Daily Papers

Task-oriented dialogue systems typically rely on large amounts of high-quality training data or require complex handcrafted rules. However, existing datasets are often limited in size considering the complexity of the dialogues. Additionally, conventional training signal inference is not suitable for non-deterministic agent behaviour, i.e. considering multiple actions as valid in identical dialogue states. We propose the Conversation Graph (ConvGraph), a graph-based representation of dialogues that can be exploited for data augmentation, multi-reference training and evaluation of non-deterministic agents. ConvGraph generates novel dialogue paths to augment data volume and diversity. Intrinsic and extrinsic evaluation across three datasets shows that data augmentation and/or multi-reference training with ConvGraph can improve dialogue success rates by up to 6.4%.

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

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

Graph representation learning is fundamental for analyzing graph-structured data. Exploring invariant graph representations remains a challenge for most existing graph representation learning methods. In this paper, we propose a cross-view graph consistency learning (CGCL) method that learns invariant graph representations for link prediction. First, two complementary augmented views are derived from an incomplete graph structure through a bidirectional graph structure augmentation scheme. This augmentation scheme mitigates the potential information loss that is commonly associated with various data augmentation techniques involving raw graph data, such as edge perturbation, node removal, and attribute masking. Second, we propose a CGCL model that can learn invariant graph representations. A cross-view training scheme is proposed to train the proposed CGCL model. This scheme attempts to maximize the consistency information between one augmented view and the graph structure reconstructed from the other augmented view. Furthermore, we offer a comprehensive theoretical CGCL analysis. This paper empirically and experimentally demonstrates the effectiveness of the proposed CGCL method, achieving competitive results on graph datasets in comparisons with several state-of-the-art algorithms.

The rapid growth of deep learning has driven exponential increases in model parameters and computational demands. NVIDIA GPUs and their CUDA-based software ecosystem provide robust support for parallel computing, significantly alleviating computational bottlenecks. Meanwhile, due to the cultivation of user programming habits and the high performance of GPUs, the CUDA ecosystem has established a dominant position in the field of parallel software. This dominance requires other hardware platforms to support CUDA-based software with performance portability. However, translating CUDA code to other platforms poses significant challenges due to differences in parallel programming paradigms and hardware architectures. Existing approaches rely on language extensions, domain-specific languages (DSLs), or compilers but face limitations in workload coverage and generalizability. Moreover, these methods often incur substantial development costs. Recently, LLMs have demonstrated extraordinary potential in various vertical domains, especially in code-related tasks. However, the performance of existing LLMs in CUDA transpilation, particularly for high-performance code, remains suboptimal. To address these challenges, we propose a novel framework for generating high-performance CUDA and corresponding platform code pairs, leveraging AI compiler and automatic optimization technology. We further enhance the framework with a graph-based data augmentation method and introduce HPCTransEval, a benchmark for evaluating LLM performance on CUDA transpilation. We conduct experiments using CUDA-to-CPU transpilation as a case study on leading LLMs. The speedup ratio of the CPU operators has an average improvemnet of 43.8\%, highlighting the potential of LLMs to address compatibility challenges within the CUDA ecosystem. Our code is available at https://github.com/PJLAB-CHIP/HPCTransCompile.

Contrastive learning is an effective unsupervised method in graph representation learning, and the key component of contrastive learning lies in the construction of positive and negative samples. Previous methods usually utilize the proximity of nodes in the graph as the principle. Recently, the data-augmentation-based contrastive learning method has advanced to show great power in the visual domain, and some works extended this method from images to graphs. However, unlike the data augmentation on images, the data augmentation on graphs is far less intuitive and much harder to provide high-quality contrastive samples, which leaves much space for improvement. In this work, by introducing an adversarial graph view for data augmentation, we propose a simple but effective method, Adversarial Graph Contrastive Learning (ARIEL), to extract informative contrastive samples within reasonable constraints. We develop a new technique called information regularization for stable training and use subgraph sampling for scalability. We generalize our method from node-level contrastive learning to the graph level by treating each graph instance as a super-node. ARIEL consistently outperforms the current graph contrastive learning methods for both node-level and graph-level classification tasks on real-world datasets. We further demonstrate that ARIEL is more robust in the face of adversarial attacks.

Tables are widely used in documents because of their compact and structured representation of information. In particular, in scientific papers, tables can sum up novel discoveries and summarize experimental results, making the research comparable and easily understandable by scholars. Since the layout of tables is highly variable, it would be useful to interpret their content and classify them into categories. This could be helpful to directly extract information from scientific papers, for instance comparing performance of some models given their paper result tables. In this work, we address the classification of tables using a Graph Neural Network, exploiting the table structure for the message passing algorithm in use. We evaluate our model on a subset of the Tab2Know dataset. Since it contains few examples manually annotated, we propose data augmentation techniques directly on the table graph structures. We achieve promising preliminary results, proposing a data augmentation method suitable for graph-based table representation.

Data augmentation has been widely used in machine learning for natural language processing and computer vision tasks to improve model performance. However, little research has studied data augmentation on graph neural networks, particularly using augmentation at both train- and test-time. Inspired by the success of augmentation in other domains, we have designed a method for social influence prediction using graph neural networks with train- and test-time augmentation, which can effectively generate multiple augmented graphs for social networks by utilising a variational graph autoencoder in both scenarios. We have evaluated the performance of our method on predicting user influence on multiple social network datasets. Our experimental results show that our end-to-end approach, which jointly trains a graph autoencoder and social influence behaviour classification network, can outperform state-of-the-art approaches, demonstrating the effectiveness of train- and test-time augmentation on graph neural networks for social influence prediction. We observe that this is particularly effective on smaller graphs.

Generalizable, transferrable, and robust representation learning on graph-structured data remains a challenge for current graph neural networks (GNNs). Unlike what has been developed for convolutional neural networks (CNNs) for image data, self-supervised learning and pre-training are less explored for GNNs. In this paper, we propose a graph contrastive learning (GraphCL) framework for learning unsupervised representations of graph data. We first design four types of graph augmentations to incorporate various priors. We then systematically study the impact of various combinations of graph augmentations on multiple datasets, in four different settings: semi-supervised, unsupervised, and transfer learning as well as adversarial attacks. The results show that, even without tuning augmentation extents nor using sophisticated GNN architectures, our GraphCL framework can produce graph representations of similar or better generalizability, transferrability, and robustness compared to state-of-the-art methods. We also investigate the impact of parameterized graph augmentation extents and patterns, and observe further performance gains in preliminary experiments. Our codes are available at https://github.com/Shen-Lab/GraphCL.

