Daily Papers

Large Language Models (LLMs) may suffer from hallucinations in real-world applications due to the lack of relevant knowledge. In contrast, knowledge graphs encompass extensive, multi-relational structures that store a vast array of symbolic facts. Consequently, integrating LLMs with knowledge graphs has been extensively explored, with Knowledge Graph Question Answering (KGQA) serving as a critical touchstone for the integration. This task requires LLMs to answer natural language questions by retrieving relevant triples from knowledge graphs. However, existing methods face two significant challenges: excessively long reasoning paths distracting from the answer generation, and false-positive relations hindering the path refinement. In this paper, we propose an iterative interactive KGQA framework that leverages the interactive learning capabilities of LLMs to perform reasoning and Debating over Graphs (DoG). Specifically, DoG employs a subgraph-focusing mechanism, allowing LLMs to perform answer trying after each reasoning step, thereby mitigating the impact of lengthy reasoning paths. On the other hand, DoG utilizes a multi-role debate team to gradually simplify complex questions, reducing the influence of false-positive relations. This debate mechanism ensures the reliability of the reasoning process. Experimental results on five public datasets demonstrate the effectiveness and superiority of our architecture. Notably, DoG outperforms the state-of-the-art method ToG by 23.7\% and 9.1\% in accuracy on WebQuestions and GrailQA, respectively. Furthermore, the integration experiments with various LLMs on the mentioned datasets highlight the flexibility of DoG. Code is available at https://github.com/reml-group/DoG.

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.

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

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

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.

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

With the increasing prevalence of graph-structured data, multi-view graph clustering has been widely used in various downstream applications. Existing approaches primarily rely on a unified message passing mechanism, which significantly enhances clustering performance. Nevertheless, this mechanism limits its applicability to heterophilous situations, as it is fundamentally predicated on the assumption of homophily, i.e., the connected nodes often belong to the same class. In reality, this assumption does not always hold; a moderately or even mildly homophilous graph is more common than a fully homophilous one due to inevitable heterophilous information in the graph. To address this issue, in this paper, we propose a novel SiMilarity-enhanced Homophily for Multi-view Heterophilous Graph Clustering (SMHGC) approach. By analyzing the relationship between similarity and graph homophily, we propose to enhance the homophily by introducing three similarity terms, i.e., neighbor pattern similarity, node feature similarity, and multi-view global similarity, in a label-free manner. Then, a consensus-based inter- and intra-view fusion paradigm is proposed to fuse the improved homophilous graph from different views and utilize them for clustering. The state-of-the-art experimental results on both multi-view heterophilous and homophilous datasets collectively demonstrate the strong capacity of similarity for unsupervised multi-view heterophilous graph learning. Additionally, the consistent performance across semi-synthetic datasets with varying levels of homophily serves as further evidence of SMHGC's resilience to heterophily.

State-of-the-art Graph Neural Networks (GNNs) have limited scalability with respect to the graph and model sizes. On large graphs, increasing the model depth often means exponential expansion of the scope (i.e., receptive field). Beyond just a few layers, two fundamental challenges emerge: 1. degraded expressivity due to oversmoothing, and 2. expensive computation due to neighborhood explosion. We propose a design principle to decouple the depth and scope of GNNs -- to generate representation of a target entity (i.e., a node or an edge), we first extract a localized subgraph as the bounded-size scope, and then apply a GNN of arbitrary depth on top of the subgraph. A properly extracted subgraph consists of a small number of critical neighbors, while excluding irrelevant ones. The GNN, no matter how deep it is, smooths the local neighborhood into informative representation rather than oversmoothing the global graph into "white noise". Theoretically, decoupling improves the GNN expressive power from the perspectives of graph signal processing (GCN), function approximation (GraphSAGE) and topological learning (GIN). Empirically, on seven graphs (with up to 110M nodes) and six backbone GNN architectures, our design achieves significant accuracy improvement with orders of magnitude reduction in computation and hardware cost.

Cross-domain few-shot medical image segmentation (CD-FSMIS) offers a promising and data-efficient solution for medical applications where annotations are severely scarce and multimodal analysis is required. However, existing methods typically filter out domain-specific information to improve generalization, which inadvertently limits cross-domain performance and degrades source-domain accuracy. To address this, we present Contrastive Graph Modeling (C-Graph), a framework that leverages the structural consistency of medical images as a reliable domain-transferable prior. We represent image features as graphs, with pixels as nodes and semantic affinities as edges. A Structural Prior Graph (SPG) layer is proposed to capture and transfer target-category node dependencies and enable global structure modeling through explicit node interactions. Building upon SPG layers, we introduce a Subgraph Matching Decoding (SMD) mechanism that exploits semantic relations among nodes to guide prediction. Furthermore, we design a Confusion-minimizing Node Contrast (CNC) loss to mitigate node ambiguity and subgraph heterogeneity by contrastively enhancing node discriminability in the graph space. Our method significantly outperforms prior CD-FSMIS approaches across multiple cross-domain benchmarks, achieving state-of-the-art performance while simultaneously preserving strong segmentation accuracy on the source domain.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present IsoNet++, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an injective alignment between their nodes. Second, we update this alignment in a lazy fashion over multiple rounds. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, IsoNet++ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. In contrast, we consider node pairs (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

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

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

Pan-cancer screening in large-scale CT scans remains challenging for existing AI methods, primarily due to the difficulty of localizing diverse types of tiny lesions in large CT volumes. The extreme foreground-background imbalance significantly hinders models from focusing on diseased regions, while redundant focus on healthy regions not only decreases the efficiency but also increases false positives. Inspired by radiologists' glance and focus diagnostic strategy, we introduce GF-Screen, a Glance and Focus reinforcement learning framework for pan-cancer screening. GF-Screen employs a Glance model to localize the diseased regions and a Focus model to precisely segment the lesions, where segmentation results of the Focus model are leveraged to reward the Glance model via Reinforcement Learning (RL). Specifically, the Glance model crops a group of sub-volumes from the entire CT volume and learns to select the sub-volumes with lesions for the Focus model to segment. Given that the selecting operation is non-differentiable for segmentation training, we propose to employ the segmentation results to reward the Glance model. To optimize the Glance model, we introduce a novel group relative learning paradigm, which employs group relative comparison to prioritize high-advantage predictions and discard low-advantage predictions within sub-volume groups, not only improving efficiency but also reducing false positives. In this way, for the first time, we effectively extend cutting-edge RL techniques to tackle the specific challenges in pan-cancer screening. Extensive experiments on 16 internal and 7 external datasets across 9 lesion types demonstrated the effectiveness of GF-Screen. Notably, GF-Screen leads the public validation leaderboard of MICCAI FLARE25 pan-cancer challenge, surpassing the FLARE24 champion solution by a large margin (+25.6% DSC and +28.2% NSD).

We present an attention mechanism inspired from definition of screened Coulomb potential. This attention mechanism was used to interpret the Graph Attention (GAT) model layers and training dataset by using a flexible and scalable framework (CoulGAT) developed for this purpose. Using CoulGAT, a forest of plain and resnet models were trained and characterized using this attention mechanism against CHAMPS dataset. The learnable variables of the attention mechanism are used to extract node-node and node-feature interactions to define an empirical standard model for the graph structure and hidden layer. This representation of graph and hidden layers can be used as a tool to compare different models, optimize hidden layers and extract a compact definition of graph structure of the dataset.

We present a geometric framework for filtered approximate nearest neighbor (ANN) search. Filtering a proximity graph by a metadata predicate produces a subgraph, a fiber, whose connectivity and geometry can differ sharply from the full graph. Using local signals, we propose a two-phase search algorithm that combines full-graph exploration with filtered-neighbor descent when the local geometry is favorable. These signals also classify search failures into three regimes: topological cuts, geometric folds, and genuine basins. A key observation is that all three share a common resolution: restarting the search in a fiber-present cluster near the query. To support this, we introduce a lightweight anchor structure that identifies such regions and restarts the search accordingly. We show empirically that the method outperforms FAISS HNSW on filtered search and the three failure regimes separate cleanly and shift predictably with filter selectivity.

Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topological heuristics with the feature-learning ability of neural networks. It summarizes a putative link by random walk probabilities of adjacent paths. Instead of extracting transition probabilities from the original graph, it computes the transition matrix of a "predictive" latent graph by applying attention to learned features; this may be interpreted as feature-sensitive topology fingerprinting. WalkPool can leverage unsupervised node features or be combined with GNNs and trained end-to-end. It outperforms state-of-the-art methods on all common link prediction benchmarks, both homophilic and heterophilic, with and without node attributes. Applying WalkPool to a set of unsupervised GNNs significantly improves prediction accuracy, suggesting that it may be used as a general-purpose graph pooling scheme.

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

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.

Attention mechanism in graph neural networks is designed to assign larger weights to important neighbor nodes for better representation. However, what graph attention learns is not understood well, particularly when graphs are noisy. In this paper, we propose a self-supervised graph attention network (SuperGAT), an improved graph attention model for noisy graphs. Specifically, we exploit two attention forms compatible with a self-supervised task to predict edges, whose presence and absence contain the inherent information about the importance of the relationships between nodes. By encoding edges, SuperGAT learns more expressive attention in distinguishing mislinked neighbors. We find two graph characteristics influence the effectiveness of attention forms and self-supervision: homophily and average degree. Thus, our recipe provides guidance on which attention design to use when those two graph characteristics are known. Our experiment on 17 real-world datasets demonstrates that our recipe generalizes across 15 datasets of them, and our models designed by recipe show improved performance over baselines.

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

Most real-world networks are noisy and incomplete samples from an unknown target distribution. Refining them by correcting corruptions or inferring unobserved regions typically improves downstream performance. Inspired by the impressive generative capabilities that have been used to correct corruptions in images, and the similarities between "in-painting" and filling in missing nodes and edges conditioned on the observed graph, we propose a novel graph generative framework, SGDM, which is based on subgraph diffusion. Our framework not only improves the scalability and fidelity of graph diffusion models, but also leverages the reverse process to perform novel, conditional generation tasks. In particular, through extensive empirical analysis and a set of novel metrics, we demonstrate that our proposed model effectively supports the following refinement tasks for partially observable networks: T1: denoising extraneous subgraphs, T2: expanding existing subgraphs and T3: performing "style" transfer by regenerating a particular subgraph to match the characteristics of a different node or subgraph.

Modeling networks as different graph types and researching on route finding strategies, to avoid congestion in dense subnetworks via graph-theoretic approaches, contributes to overall blocking probability reduction in networks. Our main focus is to study methods for modeling congested subnetworks and graph density measures, in order to identify routes that avoid dense subgraphs for global congestion avoidance, along with covering related algorithmic issues.

