Daily Papers

Construction-safety models must handle concrete deployment risks, such as a worker standing near a scaffold edge without guardrails, rather than only recognize common objects in curated images. Yet real inspection archives are redundant, long-tailed, and collected across changing sites and months. We introduce SafeBuild-Bench, a metadata-driven benchmark for evaluating multimodal large language models on construction safety under realistic temporal and site variation. It is mined from 100K+ industrial image-text records and contains 3,314 task instances from over 3,000 expert-verified images, covering multiple-choice hazard identification and free-form hazard description. To make expert verification scalable, we develop GEMS, a graph-enhanced multimodal selection pipeline that combines a proxy-model confusion signal with graph-based diversity to identify informative candidates from redundant streams. On public instruction-tuning data, GEMS-selected subsets preserve robustness-oriented performance under small data budgets. On SafeBuild-Bench, current MLLMs remain far from reliable construction-safety understanding, with the best overall score near 60. We release the benchmark, evaluation scripts, and GEMS codebase at https://github.com/safebuild/gems.

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.

Learning the solution operators of PDEs on arbitrary domains is challenging due to the diversity of possible domain shapes, in addition to the often intricate underlying physics. We propose an end-to-end graph neural network (GNN) based neural operator to learn PDE solution operators from data on point clouds in arbitrary domains. Our multi-scale model maps data between input/output point clouds by passing it through a downsampled regional mesh. Many novel elements are also incorporated to ensure resolution invariance and temporal continuity. Our model, termed RIGNO, is tested on a challenging suite of benchmarks, composed of various time-dependent and steady PDEs defined on a diverse set of domains. We demonstrate that RIGNO is significantly more accurate than neural operator baselines and robustly generalizes to unseen spatial resolutions and time instances.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (https://baskargroup.github.io/AgriField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

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.

Understanding egocentric videos plays a vital role for embodied intelligence. Recent multi-modal large language models (MLLMs) can accept both visual and audio inputs. However, due to the challenge of obtaining text labels with coherent joint-modality information, whether MLLMs can jointly understand both modalities in egocentric videos remains under-explored. To address this problem, we introduce EgoAVU, a scalable data engine to automatically generate egocentric audio-visual narrations, questions, and answers. EgoAVU enriches human narrations with multimodal context and generates audio-visual narrations through cross-modal correlation modeling. Token-based video filtering and modular, graph-based curation ensure both data diversity and quality. Leveraging EgoAVU, we construct EgoAVU-Instruct, a large-scale training dataset of 3M samples, and EgoAVU-Bench, a manually verified evaluation split covering diverse tasks. EgoAVU-Bench clearly reveals the limitations of existing MLLMs: they bias heavily toward visual signals, often neglecting audio cues or failing to correspond audio with the visual source. Finetuning MLLMs on EgoAVU-Instruct effectively addresses this issue, enabling up to 113% performance improvement on EgoAVU-Bench. Such benefits also transfer to other benchmarks such as EgoTempo and EgoIllusion, achieving up to 28% relative performance gain. Code will be released to the community.

Data quality and diversity are key to the construction of effective instruction-tuning datasets. % With the increasing availability of open-source instruction-tuning datasets, it is advantageous to automatically select high-quality and diverse subsets from a vast amount of data. % Existing methods typically prioritize instance quality and use heuristic rules to maintain diversity. % However, this absence of a comprehensive view of the entire collection often leads to suboptimal results. % Moreover, heuristic rules generally focus on distance or clustering within the embedding space, which fails to accurately capture the intent of complex instructions in the semantic space. % To bridge this gap, we propose a unified method for quantifying the information content of datasets. This method models the semantic space by constructing a label graph and quantifies diversity based on the distribution of information within the graph. % Based on such a measurement, we further introduce an efficient sampling method that selects data samples iteratively to Maximize the Information Gain (MIG) in semantic space. % Experiments on various datasets and base models demonstrate that MIG consistently outperforms state-of-the-art methods. % Notably, the model fine-tuned with 5\% Tulu3 data sampled by MIG achieves comparable performance to the official SFT model trained on the full dataset, with improvements of +5.73\% on AlpacaEval and +6.89\% on Wildbench.

Panorama images have a much larger field-of-view thus naturally encode enriched scene context information compared to standard perspective images, which however is not well exploited in the previous scene understanding methods. In this paper, we propose a novel method for panoramic 3D scene understanding which recovers the 3D room layout and the shape, pose, position, and semantic category for each object from a single full-view panorama image. In order to fully utilize the rich context information, we design a novel graph neural network based context model to predict the relationship among objects and room layout, and a differentiable relationship-based optimization module to optimize object arrangement with well-designed objective functions on-the-fly. Realizing the existing data are either with incomplete ground truth or overly-simplified scene, we present a new synthetic dataset with good diversity in room layout and furniture placement, and realistic image quality for total panoramic 3D scene understanding. Experiments demonstrate that our method outperforms existing methods on panoramic scene understanding in terms of both geometry accuracy and object arrangement. Code is available at https://chengzhag.github.io/publication/dpc.

Chest X-ray multi-label classification is a core task in intelligent medical imaging diagnosis. However, real clinical data often exhibit extreme long-tailed distributions, leading to degraded performance on rare diseases in tail classes. This issue is not only driven by data scarcity but also by two intrinsic factors:1) attenuation of tail-class lesion representations under complex anatomical backgrounds, and 2) dominance of head classes in modeling label co-occurrence relationships. To address these challenges, we propose TRCGL-Net. First, a learnable text-guided conditional diffusion model is employed to generate high-quality tail-class chest X-ray image samples under disease semantic constraints, improving data diversity and realism of rare disease patterns while alleviating class imbalance and preserving pathology-consistent semantics.Second, a channel reweighting mechanism is introduced to perform feature recalibration by emphasizing disease-relevant feature channels, thereby improving feature discriminability under long-tailed distributions.A class-aware attention mechanism is further applied to generate class-specific attention maps, enabling the model to localize disease-relevant regions and focus on fine-grained lesion areas.Finally, a graph convolution network based on label co occurrence is introduced to establish an information propagation mechanism among categories. Experiments on the PadChest dataset show that the proposed method achieves a tail-class mAP of 0.4904, an overall mAP of 0.4408, and an mAUC of 0.8989, outperforming state-of-the-art methods. TRCGL-Net effectively improves recognition performance for rare diseases under long-tailed distributions and mitigates the impact of extreme class imbalance in chest X-ray multi-label classification.

The scene graph generation (SGG) task involves detecting objects within an image and predicting predicates that represent the relationships between the objects. However, in SGG benchmark datasets, each subject-object pair is annotated with a single predicate even though a single predicate may exhibit diverse semantics (i.e., semantic diversity), existing SGG models are trained to predict the one and only predicate for each pair. This in turn results in the SGG models to overlook the semantic diversity that may exist in a predicate, thus leading to biased predictions. In this paper, we propose a novel model-agnostic Semantic Diversity-aware Prototype-based Learning (DPL) framework that enables unbiased predictions based on the understanding of the semantic diversity of predicates. Specifically, DPL learns the regions in the semantic space covered by each predicate to distinguish among the various different semantics that a single predicate can represent. Extensive experiments demonstrate that our proposed model-agnostic DPL framework brings significant performance improvement on existing SGG models, and also effectively understands the semantic diversity of predicates.

Graph Neural Networks (GNNs) have shown great promise in tasks like node and graph classification, but they often struggle to generalize, particularly to unseen or out-of-distribution (OOD) data. These challenges are exacerbated when training data is limited in size or diversity. To address these issues, we introduce a theoretical framework using Rademacher complexity to compute a regret bound on the generalization error and then characterize the effect of data augmentation. This framework informs the design of GRATIN, an efficient graph data augmentation algorithm leveraging the capability of Gaussian Mixture Models (GMMs) to approximate any distribution. Our approach not only outperforms existing augmentation techniques in terms of generalization but also offers improved time complexity, making it highly suitable for real-world applications.