In the face of the deep learning model's vulnerability to domain shift, source-free domain adaptation (SFDA) methods have been proposed to adapt models to new, unseen target domains without requiring access to source domain data. Although the potential benefits of applying data augmentation to SFDA are attractive, several challenges arise such as the dependence on prior knowledge of class-preserving transformations and the increase in memory and computational requirements. In this paper, we propose Source-free Domain Adaptation Through the Lens of Data Augmentation (SF(DA)^2), a novel approach that leverages the benefits of data augmentation without suffering from these challenges. We construct an augmentation graph in the feature space of the pretrained model using the neighbor relationships between target features and propose spectral neighborhood clustering to identify partitions in the prediction space. Furthermore, we propose implicit feature augmentation and feature disentanglement as regularization loss functions that effectively utilize class semantic information within the feature space. These regularizers simulate the inclusion of an unlimited number of augmented target features into the augmentation graph while minimizing computational and memory demands. Our method shows superior adaptation performance in SFDA scenarios, including 2D image and 3D point cloud datasets and a highly imbalanced dataset.

Graph Neural Networks (GNNs) have achieved remarkable performance on graph-based tasks. The key idea for GNNs is to obtain informative representation through aggregating information from local neighborhoods. However, it remains an open question whether the neighborhood information is adequately aggregated for learning representations of nodes with few neighbors. To address this, we propose a simple and efficient data augmentation strategy, local augmentation, to learn the distribution of the node features of the neighbors conditioned on the central node's feature and enhance GNN's expressive power with generated features. Local augmentation is a general framework that can be applied to any GNN model in a plug-and-play manner. It samples feature vectors associated with each node from the learned conditional distribution as additional input for the backbone model at each training iteration. Extensive experiments and analyses show that local augmentation consistently yields performance improvement when applied to various GNN architectures across a diverse set of benchmarks. For example, experiments show that plugging in local augmentation to GCN and GAT improves by an average of 3.4\% and 1.6\% in terms of test accuracy on Cora, Citeseer, and Pubmed. Besides, our experimental results on large graphs (OGB) show that our model consistently improves performance over backbones. Code is available at https://github.com/SongtaoLiu0823/LAGNN.

Pre-trained large language model (LLM) is under exploration to perform NLP tasks that may require logical reasoning. Logic-driven data augmentation for representation learning has been shown to improve the performance of tasks requiring logical reasoning, but most of these data rely on designed templates and therefore lack generalization. In this regard, we propose an AMR-based logical equivalence-driven data augmentation method (AMR-LE) for generating logically equivalent data. Specifically, we first parse a text into the form of an AMR graph, next apply four logical equivalence laws (contraposition, double negation, commutative and implication laws) on the AMR graph to construct a logically equivalent/inequivalent AMR graph, and then convert it into a logically equivalent/inequivalent sentence. To help the model to better learn these logical equivalence laws, we propose a logical equivalence-driven contrastive learning training paradigm, which aims to distinguish the difference between logical equivalence and inequivalence. Our AMR-LE (Ensemble) achieves #2 on the ReClor leaderboard https://eval.ai/web/challenges/challenge-page/503/leaderboard/1347 . Our model shows better performance on seven downstream tasks, including ReClor, LogiQA, MNLI, MRPC, RTE, QNLI, and QQP. The source code and dataset are public at https://github.com/Strong-AI-Lab/Logical-Equivalence-driven-AMR-Data-Augmentation-for-Representation-Learning .

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

This paper presents a novel approach to representation learning in recommender systems by integrating generative self-supervised learning with graph transformer architecture. We highlight the importance of high-quality data augmentation with relevant self-supervised pretext tasks for improving performance. Towards this end, we propose a new approach that automates the self-supervision augmentation process through a rationale-aware generative SSL that distills informative user-item interaction patterns. The proposed recommender with Graph TransFormer (GFormer) that offers parameterized collaborative rationale discovery for selective augmentation while preserving global-aware user-item relationships. In GFormer, we allow the rationale-aware SSL to inspire graph collaborative filtering with task-adaptive invariant rationalization in graph transformer. The experimental results reveal that our GFormer has the capability to consistently improve the performance over baselines on different datasets. Several in-depth experiments further investigate the invariant rationale-aware augmentation from various aspects. The source code for this work is publicly available at: https://github.com/HKUDS/GFormer.

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.

In diffraction-based crystal structure analysis, thermal ellipsoids, quantified via Anisotropic Displacement Parameters (ADPs), are critical yet challenging to determine. ADPs capture atomic vibrations, reflecting thermal and structural properties, but traditional computation is often expensive. This paper introduces CartNet, a novel graph neural network (GNN) for efficiently predicting crystal properties by encoding atomic geometry into Cartesian coordinates alongside the crystal temperature. CartNet integrates a neighbour equalization technique to emphasize covalent and contact interactions, and a Cholesky-based head to ensure valid ADP predictions. We also propose a rotational SO(3) data augmentation strategy during training to handle unseen orientations. An ADP dataset with over 200,000 experimental crystal structures from the Cambridge Structural Database (CSD) was curated to validate the approach. CartNet significantly reduces computational costs and outperforms existing methods in ADP prediction by 10.87%, while delivering a 34.77% improvement over theoretical approaches. We further evaluated CartNet on other datasets covering formation energy, band gap, total energy, energy above the convex hull, bulk moduli, and shear moduli, achieving 7.71% better results on the Jarvis Dataset and 13.16% on the Materials Project Dataset. These gains establish CartNet as a state-of-the-art solution for diverse crystal property predictions. Project website and online demo: https://www.ee.ub.edu/cartnet

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

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.

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.

