective attention, and spectral rule grounding. Experiments on benchmark reasoning datasets (ProofWriter, EntailmentBank, bAbI, CLUTRR, and ARC-Challenge) demonstrate improvements in logical consistency, interpretability, and computational efficiency over state\-of\-the\-art neuro\-symbolic models. Our results suggest that GSP provides a mathematically grounded and computationally efficient substrate for robust and interpretable reasoning systems.

We study a graph bandit setting where the objective of the learner is to detect the most influential node of a graph by requesting as little information from the graph as possible. One of the relevant applications for this setting is marketing in social networks, where the marketer aims at finding and taking advantage of the most influential customers. The existing approaches for bandit problems on graphs require either partial or complete knowledge of the graph. In this paper, we do not assume any knowledge of the graph, but we consider a setting where it can be gradually discovered in a sequential and active way. At each round, the learner chooses a node of the graph and the only information it receives is a stochastic set of the nodes that the chosen node is currently influencing. To address this setting, we propose BARE, a bandit strategy for which we prove a regret guarantee that scales with the detectable dimension, a problem dependent quantity that is often much smaller than the number of nodes.

Methods that use Large Language Models (LLM) as planners for embodied instruction following tasks have become widespread. To successfully complete tasks, the LLM must be grounded in the environment in which the robot operates. One solution is to use a scene graph that contains all the necessary information. Modern methods rely on prebuilt scene graphs and assume that all task-relevant information is available at the start of planning. However, these approaches do not account for changes in the environment that may occur between the graph construction and the task execution. We propose LookPlanGraph - a method that leverages a scene graph composed of static assets and object priors. During plan execution, LookPlanGraph continuously updates the graph with relevant objects, either by verifying existing priors or discovering new entities. This is achieved by processing the agents egocentric camera view using a Vision Language Model. We conducted experiments with changed object positions VirtualHome and OmniGibson simulated environments, demonstrating that LookPlanGraph outperforms methods based on predefined static scene graphs. To demonstrate the practical applicability of our approach, we also conducted experiments in a real-world setting. Additionally, we introduce the GraSIF (Graph Scenes for Instruction Following) dataset with automated validation framework, comprising 514 tasks drawn from SayPlan Office, BEHAVIOR-1K, and VirtualHome RobotHow. Project page available at https://lookplangraph.github.io .

Ensuring that Software Requirements Specifications (SRS) align with higher-level organizational or national requirements is vital, particularly in regulated environments such as finance and aerospace. In these domains, maintaining consistency, adhering to regulatory frameworks, minimizing errors, and meeting critical expectations are essential for the reliable functioning of systems. The widespread adoption of large language models (LLMs) highlights their immense potential, yet there remains considerable scope for improvement in retrieving relevant information and enhancing reasoning capabilities. This study demonstrates that integrating a robust Graph-RAG framework with advanced prompt engineering techniques, such as Chain of Thought and Tree of Thought, can significantly enhance performance. Compared to baseline RAG methods and simple prompting strategies, this approach delivers more accurate and context-aware results. While this method demonstrates significant improvements in performance, it comes with challenges. It is both costly and more complex to implement across diverse contexts, requiring careful adaptation to specific scenarios. Additionally, its effectiveness heavily relies on having complete and accurate input data, which may not always be readily available, posing further limitations to its scalability and practicality.

Neural network-based Combinatorial Optimization (CO) methods have shown promising results in solving various NP-complete (NPC) problems without relying on hand-crafted domain knowledge. This paper broadens the current scope of neural solvers for NPC problems by introducing a new graph-based diffusion framework, namely DIFUSCO. Our framework casts NPC problems as discrete {0, 1}-vector optimization problems and leverages graph-based denoising diffusion models to generate high-quality solutions. We investigate two types of diffusion models with Gaussian and Bernoulli noise, respectively, and devise an effective inference schedule to enhance the solution quality. We evaluate our methods on two well-studied NPC combinatorial optimization problems: Traveling Salesman Problem (TSP) and Maximal Independent Set (MIS). Experimental results show that DIFUSCO strongly outperforms the previous state-of-the-art neural solvers, improving the performance gap between ground-truth and neural solvers from 1.76% to 0.46% on TSP-500, from 2.46% to 1.17% on TSP-1000, and from 3.19% to 2.58% on TSP10000. For the MIS problem, DIFUSCO outperforms the previous state-of-the-art neural solver on the challenging SATLIB benchmark.

Recent works integrating Knowledge Graphs (KGs) have led to promising improvements in enhancing the reasoning accuracy of Large Language Models (LLMs). However, current benchmarks focus mainly on closed-ended tasks, leaving a gap in the assessment of more complex real-world scenarios. This gap has also obscured the evaluation of KGs' potential to mitigate the problem of hallucination in LLMs. To fill the gap, we introduce OKGQA, a new benchmark specifically designed to assess LLMs enhanced with KGs under open-ended, real-world question answering scenarios. OKGQA is designed to closely reflect the complexities of practical applications using questions from different types, and incorporates specific metrics to measure both hallucination ratio and the enhancement in reasoning capabilities. To consider the scenario in which KGs may have varying levels of mistakes, we propose another benchmark variant OKGQA-P to assess model performance when the semantics and structure of KGs are deliberately perturbed and contaminated. OKGQA aims to (1) explore whether KGs can make LLMs more trustworthy in an open-ended setting, and (2) conduct a comparative analysis to shed light on method design. We believe that this study can facilitate a more complete performance comparison and encourage continuous improvement in integrating KGs with LLMs to reduce hallucination.

The automated extraction of complete and precise road network graphs from remote sensing imagery remains a critical challenge in geospatial computer vision. Segmentation-based approaches, while effective in pixel-level recognition, struggle to maintain topology fidelity after vectorization postprocessing. Graph-growing methods build more topologically faithful graphs but suffer from computationally prohibitive iterative ROI cropping. Graph-generating methods first predict global static candidate road network vertices, and then infer possible edges between vertices. They achieve fast topology-aware inference, but limits the dynamic insertion of vertices. To address these challenges, we propose DeH4R, a novel hybrid model that combines graph-generating efficiency and graph-growing dynamics. This is achieved by decoupling the task into candidate vertex detection, adjacent vertex prediction, initial graph contruction, and graph expansion. This architectural innovation enables dynamic vertex (edge) insertions while retaining fast inference speed and enhancing both topology fidelity and spatial consistency. Comprehensive evaluations on CityScale and SpaceNet benchmarks demonstrate state-of-the-art (SOTA) performance. DeH4R outperforms the prior SOTA graph-growing method RNGDet++ by 4.62 APLS and 10.18 IoU on CityScale, while being approximately 10 times faster. The code will be made publicly available at https://github.com/7777777FAN/DeH4R.

Propositional satisfiability (SAT) is an NP-complete problem that impacts many research fields, such as planning, verification, and security. Mainstream modern SAT solvers are based on the Conflict-Driven Clause Learning (CDCL) algorithm. Recent work aimed to enhance CDCL SAT solvers using Graph Neural Networks (GNNs). However, so far this approach either has not made solving more effective, or required substantial GPU resources for frequent online model inferences. Aiming to make GNN improvements practical, this paper proposes an approach called NeuroBack, which builds on two insights: (1) predicting phases (i.e., values) of variables appearing in the majority (or even all) of the satisfying assignments are essential for CDCL SAT solving, and (2) it is sufficient to query the neural model only once for the predictions before the SAT solving starts. Once trained, the offline model inference allows NeuroBack to execute exclusively on the CPU, removing its reliance on GPU resources. To train NeuroBack, a new dataset called DataBack containing 120,286 data samples is created. Finally, NeuroBack is implemented as an enhancement to a state-of-the-art SAT solver called Kissat. As a result, it allowed Kissat to solve 5.2% more problems on the recent SAT competition problem set, SATCOMP-2022. NeuroBack therefore shows how machine learning can be harnessed to improve SAT solving in an effective and practical manner.

Parse graphs of the human body can be obtained in the human brain to help humans complete the human pose estimation (HPE). It contains a hierarchical structure, like a tree structure, and context relations among nodes. Many researchers pre-design the parse graph of body structure, and then design framework for HPE. However, these frameworks are difficulty adapting when encountering situations that differ from the preset human structure. Different from them, we regard the feature map as a whole, similarly to human body, so the feature map can be optimized based on parse graphs and each node feature is learned implicitly instead of explicitly, which means it can flexibly respond to different human body structure. In this paper, we design the Refinement Module based on the Parse Graph of feature map (RMPG), which includes two stages: top-down decomposition and bottom-up combination. In the top-down decomposition stage, the feature map is decomposed into multiple sub-feature maps along the channel and their context relations are calculated to obtain their respective context information. In the bottom-up combination stage, the sub-feature maps and their context information are combined to obtain refined sub-feature maps, and then these refined sub-feature maps are concatenated to obtain the refined feature map. Additionally ,we design a top-down framework by using multiple RMPG modules for HPE, some of which are supervised to obtain context relations among body parts. Our framework achieves excellent results on the COCO keypoint detection, CrowdPose and MPII human pose datasets. More importantly, our experiments also demonstrate the effectiveness of RMPG on different methods, including SimpleBaselines, Hourglass, and ViTPose.

Automatically generating function summaries for binaries is an extremely valuable but challenging task, since it involves translating the execution behavior and semantics of the low-level language (assembly code) into human-readable natural language. However, most current works on understanding assembly code are oriented towards generating function names, which involve numerous abbreviations that make them still confusing. To bridge this gap, we focus on generating complete summaries for binary functions, especially for stripped binary (no symbol table and debug information in reality). To fully exploit the semantics of assembly code, we present a control flow graph and pseudo code guided binary code summarization framework called CP-BCS. CP-BCS utilizes a bidirectional instruction-level control flow graph and pseudo code that incorporates expert knowledge to learn the comprehensive binary function execution behavior and logic semantics. We evaluate CP-BCS on 3 different binary optimization levels (O1, O2, and O3) for 3 different computer architectures (X86, X64, and ARM). The evaluation results demonstrate CP-BCS is superior and significantly improves the efficiency of reverse engineering.