Large language models (LLMs) are increasingly used to evolve programs and multi-agent systems, yet most existing approaches rely on overwrite-based mutations that maintain only a single candidate at a time. Such methods discard useful variants, suffer from destructive edits, and explore a brittle search space prone to structural failure. We introduce EvoLattice, a framework that represents an entire population of candidate programs or agent behaviors within a single directed acyclic graph. Each node stores multiple persistent alternatives, and every valid path through the graph defines a distinct executable candidate, yielding a large combinatorial search space without duplicating structure. EvoLattice enables fine-grained alternative-level evaluation by scoring each alternative across all paths in which it appears, producing statistics that reveal how local design choices affect global performance. These statistics provide a dense, data-driven feedback signal for LLM-guided mutation, recombination, and pruning, while preserving successful components. Structural correctness is guaranteed by a deterministic self-repair mechanism that enforces acyclicity and dependency consistency independently of the LLM. EvoLattice naturally extends to agent evolution by interpreting alternatives as prompt fragments or sub-agent behaviors. Across program synthesis (proxy and optimizer meta-learning), EvoLattice yields more stable evolution, greater expressivity, and stronger improvement trajectories than prior LLM-guided methods. The resulting dynamics resemble quality-diversity optimization, emerging implicitly from EvoLattice's internal multi-alternative representation rather than an explicit external archive.

Generative commonsense reasoning (GCR) in natural language is to reason about the commonsense while generating coherent text. Recent years have seen a surge of interest in improving the generation quality of commonsense reasoning tasks. Nevertheless, these approaches have seldom investigated diversity in the GCR tasks, which aims to generate alternative explanations for a real-world situation or predict all possible outcomes. Diversifying GCR is challenging as it expects to generate multiple outputs that are not only semantically different but also grounded in commonsense knowledge. In this paper, we propose MoKGE, a novel method that diversifies the generative reasoning by a mixture of expert (MoE) strategy on commonsense knowledge graphs (KG). A set of knowledge experts seek diverse reasoning on KG to encourage various generation outputs. Empirical experiments demonstrated that MoKGE can significantly improve the diversity while achieving on par performance on accuracy on two GCR benchmarks, based on both automatic and human evaluations.

Retrieval-Augmented Generation (RAG) enables large language models to provide more precise and pertinent responses by incorporating external knowledge. In the Query-Focused Summarization (QFS) task, GraphRAG-based approaches have notably enhanced the comprehensiveness and diversity of generated responses. However, existing GraphRAG-based approaches predominantly focus on coarse-grained information summarization without being aware of the specific query, and the retrieved content lacks sufficient contextual information to generate comprehensive responses. To address the deficiencies of current RAG systems, we propose Context-Aware Fine-Grained Graph RAG (FG-RAG) to enhance the performance of the QFS task. FG-RAG employs Context-Aware Entity Expansion in graph retrieval to expand the coverage of retrieved entities in the graph, thus providing enough contextual information for the retrieved content. Furthermore, FG-RAG utilizes Query-Level Fine-Grained Summarization to incorporate fine-grained details during response generation, enhancing query awareness for the generated summarization. Our evaluation demonstrates that FG-RAG outperforms other RAG systems in multiple metrics of comprehensiveness, diversity, and empowerment when handling the QFS task. Our implementation is available at https://github.com/BuptWululu/FG-RAG.

Automatic generation of device-level analog circuit topologies remains a fundamental challenge in analog design automation. Recent transformer-based approaches have shown promise, yet they often suffer from limited functional controllability, memorization of training data, and the generation of electrically invalid circuits. We propose AnalogToBi, a device-level analog circuit topology generation framework that addresses these limitations. AnalogToBi enables explicit functional control via a circuit type token and adopts a bipartite graph-based circuit representation that decouples positional ordering from functional semantics, encouraging structural reasoning over sequence memorization. In addition, grammar-guided decoding enforces electrical validity during generation, while apply device renaming-based data augmentation improves generalization by increasing sequence diversity without altering circuit functionality. Experimental results show that AnalogToBi achieves 97.8% validity and 92.1% novelty, resulting in 89.9% valid and novel circuits under conditional generation, without human expert involvement. We further present that generated circuits can be automatically translated into SPICE netlists, and SPICE simulations confirm that AnalogToBi discovers high-quality analog topologies that outperform prior methods. For code and supplementary materials, see https://github.com/Seungmin0825/AnalogToBi

Scripting interfaces enable users to automate tasks and customize software workflows, but creating scripts traditionally requires programming expertise and familiarity with specific APIs, posing barriers for many users. While Large Language Models (LLMs) can generate code from natural language queries, runtime code generation is severely limited due to unverified code, security risks, longer response times, and higher computational costs. To bridge the gap, we propose an offline simulation framework to curate a software-specific skillset, a collection of verified scripts, by exploiting LLMs and publicly available scripting guides. Our framework comprises two components: (1) task creation, using top-down functionality guidance and bottom-up API synergy exploration to generate helpful tasks; and (2) skill generation with trials, refining and validating scripts based on execution feedback. To efficiently navigate the extensive API landscape, we introduce a Graph Neural Network (GNN)-based link prediction model to capture API synergy, enabling the generation of skills involving underutilized APIs and expanding the skillset's diversity. Experiments with Adobe Illustrator demonstrate that our framework significantly improves automation success rates, reduces response time, and saves runtime token costs compared to traditional runtime code generation. This is the first attempt to use software scripting interfaces as a testbed for LLM-based systems, highlighting the advantages of leveraging execution feedback in a controlled environment and offering valuable insights into aligning AI capabilities with user needs in specialized software domains.

The open-source software (OSS) ecosystem suffers from security threats caused by malware.However, OSS malware research has three limitations: a lack of high-quality datasets, a lack of malware diversity, and a lack of attack campaign contexts. In this paper, we first build the largest dataset of 24,356 malicious packages from online sources, then propose a knowledge graph to represent the OSS malware corpus and conduct malware analysis in the wild.Our main findings include (1) it is essential to collect malicious packages from various online sources because their data overlapping degrees are small;(2) despite the sheer volume of malicious packages, many reuse similar code, leading to a low diversity of malware;(3) only 28 malicious packages were repeatedly hidden via dependency libraries of 1,354 malicious packages, and dependency-hidden malware has a shorter active time;(4) security reports are the only reliable source for disclosing the malware-based context. Index Terms: Malicious Packages, Software Analysis

Despite advances in generation quality, current text-to-image (T2I) models often lack diversity, generating homogeneous outputs. This work introduces a framework to address the need for robust diversity evaluation in T2I models. Our framework systematically assesses diversity by evaluating individual concepts and their relevant factors of variation. Key contributions include: (1) a novel human evaluation template for nuanced diversity assessment; (2) a curated prompt set covering diverse concepts with their identified factors of variation (e.g. prompt: An image of an apple, factor of variation: color); and (3) a methodology for comparing models in terms of human annotations via binomial tests. Furthermore, we rigorously compare various image embeddings for diversity measurement. Notably, our principled approach enables ranking of T2I models by diversity, identifying categories where they particularly struggle. This research offers a robust methodology and insights, paving the way for improvements in T2I model diversity and metric development.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

Artificial general intelligence on graphs has shown significant advancements across various applications, yet the traditional 'Pre-train & Fine-tune' paradigm faces inefficiencies and negative transfer issues, particularly in complex and few-shot settings. Graph prompt learning emerges as a promising alternative, leveraging lightweight prompts to manipulate data and fill the task gap by reformulating downstream tasks to the pretext. However, several critical challenges still remain: how to unify diverse graph prompt models, how to evaluate the quality of graph prompts, and to improve their usability for practical comparisons and selection. In response to these challenges, we introduce the first comprehensive benchmark for graph prompt learning. Our benchmark integrates SIX pre-training methods and FIVE state-of-the-art graph prompt techniques, evaluated across FIFTEEN diverse datasets to assess performance, flexibility, and efficiency. We also present 'ProG', an easy-to-use open-source library that streamlines the execution of various graph prompt models, facilitating objective evaluations. Additionally, we propose a unified framework that categorizes existing graph prompt methods into two main approaches: prompts as graphs and prompts as tokens. This framework enhances the applicability and comparison of graph prompt techniques. The code is available at: https://github.com/sheldonresearch/ProG.

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

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

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.

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.