Cortical surface registration plays a crucial role in aligning cortical functional and anatomical features across individuals. However, conventional registration algorithms are computationally inefficient. Recently, learning-based registration algorithms have emerged as a promising solution, significantly improving processing efficiency. Nonetheless, there remains a gap in the development of a learning-based method that exceeds the state-of-the-art conventional methods simultaneously in computational efficiency, registration accuracy, and distortion control, despite the theoretically greater representational capabilities of deep learning approaches. To address the challenge, we present SUGAR, a unified unsupervised deep-learning framework for both rigid and non-rigid registration. SUGAR incorporates a U-Net-based spherical graph attention network and leverages the Euler angle representation for deformation. In addition to the similarity loss, we introduce fold and multiple distortion losses, to preserve topology and minimize various types of distortions. Furthermore, we propose a data augmentation strategy specifically tailored for spherical surface registration, enhancing the registration performance. Through extensive evaluation involving over 10,000 scans from 7 diverse datasets, we showed that our framework exhibits comparable or superior registration performance in accuracy, distortion, and test-retest reliability compared to conventional and learning-based methods. Additionally, SUGAR achieves remarkable sub-second processing times, offering a notable speed-up of approximately 12,000 times in registering 9,000 subjects from the UK Biobank dataset in just 32 minutes. This combination of high registration performance and accelerated processing time may greatly benefit large-scale neuroimaging studies.

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.

Automated detection of vulnerabilities in source code is an essential cybersecurity challenge, underpinning trust in digital systems and services. Graph Neural Networks (GNNs) have emerged as a promising approach as they can learn structural and logical code relationships in a data-driven manner. However, their performance is severely constrained by training data imbalances and label noise. GNNs often learn 'spurious' correlations from superficial code similarities, producing detectors that fail to generalize well to unseen real-world data. In this work, we propose a unified framework for robust and interpretable vulnerability detection, called VISION, to mitigate spurious correlations by systematically augmenting a counterfactual training dataset. Counterfactuals are samples with minimal semantic modifications but opposite labels. Our framework includes: (i) generating counterfactuals by prompting a Large Language Model (LLM); (ii) targeted GNN training on paired code examples with opposite labels; and (iii) graph-based interpretability to identify the crucial code statements relevant for vulnerability predictions while ignoring spurious ones. We find that VISION reduces spurious learning and enables more robust, generalizable detection, improving overall accuracy (from 51.8% to 97.8%), pairwise contrast accuracy (from 4.5% to 95.8%), and worst-group accuracy (from 0.7% to 85.5%) on the Common Weakness Enumeration (CWE)-20 vulnerability. We further demonstrate gains using proposed metrics: intra-class attribution variance, inter-class attribution distance, and node score dependency. We also release CWE-20-CFA, a benchmark of 27,556 functions (real and counterfactual) from the high-impact CWE-20 category. Finally, VISION advances transparent and trustworthy AI-based cybersecurity systems through interactive visualization for human-in-the-loop analysis.

Graph neural network (GNN) is a powerful learning approach for graph-based recommender systems. Recently, GNNs integrated with contrastive learning have shown superior performance in recommendation with their data augmentation schemes, aiming at dealing with highly sparse data. Despite their success, most existing graph contrastive learning methods either perform stochastic augmentation (e.g., node/edge perturbation) on the user-item interaction graph, or rely on the heuristic-based augmentation techniques (e.g., user clustering) for generating contrastive views. We argue that these methods cannot well preserve the intrinsic semantic structures and are easily biased by the noise perturbation. In this paper, we propose a simple yet effective graph contrastive learning paradigm LightGCL that mitigates these issues impairing the generality and robustness of CL-based recommenders. Our model exclusively utilizes singular value decomposition for contrastive augmentation, which enables the unconstrained structural refinement with global collaborative relation modeling. Experiments conducted on several benchmark datasets demonstrate the significant improvement in performance of our model over the state-of-the-arts. Further analyses demonstrate the superiority of LightGCL's robustness against data sparsity and popularity bias. The source code of our model is available at https://github.com/HKUDS/LightGCL.

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.

Heterophilic Graph Neural Networks (HGNNs) have shown promising results for semi-supervised learning tasks on graphs. Notably, most real-world heterophilic graphs are composed of a mixture of nodes with different neighbor patterns, exhibiting local node-level homophilic and heterophilic structures. However, existing works are only devoted to designing better HGNN backbones or architectures for node classification tasks on heterophilic and homophilic graph benchmarks simultaneously, and their analyses of HGNN performance with respect to nodes are only based on the determined data distribution without exploring the effect caused by this structural difference between training and testing nodes. How to learn invariant node representations on heterophilic graphs to handle this structure difference or distribution shifts remains unexplored. In this paper, we first discuss the limitations of previous graph-based invariant learning methods from the perspective of data augmentation. Then, we propose HEI, a framework capable of generating invariant node representations through incorporating heterophily information to infer latent environments without augmentation, which are then used for invariant prediction, under heterophilic graph structure distribution shifts. We theoretically show that our proposed method can achieve guaranteed performance under heterophilic graph structure distribution shifts. Extensive experiments on various benchmarks and backbones can also demonstrate the effectiveness of our method compared with existing state-of-the-art baselines.

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

Learning-based visual localization methods that use scene coordinate regression (SCR) offer the advantage of smaller map sizes. However, on datasets with complex illumination changes or image-level ambiguities, it remains a less robust alternative to feature matching methods. This work aims to close the gap. We introduce a covisibility graph-based global encoding learning and data augmentation strategy, along with a depth-adjusted reprojection loss to facilitate implicit triangulation. Additionally, we revisit the network architecture and local feature extraction module. Our method achieves state-of-the-art on challenging large-scale datasets without relying on network ensembles or 3D supervision. On Aachen Day-Night, we are 10times more accurate than previous SCR methods with similar map sizes and require at least 5times smaller map sizes than any other SCR method while still delivering superior accuracy. Code will be available at: https://github.com/cvg/scrstudio .

We address a fundamental challenge in Reinforcement Learning from Interaction Demonstration (RLID): demonstration noise and coverage limitations. While existing data collection approaches provide valuable interaction demonstrations, they often yield sparse, disconnected, and noisy trajectories that fail to capture the full spectrum of possible skill variations and transitions. Our key insight is that despite noisy and sparse demonstrations, there exist infinite physically feasible trajectories that naturally bridge between demonstrated skills or emerge from their neighboring states, forming a continuous space of possible skill variations and transitions. Building upon this insight, we present two data augmentation techniques: a Stitched Trajectory Graph (STG) that discovers potential transitions between demonstration skills, and a State Transition Field (STF) that establishes unique connections for arbitrary states within the demonstration neighborhood. To enable effective RLID with augmented data, we develop an Adaptive Trajectory Sampling (ATS) strategy for dynamic curriculum generation and a historical encoding mechanism for memory-dependent skill learning. Our approach enables robust skill acquisition that significantly generalizes beyond the reference demonstrations. Extensive experiments across diverse interaction tasks demonstrate substantial improvements over state-of-the-art methods in terms of convergence stability, generalization capability, and recovery robustness.

