Daily Papers

Domain generalization (DG) seeks robust Vision Transformer (ViT) performance on unseen domains. Efficiently adapting pretrained ViTs for DG is challenging; standard fine-tuning is costly and can impair generalization. We propose GNN-MoE, enhancing Parameter-Efficient Fine-Tuning (PEFT) for DG with a Mixture-of-Experts (MoE) framework using efficient Kronecker adapters. Instead of token-based routing, a novel Graph Neural Network (GNN) router (GCN, GAT, SAGE) operates on inter-patch graphs to dynamically assign patches to specialized experts. This context-aware GNN routing leverages inter-patch relationships for better adaptation to domain shifts. GNN-MoE achieves state-of-the-art or competitive DG benchmark performance with high parameter efficiency, highlighting the utility of graph-based contextual routing for robust, lightweight DG.

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 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.

The digitization of complex technical systems, such as Piping and Instrumentation Diagrams (P&IDs), is crucial for efficient maintenance and operation of complex systems in hydraulic and process engineering. Previous approaches often rely on separate modules that analyze diagram elements individually, neglecting the diagram's overall structure. We address this limitation by proposing a novel approach that utilizes the Relationformer, a state-of-the-art deep learning architecture, to extract graphs from P&IDs. Our method leverages the ability of the Relationformer to simultaneously detect objects and their relationships in images, making it suitable for the task of graph extraction from engineering diagrams. We apply our proposed approach to both real-world and synthetically created P&ID datasets, and evaluate its effectiveness by comparing it with a modular digitization approach based on recent literature. We present PID2Graph, the first publicly accessible P&ID dataset featuring comprehensive labels for the graph structure, including symbols, nodes and their connections that is used for evaluation. To understand the effect of patching and stitching of both of the approaches, we compare values before and after merging the patches. For the real-world data, the Relationformer achieves convincing results, outperforming the modular digitization approach for edge detection by more than 25%. Our work provides a comprehensive framework for assessing the performance of P&ID digitization methods and opens up new avenues for research in this area using transformer architectures. The P&ID dataset used for evaluation will be published and publicly available upon acceptance of the paper.

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\%.

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

We consider the problem of graph matching, or learning vertex correspondence, between two correlated stochastic block models (SBMs). The graph matching problem arises in various fields, including computer vision, natural language processing and bioinformatics, and in particular, matching graphs with inherent community structure has significance related to de-anonymization of correlated social networks. Compared to the correlated Erdos-Renyi (ER) model, where various efficient algorithms have been developed, among which a few algorithms have been proven to achieve the exact matching with constant edge correlation, no low-order polynomial algorithm has been known to achieve exact matching for the correlated SBMs with constant correlation. In this work, we propose an efficient algorithm for matching graphs with community structure, based on the comparison between partition trees rooted from each vertex, by extending the idea of Mao et al. (2021) to graphs with communities. The partition tree divides the large neighborhoods of each vertex into disjoint subsets using their edge statistics to different communities. Our algorithm is the first low-order polynomial-time algorithm achieving exact matching between two correlated SBMs with high probability in dense graphs.

Multivariate time series is prevalent in many scientific and industrial domains. Modeling multivariate signals is challenging due to their long-range temporal dependencies and intricate interactions--both direct and indirect. To confront these complexities, we introduce a method of representing multivariate signals as nodes in a graph with edges indicating interdependency between them. Specifically, we leverage graph neural networks (GNN) and attention mechanisms to efficiently learn the underlying relationships within the time series data. Moreover, we suggest employing hierarchical signal decompositions running over the graphs to capture multiple spatial dependencies. The effectiveness of our proposed model is evaluated across various real-world benchmark datasets designed for long-term forecasting tasks. The results consistently showcase the superiority of our model, achieving an average 23\% reduction in mean squared error (MSE) compared to existing models.

Random walks are widely used for mining networks due to the computational efficiency of computing them. For instance, graph representation learning learns a d-dimensional embedding space, so that the nodes that tend to co-occur on random walks (a proxy of being in the same network neighborhood) are close in the embedding space. Specific local network topology (i.e., structure) influences the co-occurrence of nodes on random walks, so random walks of limited length capture only partial topological information, hence diminishing the performance of downstream methods. We explicitly capture all topological neighborhood information and improve performance by introducing orbit adjacencies that quantify the adjacencies of two nodes as co-occurring on a given pair of graphlet orbits, which are symmetric positions on graphlets (small, connected, non-isomorphic, induced subgraphs of a large network). Importantly, we mathematically prove that random walks on up to k nodes capture only a subset of all the possible orbit adjacencies for up to k-node graphlets. Furthermore, we enable orbit adjacency-based analysis of networks by developing an efficient GRaphlet-orbit ADjacency COunter (GRADCO), which exhaustively computes all 28 orbit adjacency matrices for up to four-node graphlets. Note that four-node graphlets suffice, because real networks are usually small-world. In large networks on around 20,000 nodes, GRADCOcomputesthe28matricesinminutes. Onsixrealnetworksfromvarious domains, we compare the performance of node-label predictors obtained by using the network embeddings based on our orbit adjacencies to those based on random walks. We find that orbit adjacencies, which include those unseen by random walks, outperform random walk-based adjacencies, demonstrating the importance of the inclusion of the topological neighborhood information that is unseen by random walks.

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.

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.

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.

Latent Diffusion Models (LDMs) are generally trained at fixed resolutions, limiting their capability when scaling up to high-resolution images. While training-based approaches address this limitation by training on high-resolution datasets, they require large amounts of data and considerable computational resources, making them less practical. Consequently, training-free methods, particularly patch-based approaches, have become a popular alternative. These methods divide an image into patches and fuse the denoising paths of each patch, showing strong performance on high-resolution generation. However, we observe two critical issues for patch-based approaches, which we call ``patch-level distribution shift" and ``increased patch monotonicity." To address these issues, we propose Adaptive Path Tracing (APT), a framework that combines Statistical Matching to ensure patch distributions remain consistent in upsampled latents and Scale-aware Scheduling to deal with the patch monotonicity. As a result, APT produces clearer and more refined details in high-resolution images. In addition, APT enables a shortcut denoising process, resulting in faster sampling with minimal quality degradation. Our experimental results confirm that APT produces more detailed outputs with improved inference speed, providing a practical approach to high-resolution image generation.

Observing certain patches in an image reduces the uncertainty of others. Their realization lowers the distribution entropy of each remaining patch feature, analogous to collapsing a particle's wave function in quantum mechanics. This phenomenon can intuitively be called patch collapse. To identify which patches are most relied on during a target region's collapse, we learn an autoencoder that softly selects a subset of patches to reconstruct each target patch. Graphing these learned dependencies for each patch's PageRank score reveals the optimal patch order to realize an image. We show that respecting this order benefits various masked image modeling methods. First, autoregressive image generation can be boosted by retraining the state-of-the-art model MAR. Next, we introduce a new setup for image classification by exposing Vision Transformers only to high-rank patches in the collapse order. Seeing 22\% of such patches is sufficient to achieve high accuracy. With these experiments, we propose patch collapse as a novel image modeling perspective that promotes vision efficiency. Our project is available at https://github.com/wguo-ai/CoP .

A graph homomorphism is a map between two graphs that preserves adjacency relations. We consider the problem of sampling a random graph homomorphism from a graph into a large network. We propose two complementary MCMC algorithms for sampling random graph homomorphisms and establish bounds on their mixing times and the concentration of their time averages. Based on our sampling algorithms, we propose a novel framework for network data analysis that circumvents some of the drawbacks in methods based on independent and neighborhood sampling. Various time averages of the MCMC trajectory give us various computable observables, including well-known ones such as homomorphism density and average clustering coefficient and their generalizations. Furthermore, we show that these network observables are stable with respect to a suitably renormalized cut distance between networks. We provide various examples and simulations demonstrating our framework through synthetic networks. We also demonstrate the performance of our framework on the tasks of network clustering and subgraph classification on the Facebook100 dataset and on Word Adjacency Networks of a set of classic novels.