Graph-structured scene descriptions can be efficiently used in generative models to control the composition of the generated image. Previous approaches are based on the combination of graph convolutional networks and adversarial methods for layout prediction and image generation, respectively. In this work, we show how employing multi-head attention to encode the graph information, as well as using a transformer-based model in the latent space for image generation can improve the quality of the sampled data, without the need to employ adversarial models with the subsequent advantage in terms of training stability. The proposed approach, specifically, is entirely based on transformer architectures both for encoding scene graphs into intermediate object layouts and for decoding these layouts into images, passing through a lower dimensional space learned by a vector-quantized variational autoencoder. Our approach shows an improved image quality with respect to state-of-the-art methods as well as a higher degree of diversity among multiple generations from the same scene graph. We evaluate our approach on three public datasets: Visual Genome, COCO, and CLEVR. We achieve an Inception Score of 13.7 and 12.8, and an FID of 52.3 and 60.3, on COCO and Visual Genome, respectively. We perform ablation studies on our contributions to assess the impact of each component. Code is available at https://github.com/perceivelab/trf-sg2im

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

There is growing evidence that data diversity is crucial for developing fair and robust NLP models. However, current approaches to measure diversity remain inconsistent and fragmented: While there exist a number of tools for measuring the lexical diversity of texts, researchers lack standardized tools for quantifying diversity based on embeddings. Embedding-based diversity measures are highly flexible: They work with any embedding model and any data that can be embedded, and are thus applicable to many notions of diversity. With emb-diversity, we provide a comprehensive embedding-based diversity measurement tool, spanning a broad range of measures. We demonstrate its potential for several use cases: measuring the stylistic, semantic, language and speaker diversity of datasets. https://github.com/nlpsoc/emb-diversity/

We propose refined GRFs (GRFs++), a new class of Graph Random Features (GRFs) for efficient and accurate computations involving kernels defined on the nodes of a graph. GRFs++ resolve some of the long-standing limitations of regular GRFs, including difficulty modeling relationships between more distant nodes. They reduce dependence on sampling long graph random walks via a novel walk-stitching technique, concatenating several shorter walks without breaking unbiasedness. By applying these techniques, GRFs++ inherit the approximation quality provided by longer walks but with greater efficiency, trading sequential, inefficient sampling of a long walk for parallel computation of short walks and matrix-matrix multiplication. Furthermore, GRFs++ extend the simplistic GRFs walk termination mechanism (Bernoulli schemes with fixed halting probabilities) to a broader class of strategies, applying general distributions on the walks' lengths. This improves the approximation accuracy of graph kernels, without incurring extra computational cost. We provide empirical evaluations to showcase all our claims and complement our results with theoretical analysis.

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.

Data diversity is crucial for the instruction tuning of large language models. Existing studies have explored various diversity-aware data selection methods to construct high-quality datasets and enhance model performance. However, the fundamental problem of precisely defining and measuring data diversity remains underexplored, limiting clear guidance for data engineering. To address this, we systematically analyze 11 existing diversity measurement methods by evaluating their correlation with model performance through extensive fine-tuning experiments. Our results indicate that a reliable diversity measure should properly account for both inter-sample differences and the information distribution in the sample space. Building on this, we propose NovelSum, a new diversity metric based on sample-level "novelty." Experiments on both simulated and real-world data show that NovelSum accurately captures diversity variations and achieves a 0.97 correlation with instruction-tuned model performance, highlighting its value in guiding data engineering practices. With NovelSum as an optimization objective, we further develop a greedy, diversity-oriented data selection strategy that outperforms existing approaches, validating both the effectiveness and practical significance of our metric.

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.

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.

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

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

Many real-world graphs frequently present challenges for graph learning due to the presence of both heterophily and heterogeneity. However, existing benchmarks for graph learning often focus on heterogeneous graphs with homophily or homogeneous graphs with heterophily, leaving a gap in understanding how methods perform on graphs that are both heterogeneous and heterophilic. To bridge this gap, we introduce H2GB, a novel graph benchmark that brings together the complexities of both the heterophily and heterogeneity properties of graphs. Our benchmark encompasses 9 diverse real-world datasets across 5 domains, 28 baseline model implementations, and 26 benchmark results. In addition, we present a modular graph transformer framework UnifiedGT and a new model variant, H2G-former, that excels at this challenging benchmark. By integrating masked label embeddings, cross-type heterogeneous attention, and type-specific FFNs, H2G-former effectively tackles graph heterophily and heterogeneity. Extensive experiments across 26 baselines on H2GB reveal inadequacies of current models on heterogeneous heterophilic graph learning, and demonstrate the superiority of our H2G-former over existing solutions. Both the benchmark and the framework are available on GitHub (https://github.com/junhongmit/H2GB) and PyPI (https://pypi.org/project/H2GB), and documentation can be found at https://junhongmit.github.io/H2GB/.

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.

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.

Proximity preserving and structural role-based node embeddings have become a prime workhorse of applied graph mining. Novel node embedding techniques are often tested on a restricted set of benchmark datasets. In this paper, we propose a new diverse social network dataset called Twitch Gamers with multiple potential target attributes. Our analysis of the social network and node classification experiments illustrate that Twitch Gamers is suitable for assessing the predictive performance of novel proximity preserving and structural role-based node embedding algorithms.

Diversity is an important criterion for many areas of machine learning (ML), including generative modeling and dataset curation. Yet little work has gone into understanding, formalizing, and measuring diversity in ML. In this paper, we address the diversity evaluation problem by proposing the Vendi Score, which connects and extends ideas from ecology and quantum statistical mechanics to ML. The Vendi Score is defined as the exponential of the Shannon entropy of the eigenvalues of a similarity matrix. This matrix is induced by a user-defined similarity function applied to the sample to be evaluated for diversity. In taking a similarity function as input, the Vendi Score enables its user to specify any desired form of diversity. Importantly, unlike many existing metrics in ML, the Vendi Score doesn't require a reference dataset or distribution over samples or labels, it is therefore general and applicable to any generative model, decoding algorithm, and dataset from any domain where similarity can be defined. We showcased the Vendi Score on molecular generative modeling, a domain where diversity plays an important role in enabling the discovery of novel molecules. We found that the Vendi Score addresses shortcomings of the current diversity metric of choice in that domain. We also applied the Vendi Score to generative models of images and decoding algorithms of text and found it confirms known results about diversity in those domains. Furthermore, we used the Vendi Score to measure mode collapse, a known limitation of generative adversarial networks (GANs). In particular, the Vendi Score revealed that even GANs that capture all the modes of a labeled dataset can be less diverse than the original dataset. Finally, the interpretability of the Vendi Score allowed us to diagnose several benchmark ML datasets for diversity, opening the door for diversity-informed data augmentation.

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by using graph structures based on the relational inductive bias (homophily assumption). While GNNs have been commonly believed to outperform NNs in real-world tasks, recent work has identified a non-trivial set of datasets where their performance compared to NNs is not satisfactory. Heterophily has been considered the main cause of this empirical observation and numerous works have been put forward to address it. In this paper, we first revisit the widely used homophily metrics and point out that their consideration of only graph-label consistency is a shortcoming. Then, we study heterophily from the perspective of post-aggregation node similarity and define new homophily metrics, which are potentially advantageous compared to existing ones. Based on this investigation, we prove that some harmful cases of heterophily can be effectively addressed by local diversification operation. Then, we propose the Adaptive Channel Mixing (ACM), a framework to adaptively exploit aggregation, diversification and identity channels node-wisely to extract richer localized information for diverse node heterophily situations. ACM is more powerful than the commonly used uni-channel framework for node classification tasks on heterophilic graphs and is easy to be implemented in baseline GNN layers. When evaluated on 10 benchmark node classification tasks, ACM-augmented baselines consistently achieve significant performance gain, exceeding state-of-the-art GNNs on most tasks without incurring significant computational burden.

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.

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

Heterogeneous graph learning aims to capture complex relationships and diverse relational semantics among entities in a heterogeneous graph to obtain meaningful representations for nodes and edges. Recent advancements in heterogeneous graph neural networks (HGNNs) have achieved state-of-the-art performance by considering relation heterogeneity and using specialized message functions and aggregation rules. However, existing frameworks for heterogeneous graph learning have limitations in generalizing across diverse heterogeneous graph datasets. Most of these frameworks follow the "pre-train" and "fine-tune" paradigm on the same dataset, which restricts their capacity to adapt to new and unseen data. This raises the question: "Can we generalize heterogeneous graph models to be well-adapted to diverse downstream learning tasks with distribution shifts in both node token sets and relation type heterogeneity?'' To tackle those challenges, we propose HiGPT, a general large graph model with Heterogeneous graph instruction-tuning paradigm. Our framework enables learning from arbitrary heterogeneous graphs without the need for any fine-tuning process from downstream datasets. To handle distribution shifts in heterogeneity, we introduce an in-context heterogeneous graph tokenizer that captures semantic relationships in different heterogeneous graphs, facilitating model adaptation. We incorporate a large corpus of heterogeneity-aware graph instructions into our HiGPT, enabling the model to effectively comprehend complex relation heterogeneity and distinguish between various types of graph tokens. Furthermore, we introduce the Mixture-of-Thought (MoT) instruction augmentation paradigm to mitigate data scarcity by generating diverse and informative instructions. Through comprehensive evaluations, our proposed framework demonstrates exceptional performance in terms of generalization performance.