Skill usage has become a core component of modern agent systems and can substantially improve agents' ability to complete complex tasks. In real-world settings, where agents must monitor and interact with numerous personal applications, web browsers, and other environment interfaces, skill libraries can scale to thousands of reusable skills. Scaling to larger skill sets introduces two key challenges. First, loading the full skill set saturates the context window, driving up token costs, hallucination, and latency. In this paper, we present Graph of Skills (GoS), an inference-time structural retrieval layer for large skill libraries. GoS constructs an executable skill graph offline from skill packages, then at inference time retrieves a bounded, dependency-aware skill bundle through hybrid semantic-lexical seeding, reverse-weighted Personalized PageRank, and context-budgeted hydration. On SkillsBench and ALFWorld, GoS improves average reward by 43.6% over the vanilla full skill-loading baseline while reducing input tokens by 37.8%, and generalizes across three model families: Claude Sonnet, GPT-5.2 Codex, and MiniMax. Additional ablation studies across skill libraries ranging from 200 to 2,000 skills further demonstrate that GoS consistently outperforms both vanilla skills loading and simple vector retrieval in balancing reward, token efficiency, and runtime.

Half a billion citation edges extracted from 100.7 million Ukrainian court decisions reveal that judicial citation structure encodes legal domain boundaries without supervision and predicts future legislative importance with near-perfect accuracy. We construct the first large-scale citation graph from the complete EDRSR registry (99.5 million full texts, 1.1 TB), extracting 502 million citation links across six types via regex on commodity hardware in approximately 5 hours, with precision of 1.00 on a 200-decision validation sample (95% Wilson CI: [0.982, 1.000]). Three principal findings emerge. (1) The degree distribution follows a power law (alpha = 1.57 +/- 0.008), placing the Ukrainian court network near the EU Court of Justice and below the US Supreme Court, with hub articles cited by millions of decisions. (2) Louvain community detection on the co-citation projection recovers legal domain boundaries (civil, criminal, administrative, commercial) with modularity Q = 0.44-0.55 and temporal stability (NMI = 0.83-0.86 across periods), constituting an automatically constructed legal ontology grounded in judicial practice. (3) Citation features predict top-1000 articles with AUC = 0.9984, substantially outperforming a naive frequency baseline (P@1000 = 0.655); temporal dynamics detect legislative regime changes as phase transitions and the 2022 invasion as a citation entropy spike (H: 11.02 -> 13.49) with emergent wartime legislation nodes. The citation-derived ontology is operationalized as the domain layer of a workflow memory system for LLM-assisted legal analysis, connecting to the ontology-controlled paradigm. The extraction pipeline, analysis code, and aggregated statistics are released as open data.

Generative Knowledge Graph Construction (KGC) refers to those methods that leverage the sequence-to-sequence framework for building knowledge graphs, which is flexible and can be adapted to widespread tasks. In this study, we summarize the recent compelling progress in generative knowledge graph construction. We present the advantages and weaknesses of each paradigm in terms of different generation targets and provide theoretical insight and empirical analysis. Based on the review, we suggest promising research directions for the future. Our contributions are threefold: (1) We present a detailed, complete taxonomy for the generative KGC methods; (2) We provide a theoretical and empirical analysis of the generative KGC methods; (3) We propose several research directions that can be developed in the future.

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.

Autonomous scientific discovery with large language model (LLM)-based agents has recently made substantial progress, demonstrating the ability to automate end-to-end research workflows. However, existing systems largely rely on runtime-centric execution paradigms, repeatedly reading, summarizing, and reasoning over large volumes of scientific literature online. This on-the-spot computation strategy incurs high computational cost, suffers from context window limitations, and often leads to brittle reasoning and hallucination. We propose Idea2Story, a pre-computation-driven framework for autonomous scientific discovery that shifts literature understanding from online reasoning to offline knowledge construction. Idea2Story continuously collects peer-reviewed papers together with their review feedback, extracts core methodological units, composes reusable research patterns, and organizes them into a structured methodological knowledge graph. At runtime, underspecified user research intents are aligned to established research paradigms, enabling efficient retrieval and reuse of high-quality research patterns instead of open-ended generation and trial-and-error. By grounding research planning and execution in a pre-built knowledge graph, Idea2Story alleviates the context window bottleneck of LLMs and substantially reduces repeated runtime reasoning over literature. We conduct qualitative analyses and preliminary empirical studies demonstrating that Idea2Story can generate coherent, methodologically grounded, and novel research patterns, and can produce several high-quality research demonstrations in an end-to-end setting. These results suggest that offline knowledge construction provides a practical and scalable foundation for reliable autonomous scientific discovery.

Modeling human language requires the ability to not only generate fluent text but also encode factual knowledge. However, traditional language models are only capable of remembering facts seen at training time, and often have difficulty recalling them. To address this, we introduce the knowledge graph language model (KGLM), a neural language model with mechanisms for selecting and copying facts from a knowledge graph that are relevant to the context. These mechanisms enable the model to render information it has never seen before, as well as generate out-of-vocabulary tokens. We also introduce the Linked WikiText-2 dataset, a corpus of annotated text aligned to the Wikidata knowledge graph whose contents (roughly) match the popular WikiText-2 benchmark. In experiments, we demonstrate that the KGLM achieves significantly better performance than a strong baseline language model. We additionally compare different language model's ability to complete sentences requiring factual knowledge, showing that the KGLM outperforms even very large language models in generating facts.

Vector graphic documents present visual elements in a resolution free, compact format and are often seen in creative applications. In this work, we attempt to learn a generative model of vector graphic documents. We define vector graphic documents by a multi-modal set of attributes associated to a canvas and a sequence of visual elements such as shapes, images, or texts, and train variational auto-encoders to learn the representation of the documents. We collect a new dataset of design templates from an online service that features complete document structure including occluded elements. In experiments, we show that our model, named CanvasVAE, constitutes a strong baseline for generative modeling of vector graphic documents.

Effective scheduling under tight resource, timing, and operational constraints underpins large-scale planning across sectors such as capital projects, manufacturing, logistics, and IT fleet transitions. However, the reliability of large language models (LLMs) when reasoning under high-constraint regimes is insufficiently characterized. To address this gap, we present R-ConstraintBench, a scalable framework that evaluates models on Resource-Constrained Project Scheduling Problems (RCPSP), an NP-Complete feasibility class, while difficulty increases via linear growth in constraints. R-ConstraintBench incrementally increases non-redundant precedence constraints in Directed Acyclic Graphs (DAGs) and then introduces downtime, temporal windows, and disjunctive constraints. As an illustrative example, we instantiate the benchmark in a data center migration setting and evaluate multiple LLMs using feasibility and error analysis, identifying degradation thresholds and constraint types most associated with failure. Empirically, strong models are near-ceiling on precedence-only DAGs, but feasibility performance collapses when downtime, temporal windows, and disjunctive constraints interact, implicating constraint interaction, not graph depth, as the principal bottleneck. Performance on clean synthetic ramps also does not guarantee transfer to domain-grounded scenarios, underscoring limited generalization.

Program source code contains complex structure information, which can be represented in structured data forms like trees or graphs. To acquire the structural information in source code, most existing researches use abstract syntax trees (AST). A group of works add additional edges to ASTs to convert source code into graphs and use graph neural networks to learn representations for program graphs. Although these works provide additional control or data flow information to ASTs for downstream tasks, they neglect an important aspect of structure information in AST itself: the different types of nodes and edges. In ASTs, different nodes contain different kinds of information like variables or control flow, and the relation between a node and all its children can also be different. To address the information of node and edge types, we bring the idea of heterogeneous graphs to learning on source code and present a new formula of building heterogeneous program graphs from ASTs with additional type information for nodes and edges. We use the ASDL grammar of programming language to define the node and edge types of program graphs. Then we use heterogeneous graph neural networks to learn on these graphs. We evaluate our approach on two tasks: code comment generation and method naming. Both tasks require reasoning on the semantics of complete code snippets. Experiment results show that our approach outperforms baseline models, including homogeneous graph-based models, showing that leveraging the type information of nodes and edges in program graphs can help in learning program semantics.

Recent advances in Retrieval-Augmented Generation (RAG) have shifted from simple vector similarity to structure-aware approaches like HippoRAG, which leverage Knowledge Graphs (KGs) and Personalized PageRank (PPR) to capture multi-hop dependencies. However, these methods suffer from a "Static Graph Fallacy": they rely on fixed transition probabilities determined during indexing. This rigidity ignores the query-dependent nature of edge relevance, causing semantic drift where random walks are diverted into high-degree "hub" nodes before reaching critical downstream evidence. Consequently, models often achieve high partial recall but fail to retrieve the complete evidence chain required for multi-hop queries. To address this, we propose CatRAG, Context-Aware Traversal for robust RAG, a framework that builds on the HippoRAG 2 architecture and transforms the static KG into a query-adaptive navigation structure. We introduce a multi-faceted framework to steer the random walk: (1) Symbolic Anchoring, which injects weak entity constraints to regularize the random walk; (2) Query-Aware Dynamic Edge Weighting, which dynamically modulates graph structure, to prune irrelevant paths while amplifying those aligned with the query's intent; and (3) Key-Fact Passage Weight Enhancement, a cost-efficient bias that structurally anchors the random walk to likely evidence. Experiments across four multi-hop benchmarks demonstrate that CatRAG consistently outperforms state of the art baselines. Our analysis reveals that while standard Recall metrics show modest gains, CatRAG achieves substantial improvements in reasoning completeness, the capacity to recover the entire evidence path without gaps. These results reveal that our approach effectively bridges the gap between retrieving partial context and enabling fully grounded reasoning. Resources are available at https://github.com/kwunhang/CatRAG.