Information flows by routes inside the network via mechanisms implemented in the model. These routes can be represented as graphs where nodes correspond to token representations and edges to operations inside the network. We automatically build these graphs in a top-down manner, for each prediction leaving only the most important nodes and edges. In contrast to the existing workflows relying on activation patching, we do this through attribution: this allows us to efficiently uncover existing circuits with just a single forward pass. Additionally, the applicability of our method is far beyond patching: we do not need a human to carefully design prediction templates, and we can extract information flow routes for any prediction (not just the ones among the allowed templates). As a result, we can talk about model behavior in general, for specific types of predictions, or different domains. We experiment with Llama 2 and show that the role of some attention heads is overall important, e.g. previous token heads and subword merging heads. Next, we find similarities in Llama 2 behavior when handling tokens of the same part of speech. Finally, we show that some model components can be specialized on domains such as coding or multilingual texts.

Federated learning is an active research topic since it enables several participants to jointly train a model without sharing local data. Currently, cross-silo federated learning is a popular training setting that utilizes a few hundred reliable data silos with high-speed access links to training a model. While this approach has been widely applied in real-world scenarios, designing a robust topology to reduce the training time remains an open problem. In this paper, we present a new multigraph topology for cross-silo federated learning. We first construct the multigraph using the overlay graph. We then parse this multigraph into different simple graphs with isolated nodes. The existence of isolated nodes allows us to perform model aggregation without waiting for other nodes, hence effectively reducing the training time. Intensive experiments on three public datasets show that our proposed method significantly reduces the training time compared with recent state-of-the-art topologies while maintaining the accuracy of the learned model. Our code can be found at https://github.com/aioz-ai/MultigraphFL

Deep graph learning has gained grand popularity over the past years due to its versatility and success in representing graph data across a wide range of domains. However, the pervasive issue of imbalanced graph data distributions, where certain parts exhibit disproportionally abundant data while others remain sparse, undermines the efficacy of conventional graph learning algorithms, leading to biased outcomes. To address this challenge, Imbalanced Graph Learning (IGL) has garnered substantial attention, enabling more balanced data distributions and better task performance. Despite the proliferation of IGL algorithms, the absence of consistent experimental protocols and fair performance comparisons pose a significant barrier to comprehending advancements in this field. To bridge this gap, we introduce IGL-Bench, a foundational comprehensive benchmark for imbalanced graph learning, embarking on 16 diverse graph datasets and 24 distinct IGL algorithms with uniform data processing and splitting strategies. Specifically, IGL-Bench systematically investigates state-of-the-art IGL algorithms in terms of effectiveness, robustness, and efficiency on node-level and graph-level tasks, with the scope of class-imbalance and topology-imbalance. Extensive experiments demonstrate the potential benefits of IGL algorithms on various imbalanced conditions, offering insights and opportunities in the IGL field. Further, we have developed an open-sourced and unified package to facilitate reproducible evaluation and inspire further innovative research, which is available at https://github.com/RingBDStack/IGL-Bench.

Graphs have often been used to answer questions about the interaction between real-world entities by taking advantage of their capacity to represent complex topologies. Complex networks are known to be graphs that capture such non-trivial topologies; they are able to represent human phenomena such as epidemic processes, the dynamics of populations, and the urbanization of cities. The investigation of complex networks has been extrapolated to many fields of science, with particular emphasis on computing techniques, including artificial intelligence. In such a case, the analysis of the interaction between entities of interest is transposed to the internal learning of algorithms, a paradigm whose investigation is able to expand the state of the art in Computer Science. By exploring this paradigm, this thesis puts together complex networks and machine learning techniques to improve the understanding of the human phenomena observed in pandemics, pendular migration, and street networks. Accordingly, we contribute with: (i) a new neural network architecture capable of modeling dynamic processes observed in spatial and temporal data with applications in epidemics propagation, weather forecasting, and patient monitoring in intensive care units; (ii) a machine-learning methodology for analyzing and predicting links in the scope of human mobility between all the cities of Brazil; and, (iii) techniques for identifying inconsistencies in the urban planning of cities while tracking the most influential vertices, with applications over Brazilian and worldwide cities. We obtained results sustained by sound evidence of advances to the state of the art in artificial intelligence, rigorous formalisms, and ample experimentation. Our findings rely upon real-world applications in a range of domains, demonstrating the applicability of our methodologies.

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

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

Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over 10^5 nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

We present network embedding algorithms that capture information about a node from the local distribution over node attributes around it, as observed over random walks following an approach similar to Skip-gram. Observations from neighborhoods of different sizes are either pooled (AE) or encoded distinctly in a multi-scale approach (MUSAE). Capturing attribute-neighborhood relationships over multiple scales is useful for a diverse range of applications, including latent feature identification across disconnected networks with similar attributes. We prove theoretically that matrices of node-feature pointwise mutual information are implicitly factorized by the embeddings. Experiments show that our algorithms are robust, computationally efficient and outperform comparable models on social networks and web graphs.

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.

Many graph representation learning (GRL) problems are dynamic, with millions of edges added or removed per second. A fundamental workload in this setting is dynamic link prediction: using a history of graph updates to predict whether a given pair of vertices will become connected. Recent schemes for link prediction in such dynamic settings employ Transformers, modeling individual graph updates as single tokens. In this work, we propose HOT: a model that enhances this line of works by harnessing higher-order (HO) graph structures; specifically, k-hop neighbors and more general subgraphs containing a given pair of vertices. Harnessing such HO structures by encoding them into the attention matrix of the underlying Transformer results in higher accuracy of link prediction outcomes, but at the expense of increased memory pressure. To alleviate this, we resort to a recent class of schemes that impose hierarchy on the attention matrix, significantly reducing memory footprint. The final design offers a sweetspot between high accuracy and low memory utilization. HOT outperforms other dynamic GRL schemes, for example achieving 9%, 7%, and 15% higher accuracy than - respectively - DyGFormer, TGN, and GraphMixer, for the MOOC dataset. Our design can be seamlessly extended towards other dynamic GRL workloads.

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.

Network embedding has been intensively studied in the literature and widely used in various applications, such as link prediction and node classification. While previous work focus on the design of new algorithms or are tailored for various problem settings, the discussion of initialization strategies in the learning process is often missed. In this work, we address this important issue of initialization for network embedding that could dramatically improve the performance of the algorithms on both effectiveness and efficiency. Specifically, we first exploit the graph partition technique that divides the graph into several disjoint subsets, and then construct an abstract graph based on the partitions. We obtain the initialization of the embedding for each node in the graph by computing the network embedding on the abstract graph, which is much smaller than the input graph, and then propagating the embedding among the nodes in the input graph. With extensive experiments on various datasets, we demonstrate that our initialization technique significantly improves the performance of the state-of-the-art algorithms on the evaluations of link prediction and node classification by up to 7.76% and 8.74% respectively. Besides, we show that the technique of initialization reduces the running time of the state-of-the-arts by at least 20%.

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.

Tangles were originally introduced as a concept to formalize regions of high connectivity in graphs. In recent years, they have also been discovered as a link between structural graph theory and data science: when interpreting similarity in data sets as connectivity between points, finding clusters in the data essentially amounts to finding tangles in the underlying graphs. This paper further explores the potential of tangles in data sets as a means for a formal study of clusters. Real-world data often follow a normal distribution. Accounting for this, we develop a quantitative theory of tangles in data sets drawn from Gaussian mixtures. To this end, we equip the data with a graph structure that models similarity between the points and allows us to apply tangle theory to the data. We provide explicit conditions under which tangles associated with the marginal Gaussian distributions exist asymptotically almost surely. This can be considered as a sufficient formal criterion for the separabability of clusters in the data.

We target a 3D generative model for general natural scenes that are typically unique and intricate. Lacking the necessary volumes of training data, along with the difficulties of having ad hoc designs in presence of varying scene characteristics, renders existing setups intractable. Inspired by classical patch-based image models, we advocate for synthesizing 3D scenes at the patch level, given a single example. At the core of this work lies important algorithmic designs w.r.t the scene representation and generative patch nearest-neighbor module, that address unique challenges arising from lifting classical 2D patch-based framework to 3D generation. These design choices, on a collective level, contribute to a robust, effective, and efficient model that can generate high-quality general natural scenes with both realistic geometric structure and visual appearance, in large quantities and varieties, as demonstrated upon a variety of exemplar scenes.