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.

Text-to-image (T2I) models are remarkable at generating realistic images based on textual descriptions. However, textual prompts are inherently underspecified: they do not specify all possible attributes of the required image. This raises two key questions: Do T2I models generate diverse outputs on underspecified prompts? How can we automatically measure diversity? We propose GRADE: Granular Attribute Diversity Evaluation, an automatic method for quantifying sample diversity. GRADE leverages the world knowledge embedded in large language models and visual question-answering systems to identify relevant concept-specific axes of diversity (e.g., ``shape'' and ``color'' for the concept ``cookie''). It then estimates frequency distributions of concepts and their attributes and quantifies diversity using (normalized) entropy. GRADE achieves over 90% human agreement while exhibiting weak correlation to commonly used diversity metrics. We use GRADE to measure the overall diversity of 12 T2I models using 400 concept-attribute pairs, revealing that all models display limited variation. Further, we find that these models often exhibit default behaviors, a phenomenon where the model consistently generates concepts with the same attributes (e.g., 98% of the cookies are round). Finally, we demonstrate that a key reason for low diversity is due to underspecified captions in training data. Our work proposes a modern, semantically-driven approach to measure sample diversity and highlights the stunning homogeneity in outputs by T2I models.

Neural networks that process the parameters of other neural networks find applications in domains as diverse as classifying implicit neural representations, generating neural network weights, and predicting generalization errors. However, existing approaches either overlook the inherent permutation symmetry in the neural network or rely on intricate weight-sharing patterns to achieve equivariance, while ignoring the impact of the network architecture itself. In this work, we propose to represent neural networks as computational graphs of parameters, which allows us to harness powerful graph neural networks and transformers that preserve permutation symmetry. Consequently, our approach enables a single model to encode neural computational graphs with diverse architectures. We showcase the effectiveness of our method on a wide range of tasks, including classification and editing of implicit neural representations, predicting generalization performance, and learning to optimize, while consistently outperforming state-of-the-art methods. The source code is open-sourced at https://github.com/mkofinas/neural-graphs.

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.

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.

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

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

Graph neural networks have moved from a niche representation-learning technique to the default model class wherever data carry relational structure. The interesting question is no longer whether message passing helps on a given dataset, but where graph structure earns its computational cost and where it does not. This survey organises the field around a single design space, derives the spectral and spatial formulations from shared first principles, and connects expressive power to the Weisfeiler-Leman hierarchy with explicit statements of what current architectures can and cannot separate. Against that methodological backbone we examine twelve application domains, among them recommendation and social networks, knowledge graphs and language-model integration, drug discovery and molecular property learning, healthcare and neuroscience, computer vision, traffic and urban computing, power and renewable-energy systems, wireless and sixth-generation networks, fraud and cybersecurity, industrial prognostics, materials science, and climate modelling. For each domain we specify the graph-construction choices and their costs, identify which architecture families dominate and why, and separate reported gains from artefacts of weak baselines or favourable splits. A cross-domain comparison exposes recurring patterns: heterophily and scale undercut the same models almost everywhere, temporal graphs remain harder than their static counterparts, and the architectures that top public leaderboards are seldom the ones that reach deployment. We treat over-smoothing, over-squashing, robustness, distribution shift, fairness, and explainability not as a closing checklist but as the constraints that decide adoption.

Graph pre-training has achieved remarkable success in recent years, delivering transferable representations for downstream adaptation. However, most existing methods are designed for either homogeneous or heterogeneous graphs, thereby hindering unified graph modeling across diverse graph types. This separation contradicts real-world applications, where mixed homogeneous and heterogeneous graphs are ubiquitous, and distribution shifts between upstream pre-training and downstream deployment are common. In this paper, we empirically demonstrate that a balanced mixture of homogeneous and heterogeneous graph pre-training benefits downstream tasks and propose a unified multi-domain Graph Pre-training method across Homogeneous and Heterogeneous graphs (GPH^{2}). To address the lack of a unified encoder for homogeneous and heterogeneous graphs, we propose a Unified Multi-View Graph Construction that simultaneously encodes both without explicit graph-type-specific designs. To cope with the increased cross-domain distribution discrepancies arising from mixed graphs, we introduce domain-specific expert encoding. Each expert is independently pre-trained on a single graph to capture domain-specific knowledge, thereby shielding the pre-training encoder from the adverse effects of cross-domain discrepancies. For downstream tasks, we further design a Task-oriented Expert Fusion Strategy that adaptively integrates multiple experts based on their discriminative strengths. Extensive experiments on mixed graphs demonstrate that GPH^{2} enables stable transfer across graph types and domains, significantly outperforming existing graph pre-training methods.

Graph neural networks (GNNs) based methods have achieved impressive performance on node clustering task. However, they are designed on the homophilic assumption of graph and clustering on heterophilic graph is overlooked. Due to the lack of labels, it is impossible to first identify a graph as homophilic or heterophilic before a suitable GNN model can be found. Hence, clustering on real-world graph with various levels of homophily poses a new challenge to the graph research community. To fill this gap, we propose a novel graph clustering method, which contains three key components: graph reconstruction, a mixed filter, and dual graph clustering network. To be graph-agnostic, we empirically construct two graphs which are high homophily and heterophily from each data. The mixed filter based on the new graphs extracts both low-frequency and high-frequency information. To reduce the adverse coupling between node attribute and topological structure, we separately map them into two subspaces in dual graph clustering network. Extensive experiments on 11 benchmark graphs demonstrate our promising performance. In particular, our method dominates others on heterophilic graphs.

Candidate generation is the first stage in recommendation systems, where a light-weight system is used to retrieve potentially relevant items for an input user. These candidate items are then ranked and pruned in later stages of recommender systems using a more complex ranking model. Since candidate generation is the top of the recommendation funnel, it is important to retrieve a high-recall candidate set to feed into downstream ranking models. A common approach for candidate generation is to leverage approximate nearest neighbor (ANN) search from a single dense query embedding; however, this approach this can yield a low-diversity result set with many near duplicates. As users often have multiple interests, candidate retrieval should ideally return a diverse set of candidates reflective of the user's multiple interests. To this end, we introduce kNN-Embed, a general approach to improving diversity in dense ANN-based retrieval. kNN-Embed represents each user as a smoothed mixture over learned item clusters that represent distinct `interests' of the user. By querying each of a user's mixture component in proportion to their mixture weights, we retrieve a high-diversity set of candidates reflecting elements from each of a user's interests. We experimentally compare kNN-Embed to standard ANN candidate retrieval, and show significant improvements in overall recall and improved diversity across three datasets. Accompanying this work, we open source a large Twitter follow-graph dataset, to spur further research in graph-mining and representation learning for recommender systems.

Node classification is a classical graph machine learning task on which Graph Neural Networks (GNNs) have recently achieved strong results. However, it is often believed that standard GNNs only work well for homophilous graphs, i.e., graphs where edges tend to connect nodes of the same class. Graphs without this property are called heterophilous, and it is typically assumed that specialized methods are required to achieve strong performance on such graphs. In this work, we challenge this assumption. First, we show that the standard datasets used for evaluating heterophily-specific models have serious drawbacks, making results obtained by using them unreliable. The most significant of these drawbacks is the presence of a large number of duplicate nodes in the datasets Squirrel and Chameleon, which leads to train-test data leakage. We show that removing duplicate nodes strongly affects GNN performance on these datasets. Then, we propose a set of heterophilous graphs of varying properties that we believe can serve as a better benchmark for evaluating the performance of GNNs under heterophily. We show that standard GNNs achieve strong results on these heterophilous graphs, almost always outperforming specialized models. Our datasets and the code for reproducing our experiments are available at https://github.com/yandex-research/heterophilous-graphs

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.

