Daily Papers

Large Generative Models (LGMs) such as GPT, Stable Diffusion, Sora, and Suno are trained on a huge amount of language corpus, images, videos, and audio that are extremely diverse from numerous domains. This training paradigm over diverse well-curated data lies at the heart of generating creative and sensible content. However, all previous graph generative models (e.g., GraphRNN, MDVAE, MoFlow, GDSS, and DiGress) have been trained only on one dataset each time, which cannot replicate the revolutionary success achieved by LGMs in other fields. To remedy this crucial gap, we propose a new class of graph generative model called Large Graph Generative Model (LGGM) that is trained on a large corpus of graphs (over 5000 graphs) from 13 different domains. We empirically demonstrate that the pre-trained LGGM has superior zero-shot generative capability to existing graph generative models. Furthermore, our pre-trained LGGM can be easily fine-tuned with graphs from target domains and demonstrate even better performance than those directly trained from scratch, behaving as a solid starting point for real-world customization. Inspired by Stable Diffusion, we further equip LGGM with the capability to generate graphs given text prompts (Text-to-Graph), such as the description of the network name and domain (i.e., "The power-1138-bus graph represents a network of buses in a power distribution system."), and network statistics (i.e., "The graph has a low average degree, suitable for modeling social media interactions."). This Text-to-Graph capability integrates the extensive world knowledge in the underlying language model, offering users fine-grained control of the generated graphs. We release the code, the model checkpoint, and the datasets at https://lggm-lg.github.io/.

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.

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.

As the field of Graph Neural Networks (GNN) continues to grow, it experiences a corresponding increase in the need for large, real-world datasets to train and test new GNN models on challenging, realistic problems. Unfortunately, such graph datasets are often generated from online, highly privacy-restricted ecosystems, which makes research and development on these datasets hard, if not impossible. This greatly reduces the amount of benchmark graphs available to researchers, causing the field to rely only on a handful of publicly-available datasets. To address this problem, we introduce a novel graph generative model, Computation Graph Transformer (CGT) that learns and reproduces the distribution of real-world graphs in a privacy-controlled way. More specifically, CGT (1) generates effective benchmark graphs on which GNNs show similar task performance as on the source graphs, (2) scales to process large-scale graphs, (3) incorporates off-the-shelf privacy modules to guarantee end-user privacy of the generated graph. Extensive experiments across a vast body of graph generative models show that only our model can successfully generate privacy-controlled, synthetic substitutes of large-scale real-world graphs that can be effectively used to benchmark GNN models.

Graph generative models become increasingly effective for data distribution approximation and data augmentation. While they have aroused public concerns about their malicious misuses or misinformation broadcasts, just as what Deepfake visual and auditory media has been delivering to society. Hence it is essential to regulate the prevalence of generated graphs. To tackle this problem, we pioneer the formulation of the generated graph detection problem to distinguish generated graphs from real ones. We propose the first framework to systematically investigate a set of sophisticated models and their performance in four classification scenarios. Each scenario switches between seen and unseen datasets/generators during testing to get closer to real-world settings and progressively challenge the classifiers. Extensive experiments evidence that all the models are qualified for generated graph detection, with specific models having advantages in specific scenarios. Resulting from the validated generality and oblivion of the classifiers to unseen datasets/generators, we draw a safe conclusion that our solution can sustain for a decent while to curb generated graph misuses.

Graph-based collaborative filtering methods have prevailing performance for recommender systems since they can capture high-order information between users and items, in which the graphs are constructed from the observed user-item interactions that might miss links or contain spurious positive interactions in industrial scenarios. The Bayesian Graph Neural Network framework approaches this issue with generative models for the interaction graphs. The critical problem is to devise a proper family of graph generative models tailored to recommender systems. We propose an efficient generative model that jointly considers the preferences of users, the concurrence of items and some important graph structure information. Experiments on four popular benchmark datasets demonstrate the effectiveness of our proposed graph generative methods for recommender systems.

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

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

Discovering novel drug candidate molecules is one of the most fundamental and critical steps in drug development. Generative deep learning models, which create synthetic data given a probability distribution, have been developed with the purpose of picking completely new samples from a partially known space. Generative models offer high potential for designing de novo molecules; however, in order for them to be useful in real-life drug development pipelines, these models should be able to design target-specific molecules, which is the next step in this field. In this study, we propose DrugGEN, for the de novo design of drug candidate molecules that interact with selected target proteins. The proposed system represents compounds and protein structures as graphs and processes them via serially connected two generative adversarial networks comprising graph transformers. DrugGEN is trained using a large dataset of compounds from ChEMBL and target-specific bioactive molecules, to design effective and specific inhibitory molecules against the AKT1 protein, which has critical importance for developing treatments against various types of cancer. On fundamental benchmarks, DrugGEN models have either competitive or better performance against other methods. To assess the target-specific generation performance, we conducted further in silico analysis with molecular docking and deep learning-based bioactivity prediction. Results indicate that de novo molecules have high potential for interacting with the AKT1 protein structure in the level of its native ligand. DrugGEN can be used to design completely novel and effective target-specific drug candidate molecules for any druggable protein, given target features and a dataset of experimental bioactivities. Code base, datasets, results and trained models of DrugGEN are available at https://github.com/HUBioDataLab/DrugGEN

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.

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

Diffusion models have established themselves as state-of-the-art generative models across various data modalities, including images and videos, due to their ability to accurately approximate complex data distributions. Unlike traditional generative approaches such as VAEs and GANs, diffusion models employ a progressive denoising process that transforms noise into meaningful data over multiple iterative steps. This gradual approach enhances their expressiveness and generation quality. Not only that, diffusion models have also been shown to extract meaningful representations from data while learning to generate samples. Despite their success, the application of diffusion models to graph-structured data remains relatively unexplored, primarily due to the discrete nature of graphs, which necessitates discrete diffusion processes distinct from the continuous methods used in other domains. In this work, we leverage the representational capabilities of diffusion models to learn meaningful embeddings for graph data. By training a discrete diffusion model within an autoencoder framework, we enable both effective autoencoding and representation learning tailored to the unique characteristics of graph-structured data. We only need the encoder at the end to extract representations. Our approach demonstrates the potential of discrete diffusion models to be used for graph representation learning.

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.

Advancements in generative models have sparked significant interest in generating images while adhering to specific structural guidelines. Scene graph to image generation is one such task of generating images which are consistent with the given scene graph. However, the complexity of visual scenes poses a challenge in accurately aligning objects based on specified relations within the scene graph. Existing methods approach this task by first predicting a scene layout and generating images from these layouts using adversarial training. In this work, we introduce a novel approach to generate images from scene graphs which eliminates the need of predicting intermediate layouts. We leverage pre-trained text-to-image diffusion models and CLIP guidance to translate graph knowledge into images. Towards this, we first pre-train our graph encoder to align graph features with CLIP features of corresponding images using a GAN based training. Further, we fuse the graph features with CLIP embedding of object labels present in the given scene graph to create a graph consistent CLIP guided conditioning signal. In the conditioning input, object embeddings provide coarse structure of the image and graph features provide structural alignment based on relationships among objects. Finally, we fine tune a pre-trained diffusion model with the graph consistent conditioning signal with reconstruction and CLIP alignment loss. Elaborate experiments reveal that our method outperforms existing methods on standard benchmarks of COCO-stuff and Visual Genome dataset.

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

Recent success in deep learning has generated immense interest among practitioners and students, inspiring many to learn about this new technology. While visual and interactive approaches have been successfully developed to help people more easily learn deep learning, most existing tools focus on simpler models. In this work, we present GAN Lab, the first interactive visualization tool designed for non-experts to learn and experiment with Generative Adversarial Networks (GANs), a popular class of complex deep learning models. With GAN Lab, users can interactively train generative models and visualize the dynamic training process's intermediate results. GAN Lab tightly integrates an model overview graph that summarizes GAN's structure, and a layered distributions view that helps users interpret the interplay between submodels. GAN Lab introduces new interactive experimentation features for learning complex deep learning models, such as step-by-step training at multiple levels of abstraction for understanding intricate training dynamics. Implemented using TensorFlow.js, GAN Lab is accessible to anyone via modern web browsers, without the need for installation or specialized hardware, overcoming a major practical challenge in deploying interactive tools for deep learning.

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.

SLEDGE is the first generative simulator for vehicle motion planning trained on real-world driving logs. Its core component is a learned model that is able to generate agent bounding boxes and lane graphs. The model's outputs serve as an initial state for traffic simulation. The unique properties of the entities to be generated for SLEDGE, such as their connectivity and variable count per scene, render the naive application of most modern generative models to this task non-trivial. Therefore, together with a systematic study of existing lane graph representations, we introduce a novel raster-to-vector autoencoder (RVAE). It encodes agents and the lane graph into distinct channels in a rasterized latent map. This facilitates both lane-conditioned agent generation and combined generation of lanes and agents with a Diffusion Transformer. Using generated entities in SLEDGE enables greater control over the simulation, e.g. upsampling turns or increasing traffic density. Further, SLEDGE can support 500m long routes, a capability not found in existing data-driven simulators like nuPlan. It presents new challenges for planning algorithms, evidenced by failure rates of over 40% for PDM, the winner of the 2023 nuPlan challenge, when tested on hard routes and dense traffic generated by our model. Compared to nuPlan, SLEDGE requires 500times less storage to set up (<4GB), making it a more accessible option and helping with democratizing future research in this field.

Recent embedding-based methods have achieved great successes on exploiting entity alignment from knowledge graph (KG) embeddings of multiple modals. In this paper, we study embedding-based entity alignment (EEA) from a perspective of generative models. We show that EEA is a special problem where the main objective is analogous to that in a typical generative model, based on which we theoretically prove the effectiveness of the recently developed generative adversarial network (GAN)-based EEA methods. We then reveal that their incomplete objective limits the capacity on both entity alignment and entity synthesis (i.e., generating new entities). We mitigate this problem by introducing a generative EEA (abbr., GEEA) framework with the proposed mutual variational autoencoder (M-VAE) as the generative model. M-VAE can convert an entity from one KG to another and generate new entities from random noise vectors. We demonstrate the power of GEEA with theoretical analysis and empirical experiments on both entity alignment and entity synthesis tasks.

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 current research direction in generative models, such as the recently developed GPT4, aims to find relevant knowledge information for multimodal and multilingual inputs to provide answers. Under these research circumstances, the demand for multilingual evaluation of visual question answering (VQA) tasks, a representative task of multimodal systems, has increased. Accordingly, we propose a bilingual outside-knowledge VQA (BOK-VQA) dataset in this study that can be extended to multilingualism. The proposed data include 17K images, 17K question-answer pairs for both Korean and English and 280K instances of knowledge information related to question-answer content. We also present a framework that can effectively inject knowledge information into a VQA system by pretraining the knowledge information of BOK-VQA data in the form of graph embeddings. Finally, through in-depth analysis, we demonstrated the actual effect of the knowledge information contained in the constructed training data on VQA.

We introduce a new framework for molecular graph generation with 3D molecular generative models. Our Synthetic Coordinate Embedding (SyCo) framework maps molecular graphs to Euclidean point clouds via synthetic conformer coordinates and learns the inverse map using an E(n)-Equivariant Graph Neural Network (EGNN). The induced point cloud-structured latent space is well-suited to apply existing 3D molecular generative models. This approach simplifies the graph generation problem - without relying on molecular fragments nor autoregressive decoding - into a point cloud generation problem followed by node and edge classification tasks. Further, we propose a novel similarity-constrained optimization scheme for 3D diffusion models based on inpainting and guidance. As a concrete implementation of our framework, we develop EDM-SyCo based on the E(3) Equivariant Diffusion Model (EDM). EDM-SyCo achieves state-of-the-art performance in distribution learning of molecular graphs, outperforming the best non-autoregressive methods by more than 30% on ZINC250K and 16% on the large-scale GuacaMol dataset while improving conditional generation by up to 3.9 times.