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

Complex networks can be used for modeling street meshes and urban agglomerates. With such a model, many aspects of a city can be investigated to promote a better quality of life to its citizens. Along these lines, this paper proposes a set of distance-based pattern-discovery algorithmic instruments to improve urban structures modeled as complex networks, detecting nodes that lack access from/to points of interest in a given city. Furthermore, we introduce a greedy algorithm that is able to recommend improvements to the structure of a city by suggesting where points of interest are to be placed. We contribute to a thorough process to deal with complex networks, including mathematical modeling and algorithmic innovation. The set of our contributions introduces a systematic manner to treat a recurrent problem of broad interest in cities.

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

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

Graph In-Context Learning, with the ability to adapt pre-trained graph models to novel and diverse downstream graphs without updating any parameters, has gained much attention in the community. The key to graph in-context learning is to perform downstream graphs conditioned on chosen prompt examples. Existing methods randomly select subgraphs or edges as prompts, leading to noisy graph prompts and inferior model performance. Additionally, due to the gap between pre-training and testing graphs, when the number of classes in the testing graphs is much greater than that in the training, the in-context learning ability will also significantly deteriorate. To tackle the aforementioned challenges, we develop a multi-stage adaptive prompt optimization method GraphPrompter, which optimizes the entire process of generating, selecting, and using graph prompts for better in-context learning capabilities. Firstly, Prompt Generator introduces a reconstruction layer to highlight the most informative edges and reduce irrelevant noise for graph prompt construction. Furthermore, in the selection stage, Prompt Selector employs the k-nearest neighbors algorithm and pre-trained selection layers to dynamically choose appropriate samples and minimize the influence of irrelevant prompts. Finally, we leverage a Prompt Augmenter with a cache replacement strategy to enhance the generalization capability of the pre-trained model on new datasets. Extensive experiments show that GraphPrompter effectively enhances the in-context learning ability of graph models. On average across all the settings, our approach surpasses the state-of-the-art baselines by over 8%. Our code is released at https://github.com/karin0018/GraphPrompter.

We propose a novel feed-forward network for video inpainting. We use a set of sampled video frames as the reference to take visible contents to fill the hole of a target frame. Our video inpainting network consists of two stages. The first stage is an alignment module that uses computed homographies between the reference frames and the target frame. The visible patches are then aggregated based on the frame similarity to fill in the target holes roughly. The second stage is a non-local attention module that matches the generated patches with known reference patches (in space and time) to refine the previous global alignment stage. Both stages consist of large spatial-temporal window size for the reference and thus enable modeling long-range correlations between distant information and the hole regions. Therefore, even challenging scenes with large or slowly moving holes can be handled, which have been hardly modeled by existing flow-based approach. Our network is also designed with a recurrent propagation stream to encourage temporal consistency in video results. Experiments on video object removal demonstrate that our method inpaints the holes with globally and locally coherent contents.

To characterize the location (mean, median) of a set of graphs, one needs a notion of centrality that is adapted to metric spaces, since graph sets are not Euclidean spaces. A standard approach is to consider the Frechet mean. In this work, we equip a set of graphs with the pseudometric defined by the norm between the eigenvalues of their respective adjacency matrix. Unlike the edit distance, this pseudometric reveals structural changes at multiple scales, and is well adapted to studying various statistical problems for graph-valued data. We describe an algorithm to compute an approximation to the sample Frechet mean of a set of undirected unweighted graphs with a fixed size using this pseudometric.

Masked graph autoencoders have emerged as a powerful graph self-supervised learning method that has yet to be fully explored. In this paper, we unveil that the existing discrete edge masking and binary link reconstruction strategies are insufficient to learn topologically informative representations, from the perspective of message propagation on graph neural networks. These limitations include blocking message flows, vulnerability to over-smoothness, and suboptimal neighborhood discriminability. Inspired by these understandings, we explore non-discrete edge masks, which are sampled from a continuous and dispersive probability distribution instead of the discrete Bernoulli distribution. These masks restrict the amount of output messages for each edge, referred to as "bandwidths". We propose a novel, informative, and effective topological masked graph autoencoder using bandwidth masking and a layer-wise bandwidth prediction objective. We demonstrate its powerful graph topological learning ability both theoretically and empirically. Our proposed framework outperforms representative baselines in both self-supervised link prediction (improving the discrete edge reconstructors by at most 20%) and node classification on numerous datasets, solely with a structure-learning pretext. Our implementation is available at https://github.com/Newiz430/Bandana.

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

Feature-based image matching has extensive applications in computer vision. Keypoints detected in images can be naturally represented as graph structures, and Graph Neural Networks (GNNs) have been shown to outperform traditional deep learning techniques. Consequently, the paradigm of image matching via GNNs has gained significant prominence in recent academic research. In this paper, we first introduce an innovative adaptive graph construction method that utilizes a filtering mechanism based on distance and dynamic threshold similarity. This method dynamically adjusts the criteria for incorporating new vertices based on the characteristics of existing vertices, allowing for the construction of more precise and robust graph structures while avoiding redundancy. We further combine the vertex processing capabilities of GNNs with the global awareness capabilities of Transformers to enhance the model's representation of spatial and feature information within graph structures. This hybrid model provides a deeper understanding of the interrelationships between vertices and their contributions to the matching process. Additionally, we employ the Sinkhorn algorithm to iteratively solve for optimal matching results. Finally, we validate our system using extensive image datasets and conduct comprehensive comparative experiments. Experimental results demonstrate that our system achieves an average improvement of 3.8x-40.3x in overall matching performance. Additionally, the number of vertices and edges significantly impacts training efficiency and memory usage; therefore, we employ multi-GPU technology to accelerate the training process. Our code is available at https://github.com/songxf1024/GIMS.

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.

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

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.

Aiming at better representing multivariate relationships, this paper investigates a motif dimensional framework for higher-order graph learning. The graph learning effectiveness can be improved through OFFER. The proposed framework mainly aims at accelerating and improving higher-order graph learning results. We apply the acceleration procedure from the dimensional of network motifs. Specifically, the refined degree for nodes and edges are conducted in two stages: (1) employ motif degree of nodes to refine the adjacency matrix of the network; and (2) employ motif degree of edges to refine the transition probability matrix in the learning process. In order to assess the efficiency of the proposed framework, four popular network representation algorithms are modified and examined. By evaluating the performance of OFFER, both link prediction results and clustering results demonstrate that the graph representation learning algorithms enhanced with OFFER consistently outperform the original algorithms with higher efficiency.

Over the last few years, deep learning techniques have yielded significant improvements in image inpainting. However, many of these techniques fail to reconstruct reasonable structures as they are commonly over-smoothed and/or blurry. This paper develops a new approach for image inpainting that does a better job of reproducing filled regions exhibiting fine details. We propose a two-stage adversarial model EdgeConnect that comprises of an edge generator followed by an image completion network. The edge generator hallucinates edges of the missing region (both regular and irregular) of the image, and the image completion network fills in the missing regions using hallucinated edges as a priori. We evaluate our model end-to-end over the publicly available datasets CelebA, Places2, and Paris StreetView, and show that it outperforms current state-of-the-art techniques quantitatively and qualitatively. Code and models available at: https://github.com/knazeri/edge-connect

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

With the increasing number of new neural architecture designs and substantial existing neural architectures, it becomes difficult for the researchers to situate their contributions compared with existing neural architectures or establish the connections between their designs and other relevant ones. To discover similar neural architectures in an efficient and automatic manner, we define a new problem Neural Architecture Retrieval which retrieves a set of existing neural architectures which have similar designs to the query neural architecture. Existing graph pre-training strategies cannot address the computational graph in neural architectures due to the graph size and motifs. To fulfill this potential, we propose to divide the graph into motifs which are used to rebuild the macro graph to tackle these issues, and introduce multi-level contrastive learning to achieve accurate graph representation learning. Extensive evaluations on both human-designed and synthesized neural architectures demonstrate the superiority of our algorithm. Such a dataset which contains 12k real-world network architectures, as well as their embedding, is built for neural architecture retrieval.

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.