We aim to select data subsets for the fine-tuning of large language models to more effectively follow instructions. Prior work has emphasized the importance of diversity in dataset curation but relied on heuristics such as the number of tasks. In this paper, we use determinantal point processes to capture the diversity and quality of instruction tuning datasets for subset selection. We propose to measure dataset diversity with log determinant distance that is the distance between the dataset of interest and a maximally diverse reference dataset. Our experiments demonstrate that the proposed diversity measure in the normalized weight gradient space is correlated with downstream instruction-following performance. Consequently, it can be used to inform when data selection is the most helpful and to analyze dataset curation strategies. We demonstrate the utility of our approach on various instruction tuning datasets.

Current trends to pre-train capable Large Language Models (LLMs) mostly focus on scaling of model and dataset size. However, the quality of pre-training data is an important factor for training powerful LLMs, yet it is a nebulous concept that has not been fully characterized. Therefore, we use the recently proposed Task2Vec diversity coefficient to ground and understand formal aspects of data quality, to go beyond scale alone. Specifically, we measure the diversity coefficient of publicly available pre-training datasets to demonstrate that their formal diversity is high when compared to theoretical lower and upper bounds. In addition, to build confidence in the diversity coefficient, we conduct interpretability experiments and find that the coefficient aligns with intuitive properties of diversity, e.g., it increases as the number of latent concepts increases. We conclude the diversity coefficient is reliable, show it's high for publicly available LLM datasets, and conjecture it can be used to build useful diverse datasets for LLMs.

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.

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

Diverse outputs in text generation are necessary for effective exploration in complex reasoning tasks, such as code generation and mathematical problem solving. Such Pass@k problems benefit from distinct candidates covering the solution space. However, traditional sampling approaches often waste computational resources on repetitive failure modes. While Diffusion Language Models have emerged as a competitive alternative to the prevailing Autoregressive paradigm, they remain susceptible to this redundancy, with independent samples frequently collapsing into similar modes. To address this, we propose a training free, low cost intervention to enhance generative diversity in Diffusion Language Models. Our approach modifies intermediate samples in a batch sequentially, where each sample is repelled from the feature space of previous samples, actively penalising redundancy. Unlike prior methods that require retraining or beam search, our strategy incurs negligible computational overhead, while ensuring that each sample contributes a unique perspective to the batch. We evaluate our method on the HumanEval and GSM8K benchmarks using the LLaDA-8B-Instruct model. Our results demonstrate significantly improved diversity and Pass@k performance across various temperature settings. As a simple modification to the sampling process, our method offers an immediate, low-cost improvement for current and future Diffusion Language Models in tasks that benefit from diverse solution search. We make our code available at https://github.com/sean-lamont/odd.

Despite the prevalence of recent success in learning from static graphs, learning from time-evolving graphs remains an open challenge. In this work, we design new, more stringent evaluation procedures for link prediction specific to dynamic graphs, which reflect real-world considerations, to better compare the strengths and weaknesses of methods. First, we create two visualization techniques to understand the reoccurring patterns of edges over time and show that many edges reoccur at later time steps. Based on this observation, we propose a pure memorization baseline called EdgeBank. EdgeBank achieves surprisingly strong performance across multiple settings because easy negative edges are often used in the current evaluation setting. To evaluate against more difficult negative edges, we introduce two more challenging negative sampling strategies that improve robustness and better match real-world applications. Lastly, we introduce six new dynamic graph datasets from a diverse set of domains missing from current benchmarks, providing new challenges and opportunities for future research. Our code repository is accessible at https://github.com/fpour/DGB.git.

Result diversification (RD) is a crucial technique in Text-to-Image Retrieval for enhancing the efficiency of a practical application. Conventional methods focus solely on increasing the diversity metric of image appearances. However, the diversity metric and its desired value vary depending on the application, which limits the applications of RD. This paper proposes a novel task called CDR-CA (Contextual Diversity Refinement of Composite Attributes). CDR-CA aims to refine the diversities of multiple attributes, according to the application's context. To address this task, we propose Multi-Source DPPs, a simple yet strong baseline that extends the Determinantal Point Process (DPP) to multi-sources. We model MS-DPP as a single DPP model with a unified similarity matrix based on a manifold representation. We also introduce Tangent Normalization to reflect contexts. Extensive experiments demonstrate the effectiveness of the proposed method. Our code is publicly available at https://github.com/NEC-N-SOGI/msdpp.

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.

Despite high semantic alignment, modern text-to-image (T2I) generative models still struggle to synthesize diverse images from a given prompt. This lack of diversity not only restricts user choice, but also risks amplifying societal biases. In this work, we enhance the T2I diversity through a geometric lens. Unlike most existing methods that rely primarily on entropy-based guidance to increase sample dissimilarity, we introduce Geometry-Aware Spherical Sampling (GASS) to enhance diversity by explicitly controlling both prompt-dependent and prompt-independent sources of variation. Specifically, we decompose the diversity measure in CLIP embeddings using two orthogonal directions: the text embedding, which captures semantic variation related to the prompt, and an identified orthogonal direction that captures prompt-independent variation (e.g., backgrounds). Based on this decomposition, GASS increases the geometric projection spread of generated image embeddings along both axes and guides the T2I sampling process via expanded predictions along the generation trajectory. Our experiments on different frozen T2I backbones (U-Net and DiT, diffusion and flow) and benchmarks demonstrate the effectiveness of disentangled diversity enhancement with minimal impact on image fidelity and semantic alignment.

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.

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

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

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.

The primary goal in recommendation is to suggest relevant content to users, but optimizing for accuracy often results in recommendations that lack diversity. To remedy this, conventional approaches such as re-ranking improve diversity by presenting more diverse items. Here we argue that to promote inherent and prolonged diversity, the system must encourage its creation. Towards this, we harness the performative nature of recommendation, and show how learning can incentivize strategic content creators to create diverse content. Our approach relies on a novel form of regularization that anticipates strategic changes to content, and penalizes for content homogeneity. We provide analytic and empirical results that demonstrate when and how diversity can be incentivized, and experimentally demonstrate the utility of our approach on synthetic and semi-synthetic data.

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.

We introduce in this paper the mechanism of graph random features (GRFs). GRFs can be used to construct unbiased randomized estimators of several important kernels defined on graphs' nodes, in particular the regularized Laplacian kernel. As regular RFs for non-graph kernels, they provide means to scale up kernel methods defined on graphs to larger networks. Importantly, they give substantial computational gains also for smaller graphs, while applied in downstream applications. Consequently, GRFs address the notoriously difficult problem of cubic (in the number of the nodes of the graph) time complexity of graph kernels algorithms. We provide a detailed theoretical analysis of GRFs and an extensive empirical evaluation: from speed tests, through Frobenius relative error analysis to kmeans graph-clustering with graph kernels. We show that the computation of GRFs admits an embarrassingly simple distributed algorithm that can be applied if the graph under consideration needs to be split across several machines. We also introduce a (still unbiased) quasi Monte Carlo variant of GRFs, q-GRFs, relying on the so-called reinforced random walks, that might be used to optimize the variance of GRFs. As a byproduct, we obtain a novel approach to solve certain classes of linear equations with positive and symmetric matrices.

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.

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges in this task due to a long tail data distribution. Current scene graph generation models are trained on a tiny fraction of the distribution corresponding to the most frequent compositions, e.g. <cup, on, table>. However, test images might contain zero- and few-shot compositions of objects and relationships, e.g. <cup, on, surfboard>. Despite each of the object categories and the predicate (e.g. 'on') being frequent in the training data, the models often fail to properly understand such unseen or rare compositions. To improve generalization, it is natural to attempt increasing the diversity of the training distribution. However, in the graph domain this is non-trivial. To that end, we propose a method to synthesize rare yet plausible scene graphs by perturbing real ones. We then propose and empirically study a model based on conditional generative adversarial networks (GANs) that allows us to generate visual features of perturbed scene graphs and learn from them in a joint fashion. When evaluated on the Visual Genome dataset, our approach yields marginal, but consistent improvements in zero- and few-shot metrics. We analyze the limitations of our approach indicating promising directions for future research.

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.