This study explores the use of Large Language Models (LLMs) for automatic evaluation of knowledge graph (KG) completion models. Historically, validating information in KGs has been a challenging task, requiring large-scale human annotation at prohibitive cost. With the emergence of general-purpose generative AI and LLMs, it is now plausible that human-in-the-loop validation could be replaced by a generative agent. We introduce a framework for consistency and validation when using generative models to validate knowledge graphs. Our framework is based upon recent open-source developments for structural and semantic validation of LLM outputs, and upon flexible approaches to fact checking and verification, supported by the capacity to reference external knowledge sources of any kind. The design is easy to adapt and extend, and can be used to verify any kind of graph-structured data through a combination of model-intrinsic knowledge, user-supplied context, and agents capable of external knowledge retrieval.

In molecular research, simulation \& design of molecules are key areas with significant implications for drug development, material science, and other fields. Current classical computational power falls inadequate to simulate any more than small molecules, let alone protein chains on hundreds of peptide. Therefore these experiment are done physically in wet-lab, but it takes a lot of time \& not possible to examine every molecule due to the size of the search area, tens of billions of dollars are spent every year in these research experiments. Molecule simulation \& design has lately advanced significantly by machine learning models, A fresh perspective on the issue of chemical synthesis is provided by deep generative models for graph-structured data. By optimising differentiable models that produce molecular graphs directly, it is feasible to avoid costly search techniques in the discrete and huge space of chemical structures. But these models also suffer from computational limitations when dimensions become huge and consume huge amount of resources. Quantum Generative machine learning in recent years have shown some empirical results promising significant advantages over classical counterparts.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

We present the first comprehensive study on automatic knowledge base construction for two prevalent commonsense knowledge graphs: ATOMIC (Sap et al., 2019) and ConceptNet (Speer et al., 2017). Contrary to many conventional KBs that store knowledge with canonical templates, commonsense KBs only store loosely structured open-text descriptions of knowledge. We posit that an important step toward automatic commonsense completion is the development of generative models of commonsense knowledge, and propose COMmonsEnse Transformers (COMET) that learn to generate rich and diverse commonsense descriptions in natural language. Despite the challenges of commonsense modeling, our investigation reveals promising results when implicit knowledge from deep pre-trained language models is transferred to generate explicit knowledge in commonsense knowledge graphs. Empirical results demonstrate that COMET is able to generate novel knowledge that humans rate as high quality, with up to 77.5% (ATOMIC) and 91.7% (ConceptNet) precision at top 1, which approaches human performance for these resources. Our findings suggest that using generative commonsense models for automatic commonsense KB completion could soon be a plausible alternative to extractive methods.

Generation of graphs is a major challenge for real-world tasks that require understanding the complex nature of their non-Euclidean structures. Although diffusion models have achieved notable success in graph generation recently, they are ill-suited for modeling the topological properties of graphs since learning to denoise the noisy samples does not explicitly learn the graph structures to be generated. To tackle this limitation, we propose a generative framework that models the topology of graphs by explicitly learning the final graph structures of the diffusion process. Specifically, we design the generative process as a mixture of endpoint-conditioned diffusion processes which is driven toward the predicted graph that results in rapid convergence. We further introduce a simple parameterization of the mixture process and develop an objective for learning the final graph structure, which enables maximum likelihood training. Through extensive experimental validation on general graph and 2D/3D molecule generation tasks, we show that our method outperforms previous generative models, generating graphs with correct topology with both continuous (e.g. 3D coordinates) and discrete (e.g. atom types) features. Our code is available at https://github.com/harryjo97/GruM.

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.

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

Knowledge Graph (KG) and its variant of ontology have been widely used for knowledge representation, and have shown to be quite effective in augmenting Zero-shot Learning (ZSL). However, existing ZSL methods that utilize KGs all neglect the intrinsic complexity of inter-class relationships represented in KGs. One typical feature is that a class is often related to other classes in different semantic aspects. In this paper, we focus on ontologies for augmenting ZSL, and propose to learn disentangled ontology embeddings guided by ontology properties to capture and utilize more fine-grained class relationships in different aspects. We also contribute a new ZSL framework named DOZSL, which contains two new ZSL solutions based on generative models and graph propagation models, respectively, for effectively utilizing the disentangled ontology embeddings. Extensive evaluations have been conducted on five benchmarks across zero-shot image classification (ZS-IMGC) and zero-shot KG completion (ZS-KGC). DOZSL often achieves better performance than the state-of-the-art, and its components have been verified by ablation studies and case studies. Our codes and datasets are available at https://github.com/zjukg/DOZSL.

Diffusion models, as a novel generative paradigm, have achieved remarkable success in various image generation tasks such as image inpainting, image-to-text translation, and video generation. Graph generation is a crucial computational task on graphs with numerous real-world applications. It aims to learn the distribution of given graphs and then generate new graphs. Given the great success of diffusion models in image generation, increasing efforts have been made to leverage these techniques to advance graph generation in recent years. In this paper, we first provide a comprehensive overview of generative diffusion models on graphs, In particular, we review representative algorithms for three variants of graph diffusion models, i.e., Score Matching with Langevin Dynamics (SMLD), Denoising Diffusion Probabilistic Model (DDPM), and Score-based Generative Model (SGM). Then, we summarize the major applications of generative diffusion models on graphs with a specific focus on molecule and protein modeling. Finally, we discuss promising directions in generative diffusion models on graph-structured data. For this survey, we also created a GitHub project website by collecting the supporting resources for generative diffusion models on graphs, at the link: https://github.com/ChengyiLIU-cs/Generative-Diffusion-Models-on-Graphs

While Retrieval-Augmented Generation (RAG) enhances the accuracy and relevance of responses by generative language models, it falls short in graph-based contexts where both textual and topological information are important. Naive RAG approaches inherently neglect the structural intricacies of textual graphs, resulting in a critical gap in the generation process. To address this challenge, we introduce Graph Retrieval-Augmented Generation (GRAG), which significantly enhances both the retrieval and generation processes by emphasizing the importance of subgraph structures. Unlike RAG approaches that focus solely on text-based entity retrieval, GRAG maintains an acute awareness of graph topology, which is crucial for generating contextually and factually coherent responses. Our GRAG approach consists of four main stages: indexing of k-hop ego-graphs, graph retrieval, soft pruning to mitigate the impact of irrelevant entities, and generation with pruned textual subgraphs. GRAG's core workflow-retrieving textual subgraphs followed by soft pruning-efficiently identifies relevant subgraph structures while avoiding the computational infeasibility typical of exhaustive subgraph searches, which are NP-hard. Moreover, we propose a novel prompting strategy that achieves lossless conversion from textual subgraphs to hierarchical text descriptions. Extensive experiments on graph multi-hop reasoning benchmarks demonstrate that in scenarios requiring multi-hop reasoning on textual graphs, our GRAG approach significantly outperforms current state-of-the-art RAG methods while effectively mitigating hallucinations.

Dialogue-based Role Playing Games (RPGs) require powerful storytelling. The narratives of these may take years to write and typically involve a large creative team. In this work, we demonstrate the potential of large generative text models to assist this process. GRIM, a prototype GRaph-based Interactive narrative visualization system for gaMes, generates a rich narrative graph with branching storylines that match a high-level narrative description and constraints provided by the designer. Game designers can interactively edit the graph by automatically generating new sub-graphs that fit the edits within the original narrative and constraints. We illustrate the use of GRIM in conjunction with GPT-4, generating branching narratives for four well-known stories with different contextual constraints.

Real-world Knowledge Graphs (KGs) often suffer from incompleteness, which limits their potential performance. Knowledge Graph Completion (KGC) techniques aim to address this issue. However, traditional KGC methods are computationally intensive and impractical for large-scale KGs, necessitating the learning of dense node embeddings and computing pairwise distances. Generative transformer-based language models (e.g., T5 and recent KGT5) offer a promising solution as they can predict the tail nodes directly. In this study, we propose to include node neighborhoods as additional information to improve KGC methods based on language models. We examine the effects of this imputation and show that, on both inductive and transductive Wikidata subsets, our method outperforms KGT5 and conventional KGC approaches. We also provide an extensive analysis of the impact of neighborhood on model prediction and show its importance. Furthermore, we point the way to significantly improve KGC through more effective neighborhood selection.

Multimodal learning combines multiple data modalities, broadening the types and complexity of data our models can utilize: for example, from plain text to image-caption pairs. Most multimodal learning algorithms focus on modeling simple one-to-one pairs of data from two modalities, such as image-caption pairs, or audio-text pairs. However, in most real-world settings, entities of different modalities interact with each other in more complex and multifaceted ways, going beyond one-to-one mappings. We propose to represent these complex relationships as graphs, allowing us to capture data with any number of modalities, and with complex relationships between modalities that can flexibly vary from one sample to another. Toward this goal, we propose Multimodal Graph Learning (MMGL), a general and systematic framework for capturing information from multiple multimodal neighbors with relational structures among them. In particular, we focus on MMGL for generative tasks, building upon pretrained Language Models (LMs), aiming to augment their text generation with multimodal neighbor contexts. We study three research questions raised by MMGL: (1) how can we infuse multiple neighbor information into the pretrained LMs, while avoiding scalability issues? (2) how can we infuse the graph structure information among multimodal neighbors into the LMs? and (3) how can we finetune the pretrained LMs to learn from the neighbor context in a parameter-efficient manner? We conduct extensive experiments to answer these three questions on MMGL and analyze the empirical results to pave the way for future MMGL research.

The polygon mesh representation of 3D data exhibits great flexibility, fast rendering speed, and storage efficiency, which is widely preferred in various applications. However, given its unstructured graph representation, the direct generation of high-fidelity 3D meshes is challenging. Fortunately, with a pre-defined ordering strategy, 3D meshes can be represented as sequences, and the generation process can be seamlessly treated as an auto-regressive problem. In this paper, we validate the Neural Coordinate Field (NeurCF), an explicit coordinate representation with implicit neural embeddings, is a simple-yet-effective representation for large-scale sequential mesh modeling. After that, we present MeshXL, a family of generative pre-trained auto-regressive models, which addresses the process of 3D mesh generation with modern large language model approaches. Extensive experiments show that MeshXL is able to generate high-quality 3D meshes, and can also serve as foundation models for various down-stream applications.

In this paper, we propose a novel method for joint entity and relation extraction from unstructured text by framing it as a conditional sequence generation problem. In contrast to conventional generative information extraction models that are left-to-right token-level generators, our approach is span-based. It generates a linearized graph where nodes represent text spans and edges represent relation triplets. Our method employs a transformer encoder-decoder architecture with pointing mechanism on a dynamic vocabulary of spans and relation types. Our model can capture the structural characteristics and boundaries of entities and relations through span representations while simultaneously grounding the generated output in the original text thanks to the pointing mechanism. Evaluation on benchmark datasets validates the effectiveness of our approach, demonstrating competitive results. Code is available at https://github.com/urchade/ATG.

Advancements in generative AI have broadened the potential applications of Large Language Models (LLMs) in the development of autonomous agents. Achieving true autonomy requires accumulating and updating knowledge gained from interactions with the environment and effectively utilizing it. Current LLM-based approaches leverage past experiences using a full history of observations, summarization or retrieval augmentation. However, these unstructured memory representations do not facilitate the reasoning and planning essential for complex decision-making. In our study, we introduce AriGraph, a novel method wherein the agent constructs a memory graph that integrates semantic and episodic memories while exploring the environment. This graph structure facilitates efficient associative retrieval of interconnected concepts, relevant to the agent's current state and goals, thus serving as an effective environmental model that enhances the agent's exploratory and planning capabilities. We demonstrate that our Ariadne LLM agent, equipped with this proposed memory architecture augmented with planning and decision-making, effectively handles complex tasks on a zero-shot basis in the TextWorld environment. Our approach markedly outperforms established methods such as full-history, summarization, and Retrieval-Augmented Generation in various tasks, including the cooking challenge from the First TextWorld Problems competition and novel tasks like house cleaning and puzzle Treasure Hunting.