Graph Neural Networks (GNNs) are popular models for machine learning on graphs that typically follow the message-passing paradigm, whereby the feature of a node is updated recursively upon aggregating information over its neighbors. While exchanging messages over the input graph endows GNNs with a strong inductive bias, it can also make GNNs susceptible to over-squashing, thereby preventing them from capturing long-range interactions in the given graph. To rectify this issue, graph rewiring techniques have been proposed as a means of improving information flow by altering the graph connectivity. In this work, we identify three desiderata for graph-rewiring: (i) reduce over-squashing, (ii) respect the locality of the graph, and (iii) preserve the sparsity of the graph. We highlight fundamental trade-offs that occur between spatial and spectral rewiring techniques; while the former often satisfy (i) and (ii) but not (iii), the latter generally satisfy (i) and (iii) at the expense of (ii). We propose a novel rewiring framework that satisfies all of (i)--(iii) through a locality-aware sequence of rewiring operations. We then discuss a specific instance of such rewiring framework and validate its effectiveness on several real-world benchmarks, showing that it either matches or significantly outperforms existing rewiring approaches.

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.

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

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

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

We study the approximability of an existing framework for clustering edge-colored hypergraphs, which is closely related to chromatic correlation clustering and is motivated by machine learning and data mining applications where the goal is to cluster a set of objects based on multiway interactions of different categories or types. We present improved approximation guarantees based on linear programming, and show they are tight by proving a matching integrality gap. Our results also include new approximation hardness results, a combinatorial 2-approximation whose runtime is linear in the hypergraph size, and several new connections to well-studied objectives such as vertex cover and hypergraph multiway cut.

Graphs can be leveraged to model polyphonic multitrack symbolic music, where notes, chords and entire sections may be linked at different levels of the musical hierarchy by tonal and rhythmic relationships. Nonetheless, there is a lack of works that consider graph representations in the context of deep learning systems for music generation. This paper bridges this gap by introducing a novel graph representation for music and a deep Variational Autoencoder that generates the structure and the content of musical graphs separately, one after the other, with a hierarchical architecture that matches the structural priors of music. By separating the structure and content of musical graphs, it is possible to condition generation by specifying which instruments are played at certain times. This opens the door to a new form of human-computer interaction in the context of music co-creation. After training the model on existing MIDI datasets, the experiments show that the model is able to generate appealing short and long musical sequences and to realistically interpolate between them, producing music that is tonally and rhythmically consistent. Finally, the visualization of the embeddings shows that the model is able to organize its latent space in accordance with known musical concepts.

Text-attributed graphs are widely used across domains, offering rich opportunities for zero-shot learning via graph-text alignment. However, existing methods struggle with tasks requiring fine-grained pattern recognition, particularly on heterophilic graphs. Through empirical and theoretical analysis, we identify an over-abstraction problem: current approaches operate at excessively large hyperbolic radii, compressing multi-scale structural information into uniform high-level abstractions. This abstraction-induced information loss obscures critical local patterns essential for accurate predictions. By analyzing embeddings in hyperbolic space, we demonstrate that optimal graph learning requires faithful preservation of fine-grained structural details, better retained by representations positioned closer to the origin. To address this, we propose H4G, a framework that systematically reduces embedding radii using learnable block-diagonal scaling matrices and M\"obius matrix multiplication. This approach restores access to fine-grained patterns while maintaining global receptive ability with minimal computational overhead. Experiments show H4G achieves state-of-the-art zero-shot performance with 12.8\% improvement on heterophilic graphs and 8.4\% on homophilic graphs, confirming that radius reduction enables faithful multi-scale representation for advancing zero-shot graph learning.

Graph Structure Learning (GSL) focuses on capturing intrinsic dependencies and interactions among nodes in graph-structured data by generating novel graph structures. Graph Neural Networks (GNNs) have emerged as promising GSL solutions, utilizing recursive message passing to encode node-wise inter-dependencies. However, many existing GSL methods heavily depend on explicit graph structural information as supervision signals, leaving them susceptible to challenges such as data noise and sparsity. In this work, we propose GraphEdit, an approach that leverages large language models (LLMs) to learn complex node relationships in graph-structured data. By enhancing the reasoning capabilities of LLMs through instruction-tuning over graph structures, we aim to overcome the limitations associated with explicit graph structural information and enhance the reliability of graph structure learning. Our approach not only effectively denoises noisy connections but also identifies node-wise dependencies from a global perspective, providing a comprehensive understanding of the graph structure. We conduct extensive experiments on multiple benchmark datasets to demonstrate the effectiveness and robustness of GraphEdit across various settings. We have made our model implementation available at: https://github.com/HKUDS/GraphEdit.

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.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

Graph neural networks (GNNs), in general, are built on the assumption of a static set of features characterizing each node in a graph. This assumption is often violated in practice. Existing methods partly address this issue through feature imputation. However, these techniques (i) assume uniformity of feature set across nodes, (ii) are transductive by nature, and (iii) fail to work when features are added or removed over time. In this work, we address these limitations through a novel GNN framework called GRAFENNE. GRAFENNE performs a novel allotropic transformation on the original graph, wherein the nodes and features are decoupled through a bipartite encoding. Through a carefully chosen message passing framework on the allotropic transformation, we make the model parameter size independent of the number of features and thereby inductive to both unseen nodes and features. We prove that GRAFENNE is at least as expressive as any of the existing message-passing GNNs in terms of Weisfeiler-Leman tests, and therefore, the additional inductivity to unseen features does not come at the cost of expressivity. In addition, as demonstrated over four real-world graphs, GRAFENNE empowers the underlying GNN with high empirical efficacy and the ability to learn in continual fashion over streaming feature sets.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

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

Graph Neural Networks (GNNs) have shown great potential in the field of graph representation learning. Standard GNNs define a local message-passing mechanism which propagates information over the whole graph domain by stacking multiple layers. This paradigm suffers from two major limitations, over-squashing and poor long-range dependencies, that can be solved using global attention but significantly increases the computational cost to quadratic complexity. In this work, we propose an alternative approach to overcome these structural limitations by leveraging the ViT/MLP-Mixer architectures introduced in computer vision. We introduce a new class of GNNs, called Graph ViT/MLP-Mixer, that holds three key properties. First, they capture long-range dependency and mitigate the issue of over-squashing as demonstrated on Long Range Graph Benchmark and TreeNeighbourMatch datasets. Second, they offer better speed and memory efficiency with a complexity linear to the number of nodes and edges, surpassing the related Graph Transformer and expressive GNN models. Third, they show high expressivity in terms of graph isomorphism as they can distinguish at least 3-WL non-isomorphic graphs. We test our architecture on 4 simulated datasets and 7 real-world benchmarks, and show highly competitive results on all of them. The source code is available for reproducibility at: https://github.com/XiaoxinHe/Graph-ViT-MLPMixer.

Deep learning has revolutionized many machine learning tasks in recent years, ranging from image classification and video processing to speech recognition and natural language understanding. The data in these tasks are typically represented in the Euclidean space. However, there is an increasing number of applications where data are generated from non-Euclidean domains and are represented as graphs with complex relationships and interdependency between objects. The complexity of graph data has imposed significant challenges on existing machine learning algorithms. Recently, many studies on extending deep learning approaches for graph data have emerged. In this survey, we provide a comprehensive overview of graph neural networks (GNNs) in data mining and machine learning fields. We propose a new taxonomy to divide the state-of-the-art graph neural networks into four categories, namely recurrent graph neural networks, convolutional graph neural networks, graph autoencoders, and spatial-temporal graph neural networks. We further discuss the applications of graph neural networks across various domains and summarize the open source codes, benchmark data sets, and model evaluation of graph neural networks. Finally, we propose potential research directions in this rapidly growing field.

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

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

Following the success of Word2Vec embeddings, graph embeddings (GEs) have gained substantial traction. GEs are commonly generated and evaluated extrinsically on downstream applications, but intrinsic evaluations of the original graph properties in terms of topological structure and semantic information have been lacking. Understanding these will help identify the deficiency of the various families of GE methods when vectorizing graphs in terms of preserving the relevant knowledge or learning incorrect knowledge. To address this, we propose RESTORE, a framework for intrinsic GEs assessment through graph reconstruction. We show that reconstructing the original graph from the underlying GEs yields insights into the relative amount of information preserved in a given vector form. We first introduce the graph reconstruction task. We generate GEs from three GE families based on factorization methods, random walks, and deep learning (with representative algorithms from each family) on the CommonSense Knowledge Graph (CSKG). We analyze their effectiveness in preserving the (a) topological structure of node-level graph reconstruction with an increasing number of hops and (b) semantic information on various word semantic and analogy tests. Our evaluations show deep learning-based GE algorithm (SDNE) is overall better at preserving (a) with a mean average precision (mAP) of 0.54 and 0.35 for 2 and 3-hop reconstruction respectively, while the factorization-based algorithm (HOPE) is better at encapsulating (b) with an average Euclidean distance of 0.14, 0.17, and 0.11 for 1, 2, and 3-hop reconstruction respectively. The modest performance of these GEs leaves room for further research avenues on better graph representation learning.