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

The notion of shortcut partition, introduced recently by Chang, Conroy, Le, Milenkovi\'c, Solomon, and Than [CCLMST23], is a new type of graph partition into low-diameter clusters. Roughly speaking, the shortcut partition guarantees that for every two vertices u and v in the graph, there exists a path between u and v that intersects only a few clusters. They proved that any planar graph admits a shortcut partition and gave several applications, including a construction of tree cover for arbitrary planar graphs with stretch 1+varepsilon and O(1) many trees for any fixed varepsilon in (0,1). However, the construction heavily exploits planarity in multiple steps, and is thus inherently limited to planar graphs. In this work, we breach the "planarity barrier" to construct a shortcut partition for K_r-minor-free graphs for any r. To this end, we take a completely different approach -- our key contribution is a novel deterministic variant of the cop decomposition in minor-free graphs [And86, AGG14]. Our shortcut partition for K_r-minor-free graphs yields several direct applications. Most notably, we construct the first optimal distance oracle for K_r-minor-free graphs, with 1+varepsilon stretch, linear space, and constant query time for any fixed varepsilon in (0,1). The previous best distance oracle [AG06] uses O(nlog n) space and O(log n) query time, and its construction relies on Robertson-Seymour structural theorem and other sophisticated tools. We also obtain the first tree cover of O(1) size for minor-free graphs with stretch 1+varepsilon, while the previous best (1+varepsilon)-tree cover has size O(log^2 n) [BFN19].

Automatic extraction of chemical structures from scientific literature plays a crucial role in accelerating research across fields ranging from drug discovery to materials science. Patent documents, in particular, contain molecular information in visual form, which is often inaccessible through traditional text-based searches. In this work, we introduce SubGrapher, a method for the visual fingerprinting of chemical structure images. Unlike conventional Optical Chemical Structure Recognition (OCSR) models that attempt to reconstruct full molecular graphs, SubGrapher focuses on extracting molecular fingerprints directly from chemical structure images. Using learning-based instance segmentation, SubGrapher identifies functional groups and carbon backbones, constructing a substructure-based fingerprint that enables chemical structure retrieval. Our approach is evaluated against state-of-the-art OCSR and fingerprinting methods, demonstrating superior retrieval performance and robustness across diverse molecular depictions. The dataset, models, and code are publicly available.

Attention mechanisms are critical to the success of large language models (LLMs), driving significant advancements in multiple fields. However, for graph-structured data, which requires emphasis on topological connections, they fall short compared to message-passing mechanisms on fixed links, such as those employed by Graph Neural Networks (GNNs). This raises a question: ``Does attention fail for graphs in natural language settings?'' Motivated by these observations, we embarked on an empirical study from the perspective of attention mechanisms to explore how LLMs process graph-structured data. The goal is to gain deeper insights into the attention behavior of LLMs over graph structures. We uncovered unique phenomena regarding how LLMs apply attention to graph-structured data and analyzed these findings to improve the modeling of such data by LLMs. The primary findings of our research are: 1) While LLMs can recognize graph data and capture text-node interactions, they struggle to model inter-node relationships within graph structures due to inherent architectural constraints. 2) The attention distribution of LLMs across graph nodes does not align with ideal structural patterns, indicating a failure to adapt to graph topology nuances. 3) Neither fully connected attention nor fixed connectivity is optimal; each has specific limitations in its application scenarios. Instead, intermediate-state attention windows improve LLM training performance and seamlessly transition to fully connected windows during inference. Source code: https://github.com/millioniron/LLM_exploration{LLM4Exploration}

The topology of the hyperlink graph among pages expressing different opinions may influence the exposure of readers to diverse content. Structural bias may trap a reader in a polarized bubble with no access to other opinions. We model readers' behavior as random walks. A node is in a polarized bubble if the expected length of a random walk from it to a page of different opinion is large. The structural bias of a graph is the sum of the radii of highly-polarized bubbles. We study the problem of decreasing the structural bias through edge insertions. Healing all nodes with high polarized bubble radius is hard to approximate within a logarithmic factor, so we focus on finding the best k edges to insert to maximally reduce the structural bias. We present RePBubLik, an algorithm that leverages a variant of the random walk closeness centrality to select the edges to insert. RePBubLik obtains, under mild conditions, a constant-factor approximation. It reduces the structural bias faster than existing edge-recommendation methods, including some designed to reduce the polarization of a graph.

In pruning, the Lottery Ticket Hypothesis posits that large networks contain sparse subnetworks, or winning tickets, that can be trained in isolation to match the performance of their dense counterparts. However, most existing approaches assume a single universal winning ticket shared across all inputs, ignoring the inherent heterogeneity of real-world data. In this work, we propose Routing the Lottery (RTL), an adaptive pruning framework that discovers multiple specialized subnetworks, called adaptive tickets, each tailored to a class, semantic cluster, or environmental condition. Across diverse datasets and tasks, RTL consistently outperforms single- and multi-model baselines in balanced accuracy and recall, while using up to 10 times fewer parameters than independent models and exhibiting semantically aligned. Furthermore, we identify subnetwork collapse, a performance drop under aggressive pruning, and introduce a subnetwork similarity score that enables label-free diagnosis of oversparsification. Overall, our results recast pruning as a mechanism for aligning model structure with data heterogeneity, paving the way toward more modular and context-aware deep learning.

Attention mechanisms have been widely used to capture long-range dependencies among nodes in Graph Transformers. Bottlenecked by the quadratic computational cost, attention mechanisms fail to scale in large graphs. Recent improvements in computational efficiency are mainly achieved by attention sparsification with random or heuristic-based graph subsampling, which falls short in data-dependent context reasoning. State space models (SSMs), such as Mamba, have gained prominence for their effectiveness and efficiency in modeling long-range dependencies in sequential data. However, adapting SSMs to non-sequential graph data presents a notable challenge. In this work, we introduce Graph-Mamba, the first attempt to enhance long-range context modeling in graph networks by integrating a Mamba block with the input-dependent node selection mechanism. Specifically, we formulate graph-centric node prioritization and permutation strategies to enhance context-aware reasoning, leading to a substantial improvement in predictive performance. Extensive experiments on ten benchmark datasets demonstrate that Graph-Mamba outperforms state-of-the-art methods in long-range graph prediction tasks, with a fraction of the computational cost in both FLOPs and GPU memory consumption. The code and models are publicly available at https://github.com/bowang-lab/Graph-Mamba.

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

Computing distances and finding shortest paths in massive real-world networks is a fundamental algorithmic task in network analysis. There are two main approaches to solving this task. On one hand are traversal-based algorithms like bidirectional breadth-first search (BiBFS) with no preprocessing step and slow individual distance inquiries. On the other hand are indexing-based approaches, which maintain a large index. This allows for answering individual inquiries very fast; however, index creation is prohibitively expensive. We seek to bridge these two extremes: quickly answer distance inquiries without the need for costly preprocessing. In this work, we propose a new algorithm and data structure, WormHole, for approximate shortest path computations. WormHole leverages structural properties of social networks to build a sublinearly sized index, drawing upon the explicit core-periphery decomposition of Ben-Eliezer et al. Empirically, the preprocessing time of WormHole improves upon index-based solutions by orders of magnitude, and individual inquiries are consistently much faster than in BiBFS. The acceleration comes at the cost of a minor accuracy trade-off. Nonetheless, our empirical evidence demonstrates that WormHole accurately answers essentially all inquiries within a maximum additive error of 2. We complement these empirical results with provable theoretical guarantees, showing that WormHole requires n^{o(1)} node queries per distance inquiry in random power-law networks. In contrast, any approach without a preprocessing step requires n^{Ω(1)} queries for the same task. WormHole does not require reading the whole graph. Unlike the vast majority of index-based algorithms, it returns paths, not just distances. For faster inquiry times, it can be combined effectively with other index-based solutions, by running them only on the sublinear core.

Recently similarity graphs became the leading paradigm for efficient nearest neighbor search, outperforming traditional tree-based and LSH-based methods. Similarity graphs perform the search via greedy routing: a query traverses the graph and in each vertex moves to the adjacent vertex that is the closest to this query. In practice, similarity graphs are often susceptible to local minima, when queries do not reach its nearest neighbors, getting stuck in suboptimal vertices. In this paper we propose to learn the routing function that overcomes local minima via incorporating information about the graph global structure. In particular, we augment the vertices of a given graph with additional representations that are learned to provide the optimal routing from the start vertex to the query nearest neighbor. By thorough experiments, we demonstrate that the proposed learnable routing successfully diminishes the local minima problem and significantly improves the overall search performance.

In contrastive learning, the choice of ``view'' controls the information that the representation captures and influences the performance of the model. However, leading graph contrastive learning methods generally produce views via random corruption or learning, which could lead to the loss of essential information and alteration of semantic information. An anchor view that maintains the essential information of input graphs for contrastive learning has been hardly investigated. In this paper, based on the theory of graph information bottleneck, we deduce the definition of this anchor view; put differently, the anchor view with essential information of input graph is supposed to have the minimal structural uncertainty. Furthermore, guided by structural entropy, we implement the anchor view, termed SEGA, for graph contrastive learning. We extensively validate the proposed anchor view on various benchmarks regarding graph classification under unsupervised, semi-supervised, and transfer learning and achieve significant performance boosts compared to the state-of-the-art methods.

Local graph clustering methods aim to detect small clusters in very large graphs without the need to process the whole graph. They are fundamental and scalable tools for a wide range of tasks such as local community detection, node ranking and node embedding. While prior work on local graph clustering mainly focuses on graphs without node attributes, modern real-world graph datasets typically come with node attributes that provide valuable additional information. We present a simple local graph clustering algorithm for graphs with node attributes, based on the idea of diffusing mass locally in the graph while accounting for both structural and attribute proximities. Using high-dimensional concentration results, we provide statistical guarantees on the performance of the algorithm for the recovery of a target cluster with a single seed node. We give conditions under which a target cluster generated from a fairly general contextual random graph model, which includes both the stochastic block model and the planted cluster model as special cases, can be fully recovered with bounded false positives. Empirically, we validate all theoretical claims using synthetic data, and we show that incorporating node attributes leads to superior local clustering performances using real-world graph datasets.

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

We study efficient multi-vector retrieval for late interaction in any modality. Late interaction has emerged as a dominant paradigm for information retrieval in text, images, visual documents, and videos, but its computation and storage costs grow linearly with document length, making it costly for image-, video-, and audio-rich corpora. To address this limitation, we explore query-agnostic methods for compressing multi-vector document representations under a constant vector budget. We introduce four approaches for index compression: sequence resizing, memory tokens, hierarchical pooling, and a novel attention-guided clustering (AGC). AGC uses an attention-guided mechanism to identify the most semantically salient regions of a document as cluster centroids and to weight token aggregation. Evaluating these methods on retrieval tasks spanning text (BEIR), visual-document (ViDoRe), and video (MSR-VTT, MultiVENT 2.0), we show that attention-guided clustering consistently outperforms other parameterized compression methods (sequence resizing and memory tokens), provides greater flexibility in index size than non-parametric hierarchical clustering, and achieves competitive or improved performance compared to a full, uncompressed index. The source code is available at: github.com/hanxiangqin/omni-col-press.