GraphRAG enhances large language models (LLMs) to generate quality answers for user questions by retrieving related facts from external knowledge graphs. Existing GraphRAG methods adopt a fixed graph traversal strategy for fact retrieval but we observe that user questions come in different types and require different graph traversal strategies. As such, existing GraphRAG methods are limited in effectiveness (i.e., quality of the generated answers) and/or efficiency (i.e., response time or the number of used tokens). In this paper, we propose to classify the questions according to a complete four-class taxonomy and adaptively select the appropriate graph traversal strategy for each type of questions. Our system PolyG is essentially a query planner for GraphRAG and can handle diverse questions with an unified interface and execution engine. Compared with SOTA GraphRAG methods, PolyG achieves an overall win rate of 75% on generation quality and a speedup up to 4x on response time.

Statutory article retrieval (SAR), the task of retrieving statute law articles relevant to a legal question, is a promising application of legal text processing. In particular, high-quality SAR systems can improve the work efficiency of legal professionals and provide basic legal assistance to citizens in need at no cost. Unlike traditional ad-hoc information retrieval, where each document is considered a complete source of information, SAR deals with texts whose full sense depends on complementary information from the topological organization of statute law. While existing works ignore these domain-specific dependencies, we propose a novel graph-augmented dense statute retriever (G-DSR) model that incorporates the structure of legislation via a graph neural network to improve dense retrieval performance. Experimental results show that our approach outperforms strong retrieval baselines on a real-world expert-annotated SAR dataset.

When reading a document, glancing at the spatial layout of a document is an initial step to understand it roughly. Traditional document layout analysis (DLA) methods, however, offer only a superficial parsing of documents, focusing on basic instance detection and often failing to capture the nuanced spatial and logical relations between instances. These limitations hinder DLA-based models from achieving a gradually deeper comprehension akin to human reading. In this work, we propose a novel graph-based Document Structure Analysis (gDSA) task. This task requires that model not only detects document elements but also generates spatial and logical relations in form of a graph structure, allowing to understand documents in a holistic and intuitive manner. For this new task, we construct a relation graph-based document structure analysis dataset (GraphDoc) with 80K document images and 4.13M relation annotations, enabling training models to complete multiple tasks like reading order, hierarchical structures analysis, and complex inter-element relation inference. Furthermore, a document relation graph generator (DRGG) is proposed to address the gDSA task, which achieves performance with 57.6% at mAP_g@0.5 for a strong benchmark baseline on this novel task and dataset. We hope this graphical representation of document structure can mark an innovative advancement in document structure analysis and understanding. The new dataset and code will be made publicly available at https://yufanchen96.github.io/projects/GraphDoc.

Timely accurate traffic forecast is crucial for urban traffic control and guidance. Due to the high nonlinearity and complexity of traffic flow, traditional methods cannot satisfy the requirements of mid-and-long term prediction tasks and often neglect spatial and temporal dependencies. In this paper, we propose a novel deep learning framework, Spatio-Temporal Graph Convolutional Networks (STGCN), to tackle the time series prediction problem in traffic domain. Instead of applying regular convolutional and recurrent units, we formulate the problem on graphs and build the model with complete convolutional structures, which enable much faster training speed with fewer parameters. Experiments show that our model STGCN effectively captures comprehensive spatio-temporal correlations through modeling multi-scale traffic networks and consistently outperforms state-of-the-art baselines on various real-world traffic datasets.

Graphic design forms the cornerstone of modern visual communication, serving as a vital medium for promoting cultural and commercial events. Recent advances have explored automating this process using Large Multimodal Models (LMMs), yet existing methods often produce geometrically inaccurate layouts and lack the iterative, layer-specific editing required in professional workflows. To address these limitations, we present PosterCopilot, a framework that advances layout reasoning and controllable editing for professional graphic design. Specifically, we introduce a progressive three-stage training strategy that equips LMMs with geometric understanding and aesthetic reasoning for layout design, consisting of Perturbed Supervised Fine-Tuning, Reinforcement Learning for Visual-Reality Alignment, and Reinforcement Learning from Aesthetic Feedback. Furthermore, we develop a complete workflow that couples the trained LMM-based design model with generative models, enabling layer-controllable, iterative editing for precise element refinement while maintaining global visual consistency. Extensive experiments demonstrate that PosterCopilot achieves geometrically accurate and aesthetically superior layouts, offering unprecedented controllability for professional iterative design.

Knowledge Graph (KG)-augmented Large Language Models (LLMs) have recently propelled significant advances in complex reasoning tasks, thanks to their broad domain knowledge and contextual awareness. Unfortunately, current methods often assume KGs to be complete, which is impractical given the inherent limitations of KG construction and the potential loss of contextual cues when converting unstructured text into entity-relation triples. In response, this paper proposes the Triple Context Restoration and Query-driven Feedback (TCR-QF) framework, which reconstructs the textual context underlying each triple to mitigate information loss, while dynamically refining the KG structure by iteratively incorporating query-relevant missing knowledge. Experiments on five benchmark question-answering datasets substantiate the effectiveness of TCR-QF in KG and LLM integration, where itachieves a 29.1% improvement in Exact Match and a 15.5% improvement in F1 over its state-of-the-art GraphRAG competitors.

One of the fundamental problems in Artificial Intelligence is to perform complex multi-hop logical reasoning over the facts captured by a knowledge graph (KG). This problem is challenging, because KGs can be massive and incomplete. Recent approaches embed KG entities in a low dimensional space and then use these embeddings to find the answer entities. However, it has been an outstanding challenge of how to handle arbitrary first-order logic (FOL) queries as present methods are limited to only a subset of FOL operators. In particular, the negation operator is not supported. An additional limitation of present methods is also that they cannot naturally model uncertainty. Here, we present BetaE, a probabilistic embedding framework for answering arbitrary FOL queries over KGs. BetaE is the first method that can handle a complete set of first-order logical operations: conjunction (wedge), disjunction (vee), and negation (neg). A key insight of BetaE is to use probabilistic distributions with bounded support, specifically the Beta distribution, and embed queries/entities as distributions, which as a consequence allows us to also faithfully model uncertainty. Logical operations are performed in the embedding space by neural operators over the probabilistic embeddings. We demonstrate the performance of BetaE on answering arbitrary FOL queries on three large, incomplete KGs. While being more general, BetaE also increases relative performance by up to 25.4% over the current state-of-the-art KG reasoning methods that can only handle conjunctive queries without negation.

Real-world databases are predominantly relational, comprising multiple interlinked tables that contain complex structural and statistical dependencies. Learning generative models on relational data has shown great promise in generating synthetic data and imputing missing values. However, existing methods often struggle to capture this complexity, typically reducing relational data to conditionally generated flat tables and imposing limiting structural assumptions. To address these limitations, we introduce RelDiff, a novel diffusion generative model that synthesizes complete relational databases by explicitly modeling their foreign key graph structure. RelDiff combines a joint graph-conditioned diffusion process across all tables for attribute synthesis, and a 2K+SBM graph generator based on the Stochastic Block Model for structure generation. The decomposition of graph structure and relational attributes ensures both high fidelity and referential integrity, both of which are crucial aspects of synthetic relational database generation. Experiments on 11 benchmark datasets demonstrate that RelDiff consistently outperforms prior methods in producing realistic and coherent synthetic relational databases. Code is available at https://github.com/ValterH/RelDiff.

Knowledge Graph (KG) plays a crucial role in Medical Report Generation (MRG) because it reveals the relations among diseases and thus can be utilized to guide the generation process. However, constructing a comprehensive KG is labor-intensive and its applications on the MRG process are under-explored. In this study, we establish a complete KG on chest X-ray imaging that includes 137 types of diseases and abnormalities. Based on this KG, we find that the current MRG data sets exhibit a long-tailed problem in disease distribution. To mitigate this problem, we introduce a novel augmentation strategy that enhances the representation of disease types in the tail-end of the distribution. We further design a two-stage MRG approach, where a classifier is first trained to detect whether the input images exhibit any abnormalities. The classified images are then independently fed into two transformer-based generators, namely, ``disease-specific generator" and ``disease-free generator" to generate the corresponding reports. To enhance the clinical evaluation of whether the generated reports correctly describe the diseases appearing in the input image, we propose diverse sensitivity (DS), a new metric that checks whether generated diseases match ground truth and measures the diversity of all generated diseases. Results show that the proposed two-stage generation framework and augmentation strategies improve DS by a considerable margin, indicating a notable reduction in the long-tailed problem associated with under-represented diseases.

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.

For a positive integer k, a graph property H, and a graph parameter P, let ex_{P}(n, H; δgeq k) denote the maximum value of P over all n-vertex graphs with minimum degree at least k that do not possess the property H. The corresponding extremal families are denoted by EX_{P}(n, H; δgeq k). For two disjoint graphs H_1 and H_2, let H_1 cup H_2 denote their (disjoint) union, i.e., the graph with vertex set V(H_1) cup V(H_2) and edge set E(H_1) cup E(H_2); and let H_1 vee H_2 denote their join. In 1962, Erdős established a classical theorem on the maximum number of edges in a non-Hamiltonian graph of given order and minimum degree. Motivated by recent work on feasible graph parameters in Ai2023, we prove several extensions of Erdős's 1962 theorem on non-Hamiltonian graphs. The first result gives a common generalization of the extremal theorem due to Erdős and its spectral analogs. As direct applications, we obtain complete solutions to open problems raised in the literature since 2016, thereby improving nearly all related prior results in this direction. Our proof technique differs somewhat from those in MR3539577,MR3556876. We also prove an analog theorem for the Hamiltonian-connected property and obtain a result which extends the theorem of Füredi, Kostochka, and Luo MR3843180 on Hamilton cycles.