Logical reasoning is of vital importance to natural language understanding. Previous studies either employ graph-based models to incorporate prior knowledge about logical relations, or introduce symbolic logic into neural models through data augmentation. These methods, however, heavily depend on annotated training data, and thus suffer from over-fitting and poor generalization problems due to the dataset sparsity. To address these two problems, in this paper, we propose MERIt, a MEta-path guided contrastive learning method for logical ReasonIng of text, to perform self-supervised pre-training on abundant unlabeled text data. Two novel strategies serve as indispensable components of our method. In particular, a strategy based on meta-path is devised to discover the logical structure in natural texts, followed by a counterfactual data augmentation strategy to eliminate the information shortcut induced by pre-training. The experimental results on two challenging logical reasoning benchmarks, i.e., ReClor and LogiQA, demonstrate that our method outperforms the SOTA baselines with significant improvements.

Generative models have achieved remarkable progress, yet applying them to satellite imagery remains challenging. Unlike natural imagery, satellite scenes are structured by spatially complex and semantically distinct geometries. Prior work addresses this complexity by adapting natural image frameworks using dense rasters or sparse prompts, trading off annotation cost and fidelity while breaking compatibility with vector primitives commonly used to represent geographic information. We introduce TerraDiT-Ω, a unified spatial control framework that generates satellite imagery directly from any native geospatial primitive. By jointly leveraging precise annotations (polygons, polylines) and coarser ones (bounding boxes, points), the model supports controllable layouts across varying annotation budgets, broadening applicability to design tasks such as urban planning while remaining naturally compatible with end-to-end GeoAI workflows. To effectively leverage these primitives during generation, we propose Geometry-Aware Local Attention, a conditioning mechanism that injects explicit geometric cues into the attention space. Across all conditioning formats, our approach consistently outperforms both dense-control and sparse-control baselines. Furthermore, this flexibility enables controllable synthetic data augmentation using a single generative model, improving downstream performance on land-cover segmentation, object detection, road graph extraction, and scene classification. Code, data, and weights are available at https://github.com/mvrl/TerraDiT.

We propose a novel VQA dataset, based on picture stories designed for educating young children, that aims to facilitate comprehensive evaluation and characterization of vision-language models on comprehension tasks. Unlike current VQA datasets that often focus on fact-based memorization and simple reasoning tasks without principled scientific grounding, we collect data containing tasks reflecting different levels of comprehension and underlying cognitive processes, as laid out in Bloom's Taxonomy, a classic framework widely adopted in education research. The proposed BloomVQA dataset can be mapped to a hierarchical graph-based representation of visual stories, enabling automatic data augmentation and novel measures characterizing model consistency across the underlying taxonomy. We demonstrate graded evaluation and reliability analysis based on our proposed consistency metrics on state-of-the-art vision-language models. Our results suggest that, while current models achieve the most gain on low-level comprehension tasks, they generally fall short on high-level tasks requiring more advanced comprehension and cognitive skills, as 38.0% drop in VQA accuracy is observed comparing lowest and highest level tasks. Furthermore, current models show consistency patterns misaligned with human comprehension in various scenarios, suggesting emergent structures of model behaviors.

A key feature of neural models is that they can produce semantic vector representations of objects (texts, images, speech, etc.) ensuring that similar objects are close to each other in the vector space. While much work has focused on learning representations for other modalities, there are no aligned cross-modal representations for text and knowledge base (KB) elements. One challenge for learning such representations is the lack of parallel data, which we use contrastive training on heuristics-based datasets and data augmentation to overcome, training embedding models on (KB graph, text) pairs. On WebNLG, a cleaner manually crafted dataset, we show that they learn aligned representations suitable for retrieval. We then fine-tune on annotated data to create EREDAT (Ensembled Representations for Evaluation of DAta-to-Text), a similarity metric between English text and KB graphs. EREDAT outperforms or matches state-of-the-art metrics in terms of correlation with human judgments on WebNLG even though, unlike them, it does not require a reference text to compare against.

Rationale is defined as a subset of input features that best explains or supports the prediction by machine learning models. Rationale identification has improved the generalizability and interpretability of neural networks on vision and language data. In graph applications such as molecule and polymer property prediction, identifying representative subgraph structures named as graph rationales plays an essential role in the performance of graph neural networks. Existing graph pooling and/or distribution intervention methods suffer from lack of examples to learn to identify optimal graph rationales. In this work, we introduce a new augmentation operation called environment replacement that automatically creates virtual data examples to improve rationale identification. We propose an efficient framework that performs rationale-environment separation and representation learning on the real and augmented examples in latent spaces to avoid the high complexity of explicit graph decoding and encoding. Comparing against recent techniques, experiments on seven molecular and four polymer real datasets demonstrate the effectiveness and efficiency of the proposed augmentation-based graph rationalization framework.

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.

The problem of data sparsity has long been a challenge in recommendation systems, and previous studies have attempted to address this issue by incorporating side information. However, this approach often introduces side effects such as noise, availability issues, and low data quality, which in turn hinder the accurate modeling of user preferences and adversely impact recommendation performance. In light of the recent advancements in large language models (LLMs), which possess extensive knowledge bases and strong reasoning capabilities, we propose a novel framework called LLMRec that enhances recommender systems by employing three simple yet effective LLM-based graph augmentation strategies. Our approach leverages the rich content available within online platforms (e.g., Netflix, MovieLens) to augment the interaction graph in three ways: (i) reinforcing user-item interaction egde, (ii) enhancing the understanding of item node attributes, and (iii) conducting user node profiling, intuitively from the natural language perspective. By employing these strategies, we address the challenges posed by sparse implicit feedback and low-quality side information in recommenders. Besides, to ensure the quality of the augmentation, we develop a denoised data robustification mechanism that includes techniques of noisy implicit feedback pruning and MAE-based feature enhancement that help refine the augmented data and improve its reliability. Furthermore, we provide theoretical analysis to support the effectiveness of LLMRec and clarify the benefits of our method in facilitating model optimization. Experimental results on benchmark datasets demonstrate the superiority of our LLM-based augmentation approach over state-of-the-art techniques. To ensure reproducibility, we have made our code and augmented data publicly available at: https://github.com/HKUDS/LLMRec.git