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.

In this paper, we present a novel generative task: joint scene graph - image generation. While previous works have explored image generation conditioned on scene graphs or layouts, our task is distinctive and important as it involves generating scene graphs themselves unconditionally from noise, enabling efficient and interpretable control for image generation. Our task is challenging, requiring the generation of plausible scene graphs with heterogeneous attributes for nodes (objects) and edges (relations among objects), including continuous object bounding boxes and discrete object and relation categories. We introduce a novel diffusion model, DiffuseSG, that jointly models the adjacency matrix along with heterogeneous node and edge attributes. We explore various types of encodings for the categorical data, relaxing it into a continuous space. With a graph transformer being the denoiser, DiffuseSG successively denoises the scene graph representation in a continuous space and discretizes the final representation to generate the clean scene graph. Additionally, we introduce an IoU regularization to enhance the empirical performance. Our model significantly outperforms existing methods in scene graph generation on the Visual Genome and COCO-Stuff datasets, both on standard and newly introduced metrics that better capture the problem complexity. Moreover, we demonstrate the additional benefits of our model in two downstream applications: 1) excelling in a series of scene graph completion tasks, and 2) improving scene graph detection models by using extra training samples generated from DiffuseSG.

Text-conditioned image generation has made significant progress in recent years with generative adversarial networks and more recently, diffusion models. While diffusion models conditioned on text prompts have produced impressive and high-quality images, accurately representing complex text prompts such as the number of instances of a specific object remains challenging. To address this limitation, we propose a novel guidance approach for the sampling process in the diffusion model that leverages bounding box and segmentation map information at inference time without additional training data. Through a novel loss in the sampling process, our approach guides the model with semantic features from CLIP embeddings and enforces geometric constraints, leading to high-resolution images that accurately represent the scene. To obtain bounding box and segmentation map information, we structure the text prompt as a scene graph and enrich the nodes with CLIP embeddings. Our proposed model achieves state-of-the-art performance on two public benchmarks for image generation from scene graphs, surpassing both scene graph to image and text-based diffusion models in various metrics. Our results demonstrate the effectiveness of incorporating bounding box and segmentation map guidance in the diffusion model sampling process for more accurate text-to-image generation.

Developing intelligent agents for long-term cooperation in dynamic open-world scenarios is a major challenge in multi-agent systems. Traditional Multi-agent Reinforcement Learning (MARL) frameworks like centralized training decentralized execution (CTDE) struggle with scalability and flexibility. They require centralized long-term planning, which is difficult without custom reward functions, and face challenges in processing multi-modal data. CTDE approaches also assume fixed cooperation strategies, making them impractical in dynamic environments where agents need to adapt and plan independently. To address decentralized multi-agent cooperation, we propose Decentralized Adaptive Knowledge Graph Memory and Structured Communication System (DAMCS) in a novel Multi-agent Crafter environment. Our generative agents, powered by Large Language Models (LLMs), are more scalable than traditional MARL agents by leveraging external knowledge and language for long-term planning and reasoning. Instead of fully sharing information from all past experiences, DAMCS introduces a multi-modal memory system organized as a hierarchical knowledge graph and a structured communication protocol to optimize agent cooperation. This allows agents to reason from past interactions and share relevant information efficiently. Experiments on novel multi-agent open-world tasks show that DAMCS outperforms both MARL and LLM baselines in task efficiency and collaboration. Compared to single-agent scenarios, the two-agent scenario achieves the same goal with 63% fewer steps, and the six-agent scenario with 74% fewer steps, highlighting the importance of adaptive memory and structured communication in achieving long-term goals. We publicly release our project at: https://happyeureka.github.io/damcs.

Generative commonsense reasoning which aims to empower machines to generate sentences with the capacity of reasoning over a set of concepts is a critical bottleneck for text generation. Even the state-of-the-art pre-trained language generation models struggle at this task and often produce implausible and anomalous sentences. One reason is that they rarely consider incorporating the knowledge graph which can provide rich relational information among the commonsense concepts. To promote the ability of commonsense reasoning for text generation, we propose a novel knowledge graph augmented pre-trained language generation model KG-BART, which encompasses the complex relations of concepts through the knowledge graph and produces more logical and natural sentences as output. Moreover, KG-BART can leverage the graph attention to aggregate the rich concept semantics that enhances the model generalization on unseen concept sets. Experiments on benchmark CommonGen dataset verify the effectiveness of our proposed approach by comparing with several strong pre-trained language generation models, particularly KG-BART outperforms BART by 5.80, 4.60, in terms of BLEU-3, 4. Moreover, we also show that the generated context by our model can work as background scenarios to benefit downstream commonsense QA tasks.

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective way to reduce the labeling effort is to pre-train an expressive GNN model on unlabeled data with self-supervision and then transfer the learned model to downstream tasks with only a few labels. In this paper, we present the GPT-GNN framework to initialize GNNs by generative pre-training. GPT-GNN introduces a self-supervised attributed graph generation task to pre-train a GNN so that it can capture the structural and semantic properties of the graph. We factorize the likelihood of the graph generation into two components: 1) Attribute Generation and 2) Edge Generation. By modeling both components, GPT-GNN captures the inherent dependency between node attributes and graph structure during the generative process. Comprehensive experiments on the billion-scale Open Academic Graph and Amazon recommendation data demonstrate that GPT-GNN significantly outperforms state-of-the-art GNN models without pre-training by up to 9.1% across various downstream tasks.

Vision-Language models (VLMs) pre-trained on large corpora have demonstrated notable success across a range of downstream tasks. In light of the rapidly increasing size of pre-trained VLMs, parameter-efficient transfer learning (PETL) has garnered attention as a viable alternative to full fine-tuning. One such approach is the adapter, which introduces a few trainable parameters into the pre-trained models while preserving the original parameters during adaptation. In this paper, we present a novel modeling framework that recasts adapter tuning after attention as a graph message passing process on attention graphs, where the projected query and value features and attention matrix constitute the node features and the graph adjacency matrix, respectively. Within this framework, tuning adapters in VLMs necessitates handling heterophilic graphs, owing to the disparity between the projected query and value space. To address this challenge, we propose a new adapter architecture, p-adapter, which employs p-Laplacian message passing in Graph Neural Networks (GNNs). Specifically, the attention weights are re-normalized based on the features, and the features are then aggregated using the calibrated attention matrix, enabling the dynamic exploitation of information with varying frequencies in the heterophilic attention graphs. We conduct extensive experiments on different pre-trained VLMs and multi-modal tasks, including visual question answering, visual entailment, and image captioning. The experimental results validate our method's significant superiority over other PETL methods.

This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.

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.

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

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 Neural Networks (GNNs) have been widely applied to different tasks such as bioinformatics, drug design, and social networks. However, recent studies have shown that GNNs are vulnerable to adversarial attacks which aim to mislead the node or subgraph classification prediction by adding subtle perturbations. Detecting these attacks is challenging due to the small magnitude of perturbation and the discrete nature of graph data. In this paper, we propose a general adversarial edge detection pipeline EDoG without requiring knowledge of the attack strategies based on graph generation. Specifically, we propose a novel graph generation approach combined with link prediction to detect suspicious adversarial edges. To effectively train the graph generative model, we sample several sub-graphs from the given graph data. We show that since the number of adversarial edges is usually low in practice, with low probability the sampled sub-graphs will contain adversarial edges based on the union bound. In addition, considering the strong attacks which perturb a large number of edges, we propose a set of novel features to perform outlier detection as the preprocessing for our detection. Extensive experimental results on three real-world graph datasets including a private transaction rule dataset from a major company and two types of synthetic graphs with controlled properties show that EDoG can achieve above 0.8 AUC against four state-of-the-art unseen attack strategies without requiring any knowledge about the attack type; and around 0.85 with knowledge of the attack type. EDoG significantly outperforms traditional malicious edge detection baselines. We also show that an adaptive attack with full knowledge of our detection pipeline is difficult to bypass it.

This paper aims to generate materials for 3D meshes from text descriptions. Unlike existing methods that synthesize texture maps, we propose to generate segment-wise procedural material graphs as the appearance representation, which supports high-quality rendering and provides substantial flexibility in editing. Instead of relying on extensive paired data, i.e., 3D meshes with material graphs and corresponding text descriptions, to train a material graph generative model, we propose to leverage the pre-trained 2D diffusion model as a bridge to connect the text and material graphs. Specifically, our approach decomposes a shape into a set of segments and designs a segment-controlled diffusion model to synthesize 2D images that are aligned with mesh parts. Based on generated images, we initialize parameters of material graphs and fine-tune them through the differentiable rendering module to produce materials in accordance with the textual description. Extensive experiments demonstrate the superior performance of our framework in photorealism, resolution, and editability over existing methods. Project page: https://zhanghe3z.github.io/MaPa/

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.

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

Scene graphs offer a structured, hierarchical representation of images, with nodes and edges symbolizing objects and the relationships among them. It can serve as a natural interface for image editing, dramatically improving precision and flexibility. Leveraging this benefit, we introduce a new framework that integrates large language model (LLM) with Text2Image generative model for scene graph-based image editing. This integration enables precise modifications at the object level and creative recomposition of scenes without compromising overall image integrity. Our approach involves two primary stages: 1) Utilizing a LLM-driven scene parser, we construct an image's scene graph, capturing key objects and their interrelationships, as well as parsing fine-grained attributes such as object masks and descriptions. These annotations facilitate concept learning with a fine-tuned diffusion model, representing each object with an optimized token and detailed description prompt. 2) During the image editing phase, a LLM editing controller guides the edits towards specific areas. These edits are then implemented by an attention-modulated diffusion editor, utilizing the fine-tuned model to perform object additions, deletions, replacements, and adjustments. Through extensive experiments, we demonstrate that our framework significantly outperforms existing image editing methods in terms of editing precision and scene aesthetics.

We introduce the variational graph auto-encoder (VGAE), a framework for unsupervised learning on graph-structured data based on the variational auto-encoder (VAE). This model makes use of latent variables and is capable of learning interpretable latent representations for undirected graphs. We demonstrate this model using a graph convolutional network (GCN) encoder and a simple inner product decoder. Our model achieves competitive results on a link prediction task in citation networks. In contrast to most existing models for unsupervised learning on graph-structured data and link prediction, our model can naturally incorporate node features, which significantly improves predictive performance on a number of benchmark datasets.

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.

The generation of explanation graphs is a significant task that aims to produce explanation graphs in response to user input, revealing the internal reasoning process. This task is challenging due to the significant discrepancy between unstructured user queries and structured explanation graphs. Current research commonly fine-tunes a text-based pre-trained language model on a small downstream dataset that is annotated with labeled graphs. However, due to the limited scale of available datasets, this approach may prove to be insufficient in bridging the gap between natural language text and structured graphs. In this paper, to alleviate the above limitations, we propose a novel pre-trained framework EG3P(for Explanation Graph Generation via Generative Pre-training over synthetic graphs) for the explanation graph generation task. Specifically, we first propose a text-to-graph generative task to pre-train the model with the goal of bridging the text-graph gap. Additionally, we propose an automatic corpus synthesis strategy for synthesizing a large scale of high-quality corpus, reducing the reliance on costly manual annotation methods. Experimental results on ExplaGraphs show the effectiveness of EG3P that our model surpasses all baseline systems with remarkable margins. Besides, further analysis demonstrates that EG3P is able to generate better explanation graphs on actual reasoning tasks such as CommonsenseQA and OpenbookQA.