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

Since the pioneering work on the lottery ticket hypothesis for graph neural networks (GNNs) was proposed in Chen et al. (2021), the study on finding graph lottery tickets (GLT) has become one of the pivotal focus in the GNN community, inspiring researchers to discover sparser GLT while achieving comparable performance to original dense networks. In parallel, the graph structure has gained substantial attention as a crucial factor in GNN training dynamics, also elucidated by several recent studies. Despite this, contemporary studies on GLT, in general, have not fully exploited inherent pathways in the graph structure and identified tickets in an iterative manner, which is time-consuming and inefficient. To address these limitations, we introduce TEDDY, a one-shot edge sparsification framework that leverages structural information by incorporating edge-degree information. Following edge sparsification, we encourage the parameter sparsity during training via simple projected gradient descent on the ell_0 ball. Given the target sparsity levels for both the graph structure and the model parameters, our TEDDY facilitates efficient and rapid realization of GLT within a single training. Remarkably, our experimental results demonstrate that TEDDY significantly surpasses conventional iterative approaches in generalization, even when conducting one-shot sparsification that solely utilizes graph structures, without taking feature information into account.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Graph clustering, which aims to divide a graph into several homogeneous groups, is a critical area of study with applications that span various fields such as social network analysis, bioinformatics, and image segmentation. This paper explores both traditional and more recent approaches to graph clustering. Firstly, key concepts and definitions in graph theory are introduced. The background section covers essential topics, including graph Laplacians and the integration of Deep Learning in graph analysis. The paper then delves into traditional clustering methods, including Spectral Clustering and the Leiden algorithm. Following this, state-of-the-art clustering techniques that leverage deep learning are examined. A comprehensive comparison of these methods is made through experiments. The paper concludes with a discussion of the practical applications of graph clustering and potential future research directions.

Mechanistic interpretability aims to understand neural networks by identifying which learned features mediate specific behaviors. Attribution graphs reveal these feature pathways, but interpreting them requires extensive manual analysis -- a single prompt can take approximately 2 hours for an experienced circuit tracer. We present probe prompting, an automated pipeline that transforms attribution graphs into compact, interpretable subgraphs built from concept-aligned supernodes. Starting from a seed prompt and target logit, we select high-influence features, generate concept-targeted yet context-varying probes, and group features by cross-prompt activation signatures into Semantic, Relationship, and Say-X categories using transparent decision rules. Across five prompts including classic "capitals" circuits, probe-prompted subgraphs preserve high explanatory coverage while compressing complexity (Completeness 0.83, mean across circuits; Replacement 0.54). Compared to geometric clustering baselines, concept-aligned groups exhibit higher behavioral coherence: 2.3x higher peak-token consistency (0.425 vs 0.183) and 5.8x higher activation-pattern similarity (0.762 vs 0.130), despite lower geometric compactness. Entity-swap tests reveal a layerwise hierarchy: early-layer features transfer robustly (64% transfer rate, mean layer 6.3), while late-layer Say-X features specialize for output promotion (mean layer 16.4), supporting a backbone-and-specialization view of transformer computation. We release code (https://github.com/peppinob-ol/attribution-graph-probing), an interactive demo (https://huggingface.co/spaces/Peppinob/attribution-graph-probing), and minimal artifacts enabling immediate reproduction and community adoption.

Graphs are essential data structures for modeling complex interactions in domains such as social networks, molecular structures, and biological systems. Graph-level tasks, which predict properties or classes for the entire graph, are critical for applications, such as molecular property prediction and subgraph counting. Graph Neural Networks (GNNs) have shown promise in these tasks, but their evaluations are often limited to narrow datasets, tasks, and inconsistent experimental setups, restricting their generalizability. To address these limitations, we propose a unified evaluation framework for graph-level GNNs. This framework provides a standardized setting to evaluate GNNs across diverse datasets, various graph tasks (e.g., graph classification and regression), and challenging scenarios, including noisy, imbalanced, and few-shot graphs. Additionally, we propose a novel GNN model with enhanced expressivity and generalization capabilities. Specifically, we enhance the expressivity of GNNs through a k-path rooted subgraph approach, enabling the model to effectively count subgraphs (e.g., paths and cycles). Moreover, we introduce a unified graph contrastive learning algorithm for graphs across diverse domains, which adaptively removes unimportant edges to augment graphs, thereby significantly improving generalization performance. Extensive experiments demonstrate that our model achieves superior performance against fourteen effective baselines across twenty-seven graph datasets, establishing it as a robust and generalizable model for graph-level tasks.

Visual spatial description (VSD) aims to generate texts that describe the spatial relations of the given objects within images. Existing VSD work merely models the 2D geometrical vision features, thus inevitably falling prey to the problem of skewed spatial understanding of target objects. In this work, we investigate the incorporation of 3D scene features for VSD. With an external 3D scene extractor, we obtain the 3D objects and scene features for input images, based on which we construct a target object-centered 3D spatial scene graph (Go3D-S2G), such that we model the spatial semantics of target objects within the holistic 3D scenes. Besides, we propose a scene subgraph selecting mechanism, sampling topologically-diverse subgraphs from Go3D-S2G, where the diverse local structure features are navigated to yield spatially-diversified text generation. Experimental results on two VSD datasets demonstrate that our framework outperforms the baselines significantly, especially improving on the cases with complex visual spatial relations. Meanwhile, our method can produce more spatially-diversified generation. Code is available at https://github.com/zhaoyucs/VSD.

In this paper, we present a new MTL framework that searches for structures optimized for multiple tasks with diverse graph topologies and shares features among tasks. We design a restricted DAG-based central network with read-in/read-out layers to build topologically diverse task-adaptive structures while limiting search space and time. We search for a single optimized network that serves as multiple task adaptive sub-networks using our three-stage training process. To make the network compact and discretized, we propose a flow-based reduction algorithm and a squeeze loss used in the training process. We evaluate our optimized network on various public MTL datasets and show ours achieves state-of-the-art performance. An extensive ablation study experimentally validates the effectiveness of the sub-module and schemes in our framework.

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.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In graph machine learning context, graph rationale is defined to locate the critical subgraph in the given graph topology, which fundamentally determines the prediction results. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied. The core idea of intervention is that given any changing environment subgraphs, the semantics from the rationale subgraph is invariant, which guarantees the correct prediction result. However, most, if not all, of the existing rationalization works on graph data develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose well-tailored intervention strategies on graph data. Our idea is driven by the development of Transformer models, whose self-attention module provides rich interactions between input nodes. Based on the self-attention module, our proposed invariant graph Transformer (IGT) can achieve fine-grained, more specifically, node-level and virtual node-level intervention. Our comprehensive experiments involve 7 real-world datasets, and the proposed IGT shows significant performance advantages compared to 13 baseline methods.

Deep generative models (DGMs) have been widely developed for graph data. However, much less investigation has been carried out on understanding the latent space of such pretrained graph DGMs. These understandings possess the potential to provide constructive guidelines for crucial tasks, such as graph controllable generation. Thus in this work, we are interested in studying this problem and propose GraphCG, a method for the unsupervised discovery of steerable factors in the latent space of pretrained graph DGMs. We first examine the representation space of three pretrained graph DGMs with six disentanglement metrics, and we observe that the pretrained representation space is entangled. Motivated by this observation, GraphCG learns the steerable factors via maximizing the mutual information between semantic-rich directions, where the controlled graph moving along the same direction will share the same steerable factors. We quantitatively verify that GraphCG outperforms four competitive baselines on two graph DGMs pretrained on two molecule datasets. Additionally, we qualitatively illustrate seven steerable factors learned by GraphCG on five pretrained DGMs over five graph datasets, including two for molecules and three for point clouds.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

Subgraph matching is a fundamental building block for graph-based applications and is challenging due to its high-order combinatorial nature. Existing studies usually tackle it by combinatorial optimization or learning-based methods. However, they suffer from exponential computational costs or searching the matching without theoretical guarantees. In this paper, we develop D2Match by leveraging the efficiency of Deep learning and Degeneracy for subgraph matching. More specifically, we first prove that subgraph matching can degenerate to subtree matching, and subsequently is equivalent to finding a perfect matching on a bipartite graph. We can then yield an implementation of linear time complexity by the built-in tree-structured aggregation mechanism on graph neural networks. Moreover, circle structures and node attributes can be easily incorporated in D2Match to boost the matching performance. Finally, we conduct extensive experiments to show the superior performance of our D2Match and confirm that our D2Match indeed exploits the subtrees and differs from existing GNNs-based subgraph matching methods that depend on memorizing the data distribution divergence

Due to the advantages of hypergraphs in modeling high-order relationships in complex systems, they have been applied to higher-order clustering, hypergraph neural networks and computer vision. These applications rely heavily on access to high-quality, large-scale real-world hypergraph data. Yet, compared to traditional pairwise graphs, real hypergraph datasets remain scarce in both scale and diversity. This shortage significantly limits the development and evaluation of advanced hypergraph learning algorithms. Therefore, how to quickly generate large-scale hypergraphs that conform to the characteristics of real networks is a crucial task that has not received sufficient attention. Motivated by recent advances in large language models (LLMs), particularly their capabilities in semantic reasoning, structured generation, and simulating human behavior, we investigate whether LLMs can facilitate hypergraph generation from a fundamentally new perspective. We introduce HyperLLM, a novel LLM-driven hypergraph generator that simulates the formation and evolution of hypergraphs through a multi-agent collaboration. The framework integrates prompts and structural feedback mechanisms to ensure that the generated hypergraphs reflect key real-world patterns. Extensive experiments across diverse datasets demonstrate that HyperLLM achieves superior fidelity to structural and temporal hypergraph patterns, while requiring minimal statistical priors. Our findings suggest that LLM-based frameworks offer a promising new direction for hypergraph modeling.

Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for Adaptively Modeling the natural directed graphs as the Undirected or Directed graph to maximize the benefits from subsequent graph learning. Furthermore, we propose Adaptive Directed Pattern Aggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 14 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96\%.

A widely used strategy to discover and understand language model mechanisms is circuit analysis. A circuit is a minimal subgraph of a model's computation graph that executes a specific task. We identify a gap in existing circuit discovery methods: they assume circuits are position-invariant, treating model components as equally relevant across input positions. This limits their ability to capture cross-positional interactions or mechanisms that vary across positions. To address this gap, we propose two improvements to incorporate positionality into circuits, even on tasks containing variable-length examples. First, we extend edge attribution patching, a gradient-based method for circuit discovery, to differentiate between token positions. Second, we introduce the concept of a dataset schema, which defines token spans with similar semantics across examples, enabling position-aware circuit discovery in datasets with variable length examples. We additionally develop an automated pipeline for schema generation and application using large language models. Our approach enables fully automated discovery of position-sensitive circuits, yielding better trade-offs between circuit size and faithfulness compared to prior work.

Existing offline hierarchical reinforcement learning methods rely on high-level policy learning to generate subgoal sequences. However, their efficiency degrades as task horizons increase, and they lack effective strategies for stitching useful state transitions across different trajectories. We propose Graph-Assisted Stitching (GAS), a novel framework that formulates subgoal selection as a graph search problem rather than learning an explicit high-level policy. By embedding states into a Temporal Distance Representation (TDR) space, GAS clusters semantically similar states from different trajectories into unified graph nodes, enabling efficient transition stitching. A shortest-path algorithm is then applied to select subgoal sequences within the graph, while a low-level policy learns to reach the subgoals. To improve graph quality, we introduce the Temporal Efficiency (TE) metric, which filters out noisy or inefficient transition states, significantly enhancing task performance. GAS outperforms prior offline HRL methods across locomotion, navigation, and manipulation tasks. Notably, in the most stitching-critical task, it achieves a score of 88.3, dramatically surpassing the previous state-of-the-art score of 1.0. Our source code is available at: https://github.com/qortmdgh4141/GAS.