Effective rehabilitation assessment is essential for monitoring patient progress, particularly in home-based settings. Existing systems often face challenges such as data imbalance and difficulty detecting subtle movement errors. This paper introduces Error-Guided Pose Augmentation (EGPA), a method that generates synthetic skeleton data by simulating clinically relevant movement mistakes. Unlike standard augmentation techniques, EGPA targets biomechanical errors observed in rehabilitation. Combined with an attention-based graph convolutional network, EGPA improves performance across multiple evaluation metrics. Experiments demonstrate reductions in mean absolute error of up to 27.6 percent and gains in error classification accuracy of 45.8 percent. Attention visualizations show that the model learns to focus on clinically significant joints and movement phases, enhancing both accuracy and interpretability. EGPA offers a promising approach for improving automated movement quality assessment in both clinical and home-based rehabilitation contexts.

Legal case retrieval (LCR) is a specialised information retrieval task that aims to find relevant cases to a given query case. LCR holds pivotal significance in facilitating legal practitioners in finding precedents. Most of existing LCR methods are based on traditional lexical models and language models, which have gained promising performance in retrieval. However, the domain-specific structural information inherent in legal documents is yet to be exploited to further improve the performance. Our previous work CaseGNN successfully harnesses text-attributed graphs and graph neural networks to address the problem of legal structural information neglect. Nonetheless, there remain two aspects for further investigation: (1) The underutilization of rich edge information within text-attributed case graphs limits CaseGNN to generate informative case representation. (2) The inadequacy of labelled data in legal datasets hinders the training of CaseGNN model. In this paper, CaseGNN++, which is extended from CaseGNN, is proposed to simultaneously leverage the edge information and additional label data to discover the latent potential of LCR models. Specifically, an edge feature-based graph attention layer (EUGAT) is proposed to comprehensively update node and edge features during graph modelling, resulting in a full utilisation of structural information of legal cases. Moreover, a novel graph contrastive learning objective with graph augmentation is developed in CaseGNN++ to provide additional training signals, thereby enhancing the legal comprehension capabilities of CaseGNN++ model. Extensive experiments on two benchmark datasets from COLIEE 2022 and COLIEE 2023 demonstrate that CaseGNN++ not only significantly improves CaseGNN but also achieves supreme performance compared to state-of-the-art LCR methods. Code has been released on https://github.com/yanran-tang/CaseGNN.

Contrastive learning (CL) recently has spurred a fruitful line of research in the field of recommendation, since its ability to extract self-supervised signals from the raw data is well-aligned with recommender systems' needs for tackling the data sparsity issue. A typical pipeline of CL-based recommendation models is first augmenting the user-item bipartite graph with structure perturbations, and then maximizing the node representation consistency between different graph augmentations. Although this paradigm turns out to be effective, what underlies the performance gains is still a mystery. In this paper, we first experimentally disclose that, in CL-based recommendation models, CL operates by learning more evenly distributed user/item representations that can implicitly mitigate the popularity bias. Meanwhile, we reveal that the graph augmentations, which were considered necessary, just play a trivial role. Based on this finding, we propose a simple CL method which discards the graph augmentations and instead adds uniform noises to the embedding space for creating contrastive views. A comprehensive experimental study on three benchmark datasets demonstrates that, though it appears strikingly simple, the proposed method can smoothly adjust the uniformity of learned representations and has distinct advantages over its graph augmentation-based counterparts in terms of recommendation accuracy and training efficiency. The code is released at https://github.com/Coder-Yu/QRec.

Large Language Models (LLMs) demonstrate remarkable capabilities, yet struggle with hallucination and outdated knowledge when tasked with complex knowledge reasoning, resulting in factually incorrect outputs. Previous studies have attempted to mitigate it by retrieving factual knowledge from large-scale knowledge graphs (KGs) to assist LLMs in logical reasoning and prediction of answers. However, this kind of approach often introduces noise and irrelevant data, especially in situations with extensive context from multiple knowledge aspects. In this way, LLM attention can be potentially mislead from question and relevant information. In our study, we introduce an Adaptive Multi-Aspect Retrieval-augmented over KGs (Amar) framework. This method retrieves knowledge including entities, relations, and subgraphs, and converts each piece of retrieved text into prompt embeddings. The Amar framework comprises two key sub-components: 1) a self-alignment module that aligns commonalities among entities, relations, and subgraphs to enhance retrieved text, thereby reducing noise interference; 2) a relevance gating module that employs a soft gate to learn the relevance score between question and multi-aspect retrieved data, to determine which information should be used to enhance LLMs' output, or even filtered altogether. Our method has achieved state-of-the-art performance on two common datasets, WebQSP and CWQ, showing a 1.9\% improvement in accuracy over its best competitor and a 6.6\% improvement in logical form generation over a method that directly uses retrieved text as context prompts. These results demonstrate the effectiveness of Amar in improving the reasoning of LLMs.

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.

Graph anomaly detection has gained significant attention across various domains, particularly in critical applications like fraud detection in e-commerce platforms and insider threat detection in cybersecurity. Usually, these data are composed of multiple types (e.g., user information and transaction records for financial data), thus exhibiting view heterogeneity. However, in the era of big data, the heterogeneity of views and the lack of label information pose substantial challenges to traditional approaches. Existing unsupervised graph anomaly detection methods often struggle with high-dimensionality issues, rely on strong assumptions about graph structures or fail to handle complex multi-view graphs. To address these challenges, we propose a cluster aware multi-view graph anomaly detection method, called CARE. Our approach captures both local and global node affinities by augmenting the graph's adjacency matrix with the pseudo-label (i.e., soft membership assignments) without any strong assumption about the graph. To mitigate potential biases from the pseudo-label, we introduce a similarity-guided loss. Theoretically, we show that the proposed similarity-guided loss is a variant of contrastive learning loss, and we present how this loss alleviates the bias introduced by pseudo-label with the connection to graph spectral clustering. Experimental results on several datasets demonstrate the effectiveness and efficiency of our proposed framework. Specifically, CARE outperforms the second-best competitors by more than 39% on the Amazon dataset with respect to AUPRC and 18.7% on the YelpChi dataset with respect to AUROC. The code of our method is available at the GitHub link: https://github.com/zhenglecheng/CARE-demo.