Measuring diversity accurately is important for many scientific fields, including machine learning (ML), ecology, and chemistry. The Vendi Score was introduced as a generic similarity-based diversity metric that extends the Hill number of order q=1 by leveraging ideas from quantum statistical mechanics. Contrary to many diversity metrics in ecology, the Vendi Score accounts for similarity and does not require knowledge of the prevalence of the categories in the collection to be evaluated for diversity. However, the Vendi Score treats each item in a given collection with a level of sensitivity proportional to the item's prevalence. This is undesirable in settings where there is a significant imbalance in item prevalence. In this paper, we extend the other Hill numbers using similarity to provide flexibility in allocating sensitivity to rare or common items. This leads to a family of diversity metrics -- Vendi scores with different levels of sensitivity -- that can be used in a variety of applications. We study the properties of the scores in a synthetic controlled setting where the ground truth diversity is known. We then test their utility in improving molecular simulations via Vendi Sampling. Finally, we use the Vendi scores to better understand the behavior of image generative models in terms of memorization, duplication, diversity, and sample quality.

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

Graph-structured data pervades domains such as social networks, biological systems, knowledge graphs, and recommender systems. While foundation models have transformed natural language processing, vision, and multimodal learning through large-scale pretraining and generalization, extending these capabilities to graphs -- characterized by non-Euclidean structures and complex relational semantics -- poses unique challenges and opens new opportunities. To this end, Graph Foundation Models (GFMs) aim to bring scalable, general-purpose intelligence to structured data, enabling broad transfer across graph-centric tasks and domains. This survey provides a comprehensive overview of GFMs, unifying diverse efforts under a modular framework comprising three key components: backbone architectures, pretraining strategies, and adaptation mechanisms. We categorize GFMs by their generalization scope -- universal, task-specific, and domain-specific -- and review representative methods, key innovations, and theoretical insights within each category. Beyond methodology, we examine theoretical foundations including transferability and emergent capabilities, and highlight key challenges such as structural alignment, heterogeneity, scalability, and evaluation. Positioned at the intersection of graph learning and general-purpose AI, GFMs are poised to become foundational infrastructure for open-ended reasoning over structured data. This survey consolidates current progress and outlines future directions to guide research in this rapidly evolving field. Resources are available at https://github.com/Zehong-Wang/Awesome-Foundation-Models-on-Graphs.

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.

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.

Effective generalization in language models depends critically on the diversity of their training data. Yet existing diversity metrics often fall short of this goal, relying on surface-level heuristics that are decoupled from model behavior. This motivates us to ask: What kind of diversity in training data actually drives generalization in language models -- and how can we measure and amplify it? Through large-scale empirical analyses spanning over 300 training runs, carefully controlled for data scale and quality, we show that data diversity can be a strong predictor of generalization in LLM reasoning -- as measured by average model performance on unseen out-of-distribution benchmarks. We introduce G-Vendi, a metric that quantifies diversity via the entropy of model-induced gradients. Despite using a small off-the-shelf proxy model for gradients, G-Vendi consistently outperforms alternative measures, achieving strong correlation (Spearman's rho approx 0.9) with out-of-distribution (OOD) performance on both natural language inference (NLI) and math reasoning tasks. Building on this insight, we present Prismatic Synthesis, a framework for generating diverse synthetic data by targeting underrepresented regions in gradient space. Experimental results show that Prismatic Synthesis consistently improves model performance as we scale synthetic data -- not just on in-distribution test but across unseen, out-of-distribution benchmarks -- significantly outperforming state-of-the-art models that rely on 20 times larger data generator than ours. For example, PrismMath-7B, our model distilled from a 32B LLM, outperforms R1-Distill-Qwen-7B -- the same base model trained on proprietary data generated by 671B R1 -- on 6 out of 7 challenging benchmarks.

We present DEI: Diversity in Evolutionary Inference, a distributed Quality-Diversity (QD) search framework that assigns heterogeneous large language models (LLMs) as mutation operators across peer nodes communicating with non-blocking collective operations. Unlike homogeneous parallel search, which replicates a single model's inductive biases across all workers, DEI treats each LLM's distinct creative prior as a complementary source of behavioral novelty. Extending the Digital Red Queen framework with DEI, nodes share local optimal solutions at the end of each round to seed the next round's population. This creates cross-model adversarial pressure that drives robustness beyond intra-model self-play. Evaluated on the Core War domain, a competitive programming benchmark in which Redcode warrior programs battle inside a simulated machine, a four-node heterogeneous ensemble (GPT-5.4-mini, Claude Sonnet 4.6, GPT-5.2, and Claude Haiku 4.5) achieves 124 percent higher merged-archive QD-Score (45.90 vs. 20.46) and 28 percent higher coverage (80.6 percent vs. 63.0 percent of cells) than a single-node baseline at equal total LLM-call budget. The heterogeneous ensemble also outperforms an equally-budgeted homogeneous ensemble on QD-Score, coverage, and held-out solution generality across all four model families. These results provide the first empirical evidence that model diversity, not merely parallelism, is the key driver of gain in distributed LLM-based QD search.

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.

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

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

Modern text-to-image models excel in visual fidelity and prompt adherence. However, this strict adherence comes at the cost of diversity: generated samples tend to collapse into a single visual interpretation. Existing methods to improve diversity produce outputs driven by incidental variations rather than meaningful design choices. This motivates a new variant of the diversity task where structure is enforced on the generated samples. We introduce a method for controlled diversity that enables Semantic Browsing, where users can navigate structured image galleries and experience creative exploration through a systematic traversal of meaningful, interpretable axes of variation. Achieving this level of semantic control requires a deep understanding of the scene. We exploit the fact that recent text-to-image models are trained on elaborated captions, effectively decoupling semantic decision-making from pixel generation. This enables a paradigm shift: instead of relying on stochastic variation within the text-to-image model, we induce diversity directly at the text level. By leveraging rich textual representations, we allow a Vision Language Model (VLM) to operate on the full scene context. To overcome the generic outputs typical of standard VLMs, we employ an agentic workflow that explicitly enforces structured variation attuned to the original prompt. We demonstrate that our method produces diverse and navigable design spaces where every variation corresponds to a specific, user-understandable semantic decision.

Graph self-supervised learning (SSL) is now a go-to method for pre-training graph foundation models (GFMs). There is a wide variety of knowledge patterns embedded in the graph data, such as node properties and clusters, which are crucial to learning generalized representations for GFMs. However, existing surveys of GFMs have several shortcomings: they lack comprehensiveness regarding the most recent progress, have unclear categorization of self-supervised methods, and take a limited architecture-based perspective that is restricted to only certain types of graph models. As the ultimate goal of GFMs is to learn generalized graph knowledge, we provide a comprehensive survey of self-supervised GFMs from a novel knowledge-based perspective. We propose a knowledge-based taxonomy, which categorizes self-supervised graph models by the specific graph knowledge utilized. Our taxonomy consists of microscopic (nodes, links, etc.), mesoscopic (context, clusters, etc.), and macroscopic knowledge (global structure, manifolds, etc.). It covers a total of 9 knowledge categories and more than 25 pretext tasks for pre-training GFMs, as well as various downstream task generalization strategies. Such a knowledge-based taxonomy allows us to re-examine graph models based on new architectures more clearly, such as graph language models, as well as provide more in-depth insights for constructing GFMs.

Social networks have a vast range of applications with graphs. The available benchmark datasets are citation, co-occurrence, e-commerce networks, etc, with classes ranging from 3 to 15. However, there is no benchmark classification social network dataset for graph machine learning. This paper fills the gap and presents the Binary Classification Social Network Dataset (BiSND), designed for graph machine learning applications to predict binary classes. We present the BiSND in tabular and graph formats to verify its robustness across classical and advanced machine learning. We employ a diverse set of classifiers, including four traditional machine learning algorithms (Decision Trees, K-Nearest Neighbour, Random Forest, XGBoost), one Deep Neural Network (multi-layer perceptrons), one Graph Neural Network (Graph Convolutional Network), and three state-of-the-art Graph Contrastive Learning methods (BGRL, GRACE, DAENS). Our findings reveal that BiSND is suitable for classification tasks, with F1-scores ranging from 67.66 to 70.15, indicating promising avenues for future enhancements.