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.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

For supervised learning with tabular data, decision tree ensembles produced via boosting techniques generally dominate real-world applications involving iid training/test sets. However for graph data where the iid assumption is violated due to structured relations between samples, it remains unclear how to best incorporate this structure within existing boosting pipelines. To this end, we propose a generalized framework for iterating boosting with graph propagation steps that share node/sample information across edges connecting related samples. Unlike previous efforts to integrate graph-based models with boosting, our approach is anchored in a principled meta loss function such that provable convergence can be guaranteed under relatively mild assumptions. Across a variety of non-iid graph datasets with tabular node features, our method achieves comparable or superior performance than both tabular and graph neural network models, as well as existing hybrid strategies that combine the two. Beyond producing better predictive performance than recently proposed graph models, our proposed techniques are easy to implement, computationally more efficient, and enjoy stronger theoretical guarantees (which make our results more reproducible).

Vision transformers (ViTs) have significantly changed the computer vision landscape and have periodically exhibited superior performance in vision tasks compared to convolutional neural networks (CNNs). Although the jury is still out on which model type is superior, each has unique inductive biases that shape their learning and generalization performance. For example, ViTs have interesting properties with respect to early layer non-local feature dependence, as well as self-attention mechanisms which enhance learning flexibility, enabling them to ignore out-of-context image information more effectively. We hypothesize that this power to ignore out-of-context information (which we name patch selectivity), while integrating in-context information in a non-local manner in early layers, allows ViTs to more easily handle occlusion. In this study, our aim is to see whether we can have CNNs simulate this ability of patch selectivity by effectively hardwiring this inductive bias using Patch Mixing data augmentation, which consists of inserting patches from another image onto a training image and interpolating labels between the two image classes. Specifically, we use Patch Mixing to train state-of-the-art ViTs and CNNs, assessing its impact on their ability to ignore out-of-context patches and handle natural occlusions. We find that ViTs do not improve nor degrade when trained using Patch Mixing, but CNNs acquire new capabilities to ignore out-of-context information and improve on occlusion benchmarks, leaving us to conclude that this training method is a way of simulating in CNNs the abilities that ViTs already possess. We will release our Patch Mixing implementation and proposed datasets for public use. Project page: https://arielnlee.github.io/PatchMixing/

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

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

Complex networks provide a means to describe cities through their street mesh, expressing characteristics that refer to the structure and organization of an urban zone. Although other studies have used complex networks to model street meshes, we observed a lack of methods to characterize the relationship between cities by using their topological features. Accordingly, this paper aims to describe interactions between cities by using vectors of topological features extracted from their street meshes represented as complex networks. The methodology of this study is based on the use of digital maps. Over the computational representation of such maps, we extract global complex-network features that embody the characteristics of the cities. These vectors allow for the use of multidimensional projection and clustering techniques, enabling a similarity-based comparison of the street meshes. We experiment with 645 cities from the Brazilian state of Sao Paulo. Our results show how the joint of global features describes urban indicators that are deep-rooted in the network's topology and how they reveal characteristics and similarities among sets of cities that are separated from each other.

Associating unstructured data with structured information is crucial for real-world tasks that require relevance search. However, existing graph learning benchmarks often overlook the rich semantic information associate with each node. To bridge such gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), the first comprehensive multi-modal graph benchmark that incorporates both textual and visual information. MM-GRAPH surpasses previous efforts, which have primarily focused on text-attributed graphs with various connectivity patterns. MM-GRAPH consists of five graph learning datasets of various scales that are appropriate for different learning tasks. Their multimodal node features, enabling a more comprehensive evaluation of graph learning algorithms in real-world scenarios. To facilitate research on multimodal graph learning, we further provide an extensive study on the performance of various graph neural networks in the presence of features from various modalities. MM-GRAPH aims to foster research on multimodal graph learning and drive the development of more advanced and robust graph learning algorithms. By providing a diverse set of datasets and benchmarks, MM-GRAPH enables researchers to evaluate and compare their models in realistic settings, ultimately leading to improved performance on real-world applications that rely on multimodal graph data.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

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

Virtual sensing techniques allow for inferring signals at new unmonitored locations by exploiting spatio-temporal measurements coming from physical sensors at different locations. However, as the sensor coverage becomes sparse due to costs or other constraints, physical proximity cannot be used to support interpolation. In this paper, we overcome this challenge by leveraging dependencies between the target variable and a set of correlated variables (covariates) that can frequently be associated with each location of interest. From this viewpoint, covariates provide partial observability, and the problem consists of inferring values for unobserved channels by exploiting observations at other locations to learn how such variables can correlate. We introduce a novel graph-based methodology to exploit such relationships and design a graph deep learning architecture, named GgNet, implementing the framework. The proposed approach relies on propagating information over a nested graph structure that is used to learn dependencies between variables as well as locations. GgNet is extensively evaluated under different virtual sensing scenarios, demonstrating higher reconstruction accuracy compared to the state-of-the-art.

Graph learning has become indispensable for interpreting and harnessing relational data in diverse fields, ranging from recommendation systems to social network analysis. In this context, a variety of GNNs have emerged as promising methodologies for encoding the structural information of graphs. By effectively capturing the graph's underlying structure, these GNNs have shown great potential in enhancing performance in graph learning tasks, such as link prediction and node classification. However, despite their successes, a significant challenge persists: these advanced methods often face difficulties in generalizing to unseen graph data that significantly differs from the training instances. In this work, our aim is to advance the graph learning paradigm by developing a general graph foundation model. This model is designed to understand the complex topological patterns present in diverse graph data, enabling it to excel in zero-shot graph learning tasks across different downstream datasets. To achieve this goal, we address several key technical challenges in our OpenGraph model. Firstly, we propose a unified graph tokenizer to adapt our graph model to generalize well on unseen graph data, even when the underlying graph properties differ significantly from those encountered during training. Secondly, we develop a scalable graph transformer as the foundational encoder, which effectively captures node-wise dependencies within the global topological context. Thirdly, we introduce a data augmentation mechanism enhanced by a LLM to alleviate the limitations of data scarcity in real-world scenarios. Extensive experiments validate the effectiveness of our framework. By adapting our OpenGraph to new graph characteristics and comprehending the nuances of diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings and domains.

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

Weighted graphs are ubiquitous throughout biology, chemistry, and the social sciences, motivating the development of generative models for abstract weighted graph data using deep neural networks. However, most current deep generative models are either designed for unweighted graphs and are not easily extended to weighted topologies or incorporate edge weights without consideration of a joint distribution with topology. Furthermore, learning a distribution over weighted graphs must account for complex nonlocal dependencies between both the edges of the graph and corresponding weights of each edge. We develop an autoregressive model BiGG-E, a nontrivial extension of the BiGG model, that learns a joint distribution over weighted graphs while still exploiting sparsity to generate a weighted graph with n nodes and m edges in O((n + m)log n) time. Simulation studies and experiments on a variety of benchmark datasets demonstrate that BiGG-E best captures distributions over weighted graphs while remaining scalable and computationally efficient.

Microscopic assessment of histopathology images is vital for accurate cancer diagnosis and treatment. Whole Slide Image (WSI) classification and captioning have become crucial tasks in computer-aided pathology. However, microscopic WSI face challenges such as redundant patches and unknown patch positions due to subjective pathologist captures. Moreover, generating automatic pathology captions remains a significant challenge. To address these issues, we introduce a novel GNN-ViTCap framework for classification and caption generation from histopathological microscopic images. First, a visual feature extractor generates patch embeddings. Redundant patches are then removed by dynamically clustering these embeddings using deep embedded clustering and selecting representative patches via a scalar dot attention mechanism. We build a graph by connecting each node to its nearest neighbors in the similarity matrix and apply a graph neural network to capture both local and global context. The aggregated image embeddings are projected into the language model's input space through a linear layer and combined with caption tokens to fine-tune a large language model. We validate our method on the BreakHis and PatchGastric datasets. GNN-ViTCap achieves an F1 score of 0.934 and an AUC of 0.963 for classification, along with a BLEU-4 score of 0.811 and a METEOR score of 0.569 for captioning. Experimental results demonstrate that GNN-ViTCap outperforms state of the art approaches, offering a reliable and efficient solution for microscopy based patient diagnosis.