Long-horizon applications increasingly require large language models (LLMs) to answer queries when relevant evidence is sparse and dispersed across very long contexts. Existing memory systems largely follow two paradigms: explicit structured memories offer interpretability but often become brittle under long-context overload, while latent memory mechanisms are efficient and stable yet difficult to inspect. We propose LatentGraphMem, a memory framework that combines implicit graph memory with explicit subgraph retrieval. LatentGraphMem stores a graph-structured memory in latent space for stability and efficiency, and exposes a task-specific subgraph retrieval interface that returns a compact symbolic subgraph under a fixed budget for downstream reasoning and human inspection. During training, an explicit graph view is materialized to interface with a frozen reasoner for question-answering supervision. At inference time, retrieval is performed in latent space and only the retrieved subgraph is externalized. Experiments on long-horizon benchmarks across multiple model scales show that LatentGraphMem consistently outperforms representative explicit-graph and latent-memory baselines, while enabling parameter-efficient adaptation and flexible scaling to larger reasoners without introducing large symbolic artifacts.

Unified visual grounding pursues a simple and generic technical route to leverage multi-task data with less task-specific design. The most advanced methods typically present boxes and masks as vertex sequences to model referring detection and segmentation as an autoregressive sequential vertex generation paradigm. However, generating high-dimensional vertex sequences sequentially is error-prone because the upstream of the sequence remains static and cannot be refined based on downstream vertex information, even if there is a significant location gap. Besides, with limited vertexes, the inferior fitting of objects with complex contours restricts the performance upper bound. To deal with this dilemma, we propose a parallel vertex generation paradigm for superior high-dimension scalability with a diffusion model by simply modifying the noise dimension. An intuitive materialization of our paradigm is Parallel Vertex Diffusion (PVD) to directly set vertex coordinates as the generation target and use a diffusion model to train and infer. We claim that it has two flaws: (1) unnormalized coordinate caused a high variance of loss value; (2) the original training objective of PVD only considers point consistency but ignores geometry consistency. To solve the first flaw, Center Anchor Mechanism (CAM) is designed to convert coordinates as normalized offset values to stabilize the training loss value. For the second flaw, Angle summation loss (ASL) is designed to constrain the geometry difference of prediction and ground truth vertexes for geometry-level consistency. Empirical results show that our PVD achieves state-of-the-art in both referring detection and segmentation, and our paradigm is more scalable and efficient than sequential vertex generation with high-dimension data.

The growing interest in machine learning problems over graphs with additional node information such as texts, images, or labels has popularized methods that require the costly operation of processing the entire graph. Yet, little effort has been made to the development of fast local methods (i.e. without accessing the entire graph) that extract useful information from such data. To that end, we propose a study of local graph clustering using noisy node labels as a proxy for additional node information. In this setting, nodes receive initial binary labels based on cluster affiliation: 1 if they belong to the target cluster and 0 otherwise. Subsequently, a fraction of these labels is flipped. We investigate the benefits of incorporating noisy labels for local graph clustering. By constructing a weighted graph with such labels, we study the performance of graph diffusion-based local clustering method on both the original and the weighted graphs. From a theoretical perspective, we consider recovering an unknown target cluster with a single seed node in a random graph with independent noisy node labels. We provide sufficient conditions on the label noise under which, with high probability, using diffusion in the weighted graph yields a more accurate recovery of the target cluster. This approach proves more effective than using the given labels alone or using diffusion in the label-free original graph. Empirically, we show that reliable node labels can be obtained with just a few samples from an attributed graph. Moreover, utilizing these labels via diffusion in the weighted graph leads to significantly better local clustering performance across several real-world datasets, improving F1 scores by up to 13%.

Subgraph GNNs are provably expressive neural architectures that learn graph representations from sets of subgraphs. Unfortunately, their applicability is hampered by the computational complexity associated with performing message passing on many subgraphs. In this paper, we consider the problem of learning to select a small subset of the large set of possible subgraphs in a data-driven fashion. We first motivate the problem by proving that there are families of WL-indistinguishable graphs for which there exist efficient subgraph selection policies: small subsets of subgraphs that can already identify all the graphs within the family. We then propose a new approach, called Policy-Learn, that learns how to select subgraphs in an iterative manner. We prove that, unlike popular random policies and prior work addressing the same problem, our architecture is able to learn the efficient policies mentioned above. Our experimental results demonstrate that Policy-Learn outperforms existing baselines across a wide range of datasets.

The K-core of a graph is the unique maximum subgraph within which each vertex connects to K or more other vertices. The optimal K-core attack problem asks to delete the minimum number of vertices from the K-core to induce its complete collapse. A hierarchical cycle-tree packing model is introduced here for this challenging combinatorial optimization problem. We convert the temporally long-range correlated K-core pruning dynamics into locally tree-like static patterns and analyze this model through the replica-symmetric cavity method of statistical physics. A set of coarse-grained belief propagation equations are derived to predict single vertex marginal probabilities efficiently. The associated hierarchical cycle-tree guided attack ({\tt hCTGA}) algorithm is able to construct nearly optimal attack solutions for regular random graphs and Erd\"os-R\'enyi random graphs. Our cycle-tree packing model may also be helpful for constructing optimal initial conditions for other irreversible dynamical processes on sparse random graphs.

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.

Network pruning techniques, including weight pruning and filter pruning, reveal that most state-of-the-art neural networks can be accelerated without a significant performance drop. This work focuses on filter pruning which enables accelerated inference with any off-the-shelf deep learning library and hardware. We propose the concept of network pruning spaces that parametrize populations of subnetwork architectures. Based on this concept, we explore the structure aspect of subnetworks that result in minimal loss of accuracy in different pruning regimes and arrive at a series of observations by comparing subnetwork distributions. We conjecture through empirical studies that there exists an optimal FLOPs-to-parameter-bucket ratio related to the design of original network in a pruning regime. Statistically, the structure of a winning subnetwork guarantees an approximately optimal ratio in this regime. Upon our conjectures, we further refine the initial pruning space to reduce the cost of searching a good subnetwork architecture. Our experimental results on ImageNet show that the subnetwork we found is superior to those from the state-of-the-art pruning methods under comparable FLOPs.

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.

We present two new classes of algorithms for efficient field integration on graphs encoding point clouds. The first class, SeparatorFactorization(SF), leverages the bounded genus of point cloud mesh graphs, while the second class, RFDiffusion(RFD), uses popular epsilon-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g., shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (particularly for mesh-dynamics modeling), Wasserstein distance computations for point clouds, and the Gromov-Wasserstein variant.

Graph neural architecture search has sparked much attention as Graph Neural Networks (GNNs) have shown powerful reasoning capability in many relational tasks. However, the currently used graph search space overemphasizes learning node features and neglects mining hierarchical relational information. Moreover, due to diverse mechanisms in the message passing, the graph search space is much larger than that of CNNs. This hinders the straightforward application of classical search strategies for exploring complicated graph search space. We propose Automatic Relation-aware Graph Network Proliferation (ARGNP) for efficiently searching GNNs with a relation-guided message passing mechanism. Specifically, we first devise a novel dual relation-aware graph search space that comprises both node and relation learning operations. These operations can extract hierarchical node/relational information and provide anisotropic guidance for message passing on a graph. Second, analogous to cell proliferation, we design a network proliferation search paradigm to progressively determine the GNN architectures by iteratively performing network division and differentiation. The experiments on six datasets for four graph learning tasks demonstrate that GNNs produced by our method are superior to the current state-of-the-art hand-crafted and search-based GNNs. Codes are available at https://github.com/phython96/ARGNP.

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.

We present a novel quasi-Monte Carlo mechanism to improve graph-based sampling, coined repelling random walks. By inducing correlations between the trajectories of an interacting ensemble such that their marginal transition probabilities are unmodified, we are able to explore the graph more efficiently, improving the concentration of statistical estimators whilst leaving them unbiased. The mechanism has a trivial drop-in implementation. We showcase the effectiveness of repelling random walks in a range of settings including estimation of graph kernels, the PageRank vector and graphlet concentrations. We provide detailed experimental evaluation and robust theoretical guarantees. To our knowledge, repelling random walks constitute the first rigorously studied quasi-Monte Carlo scheme correlating the directions of walkers on a graph, inviting new research in this exciting nascent domain.

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

Pruning is a standard technique for reducing the computational cost of deep networks. Many advances in pruning leverage concepts from the Lottery Ticket Hypothesis (LTH). LTH reveals that inside a trained dense network exists sparse subnetworks (tickets) able to achieve similar accuracy (i.e., win the lottery - winning tickets). Pruning at initialization focuses on finding winning tickets without training a dense network. Studies on these concepts share the trend that subnetworks come from weight or filter pruning. In this work, we investigate LTH and pruning at initialization from the lens of layer pruning. First, we confirm the existence of winning tickets when the pruning process removes layers. Leveraged by this observation, we propose to discover these winning tickets at initialization, eliminating the requirement of heavy computational resources for training the initial (over-parameterized) dense network. Extensive experiments show that our winning tickets notably speed up the training phase and reduce up to 51% of carbon emission, an important step towards democratization and green Artificial Intelligence. Beyond computational benefits, our winning tickets exhibit robustness against adversarial and out-of-distribution examples. Finally, we show that our subnetworks easily win the lottery at initialization while tickets from filter removal (the standard structured LTH) hardly become winning tickets.

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN, enabling process-level supervision without explicit intermediate reasoning annotations. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target and pathway discovery in precision medicine.

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

Although Large Language Models (LLMs) have demonstrated potential in processing graphs, they struggle with comprehending graphical structure information through prompts of graph description sequences, especially as the graph size increases. We attribute this challenge to the uneven memory performance of LLMs across different positions in graph description sequences, known as ''positional biases''. To address this, we propose GraphInsight, a novel framework aimed at improving LLMs' comprehension of both macro- and micro-level graphical information. GraphInsight is grounded in two key strategies: 1) placing critical graphical information in positions where LLMs exhibit stronger memory performance, and 2) investigating a lightweight external knowledge base for regions with weaker memory performance, inspired by retrieval-augmented generation (RAG). Moreover, GraphInsight explores integrating these two strategies into LLM agent processes for composite graph tasks that require multi-step reasoning. Extensive empirical studies on benchmarks with a wide range of evaluation tasks show that GraphInsight significantly outperforms all other graph description methods (e.g., prompting techniques and reordering strategies) in understanding graph structures of varying sizes.

Large language models (LLMs) demonstrate proficiency across numerous computational tasks, yet their inner workings remain unclear. In theory, the combination of causal self-attention and multilayer perceptron layers allows every token to access and compute information based on all preceding tokens. In practice, to what extent are such operations present? In this paper, on mental math tasks (i.e., direct math calculation via next-token prediction without explicit reasoning), we investigate this question in three steps: inhibiting input-specific token computations in the initial layers, restricting the routes of information transfer across token positions in the next few layers, and forcing all computation to happen at the last token in the remaining layers. With two proposed techniques, Context-Aware Mean Ablation (CAMA) and Attention-Based Peeking (ABP), we identify an All-for-One subgraph (AF1) with high accuracy on a wide variety of mental math tasks, where meaningful computation occurs very late (in terms of layer depth) and only at the last token, which receives information of other tokens in few specific middle layers. Experiments on a variety of models and arithmetic expressions show that this subgraph is sufficient and necessary for high model performance, transfers across different models, and works on a variety of input styles. Ablations on different CAMA and ABP alternatives reveal their unique advantages over other methods, which may be of independent interest.