In this paper, we present Batch Informed Trees (BIT*), a planning algorithm based on unifying graph- and sampling-based planning techniques. By recognizing that a set of samples describes an implicit random geometric graph (RGG), we are able to combine the efficient ordered nature of graph-based techniques, such as A*, with the anytime scalability of sampling-based algorithms, such as Rapidly-exploring Random Trees (RRT). BIT* uses a heuristic to efficiently search a series of increasingly dense implicit RGGs while reusing previous information. It can be viewed as an extension of incremental graph-search techniques, such as Lifelong Planning A* (LPA*), to continuous problem domains as well as a generalization of existing sampling-based optimal planners. It is shown that it is probabilistically complete and asymptotically optimal. We demonstrate the utility of BIT* on simulated random worlds in R^2 and R^8 and manipulation problems on CMU's HERB, a 14-DOF two-armed robot. On these problems, BIT* finds better solutions faster than RRT, RRT*, Informed RRT*, and Fast Marching Trees (FMT*) with faster anytime convergence towards the optimum, especially in high dimensions.

We present Synergy Aware Forgetting Ensemble (SAFE), a method to adapt large models on a diverse collection of data while minimizing the expected cost to remove the influence of training samples from the trained model. This process, also known as selective forgetting or unlearning, is often conducted by partitioning a dataset into shards, training fully independent models on each, then ensembling the resulting models. Increasing the number of shards reduces the expected cost to forget but at the same time it increases inference cost and reduces the final accuracy of the model since synergistic information between samples is lost during the independent model training. Rather than treating each shard as independent, SAFE introduces the notion of a shard graph, which allows incorporating limited information from other shards during training, trading off a modest increase in expected forgetting cost with a significant increase in accuracy, all while still attaining complete removal of residual influence after forgetting. SAFE uses a lightweight system of adapters which can be trained while reusing most of the computations. This allows SAFE to be trained on shards an order-of-magnitude smaller than current state-of-the-art methods (thus reducing the forgetting costs) while also maintaining high accuracy, as we demonstrate empirically on fine-grained computer vision datasets.

Recent research on integrating Large Language Models (LLMs) with Graph Neural Networks (GNNs) typically follows two approaches: LLM-centered models, which convert graph data into tokens for LLM processing, and GNN-centered models, which use LLMs to encode text features into node and edge representations for GNN input. LLM-centered models often struggle to capture graph structures effectively, while GNN-centered models compress variable-length textual data into fixed-size vectors, limiting their ability to understand complex semantics. Additionally, GNN-centered approaches require converting tasks into a uniform, manually-designed format, restricting them to classification tasks and preventing language output. To address these limitations, we introduce a new architecture that deeply integrates GNN with LLM, featuring three key innovations: (1) Structure-Aware Transformers, which incorporate GNN's message-passing capabilities directly into LLM's transformer layers, allowing simultaneous processing of textual and structural information and generating outputs from both GNN and LLM; (2) Graph-Text Cross-Attention, which processes full, uncompressed text from graph nodes and edges, ensuring complete semantic integration; and (3) GNN-LLM Twin Predictor, enabling LLM's flexible autoregressive generation alongside GNN's scalable one-pass prediction. GL-Fusion achieves outstand performance on various tasks. Notably, it achieves state-of-the-art performance on OGBN-Arxiv and OGBG-Code2.

The k-Coloring problem on hereditary graph classes has been a deeply researched problem over the last decade. A hereditary graph class is characterized by a (possibly infinite) list of minimal forbidden induced subgraphs. We say that a graph is (H_1,H_2,ldots)-free if it does not contain any of H_1,H_2,ldots as induced subgraphs. The complexity landscape of the problem remains unclear even when restricting to the case k=4 and classes defined by a few forbidden induced subgraphs. While the case of only one forbidden induced subgraph has been completely resolved lately, the complexity when considering two forbidden induced subgraphs still has a couple of unknown cases. In particular, 4-Coloring on (P_6,C_3)-free graphs is polynomial while it is NP-hard on (P_{22},C_3)-free graphs. We provide a reduction showing NP-completeness of 4-Coloring on (P_t,C_3)-free graphs for 19leq tleq 21, thus constricting the gap of cases whose complexity remains unknown. Our proof includes a computer search ensuring that the graph family obtained through the reduction is indeed P_{19}-free.

Multi-band radiomap reconstruction (MB-RMR) is a key component in wireless communications for tasks such as spectrum management and network planning. However, traditional machine-learning-based MB-RMR methods, which rely heavily on simulated data or complete structured ground truth, face significant deployment challenges. These challenges stem from the differences between simulated and actual data, as well as the scarcity of real-world measurements. To address these challenges, our study presents RadioGAT, a novel framework based on Graph Attention Network (GAT) tailored for MB-RMR within a single area, eliminating the need for multi-region datasets. RadioGAT innovatively merges model-based spatial-spectral correlation encoding with data-driven radiomap generalization, thus minimizing the reliance on extensive data sources. The framework begins by transforming sparse multi-band data into a graph structure through an innovative encoding strategy that leverages radio propagation models to capture the spatial-spectral correlation inherent in the data. This graph-based representation not only simplifies data handling but also enables tailored label sampling during training, significantly enhancing the framework's adaptability for deployment. Subsequently, The GAT is employed to generalize the radiomap information across various frequency bands. Extensive experiments using raytracing datasets based on real-world environments have demonstrated RadioGAT's enhanced accuracy in supervised learning settings and its robustness in semi-supervised scenarios. These results underscore RadioGAT's effectiveness and practicality for MB-RMR in environments with limited data availability.

The complexity of laboratory environments requires solutions that simplify instrument interaction and enhance measurement automation. Traditional tools often require configuration, software, and programming skills, creating barriers to productivity. Previous approaches, including dedicated software suites and custom scripts, frequently fall short in providing user-friendly solutions that align with programming practices. We present LABIIUM, an AI-enhanced, zero-configuration measurement automation system designed to streamline experimental workflows and improve user productivity. LABIIUM integrates an AI assistant powered by Large Language Models (LLMs) to generate code. LABIIUM's Lab-Automation-Measurement Bridges (LAMBs) enable seamless instrument connectivity using standard tools such as VSCode and Python, eliminating setup overhead. To demonstrate its capabilities, we conducted experiments involving the measurement of the parametric transfer curve of a simple two-transistor inverting amplifier with a current source load. The AI assistant was evaluated using different prompt scenarios and compared with multiple models, including Claude Sonnet 3.5, Gemini Pro 1.5, and GPT-4o. An expert solution implementing the Gradient-Weighted Adaptive Stochastic Sampling (GWASS) method was used as a baseline. The solutions generated by the AI assistant were compared with the expert solution and a uniform linear sweep baseline with 10,000 points. The graph results show that the LLMs were able to successfully complete the most basic uniform sweep, but LLMs were unable to develop adaptive sweeping algorithms to compete with GWASS. The evaluation underscores LABIIUM's ability to enhance laboratory productivity and support digital transformation in research and industry, and emphasizes the future work required to improve LLM performance in Electronic Measurement Science Tasks.

Graphical User Interface (GUI) agents show great potential for enabling foundation models to complete real-world tasks, revolutionizing human-computer interaction and improving human productivity. In this report, we present OmegaUse, a general-purpose GUI agent model for autonomous task execution on both mobile and desktop platforms, supporting computer-use and phone-use scenarios. Building an effective GUI agent model relies on two factors: (1) high-quality data and (2) effective training methods. To address these, we introduce a carefully engineered data-construction pipeline and a decoupled training paradigm. For data construction, we leverage rigorously curated open-source datasets and introduce a novel automated synthesis framework that integrates bottom-up autonomous exploration with top-down taxonomy-guided generation to create high-fidelity synthetic data. For training, to better leverage these data, we adopt a two-stage strategy: Supervised Fine-Tuning (SFT) to establish fundamental interaction syntax, followed by Group Relative Policy Optimization (GRPO) to improve spatial grounding and sequential planning. To balance computational efficiency with agentic reasoning capacity, OmegaUse is built on a Mixture-of-Experts (MoE) backbone. To evaluate cross-terminal capabilities in an offline setting, we introduce OS-Nav, a benchmark suite spanning multiple operating systems: ChiM-Nav, targeting Chinese Android mobile environments, and Ubu-Nav, focusing on routine desktop interactions on Ubuntu. Extensive experiments show that OmegaUse is highly competitive across established GUI benchmarks, achieving a state-of-the-art (SOTA) score of 96.3% on ScreenSpot-V2 and a leading 79.1% step success rate on AndroidControl. OmegaUse also performs strongly on OS-Nav, reaching 74.24% step success on ChiM-Nav and 55.9% average success on Ubu-Nav.

Graphical user interface (GUI) agents autonomously operate across platforms (e.g., Linux) to complete tasks by interacting with visual elements. Specifically, a user instruction is decomposed into a sequence of action proposals, each corresponding to an interaction with the GUI. After each action, the agent observes the updated GUI environment to plan the next step. However, two main challenges arise: i) resolving ambiguity in task planning (i.e., the action proposal sequence), where selecting an appropriate plan is non-trivial, as many valid ones may exist; ii) accurately grounding actions in complex and high-resolution interfaces, i.e., precisely interacting with visual targets. This paper investigates the two aforementioned challenges with our GUI Test-time Scaling Agent, namely GTA1. First, to select the most appropriate action proposal, we introduce a test-time scaling method. At each step, we sample multiple candidate action proposals and leverage a judge model to evaluate and select the most suitable one. It trades off computation for better decision quality by concurrent sampling, shortening task execution steps, and improving overall performance. Second, we propose a model that achieves improved accuracy when grounding the selected action proposal to its corresponding visual elements. Our key insight is that reinforcement learning (RL) facilitates visual grounding through inherent objective alignments, rewarding successful clicks on interface elements. Experimentally, our method establishes state-of-the-art performance across diverse benchmarks. For example, GTA1-7B achieves 50.1%, 92.4%, and 67.7% accuracies on Screenspot-Pro, Screenspot-V2, and OSWorld-G, respectively. When paired with a planner applying our test-time scaling strategy, it exhibits state-of-the-art agentic performance (e.g., 45.2% task success rate on OSWorld). We open-source our code and models here.