Recent work synthesizes agentic tasks for post-training tool-using LLMs, yet robust generalization under shifts in tasks and toolsets remains an open challenge. We trace this brittleness to insufficient diversity in synthesized tasks. Scaling diversity is difficult because training requires tasks to remain executable and verifiable, while generalization demands coverage of diverse tool types, toolset combinations, and heterogeneous tool-use patterns. We propose DIVE, an evidence-driven recipe that inverts synthesis order, executing diverse, real-world tools first and reverse-deriving tasks strictly entailed by the resulting traces, thereby providing grounding by construction. DIVE scales structural diversity along two controllable axes, tool-pool coverage and per-task toolset variety, and an Evidence Collection--Task Derivation loop further induces rich multi-step tool-use patterns across 373 tools in five domains. Training Qwen3-8B on DIVE data (48k SFT + 3.2k RL) improves by +22 average points across 9 OOD benchmarks and outperforms the strongest 8B baseline by +68. Remarkably, controlled scaling analysis reveals that diversity scaling consistently outperforms quantity scaling for OOD generalization, even with 4x less data.

Being the most cutting-edge generative methods, diffusion methods have shown great advances in wide generation tasks. Among them, graph generation attracts significant research attention for its broad application in real life. In our survey, we systematically and comprehensively review on diffusion-based graph generative methods. We first make a review on three mainstream paradigms of diffusion methods, which are denoising diffusion probabilistic models, score-based genrative models, and stochastic differential equations. Then we further categorize and introduce the latest applications of diffusion models on graphs. In the end, we point out some limitations of current studies and future directions of future explorations. The summary of existing methods metioned in this survey is in https://github.com/zhejiangzhuque/Diffusion-based-Graph-Generative-Methods.

Graph neural networks have recently achieved remarkable success in representing graph-structured data, with rapid progress in both the node embedding and graph pooling methods. Yet, they mostly focus on capturing information from the nodes considering their connectivity, and not much work has been done in representing the edges, which are essential components of a graph. However, for tasks such as graph reconstruction and generation, as well as graph classification tasks for which the edges are important for discrimination, accurately representing edges of a given graph is crucial to the success of the graph representation learning. To this end, we propose a novel edge representation learning framework based on Dual Hypergraph Transformation (DHT), which transforms the edges of a graph into the nodes of a hypergraph. This dual hypergraph construction allows us to apply message-passing techniques for node representations to edges. After obtaining edge representations from the hypergraphs, we then cluster or drop edges to obtain holistic graph-level edge representations. We validate our edge representation learning method with hypergraphs on diverse graph datasets for graph representation and generation performance, on which our method largely outperforms existing graph representation learning methods. Moreover, our edge representation learning and pooling method also largely outperforms state-of-the-art graph pooling methods on graph classification, not only because of its accurate edge representation learning, but also due to its lossless compression of the nodes and removal of irrelevant edges for effective message-passing.

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.

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 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.

Existing research infrastructure is fundamentally document-centric, providing citation links between papers but lacking explicit representations of methodological evolution. In particular, it does not capture the structured relationships that explain how and why research methods emerge, adapt, and build upon one another. With the rise of AI-driven research agents as a new class of consumers of scientific knowledge, this limitation becomes increasingly consequential, as such agents cannot reliably reconstruct method evolution topologies from unstructured text. We introduce Intern-Atlas, a methodological evolution graph that automatically identifies method-level entities, infers lineage relationships among methodologies, and captures the bottlenecks that drive transitions between successive innovations. Built from 1,030,314 papers spanning AI conferences, journals, and arXiv preprints, the resulting graph comprises 9,410,201 semantically typed edges, each grounded in verbatim source evidence, forming a queryable causal network of methodological development. To operationalize this structure, we further propose a self-guided temporal tree search algorithm for constructing evolution chains that trace the progression of methods over time. We evaluate the quality of the resulting graph against expert-curated ground-truth evolution chains and observe strong alignment. In addition, we demonstrate that Intern-Atlas enables downstream applications in idea evaluation and automated idea generation. We position methodological evolution graphs as a foundational data layer for the emerging automated scientific discovery.

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.

This work aims to tackle the challenging heterogeneous graph encoding problem in the text-to-SQL task. Previous methods are typically node-centric and merely utilize different weight matrices to parameterize edge types, which 1) ignore the rich semantics embedded in the topological structure of edges, and 2) fail to distinguish local and non-local relations for each node. To this end, we propose a Line Graph Enhanced Text-to-SQL (LGESQL) model to mine the underlying relational features without constructing meta-paths. By virtue of the line graph, messages propagate more efficiently through not only connections between nodes, but also the topology of directed edges. Furthermore, both local and non-local relations are integrated distinctively during the graph iteration. We also design an auxiliary task called graph pruning to improve the discriminative capability of the encoder. Our framework achieves state-of-the-art results (62.8% with Glove, 72.0% with Electra) on the cross-domain text-to-SQL benchmark Spider at the time of writing.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

The diversity of training datasets is usually perceived as an important aspect to obtain a robust model. However, the definition of diversity is often not defined or differs across papers, and while some metrics exist, the quantification of this diversity is often overlooked when developing new algorithms. In this work, we study the behaviour of multiple dataset diversity metrics for image, text and metadata using MorphoMNIST, a toy dataset with controlled perturbations, and PadChest, a publicly available chest X-ray dataset. We evaluate whether these metrics correlate with each other but also with the intuition of a clinical expert. We also assess whether they correlate with downstream-task performance and how they impact the training dynamic of the models. We find limited correlations between the AUC and image or metadata reference-free diversity metrics, but higher correlations with the FID and the semantic diversity metrics. Finally, the clinical expert indicates that scanners are the main source of diversity in practice. However, we find that the addition of another scanner to the training set leads to shortcut learning. The code used in this study is available at https://github.com/TheoSourget/dataset_diversity_evaluation

Universal graph pre-training has emerged as a key paradigm in graph representation learning, offering a promising way to train encoders to learn transferable representations from unlabeled graphs and to effectively generalize across a wide range of downstream tasks. However, recent explorations in universal graph pre-training primarily focus on homogeneous graphs and it remains unexplored for heterogeneous graphs, which exhibit greater structural and semantic complexity. This heterogeneity makes it highly challenging to train a universal encoder for diverse heterogeneous graphs: (i) the diverse types with dataset-specific semantics hinder the construction of a unified representation space; (ii) the number and semantics of meta-paths vary across datasets, making encoding and aggregation patterns learned from one dataset difficult to apply to others. To address these challenges, we propose a novel Meta-path-aware Universal heterogeneous Graph pre-training (MUG) approach. Specifically, for challenge (i), MUG introduces a input unification module that integrates information from multiple node and relation types within each heterogeneous graph into a unified representation.This representation is then projected into a shared space by a dimension-aware encoder, enabling alignment across graphs with diverse schemas.Furthermore, for challenge (ii), MUG trains a shared encoder to capture consistent structural patterns across diverse meta-path views rather than relying on dataset-specific aggregation strategies, while a global objective encourages discriminability and reduces dataset-specific biases. Extensive experiments demonstrate the effectiveness of MUG on some real datasets.

A growing body of research has demonstrated the inability of NLP models to generalize compositionally and has tried to alleviate it through specialized architectures, training schemes, and data augmentation, among other approaches. In this work, we study a different approach: training on instances with diverse structures. We propose a model-agnostic algorithm for subsampling such sets of instances from a labeled instance pool with structured outputs. Evaluating on both compositional template splits and traditional IID splits of 5 semantic parsing datasets of varying complexity, we show that structurally diverse training using our algorithm leads to comparable or better generalization than prior algorithms in 9 out of 10 dataset-split type pairs. In general, we find structural diversity to consistently improve sample efficiency compared to random train sets. Moreover, we show that structurally diverse sampling yields comprehensive test sets that are a lot more challenging than IID test sets. Finally, we provide two explanations for improved generalization from diverse train sets: 1) improved coverage of output substructures, and 2) a reduction in spurious correlations between these substructures.

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.

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

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.

Although LLMs have demonstrated improved performance by scaling parallel test-time compute, doing so relies on generating reasoning paths that are both diverse and accurate. For challenging problems, the forking tokens that trigger diverse yet correct reasoning modes are typically deep in the sampling tree. Consequently, common strategies to encourage diversity, such as temperature scaling, encounter a worsened trade-off between diversity and accuracy. Motivated by this challenge, we treat parallel reasoning as a set-of-next-token-prediction problem, and incorporate a set-based global loss into Supervised Fine-Tuning (SFT) using self-supervised bipartite matching between our global forking tokens and unique reasoning traces. We observe that, while naive fine-tuning with multiple reasoning traces collapses these unique reasoning modes, our proposed method, Set Supervised Fine-Tuning (SSFT), preserves these modes and produces emergent global forking tokens. Experiments on multiple reasoning benchmarks show that our SSFT consistently outperforms SFT under both Pass@1 and Cons@k metrics.