Networks provide a powerful formalism for modeling complex systems by using a model of pairwise interactions. But much of the structure within these systems involves interactions that take place among more than two nodes at once; for example, communication within a group rather than person-to person, collaboration among a team rather than a pair of coauthors, or biological interaction between a set of molecules rather than just two. Such higher-order interactions are ubiquitous, but their empirical study has received limited attention, and little is known about possible organizational principles of such structures. Here we study the temporal evolution of 19 datasets with explicit accounting for higher-order interactions. We show that there is a rich variety of structure in our datasets but datasets from the same system types have consistent patterns of higher-order structure. Furthermore, we find that tie strength and edge density are competing positive indicators of higher-order organization, and these trends are consistent across interactions involving differing numbers of nodes. To systematically further the study of theories for such higher-order structures, we propose higher-order link prediction as a benchmark problem to assess models and algorithms that predict higher-order structure. We find a fundamental differences from traditional pairwise link prediction, with a greater role for local rather than long-range information in predicting the appearance of new interactions.

This paper proposes a simple but effective graph-based agglomerative algorithm, for clustering high-dimensional data. We explore the different roles of two fundamental concepts in graph theory, indegree and outdegree, in the context of clustering. The average indegree reflects the density near a sample, and the average outdegree characterizes the local geometry around a sample. Based on such insights, we define the affinity measure of clusters via the product of average indegree and average outdegree. The product-based affinity makes our algorithm robust to noise. The algorithm has three main advantages: good performance, easy implementation, and high computational efficiency. We test the algorithm on two fundamental computer vision problems: image clustering and object matching. Extensive experiments demonstrate that it outperforms the state-of-the-arts in both applications.

We study the realizability of simplicial complexes with a given pair of integer sequences, representing the node degree distribution and the facet size distribution, respectively. While the s-uniform variant of the problem is NP-complete when s geq 3, we identify two populations of input sequences, most of which can be solved in polynomial time using a recursive algorithm that we contribute. Combining with a sampler for the simplicial configuration model [J.-G. Young et al., Phys. Rev. E 96, 032312 (2017)], we facilitate the efficient sampling of simplicial ensembles from arbitrary degree and size distributions. We find that, contrary to expectations based on dyadic networks, increasing the nodes' degrees reduces the number of loops in simplicial complexes. Our work unveils a fundamental constraint on the degree-size sequences and sheds light on further analysis of higher-order phenomena based on local structures.

Integer Linear Programs (ILPs) are powerful tools for modeling and solving a large number of combinatorial optimization problems. Recently, it has been shown that Large Neighborhood Search (LNS), as a heuristic algorithm, can find high quality solutions to ILPs faster than Branch and Bound. However, how to find the right heuristics to maximize the performance of LNS remains an open problem. In this paper, we propose a novel approach, CL-LNS, that delivers state-of-the-art anytime performance on several ILP benchmarks measured by metrics including the primal gap, the primal integral, survival rates and the best performing rate. Specifically, CL-LNS collects positive and negative solution samples from an expert heuristic that is slow to compute and learns a new one with a contrastive loss. We use graph attention networks and a richer set of features to further improve its performance.

We present PatchmatchNet, a novel and learnable cascade formulation of Patchmatch for high-resolution multi-view stereo. With high computation speed and low memory requirement, PatchmatchNet can process higher resolution imagery and is more suited to run on resource limited devices than competitors that employ 3D cost volume regularization. For the first time we introduce an iterative multi-scale Patchmatch in an end-to-end trainable architecture and improve the Patchmatch core algorithm with a novel and learned adaptive propagation and evaluation scheme for each iteration. Extensive experiments show a very competitive performance and generalization for our method on DTU, Tanks & Temples and ETH3D, but at a significantly higher efficiency than all existing top-performing models: at least two and a half times faster than state-of-the-art methods with twice less memory usage.

Graph Neural Networks (GNNs) that are based on the message passing (MP) paradigm generally exchange information between 1-hop neighbors to build node representations at each layer. In principle, such networks are not able to capture long-range interactions (LRI) that may be desired or necessary for learning a given task on graphs. Recently, there has been an increasing interest in development of Transformer-based methods for graphs that can consider full node connectivity beyond the original sparse structure, thus enabling the modeling of LRI. However, MP-GNNs that simply rely on 1-hop message passing often fare better in several existing graph benchmarks when combined with positional feature representations, among other innovations, hence limiting the perceived utility and ranking of Transformer-like architectures. Here, we present the Long Range Graph Benchmark (LRGB) with 5 graph learning datasets: PascalVOC-SP, COCO-SP, PCQM-Contact, Peptides-func and Peptides-struct that arguably require LRI reasoning to achieve strong performance in a given task. We benchmark both baseline GNNs and Graph Transformer networks to verify that the models which capture long-range dependencies perform significantly better on these tasks. Therefore, these datasets are suitable for benchmarking and exploration of MP-GNNs and Graph Transformer architectures that are intended to capture LRI.

Graph Neural Networks operate through bottom-up message-passing, fundamentally differing from human visual perception, which intuitively captures global structures first. We investigate the underappreciated potential of vision models for graph understanding, finding they achieve performance comparable to GNNs on established benchmarks while exhibiting distinctly different learning patterns. These divergent behaviors, combined with limitations of existing benchmarks that conflate domain features with topological understanding, motivate our introduction of GraphAbstract. This benchmark evaluates models' ability to perceive global graph properties as humans do: recognizing organizational archetypes, detecting symmetry, sensing connectivity strength, and identifying critical elements. Our results reveal that vision models significantly outperform GNNs on tasks requiring holistic structural understanding and maintain generalizability across varying graph scales, while GNNs struggle with global pattern abstraction and degrade with increasing graph size. This work demonstrates that vision models possess remarkable yet underutilized capabilities for graph structural understanding, particularly for problems requiring global topological awareness and scale-invariant reasoning. These findings open new avenues to leverage this underappreciated potential for developing more effective graph foundation models for tasks dominated by holistic pattern recognition.

Retrieval-augmented generation (RAG) is a powerful technique that enhances downstream task execution by retrieving additional information, such as knowledge, skills, and tools from external sources. Graph, by its intrinsic "nodes connected by edges" nature, encodes massive heterogeneous and relational information, making it a golden resource for RAG in tremendous real-world applications. As a result, we have recently witnessed increasing attention on equipping RAG with Graph, i.e., GraphRAG. However, unlike conventional RAG, where the retriever, generator, and external data sources can be uniformly designed in the neural-embedding space, the uniqueness of graph-structured data, such as diverse-formatted and domain-specific relational knowledge, poses unique and significant challenges when designing GraphRAG for different domains. Given the broad applicability, the associated design challenges, and the recent surge in GraphRAG, a systematic and up-to-date survey of its key concepts and techniques is urgently desired. Following this motivation, we present a comprehensive and up-to-date survey on GraphRAG. Our survey first proposes a holistic GraphRAG framework by defining its key components, including query processor, retriever, organizer, generator, and data source. Furthermore, recognizing that graphs in different domains exhibit distinct relational patterns and require dedicated designs, we review GraphRAG techniques uniquely tailored to each domain. Finally, we discuss research challenges and brainstorm directions to inspire cross-disciplinary opportunities. Our survey repository is publicly maintained at https://github.com/Graph-RAG/GraphRAG/.

Various human-designed prompt engineering techniques have been proposed to improve problem solvers based on Large Language Models (LLMs), yielding many disparate code bases. We unify these approaches by describing LLM-based agents as computational graphs. The nodes implement functions to process multimodal data or query LLMs, and the edges describe the information flow between operations. Graphs can be recursively combined into larger composite graphs representing hierarchies of inter-agent collaboration (where edges connect operations of different agents). Our novel automatic graph optimizers (1) refine node-level LLM prompts (node optimization) and (2) improve agent orchestration by changing graph connectivity (edge optimization). Experiments demonstrate that our framework can be used to efficiently develop, integrate, and automatically improve various LLM agents. The code can be found at https://github.com/metauto-ai/gptswarm.

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.