Computer use agents (CUA) are systems that automatically interact with graphical user interfaces (GUIs) to complete tasks. CUA have made significant progress with the advent of large vision-language models (VLMs). However, these agents typically rely on cloud-based inference with substantial compute demands, raising critical privacy and scalability concerns, especially when operating on personal devices. In this work, we take a step toward privacy-preserving and resource-efficient agents by developing a lightweight vision-language model that runs entirely on local machines. To train this compact agent, we introduce an LLM-as-Judge framework that automatically evaluates and filters synthetic interaction trajectories, producing high-quality data for reinforcement learning without human annotation. Experiments on the OS-World benchmark demonstrate that our fine-tuned local model outperforms existing baselines, highlighting a promising path toward private, efficient, and generalizable GUI agents.

Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical organization inherent in protein structures. We introduce Topotein, a comprehensive framework that applies topological deep learning to PRL through the novel Protein Combinatorial Complex (PCC) and Topology-Complete Perceptron Network (TCPNet). Our PCC represents proteins at multiple hierarchical levels -- from residues to secondary structures to complete proteins -- while preserving geometric information at each level. TCPNet employs SE(3)-equivariant message passing across these hierarchical structures, enabling more effective capture of multi-scale structural patterns. Through extensive experiments on four PRL tasks, TCPNet consistently outperforms state-of-the-art geometric graph neural networks. Our approach demonstrates particular strength in tasks such as fold classification which require understanding of secondary structure arrangements, validating the importance of hierarchical topological features for protein analysis.

Motivated by applications in chemistry and other sciences, we study the expressive power of message-passing neural networks for geometric graphs, whose node features correspond to 3-dimensional positions. Recent work has shown that such models can separate generic pairs of non-isomorphic geometric graphs, though they may fail to separate some rare and complicated instances. However, these results assume a fully connected graph, where each node possesses complete knowledge of all other nodes. In contrast, often, in application, every node only possesses knowledge of a small number of nearest neighbors. This paper shows that generic pairs of non-isomorphic geometric graphs can be separated by message-passing networks with rotation equivariant features as long as the underlying graph is connected. When only invariant intermediate features are allowed, generic separation is guaranteed for generically globally rigid graphs. We introduce a simple architecture, EGENNET, which achieves our theoretical guarantees and compares favorably with alternative architecture on synthetic and chemical benchmarks. Our code is available at https://github.com/yonatansverdlov/E-GenNet.

Recent years have witnessed the rapid evolution of AI agents toward handling increasingly complex, real-world tasks. However, existing benchmarks rarely evaluate whether agents can operate graphical user interfaces to complete long-horizon, high-value professional workflows across diverse domains. Current GUI benchmarks still predominantly focus on general-purpose software, relatively simple applications, and short-horizon tasks, leaving it largely unknown whether modern agents can follow user instructions to autonomously operate domain-specific professional software and accomplish economically valuable work in an end-to-end manner. To bridge this gap, we introduce Workflow-GYM, a benchmark for long-horizon GUI tasks centered on professional domains and specialized software environments. Through extensive experiments on state-of-the-art models, we find that even the strongest models achieve only slightly above 30% success rates, highlighting that professional long-horizon GUI workflows remain highly challenging for current GUI agents. Further analysis reveals that current agents struggle to maintain long-horizon workflow consistency, frequently exhibiting workflow stage omission, error propagation, objective drift, and insufficient understanding of professional software environments. Our findings provide important insights into the limitations of current agent systems and suggest key directions for the next generation of GUI-agent research.

Recent studies in using deep reinforcement learning (DRL) to solve Job-shop scheduling problems (JSSP) focus on construction heuristics. However, their performance is still far from optimality, mainly because the underlying graph representation scheme is unsuitable for modelling partial solutions at each construction step. This paper proposes a novel DRL-guided improvement heuristic for solving JSSP, where graph representation is employed to encode complete solutions. We design a Graph Neural-Network-based representation scheme, consisting of two modules to effectively capture the information of dynamic topology and different types of nodes in graphs encountered during the improvement process. To speed up solution evaluation during improvement, we present a novel message-passing mechanism that can evaluate multiple solutions simultaneously. We prove that the computational complexity of our method scales linearly with problem size. Experiments on classic benchmarks show that the improvement policy learned by our method outperforms state-of-the-art DRL-based methods by a large margin.

Human dialogue contains evolving concepts, and speakers naturally associate multiple concepts to compose a response. However, current dialogue models with the seq2seq framework lack the ability to effectively manage concept transitions and can hardly introduce multiple concepts to responses in a sequential decoding manner. To facilitate a controllable and coherent dialogue, in this work, we devise a concept-guided non-autoregressive model (CG-nAR) for open-domain dialogue generation. The proposed model comprises a multi-concept planning module that learns to identify multiple associated concepts from a concept graph and a customized Insertion Transformer that performs concept-guided non-autoregressive generation to complete a response. The experimental results on two public datasets show that CG-nAR can produce diverse and coherent responses, outperforming state-of-the-art baselines in both automatic and human evaluations with substantially faster inference speed.

Recovering causal relationships from data is an important problem. Using observational data, one can typically only recover causal graphs up to a Markov equivalence class and additional assumptions or interventional data are needed for complete recovery. In this work, under some standard assumptions, we study causal graph discovery via adaptive interventions with node-dependent interventional costs. For this setting, we show that no algorithm can achieve an approximation guarantee that is asymptotically better than linear in the number of vertices with respect to the verification number; a well-established benchmark for adaptive search algorithms. Motivated by this negative result, we define a new benchmark that captures the worst-case interventional cost for any search algorithm. Furthermore, with respect to this new benchmark, we provide adaptive search algorithms that achieve logarithmic approximations under various settings: atomic, bounded size interventions and generalized cost objectives.

There has been considerable divergence of opinion on the reasoning abilities of Large Language Models (LLMs). While the initial optimism that reasoning might emerge automatically with scale has been tempered thanks to a slew of counterexamples, a wide spread belief in their iterative self-critique capabilities persists. In this paper, we set out to systematically investigate the effectiveness of iterative prompting of LLMs in the context of Graph Coloring, a canonical NP-complete reasoning problem that is related to propositional satisfiability as well as practical problems like scheduling and allocation. We present a principled empirical study of the performance of GPT4 in solving graph coloring instances or verifying the correctness of candidate colorings. In iterative modes, we experiment with the model critiquing its own answers and an external correct reasoner verifying proposed solutions. In both cases, we analyze whether the content of the criticisms actually affects bottom line performance. The study seems to indicate that (i) LLMs are bad at solving graph coloring instances (ii) they are no better at verifying a solution--and thus are not effective in iterative modes with LLMs critiquing LLM-generated solutions (iii) the correctness and content of the criticisms--whether by LLMs or external solvers--seems largely irrelevant to the performance of iterative prompting. We show that the observed increase in effectiveness is largely due to the correct solution being fortuitously present in the top-k completions of the prompt (and being recognized as such by an external verifier). Our results thus call into question claims about the self-critiquing capabilities of state of the art LLMs.

Code search with natural language plays a crucial role in reusing existing code snippets and accelerating software development. Thanks to the Transformer-based pretraining models, the performance of code search has been improved significantly compared to traditional information retrieval (IR) based models. However, due to the quadratic complexity of multi-head self-attention, there is a limit on the input token length. For efficient training on standard GPUs like V100, existing pretrained code models, including GraphCodeBERT, CodeBERT, RoBERTa (code), take the first 256 tokens by default, which makes them unable to represent the complete information of long code that is greater than 256 tokens. Unlike long text paragraph that can be regarded as a whole with complete semantics, the semantics of long code is discontinuous as a piece of long code may contain different code modules. Therefore, it is unreasonable to directly apply the long text processing methods to long code. To tackle the long code problem, we propose SEA (Split, Encode and Aggregate for Long Code Search), which splits long code into code blocks, encodes these blocks into embeddings, and aggregates them to obtain a comprehensive long code representation. With SEA, we could directly use Transformer-based pretraining models to model long code without changing their internal structure and repretraining. Leveraging abstract syntax tree (AST) based splitting and attention-based aggregation methods, SEA achieves significant improvements in long code search performance. We also compare SEA with two sparse Trasnformer methods. With GraphCodeBERT as the encoder, SEA achieves an overall mean reciprocal ranking score of 0.785, which is 10.1% higher than GraphCodeBERT on the CodeSearchNet benchmark.