Image diversity remains a fundamental challenge for text-to-image diffusion models. Low-diversity models tend to generate repetitive outputs, increasing sampling redundancy and hindering both creative exploration and downstream applications. A primary cause is that generation often collapses toward a strong mode in the learned distribution. Existing attempts to improve diversity, such as noise resampling, prompt rewriting, or steering-based guidance, often still collapse to dominant modes or introduce distortions that degrade image quality. In light of this, we propose Token-Prompt embedding Space Optimization (TPSO), a training-free and model-agnostic module. TPSO introduces learnable parameters to explore underrepresented regions of the token embedding space, reducing the tendency of the model to repeatedly generate samples from strong modes of the learned distribution. At the same time, the prompt-level space provides a global semantic constraint that regulates distribution shifts, preventing quality degradation while maintaining high fidelity. Extensive experiments on MS-COCO and three diffusion backbones show that TPSO significantly enhances generative diversity, improving baseline performance from 1.10 to 4.18 points, without sacrificing image quality. Code will be released upon acceptance.

Reinforcement Learning from Human Feedback (RLHF) has shown potential in qualitative tasks where easily defined performance measures are lacking. However, there are drawbacks when RLHF is commonly used to optimize for average human preferences, especially in generative tasks that demand diverse model responses. Meanwhile, Quality Diversity (QD) algorithms excel at identifying diverse and high-quality solutions but often rely on manually crafted diversity metrics. This paper introduces Quality Diversity through Human Feedback (QDHF), a novel approach that progressively infers diversity metrics from human judgments of similarity among solutions, thereby enhancing the applicability and effectiveness of QD algorithms in complex and open-ended domains. Empirical studies show that QDHF significantly outperforms state-of-the-art methods in automatic diversity discovery and matches the efficacy of QD with manually crafted diversity metrics on standard benchmarks in robotics and reinforcement learning. Notably, in open-ended generative tasks, QDHF substantially enhances the diversity of text-to-image generation from a diffusion model and is more favorably received in user studies. We conclude by analyzing QDHF's scalability, robustness, and quality of derived diversity metrics, emphasizing its strength in open-ended optimization tasks. Code and tutorials are available at https://liding.info/qdhf.

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

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.

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

Graph Edit Distance (GED) measures the (dis-)similarity between two given graphs, in terms of the minimum-cost edit sequence that transforms one graph to the other. However, the exact computation of GED is NP-Hard, which has recently motivated the design of neural methods for GED estimation. However, they do not explicitly account for edit operations with different costs. In response, we propose GRAPHEDX, a neural GED estimator that can work with general costs specified for the four edit operations, viz., edge deletion, edge addition, node deletion and node addition. We first present GED as a quadratic assignment problem (QAP) that incorporates these four costs. Then, we represent each graph as a set of node and edge embeddings and use them to design a family of neural set divergence surrogates. We replace the QAP terms corresponding to each operation with their surrogates. Computing such neural set divergence require aligning nodes and edges of the two graphs. We learn these alignments using a Gumbel-Sinkhorn permutation generator, additionally ensuring that the node and edge alignments are consistent with each other. Moreover, these alignments are cognizant of both the presence and absence of edges between node-pairs. Experiments on several datasets, under a variety of edit cost settings, show that GRAPHEDX consistently outperforms state-of-the-art methods and heuristics in terms of prediction error.

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/.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

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.

Artificial General Intelligence (AGI) has revolutionized numerous fields, yet its integration with graph data, a cornerstone in our interconnected world, remains nascent. This paper presents a pioneering survey on the emerging domain of graph prompts in AGI, addressing key challenges and opportunities in harnessing graph data for AGI applications. Despite substantial advancements in AGI across natural language processing and computer vision, the application to graph data is relatively underexplored. This survey critically evaluates the current landscape of AGI in handling graph data, highlighting the distinct challenges in cross-modality, cross-domain, and cross-task applications specific to graphs. Our work is the first to propose a unified framework for understanding graph prompt learning, offering clarity on prompt tokens, token structures, and insertion patterns in the graph domain. We delve into the intrinsic properties of graph prompts, exploring their flexibility, expressiveness, and interplay with existing graph models. A comprehensive taxonomy categorizes over 100 works in this field, aligning them with pre-training tasks across node-level, edge-level, and graph-level objectives. Additionally, we present, ProG, a Python library, and an accompanying website, to support and advance research in graph prompting. The survey culminates in a discussion of current challenges and future directions, offering a roadmap for research in graph prompting within AGI. Through this comprehensive analysis, we aim to catalyze further exploration and practical applications of AGI in graph data, underlining its potential to reshape AGI fields and beyond. ProG and the website can be accessed by https://github.com/WxxShirley/Awesome-Graph-Prompt, and https://github.com/sheldonresearch/ProG, respectively.

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.

Existing retrieval-augmented generation (RAG) systems are primarily designed under the assumption that each query has a single correct answer. This overlooks common information-seeking scenarios with multiple plausible answers, where diversity is essential to avoid collapsing to a single dominant response, thereby constraining creativity and compromising fair and inclusive information access. Our analysis reveals a commonly overlooked limitation of standard RAG systems: they underutilize retrieved context diversity, such that increasing retrieval diversity alone does not yield diverse generations. To address this limitation, we propose DIVERGE, a plug-and-play agentic RAG framework with novel reflection-guided generation and memory-augmented iterative refinement, which promotes diverse viewpoints while preserving answer quality. We introduce novel metrics tailored to evaluating the diversity-quality trade-off in open-ended questions, and show that they correlate well with human judgments. We demonstrate that DIVERGE achieves the best diversity-quality trade-off compared to competitive baselines and previous state-of-the-art methods on the real-world Infinity-Chat dataset, substantially improving diversity while maintaining quality. More broadly, our results reveal a systematic limitation of current LLM-based systems for open-ended information-seeking and show that explicitly modeling diversity can mitigate it. Our code is available at: https://github.com/au-clan/Diverge

Polygon representation learning is essential for diverse applications, encompassing tasks such as shape coding, building pattern classification, and geographic question answering. While recent years have seen considerable advancements in this field, much of the focus has been on single polygons, overlooking the intricate inner- and inter-polygonal relationships inherent in multipolygons. To address this gap, our study introduces a comprehensive framework specifically designed for learning representations of polygonal geometries, particularly multipolygons. Central to our approach is the incorporation of a heterogeneous visibility graph, which seamlessly integrates both inner- and inter-polygonal relationships. To enhance computational efficiency and minimize graph redundancy, we implement a heterogeneous spanning tree sampling method. Additionally, we devise a rotation-translation invariant geometric representation, ensuring broader applicability across diverse scenarios. Finally, we introduce Multipolygon-GNN, a novel model tailored to leverage the spatial and semantic heterogeneity inherent in the visibility graph. Experiments on five real-world and synthetic datasets demonstrate its ability to capture informative representations for polygonal geometries. Code and data are available at https://github.com/dyu62/PolyGNN{github.com/dyu62/PolyGNN}.

Text-to-image (T2I) models are rapidly gaining popularity, yet their outputs often lack geographical diversity, reinforce stereotypes, and misrepresent regions. Given their broad reach, it is critical to rigorously evaluate how these models portray the world. Existing diversity metrics either rely on curated datasets or focus on surface-level visual similarity, limiting interpretability. We introduce GeoDiv, a framework leveraging large language and vision-language models to assess geographical diversity along two complementary axes: the Socio-Economic Visual Index (SEVI), capturing economic and condition-related cues, and the Visual Diversity Index (VDI), measuring variation in primary entities and backgrounds. Applied to images generated by models such as Stable Diffusion and FLUX.1-dev across 10 entities and 16 countries, GeoDiv reveals a consistent lack of diversity and identifies fine-grained attributes where models default to biased portrayals. Strikingly, depictions of countries like India, Nigeria, and Colombia are disproportionately impoverished and worn, reflecting underlying socio-economic biases. These results highlight the need for greater geographical nuance in generative models. GeoDiv provides the first systematic, interpretable framework for measuring such biases, marking a step toward fairer and more inclusive generative systems. Project page: https://abhipsabasu.github.io/geodiv