Convolutional neural networks have allowed remarkable advances in single image super-resolution (SISR) over the last decade. Among recent advances in SISR, attention mechanisms are crucial for high-performance SR models. However, the attention mechanism remains unclear on why and how it works in SISR. In this work, we attempt to quantify and visualize attention mechanisms in SISR and show that not all attention modules are equally beneficial. We then propose attention in attention network (A^2N) for more efficient and accurate SISR. Specifically, A^2N consists of a non-attention branch and a coupling attention branch. A dynamic attention module is proposed to generate weights for these two branches to suppress unwanted attention adjustments dynamically, where the weights change adaptively according to the input features. This allows attention modules to specialize to beneficial examples without otherwise penalties and thus greatly improve the capacity of the attention network with few parameters overhead. Experimental results demonstrate that our final model A^2N could achieve superior trade-off performances comparing with state-of-the-art networks of similar sizes. Codes are available at https://github.com/haoyuc/A2N.

Task planning in language agents is emerging as an important research topic alongside the development of large language models (LLMs). It aims to break down complex user requests in natural language into solvable sub-tasks, thereby fulfilling the original requests. In this context, the sub-tasks can be naturally viewed as a graph, where the nodes represent the sub-tasks, and the edges denote the dependencies among them. Consequently, task planning is a decision-making problem that involves selecting a connected path or subgraph within the corresponding graph and invoking it. In this paper, we explore graph learning-based methods for task planning, a direction that is orthogonal to the prevalent focus on prompt design. Our interest in graph learning stems from a theoretical discovery: the biases of attention and auto-regressive loss impede LLMs' ability to effectively navigate decision-making on graphs, which is adeptly addressed by graph neural networks (GNNs). This theoretical insight led us to integrate GNNs with LLMs to enhance overall performance. Extensive experiments demonstrate that GNN-based methods surpass existing solutions even without training, and minimal training can further enhance their performance. The performance gain increases with a larger task graph size.

Mining cohesive subgraphs in attributed graphs is an essential problem in the domain of graph data analysis. The integration of fairness considerations significantly fuels interest in models and algorithms for mining fairness-aware cohesive subgraphs. Notably, the relative fair clique emerges as a robust model, ensuring not only comprehensive attribute coverage but also greater flexibility in distributing attribute vertices. Motivated by the strength of this model, we for the first time pioneer an investigation into the identification of the maximum relative fair clique in large-scale graphs. We introduce a novel concept of colorful support, which serves as the foundation for two innovative graph reduction techniques. These techniques effectively narrow the graph's size by iteratively removing edges that do not belong to relative fair cliques. Furthermore, a series of upper bounds of the maximum relative fair clique size is proposed by incorporating consideration of vertex attributes and colors. The pruning techniques derived from these upper bounds can significantly trim unnecessary search space during the branch-and-bound procedure. Adding to this, we present a heuristic algorithm with a linear time complexity, employing both a degree-based greedy strategy and a colored degree-based greedy strategy to identify a larger relative fair clique. This heuristic algorithm can serve a dual purpose by aiding in branch pruning, thereby enhancing overall search efficiency. Extensive experiments conducted on six real-life datasets demonstrate the efficiency, scalability, and effectiveness of our algorithms.

Vector databases typically rely on approximate nearest neighbor (ANN) search to retrieve the top-k closest vectors to a query in embedding space. While effective, this approach often yields semantically redundant results, missing the diversity and contextual richness required by applications such as retrieval-augmented generation (RAG), multi-hop QA, and memory-augmented agents. We introduce a new retrieval paradigm: semantic compression, which aims to select a compact, representative set of vectors that captures the broader semantic structure around a query. We formalize this objective using principles from submodular optimization and information geometry, and show that it generalizes traditional top-k retrieval by prioritizing coverage and diversity. To operationalize this idea, we propose graph-augmented vector retrieval, which overlays semantic graphs (e.g., kNN or knowledge-based links) atop vector spaces to enable multi-hop, context-aware search. We theoretically analyze the limitations of proximity-based retrieval under high-dimensional concentration and highlight how graph structures can improve semantic coverage. Our work outlines a foundation for meaning-centric vector search systems, emphasizing hybrid indexing, diversity-aware querying, and structured semantic retrieval. We make our implementation publicly available to foster future research in this area.

Organizing unstructured image collections into semantic clusters is a long-standing challenge. Traditional deep clustering techniques address this by producing a single data partition, whereas multiple clustering methods uncover diverse alternative partitions-but only when users predefine the clustering criteria. Yet expecting users to specify such criteria a priori for large, unfamiliar datasets is unrealistic. In this work, we introduce the task of Open-ended Semantic Multiple Clustering (OpenSMC), which aims to automatically discover clustering criteria from large, unstructured image collections, revealing interpretable substructures without human input. Our framework, X-Cluster: eXploratory Clustering, treats text as a reasoning proxy: it concurrently scans the entire image collection, proposes candidate criteria in natural language, and groups images into meaningful clusters per criterion. To evaluate progress, we release COCO-4c and Food-4c benchmarks, each annotated with four grouping criteria. Experiments show that X-Cluster effectively reveals meaningful partitions and enables downstream applications such as bias discovery and social media image popularity analysis. We will open-source code and data to encourage reproducibility and further research.

In this paper, we study the flow of signals through linear paths with the nonlinear condition that a node emits a signal when it receives external stimuli or when two incoming signals from other nodes arrive coincidentally with a combined amplitude above a fixed threshold. Sets of such nodes form a polychrony group and can sometimes lead to cascades. In the context of this work, cascades are polychrony groups in which the number of nodes activated as a consequence of other nodes is greater than the number of externally activated nodes. The difference between these two numbers is the so-called profit. Given the initial conditions, we predict the conditions for a vertex to activate at a prescribed time and provide an algorithm to efficiently reconstruct a cascade. We develop a dictionary between polychrony groups and graph theory. We call the graph corresponding to a cascade a chinampa. This link leads to a topological classification of chinampas. We enumerate the chinampas of profits zero and one and the description of a family of chinampas isomorphic to a family of partially ordered sets, which implies that the enumeration problem of this family is equivalent to computing the Stanley-order polynomials of those partially ordered sets.

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

We propose a filtering feature selection framework that considers subsets of features as paths in a graph, where a node is a feature and an edge indicates pairwise (customizable) relations among features, dealing with relevance and redundancy principles. By two different interpretations (exploiting properties of power series of matrices and relying on Markov chains fundamentals) we can evaluate the values of paths (i.e., feature subsets) of arbitrary lengths, eventually go to infinite, from which we dub our framework Infinite Feature Selection (Inf-FS). Going to infinite allows to constrain the computational complexity of the selection process, and to rank the features in an elegant way, that is, considering the value of any path (subset) containing a particular feature. We also propose a simple unsupervised strategy to cut the ranking, so providing the subset of features to keep. In the experiments, we analyze diverse settings with heterogeneous features, for a total of 11 benchmarks, comparing against 18 widely-known comparative approaches. The results show that Inf-FS behaves better in almost any situation, that is, when the number of features to keep are fixed a priori, or when the decision of the subset cardinality is part of the process.

Geometric Attention (GA) specifies an attention layer by four independent inputs: a finite carrier (what indices are addressable), an evidence-kernel rule (how masked proto-scores and a link induce nonnegative weights), a probe family (which observables are treated as admissible), and an anchor/update rule (which representative kernel is selected and how it is applied). Probe families induce an operational equivalence relation on kernels and therefore a gauge; anchors select representatives relative to that probe. Under a scalar relational-work representation and a multiplicative compositionality law for evidence, the admissible link family is exponential, yielding Gibbs weights; with row anchoring this includes the softmax kernel family as a subregime. After quotienting unary row/column score fields, the remaining interaction component admits a canonical rank-r normal form (Eckart-Young/SVD); dot-product score charts implement the corresponding low-rank interaction regime. Fixing the carrier and extensionalizing the update yields the standard fixed-token Transformer attention operator; allowing carrier updates yields adaptive-carrier and staged-depth regimes. The operator language also supports multihead/mixed kernels, plan-based anchors (e.g., entropic OT/Sinkhorn), and unary operators (e.g., FFN-style fields) as explicit regime choices. This separates invariant structure from modeling choice, enabling principled comparison and extension of attention mechanisms, and attention-based architectures.

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, multi-layer architectures, which are required to propagate knowledge to distant nodes in the graph, dilute the knowledge by performing extensive Laplacian smoothing at each layer and thereby consequently decrease performance. In order to still enjoy the benefit brought by the graph structure while preventing dilution of knowledge from distant nodes, we propose a Dense Graph Propagation (DGP) module with carefully designed direct links among distant nodes. DGP allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants. A weighting scheme is further used to weigh their contribution depending on the distance to the node to improve information propagation in the graph. Combined with finetuning of the representations in a two-stage training approach our method outperforms state-of-the-art zero-shot learning approaches.

Graph Neural Networks (GNNs) have emerged as powerful tools for learning on graph-structured data, but often struggle to balance local and global information. While graph Transformers aim to address this by enabling long-range interactions, they often overlook the inherent locality and efficiency of Message Passing Neural Networks (MPNNs). We propose a new concept called fractal nodes, inspired by the fractal structure observed in real-world networks. Our approach is based on the intuition that graph partitioning naturally induces fractal structure, where subgraphs often reflect the connectivity patterns of the full graph. Fractal nodes are designed to coexist with the original nodes and adaptively aggregate subgraph-level feature representations, thereby enforcing feature similarity within each subgraph. We show that fractal nodes alleviate the over-squashing problem by providing direct shortcut connections that enable long-range propagation of subgraph-level representations. Experiment results show that our method improves the expressive power of MPNNs and achieves comparable or better performance to graph Transformers while maintaining the computational efficiency of MPNN by improving the long-range dependencies of MPNN.

Existing Graph RAG methods aiming for insightful retrieval on corpus graphs typically rely on time-intensive processes that interleave Large Language Model (LLM) reasoning. To enable time-efficient insightful retrieval, we propose FastInsight. We first introduce a graph retrieval taxonomy that categorizes existing methods into three fundamental operations: vector search, graph search, and model-based search. Through this taxonomy, we identify two critical limitations in current approaches: the topology-blindness of model-based search and the semantics-blindness of graph search. FastInsight overcomes these limitations by interleaving two novel fusion operators: the Graph-based Reranker (GRanker), which functions as a graph model-based search, and Semantic-Topological eXpansion (STeX), which operates as a vector-graph search. Extensive experiments on broad retrieval and generation datasets demonstrate that FastInsight significantly improves both retrieval accuracy and generation quality compared to state-of-the-art baselines, achieving a substantial Pareto improvement in the trade-off between effectiveness and efficiency.