Knowledge about the hidden factors that determine particular system dynamics is crucial for both explaining them and pursuing goal-directed interventions. Inferring these factors from time series data without supervision remains an open challenge. Here, we focus on spatiotemporal processes, including wave propagation and weather dynamics, for which we assume that universal causes (e.g. physics) apply throughout space and time. A recently introduced DIstributed SpatioTemporal graph Artificial Neural network Architecture (DISTANA) is used and enhanced to learn such processes, requiring fewer parameters and achieving significantly more accurate predictions compared to temporal convolutional neural networks and other related approaches. We show that DISTANA, when combined with a retrospective latent state inference principle called active tuning, can reliably derive location-respective hidden causal factors. In a current weather prediction benchmark, DISTANA infers our planet's land-sea mask solely by observing temperature dynamics and, meanwhile, uses the self inferred information to improve its own future temperature predictions.

We introduce SymbolicAI, a versatile and modular framework employing a logic-based approach to concept learning and flow management in generative processes. SymbolicAI enables the seamless integration of generative models with a diverse range of solvers by treating large language models (LLMs) as semantic parsers that execute tasks based on both natural and formal language instructions, thus bridging the gap between symbolic reasoning and generative AI. We leverage probabilistic programming principles to tackle complex tasks, and utilize differentiable and classical programming paradigms with their respective strengths. The framework introduces a set of polymorphic, compositional, and self-referential operations for data stream manipulation, aligning LLM outputs with user objectives. As a result, we can transition between the capabilities of various foundation models endowed with zero- and few-shot learning capabilities and specialized, fine-tuned models or solvers proficient in addressing specific problems. In turn, the framework facilitates the creation and evaluation of explainable computational graphs. We conclude by introducing a quality measure and its empirical score for evaluating these computational graphs, and propose a benchmark that compares various state-of-the-art LLMs across a set of complex workflows. We refer to the empirical score as the "Vector Embedding for Relational Trajectory Evaluation through Cross-similarity", or VERTEX score for short. The framework codebase and benchmark are linked below.

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.

In this paper, we propose Multiresolution Equivariant Graph Variational Autoencoders (MGVAE), the first hierarchical generative model to learn and generate graphs in a multiresolution and equivariant manner. At each resolution level, MGVAE employs higher order message passing to encode the graph while learning to partition it into mutually exclusive clusters and coarsening into a lower resolution that eventually creates a hierarchy of latent distributions. MGVAE then constructs a hierarchical generative model to variationally decode into a hierarchy of coarsened graphs. Importantly, our proposed framework is end-to-end permutation equivariant with respect to node ordering. MGVAE achieves competitive results with several generative tasks including general graph generation, molecular generation, unsupervised molecular representation learning to predict molecular properties, link prediction on citation graphs, and graph-based image generation.

We present EchoScene, an interactive and controllable generative model that generates 3D indoor scenes on scene graphs. EchoScene leverages a dual-branch diffusion model that dynamically adapts to scene graphs. Existing methods struggle to handle scene graphs due to varying numbers of nodes, multiple edge combinations, and manipulator-induced node-edge operations. EchoScene overcomes this by associating each node with a denoising process and enables collaborative information exchange, enhancing controllable and consistent generation aware of global constraints. This is achieved through an information echo scheme in both shape and layout branches. At every denoising step, all processes share their denoising data with an information exchange unit that combines these updates using graph convolution. The scheme ensures that the denoising processes are influenced by a holistic understanding of the scene graph, facilitating the generation of globally coherent scenes. The resulting scenes can be manipulated during inference by editing the input scene graph and sampling the noise in the diffusion model. Extensive experiments validate our approach, which maintains scene controllability and surpasses previous methods in generation fidelity. Moreover, the generated scenes are of high quality and thus directly compatible with off-the-shelf texture generation. Code and trained models are open-sourced.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates some central challenges from multiple tasks, including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding and elicits continuous differential attention that encapsulates and evolves with latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Generative flow networks (GFlowNets) are amortized variational inference algorithms that are trained to sample from unnormalized target distributions over compositional objects. A key limitation of GFlowNets until this time has been that they are restricted to discrete spaces. We present a theory for generalized GFlowNets, which encompasses both existing discrete GFlowNets and ones with continuous or hybrid state spaces, and perform experiments with two goals in mind. First, we illustrate critical points of the theory and the importance of various assumptions. Second, we empirically demonstrate how observations about discrete GFlowNets transfer to the continuous case and show strong results compared to non-GFlowNet baselines on several previously studied tasks. This work greatly widens the perspectives for the application of GFlowNets in probabilistic inference and various modeling settings.

We propose an end-to-end variational generative model for scene layout synthesis conditioned on scene graphs. Unlike unconditional scene layout generation, we use scene graphs as an abstract but general representation to guide the synthesis of diverse scene layouts that satisfy relationships included in the scene graph. This gives rise to more flexible control over the synthesis process, allowing various forms of inputs such as scene layouts extracted from sentences or inferred from a single color image. Using our conditional layout synthesizer, we can generate various layouts that share the same structure of the input example. In addition to this conditional generation design, we also integrate a differentiable rendering module that enables layout refinement using only 2D projections of the scene. Given a depth and a semantics map, the differentiable rendering module enables optimizing over the synthesized layout to fit the given input in an analysis-by-synthesis fashion. Experiments suggest that our model achieves higher accuracy and diversity in conditional scene synthesis and allows exemplar-based scene generation from various input forms.

Self-supervised learning (SSL) has been extensively explored in recent years. Particularly, generative SSL has seen emerging success in natural language processing and other AI fields, such as the wide adoption of BERT and GPT. Despite this, contrastive learning-which heavily relies on structural data augmentation and complicated training strategies-has been the dominant approach in graph SSL, while the progress of generative SSL on graphs, especially graph autoencoders (GAEs), has thus far not reached the potential as promised in other fields. In this paper, we identify and examine the issues that negatively impact the development of GAEs, including their reconstruction objective, training robustness, and error metric. We present a masked graph autoencoder GraphMAE that mitigates these issues for generative self-supervised graph pretraining. Instead of reconstructing graph structures, we propose to focus on feature reconstruction with both a masking strategy and scaled cosine error that benefit the robust training of GraphMAE. We conduct extensive experiments on 21 public datasets for three different graph learning tasks. The results manifest that GraphMAE-a simple graph autoencoder with careful designs-can consistently generate outperformance over both contrastive and generative state-of-the-art baselines. This study provides an understanding of graph autoencoders and demonstrates the potential of generative self-supervised pre-training on graphs.

Hypergraphs are marked by complex topology, expressing higher-order interactions among multiple nodes with hyperedges, and better capturing the topology is essential for effective representation learning. Recent advances in generative self-supervised learning (SSL) suggest that hypergraph neural networks learned from generative self supervision have the potential to effectively encode the complex hypergraph topology. Designing a generative SSL strategy for hypergraphs, however, is not straightforward. Questions remain with regard to its generative SSL task, connection to downstream tasks, and empirical properties of learned representations. In light of the promises and challenges, we propose a novel generative SSL strategy for hypergraphs. We first formulate a generative SSL task on hypergraphs, hyperedge filling, and highlight its theoretical connection to node classification. Based on the generative SSL task, we propose a hypergraph SSL method, HypeBoy. HypeBoy learns effective general-purpose hypergraph representations, outperforming 16 baseline methods across 11 benchmark datasets.

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

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.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Knowledge Graphs (KGs) have emerged as invaluable resources for enriching recommendation systems by providing a wealth of factual information and capturing semantic relationships among items. Leveraging KGs can significantly enhance recommendation performance. However, not all relations within a KG are equally relevant or beneficial for the target recommendation task. In fact, certain item-entity connections may introduce noise or lack informative value, thus potentially misleading our understanding of user preferences. To bridge this research gap, we propose a novel knowledge graph diffusion model for recommendation, referred to as DiffKG. Our framework integrates a generative diffusion model with a data augmentation paradigm, enabling robust knowledge graph representation learning. This integration facilitates a better alignment between knowledge-aware item semantics and collaborative relation modeling. Moreover, we introduce a collaborative knowledge graph convolution mechanism that incorporates collaborative signals reflecting user-item interaction patterns, guiding the knowledge graph diffusion process. We conduct extensive experiments on three publicly available datasets, consistently demonstrating the superiority of our DiffKG compared to various competitive baselines. We provide the source code repository of our proposed DiffKG model at the following link: https://github.com/HKUDS/DiffKG.

We present DeepWalk, a novel approach for learning latent representations of vertices in a network. These latent representations encode social relations in a continuous vector space, which is easily exploited by statistical models. DeepWalk generalizes recent advancements in language modeling and unsupervised feature learning (or deep learning) from sequences of words to graphs. DeepWalk uses local information obtained from truncated random walks to learn latent representations by treating walks as the equivalent of sentences. We demonstrate DeepWalk's latent representations on several multi-label network classification tasks for social networks such as BlogCatalog, Flickr, and YouTube. Our results show that DeepWalk outperforms challenging baselines which are allowed a global view of the network, especially in the presence of missing information. DeepWalk's representations can provide F_1 scores up to 10% higher than competing methods when labeled data is sparse. In some experiments, DeepWalk's representations are able to outperform all baseline methods while using 60% less training data. DeepWalk is also scalable. It is an online learning algorithm which builds useful incremental results, and is trivially parallelizable. These qualities make it suitable for a broad class of real world applications such as network classification, and anomaly detection.

Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches are inherently transductive and do not naturally generalize to unseen nodes. Here we present GraphSAGE, a general, inductive framework that leverages node feature information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, we learn a function that generates embeddings by sampling and aggregating features from a node's local neighborhood. Our algorithm outperforms strong baselines on three inductive node-classification benchmarks: we classify the category of unseen nodes in evolving information graphs based on citation and Reddit post data, and we show that our algorithm generalizes to completely unseen graphs using a multi-graph dataset of protein-protein interactions.

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our G-Retriever method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, G-Retriever performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}

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

Graph Neural Networks (GNNs) are popular models for graph learning problems. GNNs show strong empirical performance in many practical tasks. However, the theoretical properties have not been completely elucidated. In this paper, we investigate whether GNNs can exploit the graph structure from the perspective of the expressive power of GNNs. In our analysis, we consider graph generation processes that are controlled by hidden (or latent) node features, which contain all information about the graph structure. A typical example of this framework is kNN graphs constructed from the hidden features. In our main results, we show that GNNs can recover the hidden node features from the input graph alone, even when all node features, including the hidden features themselves and any indirect hints, are unavailable. GNNs can further use the recovered node features for downstream tasks. These results show that GNNs can fully exploit the graph structure by themselves, and in effect, GNNs can use both the hidden and explicit node features for downstream tasks. In the experiments, we confirm the validity of our results by showing that GNNs can accurately recover the hidden features using a GNN architecture built based on our theoretical analysis.

Semantic word embeddings represent the meaning of a word via a vector, and are created by diverse methods. Many use nonlinear operations on co-occurrence statistics, and have hand-tuned hyperparameters and reweighting methods. This paper proposes a new generative model, a dynamic version of the log-linear topic model of~mnih2007three. The methodological novelty is to use the prior to compute closed form expressions for word statistics. This provides a theoretical justification for nonlinear models like PMI, word2vec, and GloVe, as well as some hyperparameter choices. It also helps explain why low-dimensional semantic embeddings contain linear algebraic structure that allows solution of word analogies, as shown by~mikolov2013efficient and many subsequent papers. Experimental support is provided for the generative model assumptions, the most important of which is that latent word vectors are fairly uniformly dispersed in space.

Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at https://github.com/hamed1375/Exphormer.