As Large Language Model (LLM) agents become increasingly capable of automating complex, multi-step tasks, the need for robust, secure, and predictable architectural patterns is paramount. This paper provides a comprehensive guide to the ``Plan-then-Execute'' (P-t-E) pattern, an agentic design that separates strategic planning from tactical execution. We explore the foundational principles of P-t-E, detailing its core components - the Planner and the Executor - and its architectural advantages in predictability, cost-efficiency, and reasoning quality over reactive patterns like ReAct (Reason + Act). A central focus is placed on the security implications of this design, particularly its inherent resilience to indirect prompt injection attacks by establishing control-flow integrity. We argue that while P-t-E provides a strong foundation, a defense-in-depth strategy is necessary, and we detail essential complementary controls such as the Principle of Least Privilege, task-scoped tool access, and sandboxed code execution. To make these principles actionable, this guide provides detailed implementation blueprints and working code references for three leading agentic frameworks: LangChain (via LangGraph), CrewAI, and AutoGen. Each framework's approach to implementing the P-t-E pattern is analyzed, highlighting unique features like LangGraph's stateful graphs for re-planning, CrewAI's declarative tool scoping for security, and AutoGen's built-in Docker sandboxing. Finally, we discuss advanced patterns, including dynamic re-planning loops, parallel execution with Directed Acyclic Graphs (DAGs), and the critical role of Human-in-the-Loop (HITL) verification, to offer a complete strategic blueprint for architects, developers, and security engineers aiming to build production-grade, resilient, and trustworthy LLM agents.

AI coding agents operate in a paradox: they possess vast parametric knowledge yet cannot remember a conversation from an hour ago. Existing memory systems store text in vector databases with single-channel retrieval, require cloud LLMs for core operations, and implement none of the cognitive processes that make human memory effective. We present SuperLocalMemory V3.3 ("The Living Brain"), a local-first agent memory system implementing the full cognitive memory taxonomy with mathematical lifecycle dynamics. Building on the information-geometric foundations of V3.2 (arXiv:2603.14588), we introduce five contributions: (1) Fisher-Rao Quantization-Aware Distance (FRQAD) -- a new metric on the Gaussian statistical manifold achieving 100% precision at preferring high-fidelity embeddings over quantized ones (vs 85.6% for cosine), with zero prior art; (2) Ebbinghaus Adaptive Forgetting with lifecycle-aware quantization -- the first mathematical forgetting curve in local agent memory coupled to progressive embedding compression, achieving 6.7x discriminative power; (3) 7-channel cognitive retrieval spanning semantic, keyword, entity graph, temporal, spreading activation, consolidation, and Hopfield associative channels, achieving 70.4% on LoCoMo in zero-LLM Mode A; (4) memory parameterization implementing Long-Term Implicit memory via soft prompts; (5) zero-friction auto-cognitive pipeline automating the complete memory lifecycle. On LoCoMo, V3.3 achieves 70.4% in Mode A (zero-LLM), with +23.8pp on multi-hop and +12.7pp on adversarial. V3.2 achieved 74.8% Mode A and 87.7% Mode C; the 4.4pp gap reflects a deliberate architectural trade-off. SLM V3.3 is open source under the Elastic License 2.0, runs entirely on CPU, with over 5,000 monthly downloads.

This tutorial serves as a comprehensive guide for understanding graph databases, focusing on the fundamentals of graph theory while showcasing practical applications across various fields. It starts by introducing foundational concepts and delves into the structure of graphs through nodes and edges, covering different types such as undirected, directed, weighted, and unweighted graphs. Key graph properties, terminologies, and essential algorithms for network analysis are outlined, including Dijkstras shortest path algorithm and methods for calculating node centrality and graph connectivity. The tutorial highlights the advantages of graph databases over traditional relational databases, particularly in efficiently managing complex, interconnected data. It examines leading graph database systems such as Neo4j, Amazon Neptune, and ArangoDB, emphasizing their unique features for handling large datasets. Practical instructions on graph operations using NetworkX and Neo4j are provided, covering node and edge creation, attribute assignment, and advanced queries with Cypher. Additionally, the tutorial explores common graph visualization techniques using tools like Plotly and Neo4j Bloom, which enhance the interpretation and usability of graph data. It also delves into community detection algorithms, including the Louvain method, which facilitates clustering in large networks. Finally, the paper concludes with recommendations for researchers interested in exploring the vast potential of graph technologies.

A Harris Graph is a tough, Eulerian, non-Hamiltonian graph. Several approaches to creating new Harris graphs from existing ones are explored, including creating families of Harris graphs and combining Harris graphs. Pictures of all Harris Graphs through order 9 and the number of Harris graphs through order 12 are included. We also prove a result about barnacle-free Harris graphs.

Large language models (LLMs), such as ChatGPT and LLaMA, are creating significant advancements in natural language processing, due to their strong text encoding/decoding ability and newly found emergent capability (e.g., reasoning). While LLMs are mainly designed to process pure texts, there are many real-world scenarios where text data are associated with rich structure information in the form of graphs (e.g., academic networks, and e-commerce networks) or scenarios where graph data are paired with rich textual information (e.g., molecules with descriptions). Besides, although LLMs have shown their pure text-based reasoning ability, it is underexplored whether such ability can be generalized to graph scenarios (i.e., graph-based reasoning). In this paper, we provide a systematic review of scenarios and techniques related to large language models on graphs. We first summarize potential scenarios of adopting LLMs on graphs into three categories, namely pure graphs, text-rich graphs, and text-paired graphs. We then discuss detailed techniques for utilizing LLMs on graphs, including LLM as Predictor, LLM as Encoder, and LLM as Aligner, and compare the advantages and disadvantages of different schools of models. Furthermore, we mention the real-world applications of such methods and summarize open-source codes and benchmark datasets. Finally, we conclude with potential future research directions in this fast-growing field. The related source can be found at https://github.com/PeterGriffinJin/Awesome-Language-Model-on-Graphs.

Graph is powerful for representing various types of real-world data. The topology (edges' presence) and edges' features of a graph decides the message passing mechanism among vertices within the graph. While most existing approaches only manually define a single-value edge to describe the connectivity or strength of association between a pair of vertices, task-specific and crucial relationship cues may be disregarded by such manually defined topology and single-value edge features. In this paper, we propose the first general graph representation learning framework (called GRATIS) which can generate a strong graph representation with a task-specific topology and task-specific multi-dimensional edge features from any arbitrary input. To learn each edge's presence and multi-dimensional feature, our framework takes both of the corresponding vertices pair and their global contextual information into consideration, enabling the generated graph representation to have a globally optimal message passing mechanism for different down-stream tasks. The principled investigation results achieved for various graph analysis tasks on 11 graph and non-graph datasets show that our GRATIS can not only largely enhance pre-defined graphs but also learns a strong graph representation for non-graph data, with clear performance improvements on all tasks. In particular, the learned topology and multi-dimensional edge features provide complementary task-related cues for graph analysis tasks. Our framework is effective, robust and flexible, and is a plug-and-play module that can be combined with different backbones and Graph Neural Networks (GNNs) to generate a task-specific graph representation from various graph and non-graph data. Our code is made publicly available at https://github.com/SSYSteve/Learning-Graph-Representation-with-Task-specific-Topology-and-Multi-dimensional-Edge-Features.

The Berge-Fulkerson conjecture states that every bridgeless cubic graph can be covered with six perfect matchings such that each edge is covered exactly twice. An equivalent reformulation is that it's possible to find a 6-cycle 4-cover. In this paper we discuss the oriented version (o6c4c) of the latter statement, pose it as a conjecture and prove it for the family of Isaacs flower snarks. Similarly to the case of oriented cycle double cover, we can always construct an orientable surface (possibly with boundary) from an o6c4c solution. If the o6c4c solution itself splits into two (not necessarily oriented) cycle double covers, then it's also possible to build another pair of orientable surfaces (also possibly with boundaries). Finally we show how to build a ribbon graph, and for some special o6c4c cases we show that this ribbon graph corresponds to an oriented 6-cycle double cover. Github: https://github.com/gexahedron/cycle-double-covers

In the realm of generative models for graphs, extensive research has been conducted. However, most existing methods struggle with large graphs due to the complexity of representing the entire joint distribution across all node pairs and capturing both global and local graph structures simultaneously. To overcome these issues, we introduce a method that generates a graph by progressively expanding a single node to a target graph. In each step, nodes and edges are added in a localized manner through denoising diffusion, building first the global structure, and then refining the local details. The local generation avoids modeling the entire joint distribution over all node pairs, achieving substantial computational savings with subquadratic runtime relative to node count while maintaining high expressivity through multiscale generation. Our experiments show that our model achieves state-of-the-art performance on well-established benchmark datasets while successfully scaling to graphs with at least 5000 nodes. Our method is also the first to successfully extrapolate to graphs outside of the training distribution, showcasing a much better generalization capability over existing methods.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Graphs can be used to represent and reason about systems and a variety of metrics have been devised to quantify their global characteristics. However, little is currently known about how to construct a graph or improve an existing one given a target objective. In this work, we formulate the construction of a graph as a decision-making process in which a central agent creates topologies by trial and error and receives rewards proportional to the value of the target objective. By means of this conceptual framework, we propose an algorithm based on reinforcement learning and graph neural networks to learn graph construction and improvement strategies. Our core case study focuses on robustness to failures and attacks, a property relevant for the infrastructure and communication networks that power modern society. Experiments on synthetic and real-world graphs show that this approach can outperform existing methods while being cheaper to evaluate. It also allows generalization to out-of-sample graphs, as well as to larger out-of-distribution graphs in some cases. The approach is applicable to the optimization of other global structural properties of graphs.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

Let G be a graph with adjacency matrix A(G). We conjecture that \[2n^+(G) \le n^-(G)(n^-(G) + 1),\] where n^+(G) and n^-(G) denote the number of positive and negative eigenvalues of A(G), respectively. This conjecture generalizes to all graphs the well-known absolute bound for strongly regular graphs. The conjecture also relates to a question posed by Torgasev. We prove the conjecture for special graph families, including line graphs and planar graphs, and provide examples where the conjecture is exact. We also conjecture that for any connected graph G, its line graph L(G) satisfies n^+(L(G)) le n^-(L(G)) + 1 and obtain partial results.

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.