Long-horizon Flexible Job-Shop Scheduling~(FJSP) presents a formidable combinatorial challenge due to complex, interdependent decisions spanning extended time horizons. While learning-based Rolling Horizon Optimization~(RHO) has emerged as a promising paradigm to accelerate solving by identifying and fixing invariant operations, its effectiveness is hindered by the structural complexity of FJSP. Existing methods often fail to capture intricate graph-structured dependencies and ignore the asymmetric costs of prediction errors, in which misclassifying critical-path operations is significantly more detrimental than misclassifying non-critical ones. Furthermore, dynamic shifts in predictive confidence during the rolling process make static pruning thresholds inadequate. To address these limitations, we propose Graph-RHO, a novel critical-path-aware graph-based RHO framework. First, we introduce a topology-aware heterogeneous graph network that encodes subproblems as operation-machine graphs with multi-relational edges, leveraging edge-feature-aware message passing to predict operation stability. Second, we incorporate a critical-path-aware mechanism that injects inductive biases during training to distinguish highly sensitive bottleneck operations from robust ones. Third, we devise an adaptive thresholding strategy that dynamically calibrates decision boundaries based on online uncertainty estimation to align model predictions with the solver's search space. Extensive experiments on standard benchmarks demonstrate that Graph-RHO establishes a new state of the art in solution quality and computational efficiency. Remarkably, it exhibits exceptional zero-shot generalization, reducing solve time by over 30\% on large-scale instances (2000 operations) while achieving superior solution quality. Our code is available https://github.com/IntelliSensing/Graph-RHO{here}.

To provide more accurate, diverse, and explainable recommendation, it is compulsory to go beyond modeling user-item interactions and take side information into account. Traditional methods like factorization machine (FM) cast it as a supervised learning problem, which assumes each interaction as an independent instance with side information encoded. Due to the overlook of the relations among instances or items (e.g., the director of a movie is also an actor of another movie), these methods are insufficient to distill the collaborative signal from the collective behaviors of users. In this work, we investigate the utility of knowledge graph (KG), which breaks down the independent interaction assumption by linking items with their attributes. We argue that in such a hybrid structure of KG and user-item graph, high-order relations --- which connect two items with one or multiple linked attributes --- are an essential factor for successful recommendation. We propose a new method named Knowledge Graph Attention Network (KGAT) which explicitly models the high-order connectivities in KG in an end-to-end fashion. It recursively propagates the embeddings from a node's neighbors (which can be users, items, or attributes) to refine the node's embedding, and employs an attention mechanism to discriminate the importance of the neighbors. Our KGAT is conceptually advantageous to existing KG-based recommendation methods, which either exploit high-order relations by extracting paths or implicitly modeling them with regularization. Empirical results on three public benchmarks show that KGAT significantly outperforms state-of-the-art methods like Neural FM and RippleNet. Further studies verify the efficacy of embedding propagation for high-order relation modeling and the interpretability benefits brought by the attention mechanism.

Despite that going deep has proven successful in many neural architectures, the existing graph transformers are relatively shallow. In this work, we explore whether more layers are beneficial to graph transformers, and find that current graph transformers suffer from the bottleneck of improving performance by increasing depth. Our further analysis reveals the reason is that deep graph transformers are limited by the vanishing capacity of global attention, restricting the graph transformer from focusing on the critical substructure and obtaining expressive features. To this end, we propose a novel graph transformer model named DeepGraph that explicitly employs substructure tokens in the encoded representation, and applies local attention on related nodes to obtain substructure based attention encoding. Our model enhances the ability of the global attention to focus on substructures and promotes the expressiveness of the representations, addressing the limitation of self-attention as the graph transformer deepens. Experiments show that our method unblocks the depth limitation of graph transformers and results in state-of-the-art performance across various graph benchmarks with deeper models.

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.

We introduce a novel score-based diffusion framework named Twigs that incorporates multiple co-evolving flows for enriching conditional generation tasks. Specifically, a central or trunk diffusion process is associated with a primary variable (e.g., graph structure), and additional offshoot or stem processes are dedicated to dependent variables (e.g., graph properties or labels). A new strategy, which we call loop guidance, effectively orchestrates the flow of information between the trunk and the stem processes during sampling. This approach allows us to uncover intricate interactions and dependencies, and unlock new generative capabilities. We provide extensive experiments to demonstrate strong performance gains of the proposed method over contemporary baselines in the context of conditional graph generation, underscoring the potential of Twigs in challenging generative tasks such as inverse molecular design and molecular optimization.

Text-to-image diffusion models (T2I) use a latent representation of a text prompt to guide the image generation process. However, the process by which the encoder produces the text representation is unknown. We propose the Diffusion Lens, a method for analyzing the text encoder of T2I models by generating images from its intermediate representations. Using the Diffusion Lens, we perform an extensive analysis of two recent T2I models. Exploring compound prompts, we find that complex scenes describing multiple objects are composed progressively and more slowly compared to simple scenes; Exploring knowledge retrieval, we find that representation of uncommon concepts requires further computation compared to common concepts, and that knowledge retrieval is gradual across layers. Overall, our findings provide valuable insights into the text encoder component in T2I pipelines.

We propose a generalization of transformer neural network architecture for arbitrary graphs. The original transformer was designed for Natural Language Processing (NLP), which operates on fully connected graphs representing all connections between the words in a sequence. Such architecture does not leverage the graph connectivity inductive bias, and can perform poorly when the graph topology is important and has not been encoded into the node features. We introduce a graph transformer with four new properties compared to the standard model. First, the attention mechanism is a function of the neighborhood connectivity for each node in the graph. Second, the positional encoding is represented by the Laplacian eigenvectors, which naturally generalize the sinusoidal positional encodings often used in NLP. Third, the layer normalization is replaced by a batch normalization layer, which provides faster training and better generalization performance. Finally, the architecture is extended to edge feature representation, which can be critical to tasks s.a. chemistry (bond type) or link prediction (entity relationship in knowledge graphs). Numerical experiments on a graph benchmark demonstrate the performance of the proposed graph transformer architecture. This work closes the gap between the original transformer, which was designed for the limited case of line graphs, and graph neural networks, that can work with arbitrary graphs. As our architecture is simple and generic, we believe it can be used as a black box for future applications that wish to consider transformer and graphs.

The Multi-Prize Lottery Ticket Hypothesis posits that randomly initialized neural networks contain several subnetworks that achieve comparable accuracy to fully trained models of the same architecture. However, current methods require that the network is sufficiently overparameterized. In this work, we propose a modification to two state-of-the-art algorithms (Edge-Popup and Biprop) that finds high-accuracy subnetworks with no additional storage cost or scaling. The algorithm, Iterative Weight Recycling, identifies subsets of important weights within a randomly initialized network for intra-layer reuse. Empirically we show improvements on smaller network architectures and higher prune rates, finding that model sparsity can be increased through the "recycling" of existing weights. In addition to Iterative Weight Recycling, we complement the Multi-Prize Lottery Ticket Hypothesis with a reciprocal finding: high-accuracy, randomly initialized subnetwork's produce diverse masks, despite being generated with the same hyperparameter's and pruning strategy. We explore the landscapes of these masks, which show high variability.

Existing graph matching methods typically assume that there are similar structures between graphs and they are matchable. However, these assumptions do not align with real-world applications. This work addresses a more realistic scenario where graphs exhibit diverse modes, requiring graph grouping before or along with matching, a task termed mixture graph matching and clustering. We introduce Minorize-Maximization Matching and Clustering (M3C), a learning-free algorithm that guarantees theoretical convergence through the Minorize-Maximization framework and offers enhanced flexibility via relaxed clustering. Building on M3C, we develop UM3C, an unsupervised model that incorporates novel edge-wise affinity learning and pseudo label selection. Extensive experimental results on public benchmarks demonstrate that our method outperforms state-of-the-art graph matching and mixture graph matching and clustering approaches in both accuracy and efficiency. Source code will be made publicly available.

Graph Neural Networks (GNNs) have shown promising potential in graph representation learning. The majority of GNNs define a local message-passing mechanism, propagating information over the graph by stacking multiple layers. These methods, however, are known to suffer from two major limitations: over-squashing and poor capturing of long-range dependencies. Recently, Graph Transformers (GTs) emerged as a powerful alternative to Message-Passing Neural Networks (MPNNs). GTs, however, have quadratic computational cost, lack inductive biases on graph structures, and rely on complex Positional/Structural Encodings (SE/PE). In this paper, we show that while Transformers, complex message-passing, and SE/PE are sufficient for good performance in practice, neither is necessary. Motivated by the recent success of State Space Models (SSMs), such as Mamba, we present Graph Mamba Networks (GMNs), a general framework for a new class of GNNs based on selective SSMs. We discuss and categorize the new challenges when adopting SSMs to graph-structured data, and present four required and one optional steps to design GMNs, where we choose (1) Neighborhood Tokenization, (2) Token Ordering, (3) Architecture of Bidirectional Selective SSM Encoder, (4) Local Encoding, and dispensable (5) PE and SE. We further provide theoretical justification for the power of GMNs. Experiments demonstrate that despite much less computational cost, GMNs attain an outstanding performance in long-range, small-scale, large-scale, and heterophilic benchmark datasets.

Graph-based Retrieval-Augmented Generation (GraphRAG) frameworks face a trade-off between the comprehensiveness of global search and the efficiency of local search. Existing methods are often challenged by navigating large-scale hierarchical graphs, optimizing retrieval paths, and balancing exploration-exploitation dynamics, frequently lacking robust multi-stage re-ranking. To overcome these deficits, we propose Deep GraphRAG, a framework designed for a balanced approach to hierarchical retrieval and adaptive integration. It introduces a hierarchical global-to-local retrieval strategy that integrates macroscopic inter-community and microscopic intra-community contextual relations. This strategy employs a three-stage process: (1) inter-community filtering, which prunes the search space using local context; (2) community-level refinement, which prioritizes relevant subgraphs via entity-interaction analysis; and (3) entity-level fine-grained search within target communities. A beam search-optimized dynamic re-ranking module guides this process, continuously filtering candidates to balance efficiency and global comprehensiveness. Deep GraphRAG also features a Knowledge Integration Module leveraging a compact LLM, trained with Dynamic Weighting Reward GRPO (DW-GRPO). This novel reinforcement learning approach dynamically adjusts reward weights to balance three key objectives: relevance, faithfulness, and conciseness. This training enables compact models (1.5B) to approach the performance of large models (70B) in the integration task. Evaluations on Natural Questions and HotpotQA demonstrate that Deep GraphRAG significantly outperforms baseline graph retrieval methods in both accuracy and efficiency.

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

Graph Neural Networks (GNNs) are a powerful tool for machine learning on graphs.GNNs combine node feature information with the graph structure by recursively passing neural messages along edges of the input graph. However, incorporating both graph structure and feature information leads to complex models, and explaining predictions made by GNNs remains unsolved. Here we propose GNNExplainer, the first general, model-agnostic approach for providing interpretable explanations for predictions of any GNN-based model on any graph-based machine learning task. Given an instance, GNNExplainer identifies a compact subgraph structure and a small subset of node features that have a crucial role in GNN's prediction. Further, GNNExplainer can generate consistent and concise explanations for an entire class of instances. We formulate GNNExplainer as an optimization task that maximizes the mutual information between a GNN's prediction and distribution of possible subgraph structures. Experiments on synthetic and real-world graphs show that our approach can identify important graph structures as well as node features, and outperforms baselines by 17.1% on average. GNNExplainer provides a variety of benefits, from the ability to visualize semantically relevant structures to interpretability, to giving insights into errors of faulty GNNs.