GraphRAG addresses significant challenges in Retrieval-Augmented Generation (RAG) by leveraging graphs with embedded knowledge to enhance the reasoning capabilities of Large Language Models (LLMs). Despite its promising potential, the GraphRAG community currently lacks a unified framework for fine-grained decomposition of the graph-based knowledge retrieval process. Furthermore, there is no systematic categorization or evaluation of existing solutions within the retrieval process. In this paper, we present LEGO-GraphRAG, a modular framework that decomposes the retrieval process of GraphRAG into three interconnected modules: subgraph-extraction, path-filtering, and path-refinement. We systematically summarize and classify the algorithms and neural network (NN) models relevant to each module, providing a clearer understanding of the design space for GraphRAG instances. Additionally, we identify key design factors, such as Graph Coupling and Computational Cost, that influence the effectiveness of GraphRAG implementations. Through extensive empirical studies, we construct high-quality GraphRAG instances using a representative selection of solutions and analyze their impact on retrieval and reasoning performance. Our findings offer critical insights into optimizing GraphRAG instance design, ultimately contributing to the advancement of more accurate and contextually relevant LLM applications.

Graph representation learning nowadays becomes fundamental in analyzing graph-structured data. Inspired by recent success of contrastive methods, in this paper, we propose a novel framework for unsupervised graph representation learning by leveraging a contrastive objective at the node level. Specifically, we generate two graph views by corruption and learn node representations by maximizing the agreement of node representations in these two views. To provide diverse node contexts for the contrastive objective, we propose a hybrid scheme for generating graph views on both structure and attribute levels. Besides, we provide theoretical justification behind our motivation from two perspectives, mutual information and the classical triplet loss. We perform empirical experiments on both transductive and inductive learning tasks using a variety of real-world datasets. Experimental experiments demonstrate that despite its simplicity, our proposed method consistently outperforms existing state-of-the-art methods by large margins. Moreover, our unsupervised method even surpasses its supervised counterparts on transductive tasks, demonstrating its great potential in real-world applications.

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.

Graph neural networks aim to learn representations for graph-structured data and show impressive performance, particularly in node classification. Recently, many methods have studied the representations of GNNs from the perspective of optimization goals and spectral graph theory. However, the feature space that dominates representation learning has not been systematically studied in graph neural networks. In this paper, we propose to fill this gap by analyzing the feature space of both spatial and spectral models. We decompose graph neural networks into determined feature spaces and trainable weights, providing the convenience of studying the feature space explicitly using matrix space analysis. In particular, we theoretically find that the feature space tends to be linearly correlated due to repeated aggregations. Motivated by these findings, we propose 1) feature subspaces flattening and 2) structural principal components to expand the feature space. Extensive experiments verify the effectiveness of our proposed more comprehensive feature space, with comparable inference time to the baseline, and demonstrate its efficient convergence capability.

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.

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

In recent years, graph pre-training has gained significant attention, focusing on acquiring transferable knowledge from unlabeled graph data to improve downstream performance. Despite these recent endeavors, the problem of negative transfer remains a major concern when utilizing graph pre-trained models to downstream tasks. Previous studies made great efforts on the issue of what to pre-train and how to pre-train by designing a variety of graph pre-training and fine-tuning strategies. However, there are cases where even the most advanced "pre-train and fine-tune" paradigms fail to yield distinct benefits. This paper introduces a generic framework W2PGNN to answer the crucial question of when to pre-train (i.e., in what situations could we take advantage of graph pre-training) before performing effortful pre-training or fine-tuning. We start from a new perspective to explore the complex generative mechanisms from the pre-training data to downstream data. In particular, W2PGNN first fits the pre-training data into graphon bases, each element of graphon basis (i.e., a graphon) identifies a fundamental transferable pattern shared by a collection of pre-training graphs. All convex combinations of graphon bases give rise to a generator space, from which graphs generated form the solution space for those downstream data that can benefit from pre-training. In this manner, the feasibility of pre-training can be quantified as the generation probability of the downstream data from any generator in the generator space. W2PGNN offers three broad applications: providing the application scope of graph pre-trained models, quantifying the feasibility of pre-training, and assistance in selecting pre-training data to enhance downstream performance. We provide a theoretically sound solution for the first application and extensive empirical justifications for the latter two applications.

We introduce a self-supervised approach for learning node and graph level representations by contrasting structural views of graphs. We show that unlike visual representation learning, increasing the number of views to more than two or contrasting multi-scale encodings do not improve performance, and the best performance is achieved by contrasting encodings from first-order neighbors and a graph diffusion. We achieve new state-of-the-art results in self-supervised learning on 8 out of 8 node and graph classification benchmarks under the linear evaluation protocol. For example, on Cora (node) and Reddit-Binary (graph) classification benchmarks, we achieve 86.8% and 84.5% accuracy, which are 5.5% and 2.4% relative improvements over previous state-of-the-art. When compared to supervised baselines, our approach outperforms them in 4 out of 8 benchmarks. Source code is released at: https://github.com/kavehhassani/mvgrl

Structured representations like graphs and parse trees play a crucial role in many Natural Language Processing systems. In recent years, the advancements in multi-turn user interfaces necessitate the need for controlling and updating these structured representations given new sources of information. Although there have been many efforts focusing on improving the performance of the parsers that map text to graphs or parse trees, very few have explored the problem of directly manipulating these representations. In this paper, we explore the novel problem of graph modification, where the systems need to learn how to update an existing scene graph given a new user's command. Our novel models based on graph-based sparse transformer and cross attention information fusion outperform previous systems adapted from the machine translation and graph generation literature. We further contribute our large graph modification datasets to the research community to encourage future research for this new problem.

Devising augmentations for graph contrastive learning is challenging due to their irregular structure, drastic distribution shifts, and nonequivalent feature spaces across datasets. We introduce LG2AR, Learning Graph Augmentations to Learn Graph Representations, which is an end-to-end automatic graph augmentation framework that helps encoders learn generalizable representations on both node and graph levels. LG2AR consists of a probabilistic policy that learns a distribution over augmentations and a set of probabilistic augmentation heads that learn distributions over augmentation parameters. We show that LG2AR achieves state-of-the-art results on 18 out of 20 graph-level and node-level benchmarks compared to previous unsupervised models under both linear and semi-supervised evaluation protocols. The source code will be released here: https://github.com/kavehhassani/lg2ar

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

Graphs can model complex relationships between objects, enabling a myriad of Web applications such as online page/article classification and social recommendation. While graph neural networks(GNNs) have emerged as a powerful tool for graph representation learning, in an end-to-end supervised setting, their performance heavily rely on a large amount of task-specific supervision. To reduce labeling requirement, the "pre-train, fine-tune" and "pre-train, prompt" paradigms have become increasingly common. In particular, prompting is a popular alternative to fine-tuning in natural language processing, which is designed to narrow the gap between pre-training and downstream objectives in a task-specific manner. However, existing study of prompting on graphs is still limited, lacking a universal treatment to appeal to different downstream tasks. In this paper, we propose GraphPrompt, a novel pre-training and prompting framework on graphs. GraphPrompt not only unifies pre-training and downstream tasks into a common task template, but also employs a learnable prompt to assist a downstream task in locating the most relevant knowledge from the pre-train model in a task-specific manner. Finally, we conduct extensive experiments on five public datasets to evaluate and analyze GraphPrompt.

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

Graph-structured data are the commonly used and have wide application scenarios in the real world. For these diverse applications, the vast variety of learning tasks, graph domains, and complex graph learning procedures present challenges for human experts when designing versatile graph learning approaches. Facing these challenges, large language models (LLMs) offer a potential solution due to the extensive knowledge and the human-like intelligence. This paper proposes a novel conceptual prototype for designing versatile graph learning methods with LLMs, with a particular focus on the "where" and "how" perspectives. From the "where" perspective, we summarize four key graph learning procedures, including task definition, graph data feature engineering, model selection and optimization, deployment and serving. We then explore the application scenarios of LLMs in these procedures across a wider spectrum. In the "how" perspective, we align the abilities of LLMs with the requirements of each procedure. Finally, we point out the promising directions that could better leverage the strength of LLMs towards versatile graph learning methods.

Large language models are extensively applied across a wide range of tasks, such as customer support, content creation, educational tutoring, and providing financial guidance. However, a well-known drawback is their predisposition to generate hallucinations. This damages the trustworthiness of the information these models provide, impacting decision-making and user confidence. We propose a method to detect hallucinations by looking at the structure of the latent space and finding associations within hallucinated and non-hallucinated generations. We create a graph structure that connects generations that lie closely in the embedding space. Moreover, we employ a Graph Attention Network which utilizes message passing to aggregate information from neighboring nodes and assigns varying degrees of importance to each neighbor based on their relevance. Our findings show that 1) there exists a structure in the latent space that differentiates between hallucinated and non-hallucinated generations, 2) Graph Attention Networks can learn this structure and generalize it to unseen generations, and 3) the robustness of our method is enhanced when incorporating contrastive learning. When evaluated against evidence-based benchmarks, our model performs similarly without access to search-based methods.

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

This paper introduces a new model to learn graph neural networks equivariant to rotations, translations, reflections and permutations called E(n)-Equivariant Graph Neural Networks (EGNNs). In contrast with existing methods, our work does not require computationally expensive higher-order representations in intermediate layers while it still achieves competitive or better performance. In addition, whereas existing methods are limited to equivariance on 3 dimensional spaces, our model is easily scaled to higher-dimensional spaces. We demonstrate the effectiveness of our method on dynamical systems modelling, representation learning in graph autoencoders and predicting molecular properties.

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

Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.

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

In this paper, we approach an overlooked yet critical task Graph2Image: generating images from multimodal attributed graphs (MMAGs). This task poses significant challenges due to the explosion in graph size, dependencies among graph entities, and the need for controllability in graph conditions. To address these challenges, we propose a graph context-conditioned diffusion model called InstructG2I. InstructG2I first exploits the graph structure and multimodal information to conduct informative neighbor sampling by combining personalized page rank and re-ranking based on vision-language features. Then, a Graph-QFormer encoder adaptively encodes the graph nodes into an auxiliary set of graph prompts to guide the denoising process of diffusion. Finally, we propose graph classifier-free guidance, enabling controllable generation by varying the strength of graph guidance and multiple connected edges to a node. Extensive experiments conducted on three datasets from different domains demonstrate the effectiveness and controllability of our approach. The code is available at https://github.com/PeterGriffinJin/InstructG2I.

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

Pre-trained sequence-to-sequence language models have led to widespread success in many natural language generation tasks. However, there has been relatively less work on analyzing their ability to generate structured outputs such as graphs. Unlike natural language, graphs have distinct structural and semantic properties in the context of a downstream NLP task, e.g., generating a graph that is connected and acyclic can be attributed to its structural constraints, while the semantics of a graph can refer to how meaningfully an edge represents the relation between two node concepts. In this work, we study pre-trained language models that generate explanation graphs in an end-to-end manner and analyze their ability to learn the structural constraints and semantics of such graphs. We first show that with limited supervision, pre-trained language models often generate graphs that either violate these constraints or are semantically incoherent. Since curating large amount of human-annotated graphs is expensive and tedious, we propose simple yet effective ways of graph perturbations via node and edge edit operations that lead to structurally and semantically positive and negative graphs. Next, we leverage these graphs in different contrastive learning models with Max-Margin and InfoNCE losses. Our methods lead to significant improvements in both structural and semantic accuracy of explanation graphs and also generalize to other similar graph generation tasks. Lastly, we show that human errors are the best negatives for contrastive learning and also that automatically generating more such human-like negative graphs can lead to further improvements. Our code and models are publicly available at https://github.com/swarnaHub/ExplagraphGen

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

Large monolithic generative models trained on massive amounts of data have become an increasingly dominant approach in AI research. In this paper, we argue that we should instead construct large generative systems by composing smaller generative models together. We show how such a compositional generative approach enables us to learn distributions in a more data-efficient manner, enabling generalization to parts of the data distribution unseen at training time. We further show how this enables us to program and construct new generative models for tasks completely unseen at training. Finally, we show that in many cases, we can discover separate compositional components from data.