Assume n, m are positive integers and G is a graph. Let P_{n,m} be the graph obtained from the path with vertices {-m, -(m-1), ldots, 0, ldots, n} by adding a loop at vertex 0. The double cone Delta_{n,m}(G) over a graph G is obtained from the direct product G times P_{n,m} by identifying V(G) times {n} into a single vertex (star, n), identifying V(G) times {-m} into a single vertex (star, -m), and adding an edge connecting (star, -m) and (star, n). This paper determines the fractional chromatic number of Delta_{n,m}(G). In particular, if n < m or n=m is even, then chi_f(Delta_{n,m}(G)) = chi_f(Delta_n(G)), where Delta_n(G) is the nth cone over G. If n=m is odd, then chi_f(Delta_{n,m}(G)) > chi_f(Delta_n(G)). The chromatic number of Delta_{n,m}(G) is also discussed.

The arXiv has collected 1.5 million pre-print articles over 28 years, hosting literature from scientific fields including Physics, Mathematics, and Computer Science. Each pre-print features text, figures, authors, citations, categories, and other metadata. These rich, multi-modal features, combined with the natural graph structure---created by citation, affiliation, and co-authorship---makes the arXiv an exciting candidate for benchmarking next-generation models. Here we take the first necessary steps toward this goal, by providing a pipeline which standardizes and simplifies access to the arXiv's publicly available data. We use this pipeline to extract and analyze a 6.7 million edge citation graph, with an 11 billion word corpus of full-text research articles. We present some baseline classification results, and motivate application of more exciting generative graph models.

Graphs are ubiquitous structures found in numerous real-world applications, such as drug discovery, recommender systems, and social network analysis. To model graph-structured data, graph neural networks (GNNs) have become a popular tool. However, existing GNN architectures encounter challenges in cross-graph learning where multiple graphs have different feature spaces. To address this, recent approaches introduce text-attributed graphs (TAGs), where each node is associated with a textual description, which can be projected into a unified feature space using textual encoders. While promising, this method relies heavily on the availability of text-attributed graph data, which is difficult to obtain in practice. To bridge this gap, we propose a novel method named Topology-Aware Node description Synthesis (TANS), leveraging large language models (LLMs) to convert existing graphs into text-attributed graphs. The key idea is to integrate topological information into LLMs to explain how graph topology influences node semantics. We evaluate our TANS on text-rich, text-limited, and text-free graphs, demonstrating its applicability. Notably, on text-free graphs, our method significantly outperforms existing approaches that manually design node features, showcasing the potential of LLMs for preprocessing graph-structured data in the absence of textual information. The code and data are available at https://github.com/Zehong-Wang/TANS.

Biological neural networks define the brain function and intelligence of humans and other mammals, and form ultra-large, spatial, structured graphs. Their neuronal organization is closely interconnected with the spatial organization of the brain's microvasculature, which supplies oxygen to the neurons and builds a complementary spatial graph. This vasculature (or the vessel structure) plays an important role in neuroscience; for example, the organization of (and changes to) vessel structure can represent early signs of various pathologies, e.g. Alzheimer's disease or stroke. Recently, advances in tissue clearing have enabled whole brain imaging and segmentation of the entirety of the mouse brain's vasculature. Building on these advances in imaging, we are presenting an extendable dataset of whole-brain vessel graphs based on specific imaging protocols. Specifically, we extract vascular graphs using a refined graph extraction scheme leveraging the volume rendering engine Voreen and provide them in an accessible and adaptable form through the OGB and PyTorch Geometric dataloaders. Moreover, we benchmark numerous state-of-the-art graph learning algorithms on the biologically relevant tasks of vessel prediction and vessel classification using the introduced vessel graph dataset. Our work paves a path towards advancing graph learning research into the field of neuroscience. Complementarily, the presented dataset raises challenging graph learning research questions for the machine learning community, in terms of incorporating biological priors into learning algorithms, or in scaling these algorithms to handle sparse,spatial graphs with millions of nodes and edges. All datasets and code are available for download at https://github.com/jocpae/VesselGraph .

Given a massive graph, how can we exploit its hierarchical structure for concisely but exactly summarizing the graph? By exploiting the structure, can we achieve better compression rates than state-of-the-art graph summarization methods? The explosive proliferation of the Web has accelerated the emergence of large graphs, such as online social networks and hyperlink networks. Consequently, graph compression has become increasingly important to process such large graphs without expensive I/O over the network or to disk. Among a number of approaches, graph summarization, which in essence combines similar nodes into a supernode and describe their connectivity concisely, protrudes with several advantages. However, we note that it fails to exploit pervasive hierarchical structures of real-world graphs as its underlying representation model enforces supernodes to be disjoint. In this work, we propose the hierarchical graph summarization model, which is an expressive graph representation model that includes the previous one proposed by Navlakha et al. as a special case. The new model represents an unweighted graph using positive and negative edges between hierarchical supernodes, each of which can contain others. Then, we propose Slugger, a scalable heuristic for concisely and exactly representing a given graph under our new model. Slugger greedily merges nodes into supernodes while maintaining and exploiting their hierarchy, which is later pruned. Slugger significantly accelerates this process by sampling, approximation, and memoization. Our experiments on 16 real-world graphs show that Slugger is (a) Effective: yielding up to 29.6% more concise summary than state-of-the-art lossless summarization methods, (b) Fast: summarizing a graph with 0.8 billion edges in a few hours, and (c) Scalable: scaling linearly with the number of edges in the input graph.

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.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

Recent advances in learning multi-modal representation have witnessed the success in biomedical domains. While established techniques enable handling multi-modal information, the challenges are posed when extended to various clinical modalities and practical modalitymissing setting due to the inherent modality gaps. To tackle these, we propose an innovative Modality-prompted Heterogeneous Graph for Omnimodal Learning (GTP-4o), which embeds the numerous disparate clinical modalities into a unified representation, completes the deficient embedding of missing modality and reformulates the cross-modal learning with a graph-based aggregation. Specially, we establish a heterogeneous graph embedding to explicitly capture the diverse semantic properties on both the modality-specific features (nodes) and the cross-modal relations (edges). Then, we design a modality-prompted completion that enables completing the inadequate graph representation of missing modality through a graph prompting mechanism, which generates hallucination graphic topologies to steer the missing embedding towards the intact representation. Through the completed graph, we meticulously develop a knowledge-guided hierarchical cross-modal aggregation consisting of a global meta-path neighbouring to uncover the potential heterogeneous neighbors along the pathways driven by domain knowledge, and a local multi-relation aggregation module for the comprehensive cross-modal interaction across various heterogeneous relations. We assess the efficacy of our methodology on rigorous benchmarking experiments against prior state-of-the-arts. In a nutshell, GTP-4o presents an initial foray into the intriguing realm of embedding, relating and perceiving the heterogeneous patterns from various clinical modalities holistically via a graph theory. Project page: https://gtp-4-o.github.io/.

Recent advances in search-augmented large reasoning models (LRMs) enable the retrieval of external knowledge to reduce hallucinations in multistep reasoning. However, their ability to operate on graph-structured data, prevalent in domains such as e-commerce, social networks, and scientific citations, remains underexplored. Unlike plain text corpora, graphs encode rich topological signals that connect related entities and can serve as valuable priors for retrieval, enabling more targeted search and improved reasoning efficiency. Yet, effectively leveraging such structure poses unique challenges, including the difficulty of generating graph-expressive queries and ensuring reliable retrieval that balances structural and semantic relevance. To address this gap, we introduce GraphSearch, the first framework that extends search-augmented reasoning to graph learning, enabling zero-shot graph learning without task-specific fine-tuning. GraphSearch combines a Graph-aware Query Planner, which disentangles search space (e.g., 1-hop, multi-hop, or global neighbors) from semantic queries, with a Graph-aware Retriever, which constructs candidate sets based on topology and ranks them using a hybrid scoring function. We further instantiate two traversal modes: GraphSearch-R, which recursively expands neighborhoods hop by hop, and GraphSearch-F, which flexibly retrieves across local and global neighborhoods without hop constraints. Extensive experiments across diverse benchmarks show that GraphSearch achieves competitive or even superior performance compared to supervised graph learning methods, setting state-of-the-art results in zero-shot node classification and link prediction. These findings position GraphSearch as a flexible and generalizable paradigm for agentic reasoning over graphs.

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.

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large graphs can be fast and easy if they are compressed sufficiently to fit in main memory or even cache. Graph summarization, which yields a coarse-grained summary graph with merged nodes, stands out with several advantages among graph compression techniques. Thus, a number of algorithms have been developed for obtaining a concise summary graph with little information loss or equivalently small reconstruction error. However, the existing methods focus solely on reducing the number of nodes, and they often yield dense summary graphs, failing to achieve better compression rates. Moreover, due to their limited scalability, they can be applied only to moderate-size graphs. In this work, we propose SSumM, a scalable and effective graph-summarization algorithm that yields a sparse summary graph. SSumM not only merges nodes together but also sparsifies the summary graph, and the two strategies are carefully balanced based on the minimum description length principle. Compared with state-of-the-art competitors, SSumM is (a) Concise: yields up to 11.2X smaller summary graphs with similar reconstruction error, (b) Accurate: achieves up to 4.2X smaller reconstruction error with similarly concise outputs, and (c) Scalable: summarizes 26X larger graphs while exhibiting linear scalability. We validate these advantages through extensive experiments on 10 real-world graphs.

As part of its scholarly data efforts, the Internet Archive (IA) releases a first version of a citation graph dataset, named refcat, derived from scholarly publications and additional data sources. It is composed of data gathered by the fatcat cataloging project (the catalog that underpins IA Scholar), related web-scale crawls targeting primary and secondary scholarly outputs, as well as metadata from the Open Library project and Wikipedia. This first version of the graph consists of over 1.3B citations. We release this dataset under a CC0 Public Domain Dedication, accessible through Internet Archive. The source code used for the derivation process, including exact and fuzzy citation matching, is released under an MIT license. The goal of this report is to describe briefly the current contents and the derivation of the dataset.