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 have achieved great success in numerous NLP tasks but continue to exhibit notable gaps in multi-step factual reasoning, especially when real-world knowledge is sparse. Recent advances in grokking have demonstrated that neural networks can transition from memorizing to perfectly generalizing once they detect underlying logical patterns - yet these studies have primarily used small, synthetic tasks. In this paper, for the first time, we extend grokking to real-world factual data and address the challenge of dataset sparsity by augmenting existing knowledge graphs with carefully designed synthetic data to raise the ratio phi_r of inferred facts to atomic facts above the threshold required for grokking. Surprisingly, we find that even factually incorrect synthetic data can strengthen emergent reasoning circuits rather than degrade accuracy, as it forces the model to rely on relational structure rather than memorization. When evaluated on multi-hop reasoning benchmarks, our approach achieves up to 95-100% accuracy on 2WikiMultiHopQA - substantially improving over strong baselines and matching or exceeding current state-of-the-art results. We further provide an in-depth analysis of how increasing phi_r drives the formation of generalizing circuits inside Transformers. Our findings suggest that grokking-based data augmentation can unlock implicit multi-hop reasoning capabilities, opening the door to more robust and interpretable factual reasoning in large-scale language models.

Recently, using large language models (LLMs) for data augmentation has led to considerable improvements in unsupervised sentence embedding models. However, existing methods encounter two primary challenges: limited data diversity and high data noise. Current approaches often neglect fine-grained knowledge, such as entities and quantities, leading to insufficient diversity. Additionally, unsupervised data frequently lacks discriminative information, and the generated synthetic samples may introduce noise. In this paper, we propose a pipeline-based data augmentation method via LLMs and introduce the Gaussian-decayed gradient-assisted Contrastive Sentence Embedding (GCSE) model to enhance unsupervised sentence embeddings. To tackle the issue of low data diversity, our pipeline utilizes knowledge graphs (KGs) to extract entities and quantities, enabling LLMs to generate more diverse, knowledge-enriched samples. To address high data noise, the GCSE model uses a Gaussian-decayed function to limit the impact of false hard negative samples, enhancing the model's discriminative capability. Experimental results show that our approach achieves state-of-the-art performance in semantic textual similarity (STS) tasks, using fewer data samples and smaller LLMs, demonstrating its efficiency and robustness across various models.

We introduce a randomized topological augmentor based on Schur complements for Graph Contrastive Learning (GCL). Given a graph laplacian matrix, the technique generates unbiased approximations of its Schur complements and treats the corresponding graphs as augmented views. We discuss the benefits of our approach, provide theoretical justifications and present connections with graph diffusion. Unlike previous efforts, we study the empirical effectiveness of the augmentor in a controlled fashion by varying the design choices for subsequent GCL phases, such as encoding and contrasting. Extensive experiments on node and graph classification benchmarks demonstrate that our technique consistently outperforms pre-defined and adaptive augmentation approaches to achieve state-of-the-art results.

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

Large language models (LLMs) learn temporal concepts from the co-occurrence of related tokens in a sequence. Compared with conventional text generation, temporal reasoning, which reaches a conclusion based on mathematical, logical and commonsense knowledge, is more challenging. In this paper, we propose TempGraph-LLM, a new paradigm towards text-based temporal reasoning. To be specific, we first teach LLMs to translate the context into a temporal graph. A synthetic dataset, which is fully controllable and requires minimal supervision, is constructed for pre-training on this task. We prove in experiments that LLMs benefit from the pre-training on other tasks. On top of that, we guide LLMs to perform symbolic reasoning with the strategies of Chain of Thoughts (CoTs) bootstrapping and special data augmentation. We observe that CoTs with symbolic reasoning bring more consistent and reliable results than those using free text.

Accurately predicting experimentally realizable 3D molecular crystal structures from their 2D chemical graphs is a long-standing open challenge in computational chemistry called crystal structure prediction (CSP). Efficiently solving this problem has implications ranging from pharmaceuticals to organic semiconductors, as crystal packing directly governs the physical and chemical properties of organic solids. In this paper, we introduce OXtal, a large-scale 100M parameter all-atom diffusion model that directly learns the conditional joint distribution over intramolecular conformations and periodic packing. To efficiently scale OXtal, we abandon explicit equivariant architectures imposing inductive bias arising from crystal symmetries in favor of data augmentation strategies. We further propose a novel crystallization-inspired lattice-free training scheme, Stoichiometric Stochastic Shell Sampling (S^4), that efficiently captures long-range interactions while sidestepping explicit lattice parametrization -- thus enabling more scalable architectural choices at all-atom resolution. By leveraging a large dataset of 600K experimentally validated crystal structures (including rigid and flexible molecules, co-crystals, and solvates), OXtal achieves orders-of-magnitude improvements over prior ab initio machine learning CSP methods, while remaining orders of magnitude cheaper than traditional quantum-chemical approaches. Specifically, OXtal recovers experimental structures with conformer RMSD_1<0.5 Å and attains over 80\% packing similarity rate, demonstrating its ability to model both thermodynamic and kinetic regularities of molecular crystallization.

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

The recent surge in contrast-based graph self-supervised learning has prominently featured an intensified exploration of spectral cues. Spectral augmentation, which involves modifying a graph's spectral properties such as eigenvalues or eigenvectors, is widely believed to enhance model performance. However, an intriguing paradox emerges, as methods grounded in seemingly conflicting assumptions regarding the spectral domain demonstrate notable enhancements in learning performance. Through extensive empirical studies, we find that simple edge perturbations - random edge dropping for node-level and random edge adding for graph-level self-supervised learning - consistently yield comparable or superior performance while being significantly more computationally efficient. This suggests that the computational overhead of sophisticated spectral augmentations may not justify their practical benefits. Our theoretical analysis of the InfoNCE loss bounds for shallow GNNs further supports this observation. The proposed insights represent a significant leap forward in the field, potentially refining the understanding and implementation of graph self-supervised learning.