We present Simplified Text-Attributed Graph Embeddings (STAGE), a straightforward yet effective method for enhancing node features in Graph Neural Network (GNN) models that encode Text-Attributed Graphs (TAGs). Our approach leverages Large-Language Models (LLMs) to generate embeddings for textual attributes. STAGE achieves competitive results on various node classification benchmarks while also maintaining a simplicity in implementation relative to current state-of-the-art (SoTA) techniques. We show that utilizing pre-trained LLMs as embedding generators provides robust features for ensemble GNN training, enabling pipelines that are simpler than current SoTA approaches which require multiple expensive training and prompting stages. We also implement diffusion-pattern GNNs in an effort to make this pipeline scalable to graphs beyond academic benchmarks.

Recently, Retrieval-Augmented Generation (RAG) has achieved remarkable success in addressing the challenges of Large Language Models (LLMs) without necessitating retraining. By referencing an external knowledge base, RAG refines LLM outputs, effectively mitigating issues such as ``hallucination'', lack of domain-specific knowledge, and outdated information. However, the complex structure of relationships among different entities in databases presents challenges for RAG systems. In response, GraphRAG leverages structural information across entities to enable more precise and comprehensive retrieval, capturing relational knowledge and facilitating more accurate, context-aware responses. Given the novelty and potential of GraphRAG, a systematic review of current technologies is imperative. This paper provides the first comprehensive overview of GraphRAG methodologies. We formalize the GraphRAG workflow, encompassing Graph-Based Indexing, Graph-Guided Retrieval, and Graph-Enhanced Generation. We then outline the core technologies and training methods at each stage. Additionally, we examine downstream tasks, application domains, evaluation methodologies, and industrial use cases of GraphRAG. Finally, we explore future research directions to inspire further inquiries and advance progress in the field.

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

Graph neural networks (GNNs) are effective models for representation learning on relational data. However, standard GNNs are limited in their expressive power, as they cannot distinguish graphs beyond the capability of the Weisfeiler-Leman graph isomorphism heuristic. In order to break this expressiveness barrier, GNNs have been enhanced with random node initialization (RNI), where the idea is to train and run the models with randomized initial node features. In this work, we analyze the expressive power of GNNs with RNI, and prove that these models are universal, a first such result for GNNs not relying on computationally demanding higher-order properties. This universality result holds even with partially randomized initial node features, and preserves the invariance properties of GNNs in expectation. We then empirically analyze the effect of RNI on GNNs, based on carefully constructed datasets. Our empirical findings support the superior performance of GNNs with RNI over standard GNNs.

We present the Evolving Graph Fourier Transform (EFT), the first invertible spectral transform that captures evolving representations on temporal graphs. We motivate our work by the inadequacy of existing methods for capturing the evolving graph spectra, which are also computationally expensive due to the temporal aspect along with the graph vertex domain. We view the problem as an optimization over the Laplacian of the continuous time dynamic graph. Additionally, we propose pseudo-spectrum relaxations that decompose the transformation process, making it highly computationally efficient. The EFT method adeptly captures the evolving graph's structural and positional properties, making it effective for downstream tasks on evolving graphs. Hence, as a reference implementation, we develop a simple neural model induced with EFT for capturing evolving graph spectra. We empirically validate our theoretical findings on a number of large-scale and standard temporal graph benchmarks and demonstrate that our model achieves state-of-the-art performance.

Graph neural networks have shown significant success in the field of graph representation learning. Graph convolutions perform neighborhood aggregation and represent one of the most important graph operations. Nevertheless, one layer of these neighborhood aggregation methods only consider immediate neighbors, and the performance decreases when going deeper to enable larger receptive fields. Several recent studies attribute this performance deterioration to the over-smoothing issue, which states that repeated propagation makes node representations of different classes indistinguishable. In this work, we study this observation systematically and develop new insights towards deeper graph neural networks. First, we provide a systematical analysis on this issue and argue that the key factor compromising the performance significantly is the entanglement of representation transformation and propagation in current graph convolution operations. After decoupling these two operations, deeper graph neural networks can be used to learn graph node representations from larger receptive fields. We further provide a theoretical analysis of the above observation when building very deep models, which can serve as a rigorous and gentle description of the over-smoothing issue. Based on our theoretical and empirical analysis, we propose Deep Adaptive Graph Neural Network (DAGNN) to adaptively incorporate information from large receptive fields. A set of experiments on citation, co-authorship, and co-purchase datasets have confirmed our analysis and insights and demonstrated the superiority of our proposed methods.

Text-attributed graphs have recently garnered significant attention due to their wide range of applications in web domains. Existing methodologies employ word embedding models for acquiring text representations as node features, which are subsequently fed into Graph Neural Networks (GNNs) for training. Recently, the advent of Large Language Models (LLMs) has introduced their powerful capabilities in information retrieval and text generation, which can greatly enhance the text attributes of graph data. Furthermore, the acquisition and labeling of extensive datasets are both costly and time-consuming endeavors. Consequently, few-shot learning has emerged as a crucial problem in the context of graph learning tasks. In order to tackle this challenge, we propose a lightweight paradigm called LLM4NG, which adopts a plug-and-play approach to empower text-attributed graphs through node generation using LLMs. Specifically, we utilize LLMs to extract semantic information from the labels and generate samples that belong to these categories as exemplars. Subsequently, we employ an edge predictor to capture the structural information inherent in the raw dataset and integrate the newly generated samples into the original graph. This approach harnesses LLMs for enhancing class-level information and seamlessly introduces labeled nodes and edges without modifying the raw dataset, thereby facilitating the node classification task in few-shot scenarios. Extensive experiments demonstrate the outstanding performance of our proposed paradigm, particularly in low-shot scenarios. For instance, in the 1-shot setting of the ogbn-arxiv dataset, LLM4NG achieves a 76% improvement over the baseline model.

Can we model non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The non-Euclidean property have posed a long term challenge in graph modeling. Despite recent GNN and Graphformer efforts encoding graphs as Euclidean vectors, recovering original graph from the vectors remains a challenge. We introduce GraphsGPT, featuring a Graph2Seq encoder that transforms non-Euclidean graphs into learnable graph words in a Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from graph words to ensure information equivalence. We pretrain GraphsGPT on 100M molecules and yield some interesting findings: (1) Pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on 8/9 graph classification and regression tasks. (2) Pretrained GraphGPT serves as a strong graph generator, demonstrated by its ability to perform both unconditional and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known non-Euclidean challenge. (4) Our proposed novel edge-centric GPT pretraining task is effective in graph fields, underscoring its success in both representation and generation.

Understanding a visual scene goes beyond recognizing individual objects in isolation. Relationships between objects also constitute rich semantic information about the scene. In this work, we explicitly model the objects and their relationships using scene graphs, a visually-grounded graphical structure of an image. We propose a novel end-to-end model that generates such structured scene representation from an input image. The model solves the scene graph inference problem using standard RNNs and learns to iteratively improves its predictions via message passing. Our joint inference model can take advantage of contextual cues to make better predictions on objects and their relationships. The experiments show that our model significantly outperforms previous methods for generating scene graphs using Visual Genome dataset and inferring support relations with NYU Depth v2 dataset.

Graph representation learning resurges as a trending research subject owing to the widespread use of deep learning for Euclidean data, which inspire various creative designs of neural networks in the non-Euclidean domain, particularly graphs. With the success of these graph neural networks (GNN) in the static setting, we approach further practical scenarios where the graph dynamically evolves. Existing approaches typically resort to node embeddings and use a recurrent neural network (RNN, broadly speaking) to regulate the embeddings and learn the temporal dynamics. These methods require the knowledge of a node in the full time span (including both training and testing) and are less applicable to the frequent change of the node set. In some extreme scenarios, the node sets at different time steps may completely differ. To resolve this challenge, we propose EvolveGCN, which adapts the graph convolutional network (GCN) model along the temporal dimension without resorting to node embeddings. The proposed approach captures the dynamism of the graph sequence through using an RNN to evolve the GCN parameters. Two architectures are considered for the parameter evolution. We evaluate the proposed approach on tasks including link prediction, edge classification, and node classification. The experimental results indicate a generally higher performance of EvolveGCN compared with related approaches. The code is available at https://github.com/IBM/EvolveGCN.

Motivated by the recent progress in generative models, we introduce a model that generates images from natural language descriptions. The proposed model iteratively draws patches on a canvas, while attending to the relevant words in the description. After training on Microsoft COCO, we compare our model with several baseline generative models on image generation and retrieval tasks. We demonstrate that our model produces higher quality samples than other approaches and generates images with novel scene compositions corresponding to previously unseen captions in the dataset.

Recent prevailing works on graph machine learning typically follow a similar methodology that involves designing advanced variants of graph neural networks (GNNs) to maintain the superior performance of GNNs on different graphs. In this paper, we aim to streamline the GNN design process and leverage the advantages of Large Language Models (LLMs) to improve the performance of GNNs on downstream tasks. We formulate a new paradigm, coined "LLMs-as-Consultants," which integrates LLMs with GNNs in an interactive manner. A framework named LOGIN (LLM Consulted GNN training) is instantiated, empowering the interactive utilization of LLMs within the GNN training process. First, we attentively craft concise prompts for spotted nodes, carrying comprehensive semantic and topological information, and serving as input to LLMs. Second, we refine GNNs by devising a complementary coping mechanism that utilizes the responses from LLMs, depending on their correctness. We empirically evaluate the effectiveness of LOGIN on node classification tasks across both homophilic and heterophilic graphs. The results illustrate that even basic GNN architectures, when employed within the proposed LLMs-as-Consultants paradigm, can achieve comparable performance to advanced GNNs with intricate designs. Our codes are available at https://github.com/QiaoYRan/LOGIN.

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.

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

Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.

Graph representation learning has emerged as a powerful technique for addressing real-world problems. Various downstream graph learning tasks have benefited from its recent developments, such as node classification, similarity search, and graph classification. However, prior arts on graph representation learning focus on domain specific problems and train a dedicated model for each graph dataset, which is usually non-transferable to out-of-domain data. Inspired by the recent advances in pre-training from natural language processing and computer vision, we design Graph Contrastive Coding (GCC) -- a self-supervised graph neural network pre-training framework -- to capture the universal network topological properties across multiple networks. We design GCC's pre-training task as subgraph instance discrimination in and across networks and leverage contrastive learning to empower graph neural networks to learn the intrinsic and transferable structural representations. We conduct extensive experiments on three graph learning tasks and ten graph datasets. The results show that GCC pre-trained on a collection of diverse datasets can achieve competitive or better performance to its task-specific and trained-from-scratch counterparts. This suggests that the pre-training and fine-tuning paradigm presents great potential for graph representation learning.

Foundation models in language and vision have the ability to run inference on any textual and visual inputs thanks to the transferable representations such as a vocabulary of tokens in language. Knowledge graphs (KGs) have different entity and relation vocabularies that generally do not overlap. The key challenge of designing foundation models on KGs is to learn such transferable representations that enable inference on any graph with arbitrary entity and relation vocabularies. In this work, we make a step towards such foundation models and present ULTRA, an approach for learning universal and transferable graph representations. ULTRA builds relational representations as a function conditioned on their interactions. Such a conditioning strategy allows a pre-trained ULTRA model to inductively generalize to any unseen KG with any relation vocabulary and to be fine-tuned on any graph. Conducting link prediction experiments on 57 different KGs, we find that the zero-shot inductive inference performance of a single pre-trained ULTRA model on unseen graphs of various sizes is often on par or better than strong baselines trained on specific graphs. Fine-tuning further boosts the performance.