Graph foundation models represent a transformative paradigm for learning transferable representations across diverse graph domains. Recent methods leverage large language models to unify graph and text modalities into a shared representation space using contrastive learning. However, systematic evaluations reveal significant performance degradation at structural boundaries where distinct topological patterns converge, with accuracy losses exceeding 20 percentage points. This issue arises from a key limitation: current methods assume all graph structures can be encoded within a single Euclidean space. In reality, tree structures require hyperbolic geometry to preserve hierarchical branching, while cyclic patterns depend on spherical geometry for closure properties. At structural boundaries, nodes experience conflicting geometric constraints that uniform encoding spaces cannot resolve. This raises a crucial challenge: Can alignment frameworks be designed to respect the intrinsic geometric diversity of graph structures? We introduce GraphShaper, a geometry-aware framework that enhances graph encoding through multi-geometric specialization. Our approach employs expert networks tailored to different geometric spaces, dynamically computing fusion weights to adaptively integrate geometric properties based on local structural characteristics. This adaptive fusion preserves structural integrity before alignment with text embeddings. Extensive experiments demonstrate that GraphShaper achieves 9.47\% accuracy improvements on citation networks and 7.63\% on social networks in zero-shot settings.

The Mamba-based image restoration backbones have recently demonstrated significant potential in balancing global reception and computational efficiency. However, the inherent causal modeling limitation of Mamba, where each token depends solely on its predecessors in the scanned sequence, restricts the full utilization of pixels across the image and thus presents new challenges in image restoration. In this work, we propose MambaIRv2, which equips Mamba with the non-causal modeling ability similar to ViTs to reach the attentive state space restoration model. Specifically, the proposed attentive state-space equation allows to attend beyond the scanned sequence and facilitate image unfolding with just one single scan. Moreover, we further introduce a semantic-guided neighboring mechanism to encourage interaction between distant but similar pixels. Extensive experiments show our MambaIRv2 outperforms SRFormer by even 0.35dB PSNR for lightweight SR even with 9.3\% less parameters and suppresses HAT on classic SR by up to 0.29dB. Code is available at https://github.com/csguoh/MambaIR.

Foundation models have emerged as critical components in a variety of artificial intelligence applications, and showcase significant success in natural language processing and several other domains. Meanwhile, the field of graph machine learning is witnessing a paradigm transition from shallow methods to more sophisticated deep learning approaches. The capabilities of foundation models to generalize and adapt motivate graph machine learning researchers to discuss the potential of developing a new graph learning paradigm. This paradigm envisions models that are pre-trained on extensive graph data and can be adapted for various graph tasks. Despite this burgeoning interest, there is a noticeable lack of clear definitions and systematic analyses pertaining to this new domain. To this end, this article introduces the concept of Graph Foundation Models (GFMs), and offers an exhaustive explanation of their key characteristics and underlying technologies. We proceed to classify the existing work related to GFMs into three distinct categories, based on their dependence on graph neural networks and large language models. In addition to providing a thorough review of the current state of GFMs, this article also outlooks potential avenues for future research in this rapidly evolving domain.

Scientific inquiry requires systems-level reasoning that integrates heterogeneous experimental data, cross-domain knowledge, and mechanistic evidence into coherent explanations. While Large Language Models (LLMs) offer inferential capabilities, they often depend on retrieval-augmented contexts that lack structural depth. Traditional Knowledge Graphs (KGs) attempt to bridge this gap, yet their pairwise constraints fail to capture the irreducible higher-order interactions that govern emergent physical behavior. To address this, we introduce a methodology for constructing hypergraph-based knowledge representations that faithfully encode multi-entity relationships. Applied to a corpus of ~1,100 manuscripts on biocomposite scaffolds, our framework constructs a global hypergraph of 161,172 nodes and 320,201 hyperedges, revealing a scale-free topology (power law exponent ~1.23) organized around highly connected conceptual hubs. This representation prevents the combinatorial explosion typical of pairwise expansions and explicitly preserves the co-occurrence context of scientific formulations. We further demonstrate that equipping agentic systems with hypergraph traversal tools, specifically using node-intersection constraints, enables them to bridge semantically distant concepts. By exploiting these higher-order pathways, the system successfully generates grounded mechanistic hypotheses for novel composite materials, such as linking cerium oxide to PCL scaffolds via chitosan intermediates. This work establishes a "teacherless" agentic reasoning system where hypergraph topology acts as a verifiable guardrail, accelerating scientific discovery by uncovering relationships obscured by traditional graph methods.

Extended-connectivity fingerprints (ECFPs) are a ubiquitous tool in current cheminformatics and molecular machine learning, and one of the most prevalent molecular feature extraction techniques used for chemical prediction. Atom features learned by graph neural networks can be aggregated to compound-level representations using a large spectrum of graph pooling methods; in contrast, sets of detected ECFP substructures are by default transformed into bit vectors using only a simple hash-based folding procedure. We introduce a general mathematical framework for the vectorisation of structural fingerprints via a formal operation called substructure pooling that encompasses hash-based folding, algorithmic substructure-selection, and a wide variety of other potential techniques. We go on to describe Sort & Slice, an easy-to-implement and bit-collision-free alternative to hash-based folding for the pooling of ECFP substructures. Sort & Slice first sorts ECFP substructures according to their relative prevalence in a given set of training compounds and then slices away all but the L most frequent substructures which are subsequently used to generate a binary fingerprint of desired length, L. We computationally compare the performance of hash-based folding, Sort & Slice, and two advanced supervised substructure-selection schemes (filtering and mutual-information maximisation) for ECFP-based molecular property prediction. Our results indicate that, despite its technical simplicity, Sort & Slice robustly (and at times substantially) outperforms traditional hash-based folding as well as the other investigated methods across prediction tasks, data splitting techniques, machine-learning models and ECFP hyperparameters. We thus recommend that Sort & Slice canonically replace hash-based folding as the default substructure-pooling technique to vectorise ECFPs for supervised molecular machine learning.

The quadratic complexity of self-attention limits its applicability and scalability on large unstructured meshes. We introduce Fast Low-rank Attention Routing Engine (FLARE), a linear complexity self-attention mechanism that routes attention through fixed-length latent sequences. Each attention head performs global communication among N tokens by projecting the input sequence onto a fixed length latent sequence of M ll N tokens using learnable query tokens. By routing attention through a bottleneck sequence, FLARE learns a low-rank form of attention that can be applied at O(NM) cost. FLARE not only scales to unprecedented problem sizes, but also delivers superior accuracy compared to state-of-the-art neural PDE surrogates across diverse benchmarks. We also release a new additive manufacturing dataset to spur further research. Our code is available at https://github.com/vpuri3/FLARE.py.

Foundation models like ChatGPT and GPT-4 have revolutionized artificial intelligence, exhibiting remarkable abilities to generalize across a wide array of tasks and applications beyond their initial training objectives. However, graph learning has predominantly focused on single-graph models, tailored to specific tasks or datasets, lacking the ability to transfer learned knowledge to different domains. This limitation stems from the inherent complexity and diversity of graph structures, along with the different feature and label spaces specific to graph data. In this paper, we recognize text as an effective unifying medium and employ Text-Attributed Graphs (TAGs) to leverage this potential. We present our UniGraph framework, designed to learn a foundation model for TAGs, which is capable of generalizing to unseen graphs and tasks across diverse domains. Unlike single-graph models that use pre-computed node features of varying dimensions as input, our approach leverages textual features for unifying node representations, even for graphs such as molecular graphs that do not naturally have textual features. We propose a novel cascaded architecture of Language Models (LMs) and Graph Neural Networks (GNNs) as backbone networks. Additionally, we propose the first pre-training algorithm specifically designed for large-scale self-supervised learning on TAGs, based on Masked Graph Modeling. We introduce graph instruction tuning using Large Language Models (LLMs) to enable zero-shot prediction ability. Our comprehensive experiments across various graph learning tasks and domains demonstrate the model's effectiveness in self-supervised representation learning on unseen graphs, few-shot in-context transfer, and zero-shot transfer, even surpassing or matching the performance of GNNs that have undergone supervised training on target datasets.

Single-stage neural combinatorial optimization solvers have achieved near-optimal results on various small-scale combinatorial optimization (CO) problems without requiring expert knowledge. However, these solvers exhibit significant performance degradation when applied to large-scale CO problems. Recently, two-stage neural methods motivated by divide-and-conquer strategies have shown efficiency in addressing large-scale CO problems. Nevertheless, the performance of these methods highly relies on problem-specific heuristics in either the dividing or the conquering procedure, which limits their applicability to general CO problems. Moreover, these methods employ separate training schemes and ignore the interdependencies between the dividing and conquering strategies, often leading to sub-optimal solutions. To tackle these drawbacks, this article develops a unified neural divide-and-conquer framework (i.e., UDC) for solving general large-scale CO problems. UDC offers a Divide-Conquer-Reunion (DCR) training method to eliminate the negative impact of a sub-optimal dividing policy. Employing a high-efficiency Graph Neural Network (GNN) for global instance dividing and a fixed-length sub-path solver for conquering divided sub-problems, the proposed UDC framework demonstrates extensive applicability, achieving superior performance in 10 representative large-scale CO problems. The code is available at https://github.com/CIAM-Group/NCO_code/tree/main/single_objective/UDC-Large-scale-CO-master.

To answer one-to-many factual queries (e.g., listing cities of a country), a language model (LM) must simultaneously recall knowledge and avoid repeating previous answers. How are these two subtasks implemented and integrated internally? Across multiple datasets and models, we identify a promote-then-suppress mechanism: the model first recalls all answers, and then suppresses previously generated ones. Specifically, LMs use both the subject and previous answer tokens to perform knowledge recall, with attention propagating subject information and MLPs promoting the answers. Then, attention attends to and suppresses previous answer tokens, while MLPs amplify the suppression signal. Our mechanism is corroborated by extensive experimental evidence: in addition to using early decoding and causal tracing, we analyze how components use different tokens by introducing both Token Lens, which decodes aggregated attention updates from specified tokens, and a knockout method that analyzes changes in MLP outputs after removing attention to specified tokens. Overall, we provide new insights into how LMs' internal components interact with different input tokens to support complex factual recall. Code is available at https://github.com/Lorenayannnnn/how-lms-answer-one-to-many-factual-queries.