We propose a novel random walk-based algorithm for unbiased estimation of arbitrary functions of a weighted adjacency matrix, coined universal graph random features (u-GRFs). This includes many of the most popular examples of kernels defined on the nodes of a graph. Our algorithm enjoys subquadratic time complexity with respect to the number of nodes, overcoming the notoriously prohibitive cubic scaling of exact graph kernel evaluation. It can also be trivially distributed across machines, permitting learning on much larger networks. At the heart of the algorithm is a modulation function which upweights or downweights the contribution from different random walks depending on their lengths. We show that by parameterising it with a neural network we can obtain u-GRFs that give higher-quality kernel estimates or perform efficient, scalable kernel learning. We provide robust theoretical analysis and support our findings with experiments including pointwise estimation of fixed graph kernels, solving non-homogeneous graph ordinary differential equations, node clustering and kernel regression on triangular meshes.

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

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

We study graph data augmentation by mixup, which has been used successfully on images. A key operation of mixup is to compute a convex combination of a pair of inputs. This operation is straightforward for grid-like data, such as images, but challenging for graph data. The key difficulty lies in the fact that different graphs typically have different numbers of nodes, and thus there lacks a node-level correspondence between graphs. In this work, we propose S-Mixup, a simple yet effective mixup method for graph classification by soft alignments. Specifically, given a pair of graphs, we explicitly obtain node-level correspondence via computing a soft assignment matrix to match the nodes between two graphs. Based on the soft assignments, we transform the adjacency and node feature matrices of one graph, so that the transformed graph is aligned with the other graph. In this way, any pair of graphs can be mixed directly to generate an augmented graph. We conduct systematic experiments to show that S-Mixup can improve the performance and generalization of graph neural networks (GNNs) on various graph classification tasks. In addition, we show that S-Mixup can increase the robustness of GNNs against noisy labels.

Learning graph generative models over latent spaces has received less attention compared to models that operate on the original data space and has so far demonstrated lacklustre performance. We present GLAD a latent space graph generative model. Unlike most previous latent space graph generative models, GLAD operates on a discrete latent space that preserves to a significant extent the discrete nature of the graph structures making no unnatural assumptions such as latent space continuity. We learn the prior of our discrete latent space by adapting diffusion bridges to its structure. By operating over an appropriately constructed latent space we avoid relying on decompositions that are often used in models that operate in the original data space. We present experiments on a series of graph benchmark datasets which clearly show the superiority of the discrete latent space and obtain state of the art graph generative performance, making GLAD the first latent space graph generative model with competitive performance. Our source code is published at: https://github.com/v18nguye/GLAD.

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

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

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

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.

The growing importance of understanding and addressing algorithmic bias in artificial intelligence (AI) has led to a surge in research on AI fairness, which often assumes that the underlying data is independent and identically distributed (IID). However, real-world data frequently exists in non-IID graph structures that capture connections among individual units. To effectively mitigate bias in AI systems, it is essential to bridge the gap between traditional fairness literature, designed for IID data, and the prevalence of non-IID graph data. This survey reviews recent advancements in fairness amidst non-IID graph data, including the newly introduced fair graph generation and the commonly studied fair graph classification. In addition, available datasets and evaluation metrics for future research are identified, the limitations of existing work are highlighted, and promising future directions are proposed.

A key requirement for graph neural networks is that they must process a graph in a way that does not depend on how the graph is described. Traditionally this has been taken to mean that a graph network must be equivariant to node permutations. Here we show that instead of equivariance, the more general concept of naturality is sufficient for a graph network to be well-defined, opening up a larger class of graph networks. We define global and local natural graph networks, the latter of which are as scalable as conventional message passing graph neural networks while being more flexible. We give one practical instantiation of a natural network on graphs which uses an equivariant message network parameterization, yielding good performance on several benchmarks.

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.

Relational databases (RDBs) are composed of interconnected tables, where relationships between them are defined through foreign keys. Recent research on applying machine learning to RDBs has explored graph-based representations of RDBs, where rows of tables are modeled as nodes, and foreign key relationships are modeled as edges. RDB-to-graph modeling helps capture cross-table dependencies, ultimately leading to enhanced performance across diverse tasks. However, there are numerous ways to model RDBs as graphs, and performance varies significantly depending on the chosen graph model. In our analysis, applying a common heuristic rule for graph modeling leads to up to a 10% drop in performance compared to the best-performing graph model, which remains non-trivial to identify. To foster research on intelligent RDB-to-graph modeling, we introduce RDB2G-Bench, the first benchmark framework for evaluating such methods. We construct extensive datasets covering 5 real-world RDBs and 12 predictive tasks, resulting in around 50k graph-performance pairs for efficient and reproducible evaluations. Thanks to our precomputed datasets, we were able to benchmark 9 automatic RDB-to-graph modeling methods on the 12 tasks over 600x faster than on-the-fly evaluation, which requires repeated model training. Our analysis of the datasets and benchmark results reveals key structural patterns affecting graph model effectiveness, along with practical implications for effective graph modeling.

Temporal hypergraphs provide a powerful paradigm for modeling time-dependent, higher-order interactions in complex systems. Representation learning for hypergraphs is essential for extracting patterns of the higher-order interactions that are critically important in real-world problems in social network analysis, neuroscience, finance, etc. However, existing methods are typically designed only for specific tasks or static hypergraphs. We present CAT-Walk, an inductive method that learns the underlying dynamic laws that govern the temporal and structural processes underlying a temporal hypergraph. CAT-Walk introduces a temporal, higher-order walk on hypergraphs, SetWalk, that extracts higher-order causal patterns. CAT-Walk uses a novel adaptive and permutation invariant pooling strategy, SetMixer, along with a set-based anonymization process that hides the identity of hyperedges. Finally, we present a simple yet effective neural network model to encode hyperedges. Our evaluation on 10 hypergraph benchmark datasets shows that CAT-Walk attains outstanding performance on temporal hyperedge prediction benchmarks in both inductive and transductive settings. It also shows competitive performance with state-of-the-art methods for node classification. (https://github.com/ubc-systopia/CATWalk)

Image classification is a computer vision task where a model analyzes an image to categorize it into a specific label. Vision Transformers (ViT) improve this task by leveraging self-attention to capture complex patterns and long range relationships between image patches. However, a key challenge for ViTs is efficiently incorporating multiscale feature representations, which is inherent in CNNs through their hierarchical structure. In this paper, we introduce the Scale-Aware Graph Attention Vision Transformer (SAG-ViT), a novel framework that addresses this challenge by integrating multi-scale features. Using EfficientNet as a backbone, the model extracts multi-scale feature maps, which are divided into patches to preserve semantic information. These patches are organized into a graph based on spatial and feature similarities, with a Graph Attention Network (GAT) refining the node embeddings. Finally, a Transformer encoder captures long-range dependencies and complex interactions. The SAG-ViT is evaluated on benchmark datasets, demonstrating its effectiveness in enhancing image classification performance.

Graph-based deep learning methods have become popular tools to process collections of correlated time series. Differently from traditional multivariate forecasting methods, neural graph-based predictors take advantage of pairwise relationships by conditioning forecasts on a (possibly dynamic) graph spanning the time series collection. The conditioning can take the form of an architectural inductive bias on the neural forecasting architecture, resulting in a family of deep learning models called spatiotemporal graph neural networks. Such relational inductive biases enable the training of global forecasting models on large time-series collections, while at the same time localizing predictions w.r.t. each element in the set (i.e., graph nodes) by accounting for local correlations among them (i.e., graph edges). Indeed, recent theoretical and practical advances in graph neural networks and deep learning for time series forecasting make the adoption of such processing frameworks appealing and timely. However, most of the studies in the literature focus on proposing variations of existing neural architectures by taking advantage of modern deep learning practices, while foundational and methodological aspects have not been subject to systematic investigation. To fill the gap, this paper aims to introduce a comprehensive methodological framework that formalizes the forecasting problem and provides design principles for graph-based predictive models and methods to assess their performance. At the same time, together with an overview of the field, we provide design guidelines, recommendations, and best practices, as well as an in-depth discussion of open challenges and future research directions.