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

Node features and structural information of a graph are both crucial for semi-supervised node classification problems. A variety of graph neural network (GNN) based approaches have been proposed to tackle these problems, which typically determine output labels through feature aggregation. This can be problematic, as it implies conditional independence of output nodes given hidden representations, despite their direct connections in the graph. To learn the direct influence among output nodes in a graph, we propose the Explicit Pairwise Factorized Graph Neural Network (EPFGNN), which models the whole graph as a partially observed Markov Random Field. It contains explicit pairwise factors to model output-output relations and uses a GNN backbone to model input-output relations. To balance model complexity and expressivity, the pairwise factors have a shared component and a separate scaling coefficient for each edge. We apply the EM algorithm to train our model, and utilize a star-shaped piecewise likelihood for the tractable surrogate objective. We conduct experiments on various datasets, which shows that our model can effectively improve the performance for semi-supervised node classification on graphs.

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable k-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

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.

Existing neural ranking models follow the text matching paradigm, where document-to-query relevance is estimated through predicting the matching score. Drawing from the rich literature of classical generative retrieval models, we introduce and formalize the paradigm of deep generative retrieval models defined via the cumulative probabilities of generating query terms. This paradigm offers a grounded probabilistic view on relevance estimation while still enabling the use of modern neural architectures. In contrast to the matching paradigm, the probabilistic nature of generative rankers readily offers a fine-grained measure of uncertainty. We adopt several current neural generative models in our framework and introduce a novel generative ranker (T-PGN), which combines the encoding capacity of Transformers with the Pointer Generator Network model. We conduct an extensive set of evaluation experiments on passage retrieval, leveraging the MS MARCO Passage Re-ranking and TREC Deep Learning 2019 Passage Re-ranking collections. Our results show the significantly higher performance of the T-PGN model when compared with other generative models. Lastly, we demonstrate that exploiting the uncertainty information of deep generative rankers opens new perspectives to query/collection understanding, and significantly improves the cut-off prediction task.

Recommender Systems are built to retrieve relevant items to satisfy users' information needs. The candidate corpus usually consists of a finite set of items that are ready to be served, such as videos, products, or articles. With recent advances in Generative AI such as GPT and Diffusion models, a new form of recommendation task is yet to be explored where items are to be created by generative models with personalized prompts. Taking image generation as an example, with a single prompt from the user and access to a generative model, it is possible to generate hundreds of new images in a few minutes. How shall we attain personalization in the presence of "infinite" items? In this preliminary study, we propose a two-stage framework, namely Prompt-Model Retrieval and Generated Item Ranking, to approach this new task formulation. We release GEMRec-18K, a prompt-model interaction dataset with 18K images generated by 200 publicly-available generative models paired with a diverse set of 90 textual prompts. Our findings demonstrate the promise of generative model recommendation as a novel personalization problem and the limitations of existing evaluation metrics. We highlight future directions for the RecSys community to advance towards generative recommender systems. Our code and dataset are available at https://github.com/MAPS-research/GEMRec.

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.

Recent advances in Graph Neural Networks (GNNs) and Graph Transformers (GTs) have been driven by innovations in architectures and Positional Encodings (PEs), which are critical for augmenting node features and capturing graph topology. PEs are essential for GTs, where topological information would otherwise be lost without message-passing. However, PEs are often tested alongside novel architectures, making it difficult to isolate their effect on established models. To address this, we present a comprehensive benchmark of PEs in a unified framework that includes both message-passing GNNs and GTs. We also establish theoretical connections between MPNNs and GTs and introduce a sparsified GRIT attention mechanism to examine the influence of global connectivity. Our findings demonstrate that previously untested combinations of GNN architectures and PEs can outperform existing methods and offer a more comprehensive picture of the state-of-the-art. To support future research and experimentation in our framework, we make the code publicly available.

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/.

Generative models for Information Retrieval, where ranking of documents is viewed as the task of generating a query from a document's language model, were very successful in various IR tasks in the past. However, with the advent of modern deep neural networks, attention has shifted to discriminative ranking functions that model the semantic similarity of documents and queries instead. Recently, deep generative models such as GPT2 and BART have been shown to be excellent text generators, but their effectiveness as rankers have not been demonstrated yet. In this work, we revisit the generative framework for information retrieval and show that our generative approaches are as effective as state-of-the-art semantic similarity-based discriminative models for the answer selection task. Additionally, we demonstrate the effectiveness of unlikelihood losses for IR.

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.

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

Generative flow networks (GFlowNets) are sequential sampling models trained to match a given distribution. GFlowNets have been successfully applied to various structured object generation tasks, sampling a diverse set of high-reward objects quickly. We propose expected flow networks (EFlowNets), which extend GFlowNets to stochastic environments. We show that EFlowNets outperform other GFlowNet formulations in stochastic tasks such as protein design. We then extend the concept of EFlowNets to adversarial environments, proposing adversarial flow networks (AFlowNets) for two-player zero-sum games. We show that AFlowNets learn to find above 80% of optimal moves in Connect-4 via self-play and outperform AlphaZero in tournaments.

In this study, we focus on the graph representation learning (a.k.a. network embedding) in attributed graphs. Different from existing embedding methods that treat the incorporation of graph structure and semantic as the simple combination of two optimization objectives, we propose a novel semantic graph representation (SGR) method to formulate the joint optimization of the two heterogeneous sources into a common high-order proximity based framework. Concretely, we first construct an auxiliary weighted graph, where the complex homogeneous and heterogeneous relations among nodes and attributes in the original graph are comprehensively encoded. Conventional embedding methods that consider high-order topology proximities can then be easily applied to the newly constructed graph to learn the representations of both node and attribute while capturing the nonlinear high-order intrinsic correlation inside or among graph structure and semantic. The learned attribute embeddings can also effectively support some semantic-oriented inference tasks (e.g., semantic community detection), helping to reveal the graph's deep semantic. The effectiveness of SGR is further verified on a series of real graphs, where it achieves impressive performance over other baselines.

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

The field of deep generative modeling has grown rapidly and consistently over the years. With the availability of massive amounts of training data coupled with advances in scalable unsupervised learning paradigms, recent large-scale generative models show tremendous promise in synthesizing high-resolution images and text, as well as structured data such as videos and molecules. However, we argue that current large-scale generative AI models do not sufficiently address several fundamental issues that hinder their widespread adoption across domains. In this work, we aim to identify key unresolved challenges in modern generative AI paradigms that should be tackled to further enhance their capabilities, versatility, and reliability. By identifying these challenges, we aim to provide researchers with valuable insights for exploring fruitful research directions, thereby fostering the development of more robust and accessible generative AI solutions.

Large Language Models (LLMs) have gained the ability to assimilate human knowledge and facilitate natural language interactions with both humans and other LLMs. However, despite their impressive achievements, LLMs have not made significant advancements in the realm of graph machine learning. This limitation arises because graphs encapsulate distinct relational data, making it challenging to transform them into natural language that LLMs understand. In this paper, we bridge this gap with a novel framework, GraphText, that translates graphs into natural language. GraphText derives a graph-syntax tree for each graph that encapsulates both the node attributes and inter-node relationships. Traversal of the tree yields a graph text sequence, which is then processed by an LLM to treat graph tasks as text generation tasks. Notably, GraphText offers multiple advantages. It introduces training-free graph reasoning: even without training on graph data, GraphText with ChatGPT can achieve on par with, or even surpassing, the performance of supervised-trained graph neural networks through in-context learning (ICL). Furthermore, GraphText paves the way for interactive graph reasoning, allowing both humans and LLMs to communicate with the model seamlessly using natural language. These capabilities underscore the vast, yet-to-be-explored potential of LLMs in the domain of graph machine learning.

This paper demonstrates how to use generative models trained for image synthesis as tools for visual data mining. Our insight is that since contemporary generative models learn an accurate representation of their training data, we can use them to summarize the data by mining for visual patterns. Concretely, we show that after finetuning conditional diffusion models to synthesize images from a specific dataset, we can use these models to define a typicality measure on that dataset. This measure assesses how typical visual elements are for different data labels, such as geographic location, time stamps, semantic labels, or even the presence of a disease. This analysis-by-synthesis approach to data mining has two key advantages. First, it scales much better than traditional correspondence-based approaches since it does not require explicitly comparing all pairs of visual elements. Second, while most previous works on visual data mining focus on a single dataset, our approach works on diverse datasets in terms of content and scale, including a historical car dataset, a historical face dataset, a large worldwide street-view dataset, and an even larger scene dataset. Furthermore, our approach allows for translating visual elements across class labels and analyzing consistent changes.

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

Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.

Graph neural networks (GNNs) have been successfully applied to learning representation on graphs in many relational tasks. Recently, researchers study neural architecture search (NAS) to reduce the dependence of human expertise and explore better GNN architectures, but they over-emphasize entity features and ignore latent relation information concealed in the edges. To solve this problem, we incorporate edge features into graph search space and propose Edge-featured Graph Neural Architecture Search to find the optimal GNN architecture. Specifically, we design rich entity and edge updating operations to learn high-order representations, which convey more generic message passing mechanisms. Moreover, the architecture topology in our search space allows to explore complex feature dependence of both entities and edges, which can be efficiently optimized by differentiable search strategy. Experiments at three graph tasks on six datasets show EGNAS can search better GNNs with higher performance than current state-of-the-art human-designed and searched-based GNNs.

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

Graph embedding methods produce unsupervised node features from graphs that can then be used for a variety of machine learning tasks. Modern graphs, particularly in industrial applications, contain billions of nodes and trillions of edges, which exceeds the capability of existing embedding systems. We present PyTorch-BigGraph (PBG), an embedding system that incorporates several modifications to traditional multi-relation embedding systems that allow it to scale to graphs with billions of nodes and trillions of edges. PBG uses graph partitioning to train arbitrarily large embeddings on either a single machine or in a distributed environment. We demonstrate comparable performance with existing embedding systems on common benchmarks, while allowing for scaling to arbitrarily large graphs and parallelization on multiple machines. We train and evaluate embeddings on several large social network graphs as well as the full Freebase dataset, which contains over 100 million nodes and 2 billion edges.

Graph transformers (GTs) have emerged as a promising architecture that is theoretically more expressive than message-passing graph neural networks (GNNs). However, typical GT models have at least quadratic complexity and thus cannot scale to large graphs. While there are several linear GTs recently proposed, they still lag behind GNN counterparts on several popular graph datasets, which poses a critical concern on their practical expressivity. To balance the trade-off between expressivity and scalability of GTs, we propose Polynormer, a polynomial-expressive GT model with linear complexity. Polynormer is built upon a novel base model that learns a high-degree polynomial on input features. To enable the base model permutation equivariant, we integrate it with graph topology and node features separately, resulting in local and global equivariant attention models. Consequently, Polynormer adopts a linear local-to-global attention scheme to learn high-degree equivariant polynomials whose coefficients are controlled by attention scores. Polynormer has been evaluated on 13 homophilic and heterophilic datasets, including large graphs with millions of nodes. Our extensive experiment results show that Polynormer outperforms state-of-the-art GNN and GT baselines on most datasets, even without the use of nonlinear activation functions.

Diffusion models have emerged as a powerful new family of deep generative models with record-breaking performance in many applications, including image synthesis, video generation, and molecule design. In this survey, we provide an overview of the rapidly expanding body of work on diffusion models, categorizing the research into three key areas: efficient sampling, improved likelihood estimation, and handling data with special structures. We also discuss the potential for combining diffusion models with other generative models for enhanced results. We further review the wide-ranging applications of diffusion models in fields spanning from computer vision, natural language generation, temporal data modeling, to interdisciplinary applications in other scientific disciplines. This survey aims to provide a contextualized, in-depth look at the state of diffusion models, identifying the key areas of focus and pointing to potential areas for further exploration. Github: https://github.com/YangLing0818/Diffusion-Models-Papers-Survey-Taxonomy.