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.

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.

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.

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

Data augmentation is one of the most prevalent tools in deep learning, underpinning many recent advances, including those from classification, generative models, and representation learning. The standard approach to data augmentation combines simple transformations like rotations and flips to generate new images from existing ones. However, these new images lack diversity along key semantic axes present in the data. Current augmentations cannot alter the high-level semantic attributes, such as animal species present in a scene, to enhance the diversity of data. We address the lack of diversity in data augmentation with image-to-image transformations parameterized by pre-trained text-to-image diffusion models. Our method edits images to change their semantics using an off-the-shelf diffusion model, and generalizes to novel visual concepts from a few labelled examples. We evaluate our approach on few-shot image classification tasks, and on a real-world weed recognition task, and observe an improvement in accuracy in tested domains.

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

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.

Relational data augmentation is a powerful technique for enhancing data analytics and improving machine learning models by incorporating columns from external datasets. However, it is challenging to efficiently discover relevant external tables to join with a given input table. Existing approaches rely on data discovery systems to identify joinable tables from external sources, typically based on overlap or containment. However, the sheer number of tables obtained from these systems results in irrelevant joins that need to be performed; this can be computationally expensive or even infeasible in practice. We address this limitation by proposing the use of efficient mutual information (MI) estimation for finding relevant joinable tables. We introduce a new sketching method that enables efficient evaluation of relationship discovery queries by estimating MI without materializing the joins and returning a smaller set of tables that are more likely to be relevant. We also demonstrate the effectiveness of our approach at approximating MI in extensive experiments using synthetic and real-world datasets.

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

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}

As an effective strategy, data augmentation (DA) alleviates data scarcity scenarios where deep learning techniques may fail. It is widely applied in computer vision then introduced to natural language processing and achieves improvements in many tasks. One of the main focuses of the DA methods is to improve the diversity of training data, thereby helping the model to better generalize to unseen testing data. In this survey, we frame DA methods into three categories based on the diversity of augmented data, including paraphrasing, noising, and sampling. Our paper sets out to analyze DA methods in detail according to the above categories. Further, we also introduce their applications in NLP tasks as well as the challenges. Some helpful resources are provided in the appendix.

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.

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/.

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

Data augmentation is an effective way to improve the performance of many neural text generation models. However, current data augmentation methods need to define or choose proper data mapping functions that map the original samples into the augmented samples. In this work, we derive an objective to formulate the problem of data augmentation on text generation tasks without any use of augmented data constructed by specific mapping functions. Our proposed objective can be efficiently optimized and applied to popular loss functions on text generation tasks with a convergence rate guarantee. Experiments on five datasets of two text generation tasks show that our approach can approximate or even surpass popular data augmentation methods.

Knowledge distillation is one of the primary methods of transferring knowledge from large to small models. However, it requires massive task-specific data, which may not be plausible in many real-world applications. Data augmentation methods such as representation interpolation, token replacement, or augmentation with models are applied to tackle this problem. However, these data augmentation methods either potentially cause shifts in decision boundaries (representation interpolation), are not expressive enough (token replacement), or introduce too much computational overhead (augmentation with models). To this end, we propose AugPro (Augmentation with Projection), an effective and efficient data augmentation method for distillation. Our method builds on top of representation interpolation augmentation methods to maintain the diversity of expressions and converts the augmented data to tokens to avoid shifting decision boundaries. It uses simple operations that come with little computational overhead. The results on multiple GLUE tasks show that our methods can improve distillation performance by a large margin at a low time cost. Codes are available at https://github.com/google-research/google-research/tree/master/augpro.

Pretraining on large-scale, unstructured internet text has enabled language models to acquire a significant amount of world knowledge. However, this knowledge acquisition is data-inefficient -- to learn a given fact, models must be trained on hundreds to thousands of diverse representations of it. This poses a challenge when adapting a pretrained model to a small corpus of domain-specific documents, where each fact may appear rarely or only once. We propose to bridge this gap with synthetic continued pretraining: using the small domain-specific corpus to synthesize a large corpus more amenable to learning, and then performing continued pretraining on the synthesized corpus. We instantiate this proposal with EntiGraph, a synthetic data augmentation algorithm that extracts salient entities from the source documents and then generates diverse text by drawing connections between the sampled entities. Synthetic continued pretraining using EntiGraph enables a language model to answer questions and follow generic instructions related to the source documents without access to them. If instead, the source documents are available at inference time, we show that the knowledge acquired through our approach compounds with retrieval-augmented generation. To better understand these results, we build a simple mathematical model of EntiGraph, and show how synthetic data augmentation can "rearrange" knowledge to enable more data-efficient learning.

Data augmentation is essential to achieve state-of-the-art performance in many deep learning applications. However, the most effective augmentation techniques become computationally prohibitive for even medium-sized datasets. To address this, we propose a rigorous technique to select subsets of data points that when augmented, closely capture the training dynamics of full data augmentation. We first show that data augmentation, modeled as additive perturbations, improves learning and generalization by relatively enlarging and perturbing the smaller singular values of the network Jacobian, while preserving its prominent directions. This prevents overfitting and enhances learning the harder to learn information. Then, we propose a framework to iteratively extract small subsets of training data that when augmented, closely capture the alignment of the fully augmented Jacobian with labels/residuals. We prove that stochastic gradient descent applied to the augmented subsets found by our approach has similar training dynamics to that of fully augmented data. Our experiments demonstrate that our method achieves 6.3x speedup on CIFAR10 and 2.2x speedup on SVHN, and outperforms the baselines by up to 10% across various subset sizes. Similarly, on TinyImageNet and ImageNet, our method beats the baselines by up to 8%, while achieving up to 3.3x speedup across various subset sizes. Finally, training on and augmenting 50% subsets using our method on a version of CIFAR10 corrupted with label noise even outperforms using the full dataset. Our code is available at: https://github.com/tianyu139/data-efficient-augmentation

Self-supervised learning provides a promising path towards eliminating the need for costly label information in representation learning on graphs. However, to achieve state-of-the-art performance, methods often need large numbers of negative examples and rely on complex augmentations. This can be prohibitively expensive, especially for large graphs. To address these challenges, we introduce Bootstrapped Graph Latents (BGRL) - a graph representation learning method that learns by predicting alternative augmentations of the input. BGRL uses only simple augmentations and alleviates the need for contrasting with negative examples, and is thus scalable by design. BGRL outperforms or matches prior methods on several established benchmarks, while achieving a 2-10x reduction in memory costs. Furthermore, we show that BGRL can be scaled up to extremely large graphs with hundreds of millions of nodes in the semi-supervised regime - achieving state-of-the-art performance and improving over supervised baselines where representations are shaped only through label information. In particular, our solution centered on BGRL constituted one of the winning entries to the Open Graph Benchmark - Large Scale Challenge at KDD Cup 2021, on a graph orders of magnitudes larger than all previously available benchmarks, thus demonstrating the scalability and effectiveness of our approach.