Recent advances in deep learning have shown exciting promise in filling large holes in natural images with semantically plausible and context aware details, impacting fundamental image manipulation tasks such as object removal. While these learning-based methods are significantly more effective in capturing high-level features than prior techniques, they can only handle very low-resolution inputs due to memory limitations and difficulty in training. Even for slightly larger images, the inpainted regions would appear blurry and unpleasant boundaries become visible. We propose a multi-scale neural patch synthesis approach based on joint optimization of image content and texture constraints, which not only preserves contextual structures but also produces high-frequency details by matching and adapting patches with the most similar mid-layer feature correlations of a deep classification network. We evaluate our method on the ImageNet and Paris Streetview datasets and achieved state-of-the-art inpainting accuracy. We show our approach produces sharper and more coherent results than prior methods, especially for high-resolution images.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

In astrophysical and cosmological analyses, the increasing quality and volume of astronomical data demand efficient and precise computational tools. This work introduces a novel adaptive algorithm for automatic knots (AutoKnots) allocation in spline interpolation, designed to meet user-defined precision requirements. Unlike traditional methods that rely on manually configured knot distributions with numerous parameters, the proposed technique automatically determines the optimal number and placement of knots based on interpolation error criteria. This simplifies configuration, often requiring only a single parameter. The algorithm progressively improves the interpolation by adaptively sampling the function-to-be-approximated, f(x), in regions where the interpolation error exceeds the desired threshold. All function evaluations contribute directly to the final approximation, ensuring efficiency. While each resampling step involves recomputing the interpolation table, this process is highly optimized and usually computationally negligible compared to the cost of evaluating f(x). We show the algorithm's efficacy through a series of precision tests on different functions. However, the study underscores the necessity for caution when dealing with certain function types, notably those featuring plateaus. To address this challenge, a heuristic enhancement is incorporated, improving accuracy in flat regions. This algorithm has been extensively used and tested over the years. NumCosmo includes a comprehensive set of unit tests that rigorously evaluate the algorithm both directly and indirectly, underscoring its robustness and reliability. As a practical application, we compute the surface mass density Sigma(R) and the average surface mass density Sigma(<R) for Navarro-Frenk-White and Hernquist halo density profiles, which provide analytical benchmarks. (abridged)

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

This paper studies the problem of embedding very large information networks into low-dimensional vector spaces, which is useful in many tasks such as visualization, node classification, and link prediction. Most existing graph embedding methods do not scale for real world information networks which usually contain millions of nodes. In this paper, we propose a novel network embedding method called the "LINE," which is suitable for arbitrary types of information networks: undirected, directed, and/or weighted. The method optimizes a carefully designed objective function that preserves both the local and global network structures. An edge-sampling algorithm is proposed that addresses the limitation of the classical stochastic gradient descent and improves both the effectiveness and the efficiency of the inference. Empirical experiments prove the effectiveness of the LINE on a variety of real-world information networks, including language networks, social networks, and citation networks. The algorithm is very efficient, which is able to learn the embedding of a network with millions of vertices and billions of edges in a few hours on a typical single machine. The source code of the LINE is available online.

Recently, learning-based algorithms have achieved promising performance on cross-spectral image patch matching, which, however, is still far from satisfactory for practical application. On the one hand, a lack of large-scale dataset with diverse scenes haunts its further improvement for learning-based algorithms, whose performances and generalization rely heavily on the dataset size and diversity. On the other hand, more emphasis has been put on feature relation in the spatial domain whereas the scale dependency between features has often been ignored, leading to performance degeneration especially when encountering significant appearance variations for cross-spectral patches. To address these issues, we publish, to be best of our knowledge, the largest visible and Long-wave Infrared (LWIR) image patch matching dataset, termed VL-CMIM, which contains 1300 pairs of strictly aligned visible and LWIR images and over 2 million patch pairs covering diverse scenes such as asteroid, field, country, build, street and water.In addition, a multi-domain feature relation learning network (MD-FRN) is proposed. Input by the features extracted from a four-branch network, both feature relations in spatial and scale domains are learned via a spatial correlation module (SCM) and multi-scale adaptive aggregation module (MSAG), respectively. To further aggregate the multi-domain relations, a deep domain interactive mechanism (DIM) is applied, where the learnt spatial-relation and scale-relation features are exchanged and further input into MSCRM and SCM. This mechanism allows our model to learn interactive cross-domain feature relations, leading to improved robustness to significant appearance changes due to different modality.

Node centralities play a pivotal role in network science, social network analysis, and recommender systems. In temporal data, static path-based centralities like closeness or betweenness can give misleading results about the true importance of nodes in a temporal graph. To address this issue, temporal generalizations of betweenness and closeness have been defined that are based on the shortest time-respecting paths between pairs of nodes. However, a major issue of those generalizations is that the calculation of such paths is computationally expensive. Addressing this issue, we study the application of De Bruijn Graph Neural Networks (DBGNN), a causality-aware graph neural network architecture, to predict temporal path-based centralities in time series data. We experimentally evaluate our approach in 13 temporal graphs from biological and social systems and show that it considerably improves the prediction of both betweenness and closeness centrality compared to a static Graph Convolutional Neural Network.

We study the problem of visualizing large-scale and high-dimensional data in a low-dimensional (typically 2D or 3D) space. Much success has been reported recently by techniques that first compute a similarity structure of the data points and then project them into a low-dimensional space with the structure preserved. These two steps suffer from considerable computational costs, preventing the state-of-the-art methods such as the t-SNE from scaling to large-scale and high-dimensional data (e.g., millions of data points and hundreds of dimensions). We propose the LargeVis, a technique that first constructs an accurately approximated K-nearest neighbor graph from the data and then layouts the graph in the low-dimensional space. Comparing to t-SNE, LargeVis significantly reduces the computational cost of the graph construction step and employs a principled probabilistic model for the visualization step, the objective of which can be effectively optimized through asynchronous stochastic gradient descent with a linear time complexity. The whole procedure thus easily scales to millions of high-dimensional data points. Experimental results on real-world data sets demonstrate that the LargeVis outperforms the state-of-the-art methods in both efficiency and effectiveness. The hyper-parameters of LargeVis are also much more stable over different data sets.

Grid-based structures are commonly used to encode explicit features for graphics primitives such as images, signed distance functions (SDF), and neural radiance fields (NeRF) due to their simple implementation. However, in n-dimensional space, calculating the value of a sampled point requires interpolating the values of its 2^n neighboring vertices. The exponential scaling with dimension leads to significant computational overheads. To address this issue, we propose a simplex-based approach for encoding graphics primitives. The number of vertices in a simplex-based structure increases linearly with dimension, making it a more efficient and generalizable alternative to grid-based representations. Using the non-axis-aligned simplicial structure property, we derive and prove a coordinate transformation, simplicial subdivision, and barycentric interpolation scheme for efficient sampling, which resembles transformation procedures in the simplex noise algorithm. Finally, we use hash tables to store multiresolution features of all interest points in the simplicial grid, which are passed into a tiny fully connected neural network to parameterize graphics primitives. We implemented a detailed simplex-based structure encoding algorithm in C++ and CUDA using the methods outlined in our approach. In the 2D image fitting task, the proposed method is capable of fitting a giga-pixel image with 9.4% less time compared to the baseline method proposed by instant-ngp, while maintaining the same quality and compression rate. In the volumetric rendering setup, we observe a maximum 41.2% speedup when the samples are dense enough.

Network pruning reduces the computation costs of an over-parameterized network without performance damage. Prevailing pruning algorithms pre-define the width and depth of the pruned networks, and then transfer parameters from the unpruned network to pruned networks. To break the structure limitation of the pruned networks, we propose to apply neural architecture search to search directly for a network with flexible channel and layer sizes. The number of the channels/layers is learned by minimizing the loss of the pruned networks. The feature map of the pruned network is an aggregation of K feature map fragments (generated by K networks of different sizes), which are sampled based on the probability distribution.The loss can be back-propagated not only to the network weights, but also to the parameterized distribution to explicitly tune the size of the channels/layers. Specifically, we apply channel-wise interpolation to keep the feature map with different channel sizes aligned in the aggregation procedure. The maximum probability for the size in each distribution serves as the width and depth of the pruned network, whose parameters are learned by knowledge transfer, e.g., knowledge distillation, from the original networks. Experiments on CIFAR-10, CIFAR-100 and ImageNet demonstrate the effectiveness of our new perspective of network pruning compared to traditional network pruning algorithms. Various searching and knowledge transfer approaches are conducted to show the effectiveness of the two components. Code is at: https://github.com/D-X-Y/NAS-Projects.