Multi-relational graphs (MRGs) are an expressive data structure for modeling diverse interactions/relations among real objects (i.e., nodes), which pervade extensive applications and scenarios. Given an MRG G with N nodes, partitioning the node set therein into K disjoint clusters (MRGC) is a fundamental task in analyzing MRGs, which has garnered considerable attention. However, the majority of existing solutions towards MRGC either yield severely compromised result quality by ineffective fusion of heterogeneous graph structures and attributes, or struggle to cope with sizable MRGs with millions of nodes and billions of edges due to the adoption of sophisticated and costly deep learning models. In this paper, we present DEMM and DEMM+, two effective MRGC approaches to address the limitations above. Specifically, our algorithms are built on novel two-stage optimization objectives, where the former seeks to derive high-caliber node feature vectors by optimizing the multi-relational Dirichlet energy specialized for MRGs, while the latter minimizes the Dirichlet energy of clustering results over the node affinity graph. In particular, DEMM+ achieves significantly higher scalability and efficiency over our based method DEMM through a suite of well-thought-out optimizations. Key technical contributions include (i) a highly efficient approximation solver for constructing node feature vectors, and (ii) a theoretically-grounded problem transformation with carefully-crafted techniques that enable linear-time clustering without explicitly materializing the NxN dense affinity matrix. Further, we extend DEMM+ to handle attribute-less MRGs through non-trivial adaptations. Extensive experiments, comparing DEMM+ against 20 baselines over 11 real MRGs, exhibit that DEMM+ is consistently superior in terms of clustering quality measured against ground-truth labels, while often being remarkably faster.

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive Graph Transformer SParsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results substantiate that GTSP effectively cuts computational costs, accompanied by only marginal decreases in accuracy or, in some cases, even improvements. For instance, GTSP yields a reduction of 30\% in Floating Point Operations while contributing to a 1.8\% increase in Area Under the Curve accuracy on OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain.

Hierarchical clustering of networks consists in finding a tree of communities, such that lower levels of the hierarchy reveal finer-grained community structures. There are two main classes of algorithms tackling this problem. Divisive (top-down) algorithms recursively partition the nodes into two communities, until a stopping rule indicates that no further split is needed. In contrast, agglomerative (bottom-up) algorithms first identify the smallest community structure and then repeatedly merge the communities using a linkage method. In this article, we establish theoretical guarantees for the recovery of the hierarchical tree and community structure of a Hierarchical Stochastic Block Model by a bottom-up algorithm. We also establish that this bottom-up algorithm attains the information-theoretic threshold for exact recovery at intermediate levels of the hierarchy. Notably, these recovery conditions are less restrictive compared to those existing for top-down algorithms. This shows that bottom-up algorithms extend the feasible region for achieving exact recovery at intermediate levels. Numerical experiments on both synthetic and real data sets confirm the superiority of bottom-up algorithms over top-down algorithms. We also observe that top-down algorithms can produce dendrograms with inversions. These findings contribute to a better understanding of hierarchical clustering techniques and their applications in network analysis.

In text-to-image generation tasks, the advancements of diffusion models have facilitated the fidelity of generated results. However, these models encounter challenges when processing text prompts containing multiple entities and attributes. The uneven distribution of attention results in the issues of entity leakage and attribute misalignment. Training from scratch to address this issue requires numerous labeled data and is resource-consuming. Motivated by this, we propose an attribution-focusing mechanism, a training-free phase-wise mechanism by modulation of attention for diffusion model. One of our core ideas is to guide the model to concentrate on the corresponding syntactic components of the prompt at distinct timesteps. To achieve this, we incorporate a temperature control mechanism within the early phases of the self-attention modules to mitigate entity leakage issues. An object-focused masking scheme and a phase-wise dynamic weight control mechanism are integrated into the cross-attention modules, enabling the model to discern the affiliation of semantic information between entities more effectively. The experimental results in various alignment scenarios demonstrate that our model attain better image-text alignment with minimal additional computational cost.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Video Object-Centric Learning seeks to decompose raw videos into a small set of object slots, but existing slot-attention models often suffer from severe over-fragmentation. This is because the model is implicitly encouraged to occupy all slots to minimize the reconstruction objective, thereby representing a single object with multiple redundant slots. We tackle this limitation with a reconstruction-guided slot curriculum (SlotCurri). Training starts with only a few coarse slots and progressively allocates new slots where reconstruction error remains high, thus expanding capacity only where it is needed and preventing fragmentation from the outset. Yet, during slot expansion, meaningful sub-parts can emerge only if coarse-level semantics are already well separated; however, with a small initial slot budget and an MSE objective, semantic boundaries remain blurry. Therefore, we augment MSE with a structure-aware loss that preserves local contrast and edge information to encourage each slot to sharpen its semantic boundaries. Lastly, we propose a cyclic inference that rolls slots forward and then backward through the frame sequence, producing temporally consistent object representations even in the earliest frames. All combined, SlotCurri addresses object over-fragmentation by allocating representational capacity where reconstruction fails, further enhanced by structural cues and cyclic inference. Notable FG-ARI gains of +6.8 on YouTube-VIS and +8.3 on MOVi-C validate the effectiveness of SlotCurri. Our code is available at github.com/wjun0830/SlotCurri.

Link prediction, a fundamental task on graphs, has proven indispensable in various applications, e.g., friend recommendation, protein analysis, and drug interaction prediction. However, since datasets span a multitude of domains, they could have distinct underlying mechanisms of link formation. Evidence in existing literature underscores the absence of a universally best algorithm suitable for all datasets. In this paper, we endeavor to explore principles of link prediction across diverse datasets from a data-centric perspective. We recognize three fundamental factors critical to link prediction: local structural proximity, global structural proximity, and feature proximity. We then unearth relationships among those factors where (i) global structural proximity only shows effectiveness when local structural proximity is deficient. (ii) The incompatibility can be found between feature and structural proximity. Such incompatibility leads to GNNs for Link Prediction (GNN4LP) consistently underperforming on edges where the feature proximity factor dominates. Inspired by these new insights from a data perspective, we offer practical instruction for GNN4LP model design and guidelines for selecting appropriate benchmark datasets for more comprehensive evaluations.

The Lottery Ticket Hypothesis asserts the existence of highly sparse, trainable subnetworks ('winning tickets') within dense, randomly initialized neural networks. However, state-of-the-art methods of drawing these tickets, like Lottery Ticket Rewinding (LTR), are computationally prohibitive, while more efficient saliency-based Pruning-at-Initialization (PaI) techniques suffer from a significant accuracy-sparsity trade-off and fail basic sanity checks. In this work, we argue that PaI's reliance on first-order saliency metrics, which ignore inter-weight dependencies, contributes substantially to this performance gap, especially in the sparse regime. To address this, we introduce Concrete Ticket Search (CTS), an algorithm that frames subnetwork discovery as a holistic combinatorial optimization problem. By leveraging a Concrete relaxation of the discrete search space and a novel gradient balancing scheme (GRADBALANCE) to control sparsity, CTS efficiently identifies high-performing subnetworks near initialization without requiring sensitive hyperparameter tuning. Motivated by recent works on lottery ticket training dynamics, we further propose a knowledge distillation-inspired family of pruning objectives, finding that minimizing the reverse Kullback-Leibler divergence between sparse and dense network outputs (CTS-KL) is particularly effective. Experiments on varying image classification tasks show that CTS produces subnetworks that robustly pass sanity checks and achieve accuracy comparable to or exceeding LTR, while requiring only a small fraction of the computation. For example, on ResNet-20 on CIFAR10, it reaches 99.3% sparsity with 74.0% accuracy in 7.9 minutes, while LTR attains the same sparsity with 68.3% accuracy in 95.2 minutes. CTS's subnetworks outperform saliency-based methods across all sparsities, but its advantage over LTR is most pronounced in the highly sparse regime.

Knowledge graph is generally incorporated into recommender systems to improve overall performance. Due to the generalization and scale of the knowledge graph, most knowledge relationships are not helpful for a target user-item prediction. To exploit the knowledge graph to capture target-specific knowledge relationships in recommender systems, we need to distill the knowledge graph to reserve the useful information and refine the knowledge to capture the users' preferences. To address the issues, we propose Knowledge-aware Conditional Attention Networks (KCAN), which is an end-to-end model to incorporate knowledge graph into a recommender system. Specifically, we use a knowledge-aware attention propagation manner to obtain the node representation first, which captures the global semantic similarity on the user-item network and the knowledge graph. Then given a target, i.e., a user-item pair, we automatically distill the knowledge graph into the target-specific subgraph based on the knowledge-aware attention. Afterward, by applying a conditional attention aggregation on the subgraph, we refine the knowledge graph to obtain target-specific node representations. Therefore, we can gain both representability and personalization to achieve overall performance. Experimental results on real-world datasets demonstrate the effectiveness of our framework over the state-of-the-art algorithms.

We aim to tackle the problem of point-based interactive segmentation, in which the key challenge is to propagate the user-provided annotations to unlabeled regions efficiently. Existing methods tackle this challenge by utilizing computationally expensive fully connected graphs or transformer architectures that sacrifice important fine-grained information required for accurate segmentation. To overcome these limitations, we propose a cascade sparse feature propagation network that learns a click-augmented feature representation for propagating user-provided information to unlabeled regions. The sparse design of our network enables efficient information propagation on high-resolution features, resulting in more detailed object segmentation. We validate the effectiveness of our method through comprehensive experiments on various benchmarks, and the results demonstrate the superior performance of our approach. Code is available at https://github.com/kleinzcy/CSFPN{https://github.com/kleinzcy/CSFPN}.

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.

Grounding has become a fundamental capability of vision-language models (VLMs). Most existing VLMs point by generating coordinates as part of their text output, which requires learning a complicated coordinate system and results in a high token count. Instead, we propose a more intuitive pointing mechanism that directly selects the visual tokens that contain the target concept. Our model generates a special pointing token that cross-attends to the input image or video tokens and selects the appropriate one. To make this model more fine-grained, we follow these pointing tokens with an additional special token that selects a fine-grained subpatch within the initially selected region, and then a third token that specifies a location within that subpatch. We further show that performance improves by generating points sequentially in a consistent order, encoding the relative position of the previously selected point, and including a special no-more-points class when selecting visual tokens. Using this method, we set a new state-of-the-art on image pointing (70.7% on PointBench), set a new state-of-the-art among fully open models on GUI pointing (61.1% on ScreenSpotPro), and improve video pointing (59.1% human preference win rate vs. a text coordinate baseline) and tracking (+6.3% gain on Molmo2Track). We additionally show that our method achieves much higher sample efficiency and discuss the qualitative differences that emerge from this design change.

In this paper, we propose the first framework that enables solving graph learning tasks of all levels (node, edge and graph) and all types (generation, regression and classification) with one model. We first propose Latent Graph Diffusion (LGD), a generative model that can generate node, edge, and graph-level features of all categories simultaneously. We achieve this goal by embedding the graph structures and features into a latent space leveraging a powerful encoder which can also be decoded, then training a diffusion model in the latent space. LGD is also capable of conditional generation through a specifically designed cross-attention mechanism. Then we formulate prediction tasks including regression and classification as (conditional) generation, which enables our LGD to solve tasks of all levels and all types with provable guarantees. We verify the effectiveness of our framework with extensive experiments, where our models achieve state-of-the-art or highly competitive results across generation and regression tasks.

We study the extent to which rotary position encodings (RoPE), a recent transformer position encoding algorithm broadly adopted in large language models (LLMs) and vision transformers (ViTs), can be applied to graph-structured data. We find that rotating tokens depending on the spectrum of the graph Laplacian efficiently injects structural information into the attention mechanism, boosting performance in synthetic and real-world graph learning tasks. This approach, coined _Wave-Induced Rotary Encodings_ (WIRE), enjoys intriguing theoretical properties: it recovers regular RoPE on grids, and depends asymptotically on the graph effective resistance. Unlike bias-based relative position encodings, WIRE is compatible with linear attention.