The complexity of a graph is the number of its labeled spanning trees. In this work complexity is studied in settings that admit regular graphs. An exact formula is established linking complexity of the complement of a regular graph to numbers of closed walks in the graph by way of an infinite alternating series. Some consequences of this result yield infinite classes of lower and upper bounds on the complexity of such graphs. Applications of these mathematical results to biological problems on neuronal activity are described.

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.

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.

In recent years, graph prompting has emerged as a promising research direction, enabling the learning of additional tokens or subgraphs appended to the original graphs without requiring retraining of pre-trained graph models across various applications. This novel paradigm, shifting from the traditional pretraining and finetuning to pretraining and prompting has shown significant empirical success in simulating graph data operations, with applications ranging from recommendation systems to biological networks and graph transferring. However, despite its potential, the theoretical underpinnings of graph prompting remain underexplored, raising critical questions about its fundamental effectiveness. The lack of rigorous theoretical proof of why and how much it works is more like a dark cloud over the graph prompt area to go further. To fill this gap, this paper introduces a theoretical framework that rigorously analyzes graph prompting from a data operation perspective. Our contributions are threefold: First, we provide a formal guarantee theorem, demonstrating graph prompts capacity to approximate graph transformation operators, effectively linking upstream and downstream tasks. Second, we derive upper bounds on the error of these data operations by graph prompts for a single graph and extend this discussion to batches of graphs, which are common in graph model training. Third, we analyze the distribution of data operation errors, extending our theoretical findings from linear graph models (e.g., GCN) to non-linear graph models (e.g., GAT). Extensive experiments support our theoretical results and confirm the practical implications of these guarantees.

Large Language Models (LLMs) have achieved impressive performance in text understanding and have become an essential tool for building smart assistants. Originally focusing on text, they have been enhanced with multimodal capabilities in recent works that successfully built visual instruction following assistants. As far as the graph modality goes, however, no such assistants have yet been developed. Graph structures are complex in that they represent relation between different features and are permutation invariant. Moreover, representing them in purely textual form does not always lead to good LLM performance even for finetuned models. As a result, there is a need to develop a new method to integrate graphs in LLMs for general graph understanding. This work explores the integration of the graph modality in LLM for general graph instruction following tasks. It aims at producing a deep learning model that enhances an underlying LLM with graph embeddings and trains it to understand them and to produce, given an instruction, an answer grounded in the graph representation. The approach performs significantly better than a graph to text approach and remains consistent even for larger graphs.

Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose One for All (OFA), the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.

Graph measures that express closeness or distance between nodes can be employed for graph nodes clustering using metric clustering algorithms. There are numerous measures applicable to this task, and which one performs better is an open question. We study the performance of 25 graph measures on generated graphs with different parameters. While usually measure comparisons are limited to general measure ranking on a particular dataset, we aim to explore the performance of various measures depending on graph features. Using an LFR graph generator, we create a dataset of 11780 graphs covering the whole LFR parameter space. For each graph, we assess the quality of clustering with k-means algorithm for each considered measure. Based on this, we determine the best measure for each area of the parameter space. We find that the parameter space consists of distinct zones where one particular measure is the best. We analyze the geometry of the resulting zones and describe it with simple criteria. Given particular graph parameters, this allows us to recommend a particular measure to use for clustering.

The execution of graph algorithms using neural networks has recently attracted significant interest due to promising empirical progress. This motivates further understanding of how neural networks can replicate reasoning steps with relational data. In this work, we study the ability of transformer networks to simulate algorithms on graphs from a theoretical perspective. The architecture that we utilize is a looped transformer with extra attention heads that interact with the graph. We prove by construction that this architecture can simulate algorithms such as Dijkstra's shortest path algorithm, Breadth- and Depth-First Search, and Kosaraju's strongly connected components algorithm. The width of the network does not increase with the size of the input graph, which implies that the network can simulate the above algorithms for any graph. Despite this property, we show that there is a limit to simulation in our solution due to finite precision. Finally, we show a Turing Completeness result with constant width when the extra attention heads are utilized.

Graphs are an essential part of many machine learning problems such as analysis of parse trees, social networks, knowledge graphs, transportation systems, and molecular structures. Applying machine learning in these areas typically involves learning the graph structure and the relationship between the nodes of the graph. However, learning the graph structure is often complex, particularly when the graph is cyclic, and the transitions from one node to another are conditioned such as graphs used to represent a finite state machine. To solve this problem, we propose to extend the memory based Neural Turing Machine (NTM) with two novel additions. We allow for transitions between nodes to be influenced by information received from external environments, and we let the NTM learn the context of those transitions. We refer to this extension as the Conditional Neural Turing Machine (CNTM). We show that the CNTM can infer conditional transition graphs by empirically verifiying the model on two data sets: a large set of randomly generated graphs, and a graph modeling the information retrieval process during certain crisis situations. The results show that the CNTM is able to reproduce the paths inside the graph with accuracy ranging from 82,12% for 10 nodes graphs to 65,25% for 100 nodes graphs.

Despite its outstanding performance in various graph tasks, vanilla Message Passing Neural Network (MPNN) usually fails in link prediction tasks, as it only uses representations of two individual target nodes and ignores the pairwise relation between them. To capture the pairwise relations, some models add manual features to the input graph and use the output of MPNN to produce pairwise representations. In contrast, others directly use manual features as pairwise representations. Though this simplification avoids applying a GNN to each link individually and thus improves scalability, these models still have much room for performance improvement due to the hand-crafted and unlearnable pairwise features. To upgrade performance while maintaining scalability, we propose Neural Common Neighbor (NCN), which uses learnable pairwise representations. To further boost NCN, we study the unobserved link problem. The incompleteness of the graph is ubiquitous and leads to distribution shifts between the training and test set, loss of common neighbor information, and performance degradation of models. Therefore, we propose two intervention methods: common neighbor completion and target link removal. Combining the two methods with NCN, we propose Neural Common Neighbor with Completion (NCNC). NCN and NCNC outperform recent strong baselines by large margins. NCNC achieves state-of-the-art performance in link prediction tasks. Our code is available at https://github.com/GraphPKU/NeuralCommonNeighbor.

Deep graph generative modeling has proven capable of learning the distribution of complex, multi-scale structures characterizing real-world graphs. However, one of the main limitations of existing methods is their large output space, which limits generation scalability and hinders accurate modeling of the underlying distribution. To overcome these limitations, we propose a novel approach that significantly reduces the output space of existing graph generative models. Specifically, starting from the observation that many real-world graphs have low graph bandwidth, we restrict graph bandwidth during training and generation. Our strategy improves both generation scalability and quality without increasing architectural complexity or reducing expressiveness. Our approach is compatible with existing graph generative methods, and we describe its application to both autoregressive and one-shot models. We extensively validate our strategy on synthetic and real datasets, including molecular graphs. Our experiments show that, in addition to improving generation efficiency, our approach consistently improves generation quality and reconstruction accuracy. The implementation is made available.

Semi-transitive graphs, defined in hps98 as examples where ``uniform percolation" holds whenever p>p_c, are a large class of graphs more general than quasi-transitive graphs. Let G be a semi-transitive graph with one end which can be properly embedded into the plane with uniformly bounded face degree for finite faces and minimal vertex degree at least 7. We show that p_u^{site}(G) +p_c^{site}(G_*)=1, where G_* denotes the matching graph of G. This fulfils and extends an observation of Sykes and Essam in 1964 (SE64) to semi-transitive graphs.

Graphs or networks are a very convenient way to represent data with lots of interaction. Recently, Machine Learning on Graph data has gained a lot of traction. In particular, vertex classification and missing edge detection have very interesting applications, ranging from drug discovery to recommender systems. To achieve such tasks, tremendous work has been accomplished to learn embedding of nodes and edges into finite-dimension vector spaces. This task is called Graph Representation Learning. However, Graph Representation Learning techniques often display prohibitive time and memory complexities, preventing their use in real-time with business size graphs. In this paper, we address this issue by leveraging a degeneracy property of Graphs - the K-Core Decomposition. We present two techniques taking advantage of this decomposition to reduce the time and memory consumption of walk-based Graph Representation Learning algorithms. We evaluate the performances, expressed in terms of quality of embedding and computational resources, of the proposed techniques on several academic datasets. Our code is available at https://github.com/SBrandeis/kcore-embedding

This work studies a central extremal graph theory problem inspired by a 1975 conjecture of Erdos, which aims to find graphs with a given size (number of nodes) that maximize the number of edges without having 3- or 4-cycles. We formulate this problem as a sequential decision-making problem and compare AlphaZero, a neural network-guided tree search, with tabu search, a heuristic local search method. Using either method, by introducing a curriculum -- jump-starting the search for larger graphs using good graphs found at smaller sizes -- we improve the state-of-the-art lower bounds for several sizes. We also propose a flexible graph-generation environment and a permutation-invariant network architecture for learning to search in the space of graphs.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being local, global or relative. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges O(N+E) by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework GraphGPS that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Knowledge Graph Completion (KGC), which aims to infer missing or incomplete facts, is a crucial task for KGs. However, integrating the vital structural information of KGs into Large Language Models (LLMs) and outputting predictions deterministically remains challenging. To address this, we propose a new method called GLTW, which encodes the structural information of KGs and merges it with LLMs to enhance KGC performance. Specifically, we introduce an improved Graph Transformer (iGT) that effectively encodes subgraphs with both local and global structural information and inherits the characteristics of language model, bypassing training from scratch. Also, we develop a subgraph-based multi-classification training objective, using all entities within KG as classification objects, to boost learning efficiency.Importantly, we combine iGT with an LLM that takes KG language prompts as input.Our extensive experiments on various KG datasets show that GLTW achieves significant performance gains compared to SOTA baselines.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.