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

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

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Graph Neural Networks (GNNs) have advanced graph structure understanding via recursive information exchange and aggregation among graph nodes. To improve model robustness, self-supervised learning (SSL) has emerged as a promising approach for data augmentation. However, existing methods for generating pre-trained graph embeddings often rely on fine-tuning with specific downstream task labels, which limits their usability in scenarios where labeled data is scarce or unavailable. To address this, our research focuses on advancing the generalization capabilities of graph models in challenging zero-shot learning scenarios. Inspired by the success of large language models (LLMs), we aim to develop a graph-oriented LLM that can achieve high generalization across diverse downstream datasets and tasks, even without any information available from the downstream graph data. In this work, we present the GraphGPT framework that aligns LLMs with graph structural knowledge with a graph instruction tuning paradigm. Our framework incorporates a text-graph grounding component to establish a connection between textual information and graph structures. Additionally, we propose a dual-stage instruction tuning paradigm, accompanied by a lightweight graph-text alignment projector. This paradigm explores self-supervised graph structural signals and task-specific graph instructions, to guide LLMs in understanding complex graph structures and improving their adaptability across different downstream tasks. Our framework is evaluated on supervised and zero-shot graph learning tasks, demonstrating superior generalization and outperforming state-of-the-art baselines.

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 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.

Transformers were originally proposed as a sequence-to-sequence model for text but have become vital for a wide range of modalities, including images, audio, video, and undirected graphs. However, transformers for directed graphs are a surprisingly underexplored topic, despite their applicability to ubiquitous domains including source code and logic circuits. In this work, we propose two direction- and structure-aware positional encodings for directed graphs: (1) the eigenvectors of the Magnetic Laplacian - a direction-aware generalization of the combinatorial Laplacian; (2) directional random walk encodings. Empirically, we show that the extra directionality information is useful in various downstream tasks, including correctness testing of sorting networks and source code understanding. Together with a data-flow-centric graph construction, our model outperforms the prior state of the art on the Open Graph Benchmark Code2 relatively by 14.7%.

Graph autoencoders are efficient at embedding graph-based data sets. Most graph autoencoder architectures have shallow depths which limits their ability to capture meaningful relations between nodes separated by multi-hops. In this paper, we propose Residual Variational Graph Autoencoder, ResVGAE, a deep variational graph autoencoder model with multiple residual modules. We show that our multiple residual modules, a convolutional layer with residual connection, improve the average precision of the graph autoencoders. Experimental results suggest that our proposed model with residual modules outperforms the models without residual modules and achieves similar results when compared with other state-of-the-art methods.

Recently, there has been an increasing interest in (supervised) learning with graph data, especially using graph neural networks. However, the development of meaningful benchmark datasets and standardized evaluation procedures is lagging, consequently hindering advancements in this area. To address this, we introduce the TUDataset for graph classification and regression. The collection consists of over 120 datasets of varying sizes from a wide range of applications. We provide Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools. Here, we give an overview of the datasets, standardized evaluation procedures, and provide baseline experiments. All datasets are available at www.graphlearning.io. The experiments are fully reproducible from the code available at www.github.com/chrsmrrs/tudataset.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

The capability to learn latent representations plays a key role in the effectiveness of recent machine learning methods. An active frontier in representation learning is understanding representations for combinatorial structures which may not admit well-behaved local neighborhoods or distance functions. For example, for polygons, slightly perturbing vertex locations might lead to significant changes in their combinatorial structure and may even lead to invalid polygons. In this paper, we investigate representations to capture the underlying combinatorial structures of polygons. Specifically, we study the open problem of Visibility Reconstruction: Given a visibility graph G, construct a polygon P whose visibility graph is G. We introduce VisDiff, a novel diffusion-based approach to reconstruct a polygon from its given visibility graph G. Our method first estimates the signed distance function (SDF) of P from G. Afterwards, it extracts ordered vertex locations that have the pairwise visibility relationship given by the edges of G. Our main insight is that going through the SDF significantly improves learning for reconstruction. In order to train VisDiff, we make two main contributions: (1) We design novel loss components for computing the visibility in a differentiable manner and (2) create a carefully curated dataset. We use this dataset to benchmark our method and achieve 21% improvement in F1-Score over standard methods. We also demonstrate effective generalization to out-of-distribution polygon types and show that learning a generative model allows us to sample the set of polygons with a given visibility graph. Finally, we extend our method to the related combinatorial problem of reconstruction from a triangulation. We achieve 95% classification accuracy of triangulation edges and a 4% improvement in Chamfer distance compared to current architectures.

Deep generative models are routinely used in generating samples from complex, high-dimensional distributions. Despite their apparent successes, their statistical properties are not well understood. A common assumption is that with enough training data and sufficiently large neural networks, deep generative model samples will have arbitrarily small errors in sampling from any continuous target distribution. We set up a unifying framework that debunks this belief. We demonstrate that broad classes of deep generative models, including variational autoencoders and generative adversarial networks, are not universal generators. Under the predominant case of Gaussian latent variables, these models can only generate concentrated samples that exhibit light tails. Using tools from concentration of measure and convex geometry, we give analogous results for more general log-concave and strongly log-concave latent variable distributions. We extend our results to diffusion models via a reduction argument. We use the Gromov--Levy inequality to give similar guarantees when the latent variables lie on manifolds with positive Ricci curvature. These results shed light on the limited capacity of common deep generative models to handle heavy tails. We illustrate the empirical relevance of our work with simulations and financial data.

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.

Large language models (LLMs) such as GPT-4 have emerged as frontrunners, showcasing unparalleled prowess in diverse applications, including answering queries, code generation, and more. Parallelly, graph-structured data, an intrinsic data type, is pervasive in real-world scenarios. Merging the capabilities of LLMs with graph-structured data has been a topic of keen interest. This paper bifurcates such integrations into two predominant categories. The first leverages LLMs for graph learning, where LLMs can not only augment existing graph algorithms but also stand as prediction models for various graph tasks. Conversely, the second category underscores the pivotal role of graphs in advancing LLMs. Mirroring human cognition, we solve complex tasks by adopting graphs in either reasoning or collaboration. Integrating with such structures can significantly boost the performance of LLMs in various complicated tasks. We also discuss and propose open questions for integrating LLMs with graph-structured data for the future direction of the field.

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

Search is an ability foundational in many important tasks, and recent studies have shown that large language models (LLMs) struggle to perform search robustly. It is unknown whether this inability is due to a lack of data, insufficient model parameters, or fundamental limitations of the transformer architecture. In this work, we use the foundational graph connectivity problem as a testbed to generate effectively limitless high-coverage data to train small transformers and test whether they can learn to perform search. We find that, when given the right training distribution, the transformer is able to learn to search. We analyze the algorithm that the transformer has learned through a novel mechanistic interpretability technique that enables us to extract the computation graph from the trained model. We find that for each vertex in the input graph, transformers compute the set of vertices reachable from that vertex. Each layer then progressively expands these sets, allowing the model to search over a number of vertices exponential in the number of layers. However, we find that as the input graph size increases, the transformer has greater difficulty in learning the task. This difficulty is not resolved even as the number of parameters is increased, suggesting that increasing model scale will not lead to robust search abilities. We also find that performing search in-context (i.e., chain-of-thought) does not resolve this inability to learn to search on larger graphs.

Graphs are a powerful tool for representing and analyzing complex relationships in real-world applications such as social networks, recommender systems, and computational finance. Reasoning on graphs is essential for drawing inferences about the relationships between entities in a complex system, and to identify hidden patterns and trends. Despite the remarkable progress in automated reasoning with natural text, reasoning on graphs with large language models (LLMs) remains an understudied problem. In this work, we perform the first comprehensive study of encoding graph-structured data as text for consumption by LLMs. We show that LLM performance on graph reasoning tasks varies on three fundamental levels: (1) the graph encoding method, (2) the nature of the graph task itself, and (3) interestingly, the very structure of the graph considered. These novel results provide valuable insight on strategies for encoding graphs as text. Using these insights we illustrate how the correct choice of encoders can boost performance on graph reasoning tasks inside LLMs by 4.8% to 61.8%, depending on the task.

As pretrained text-to-image diffusion models become increasingly powerful, recent efforts have been made to distill knowledge from these text-to-image pretrained models for optimizing a text-guided 3D model. Most of the existing methods generate a holistic 3D model from a plain text input. This can be problematic when the text describes a complex scene with multiple objects, because the vectorized text embeddings are inherently unable to capture a complex description with multiple entities and relationships. Holistic 3D modeling of the entire scene further prevents accurate grounding of text entities and concepts. To address this limitation, we propose GraphDreamer, a novel framework to generate compositional 3D scenes from scene graphs, where objects are represented as nodes and their interactions as edges. By exploiting node and edge information in scene graphs, our method makes better use of the pretrained text-to-image diffusion model and is able to fully disentangle different objects without image-level supervision. To facilitate modeling of object-wise relationships, we use signed distance fields as representation and impose a constraint to avoid inter-penetration of objects. To avoid manual scene graph creation, we design a text prompt for ChatGPT to generate scene graphs based on text inputs. We conduct both qualitative and quantitative experiments to validate the effectiveness of GraphDreamer in generating high-fidelity compositional 3D scenes with disentangled object entities.

Recent advancements in generative models have unlocked the capabilities to render photo-realistic data in a controllable fashion. Trained on the real data, these generative models are capable of producing realistic samples with minimal to no domain gap, as compared to the traditional graphics rendering. However, using the data generated using such models for training downstream tasks remains under-explored, mainly due to the lack of 3D consistent annotations. Moreover, controllable generative models are learned from massive data and their latent space is often too vast to obtain meaningful sample distributions for downstream task with limited generation. To overcome these challenges, we extract 3D consistent annotations from an existing controllable generative model, making the data useful for downstream tasks. Our experiments show competitive performance against state-of-the-art models using only generated synthetic data, demonstrating potential for solving downstream tasks. Project page: https://synth-forge.github.io

Scene graph generation (SGG) aims to predict graph-structured descriptions of input images, in the form of objects and relationships between them. This task is becoming increasingly useful for progress at the interface of vision and language. Here, it is important - yet challenging - to perform well on novel (zero-shot) or rare (few-shot) compositions of objects and relationships. In this paper, we identify two key issues that limit such generalization. Firstly, we show that the standard loss used in this task is unintentionally a function of scene graph density. This leads to the neglect of individual edges in large sparse graphs during training, even though these contain diverse few-shot examples that are important for generalization. Secondly, the frequency of relationships can create a strong bias in this task, such that a blind model predicting the most frequent relationship achieves good performance. Consequently, some state-of-the-art models exploit this bias to improve results. We show that such models can suffer the most in their ability to generalize to rare compositions, evaluating two different models on the Visual Genome dataset and its more recent, improved version, GQA. To address these issues, we introduce a density-normalized edge loss, which provides more than a two-fold improvement in certain generalization metrics. Compared to other works in this direction, our enhancements require only a few lines of code and no added computational cost. We also highlight the difficulty of accurately evaluating models using existing metrics, especially on zero/few shots, and introduce a novel weighted metric.

Graph neural networks (GNNs) are the most widely adopted model in graph-structured data oriented learning and representation. Despite their extraordinary success in real-world applications, understanding their working mechanism by theory is still on primary stage. In this paper, we move towards this goal from the perspective of generalization. To be specific, we first establish high probability bounds of generalization gap and gradients in transductive learning with consideration of stochastic optimization. After that, we provide high probability bounds of generalization gap for popular GNNs. The theoretical results reveal the architecture specific factors affecting the generalization gap. Experimental results on benchmark datasets show the consistency between theoretical results and empirical evidence. Our results provide new insights in understanding the generalization of GNNs.