Contrastive learning (CL) has recently been demonstrated critical in improving recommendation performance. The underlying principle of CL-based recommendation models is to ensure the consistency between representations derived from different graph augmentations of the user-item bipartite graph. This self-supervised approach allows for the extraction of general features from raw data, thereby mitigating the issue of data sparsity. Despite the effectiveness of this paradigm, the factors contributing to its performance gains have yet to be fully understood. This paper provides novel insights into the impact of CL on recommendation. Our findings indicate that CL enables the model to learn more evenly distributed user and item representations, which alleviates the prevalent popularity bias and promoting long-tail items. Our analysis also suggests that the graph augmentations, previously considered essential, are relatively unreliable and of limited significance in CL-based recommendation. Based on these findings, we put forward an eXtremely Simple Graph Contrastive Learning method (XSimGCL) for recommendation, which discards the ineffective graph augmentations and instead employs a simple yet effective noise-based embedding augmentation to generate views for CL. A comprehensive experimental study on four large and highly sparse benchmark datasets demonstrates that, though the proposed method is extremely simple, it can smoothly adjust the uniformity of learned representations and outperforms its graph augmentation-based counterparts by a large margin in both recommendation accuracy and training efficiency. The code and used datasets are released at https://github.com/Coder-Yu/SELFRec.

Large language models (LLMs), while exhibiting exceptional performance, suffer from hallucinations, especially on knowledge-intensive tasks. Existing works propose to augment LLMs with individual text units retrieved from external knowledge corpora to alleviate the issue. However, in many domains, texts are interconnected (e.g., academic papers in a bibliographic graph are linked by citations and co-authorships) which form a (text-attributed) graph. The knowledge in such graphs is encoded not only in single texts/nodes but also in their associated connections. To facilitate the research of augmenting LLMs with graphs, we manually construct a Graph Reasoning Benchmark dataset called GRBench, containing 1,740 questions that can be answered with the knowledge from 10 domain graphs. Then, we propose a simple and effective framework called Graph Chain-of-thought (Graph-CoT) to augment LLMs with graphs by encouraging LLMs to reason on the graph iteratively. Each Graph-CoT iteration consists of three sub-steps: LLM reasoning, LLM-graph interaction, and graph execution. We conduct systematic experiments with three LLM backbones on GRBench, where Graph-CoT outperforms the baselines consistently. The code is available at https://github.com/PeterGriffinJin/Graph-CoT.

Language Models (LMs) are increasingly challenging the dominance of domain-specific models, including Graph Neural Networks (GNNs) and Graph Transformers (GTs), in graph learning tasks. Following this trend, we propose a novel approach that empowers off-the-shelf LMs to achieve performance comparable to state-of-the-art GNNs on node classification tasks, without requiring any architectural modification. By preserving the LM's original architecture, our approach retains a key benefit of LM instruction tuning: the ability to jointly train on diverse datasets, fostering greater flexibility and efficiency. To achieve this, we introduce two key augmentation strategies: (1) Enriching LMs' input using topological and semantic retrieval methods, which provide richer contextual information, and (2) guiding the LMs' classification process through a lightweight GNN classifier that effectively prunes class candidates. Our experiments on real-world datasets show that backbone Flan-T5 models equipped with these augmentation strategies outperform state-of-the-art text-output node classifiers and are comparable to top-performing vector-output node classifiers. By bridging the gap between specialized task-specific node classifiers and general LMs, this work paves the way for more versatile and widely applicable graph learning models. We will open-source the code upon publication.

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

Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding "slow nodes" at each edge that can mediate communication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.

Knowledge graphs automatically constructed from text are increasingly used in real-world applications. However, their inherent noise, fragmentation, and semantic inconsistencies significantly affect the performance of Graph Neural Networks (GNNs) on downstream tasks. Assessing their performance and robustness remains difficult, as it is often unclear whether observed results stem from the learning model or from the quality of the constructed graph itself. In this work, we introduce a dual-purpose benchmark designed to jointly evaluate (i) the performance of GNNs on noisy, text-derived graphs and (ii) the effectiveness of graph construction methods on a downstream task. The benchmark is built in the biomedical domain from a single textual corpus and includes two automatically constructed graphs generated using different extraction methods, alongside a high-quality reference graph curated by experts that serves as an upper performance bound. This design enables controlled comparison of construction methods and systematic evaluation of GNN robustness through semi-supervised node classification. We further provide a standardized, reproducible, and extensible evaluation framework, facilitating the integration of new graph extraction methods and learning models.

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

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.

Modeling dynamic graphs, such as those found in social networks, recommendation systems, and e-commerce platforms, is crucial for capturing evolving relationships and delivering relevant insights over time. Traditional approaches primarily rely on graph neural networks with temporal components or sequence generation models, which often focus narrowly on the historical context of target nodes. This limitation restricts the ability to adapt to new and emerging patterns in dynamic graphs. To address this challenge, we propose a novel framework, Retrieval-Augmented Generation for Dynamic Graph modeling (RAG4DyG), which enhances dynamic graph predictions by incorporating contextually and temporally relevant examples from broader graph structures. Our approach includes a time- and context-aware contrastive learning module to identify high-quality demonstrations and a graph fusion strategy to effectively integrate these examples with historical contexts. The proposed framework is designed to be effective in both transductive and inductive scenarios, ensuring adaptability to previously unseen nodes and evolving graph structures. Extensive experiments across multiple real-world datasets demonstrate the effectiveness of RAG4DyG in improving predictive accuracy and adaptability for dynamic graph modeling. The code and datasets are publicly available at https://github.com/YuxiaWu/RAG4DyG.

Data augmentation has long been a cornerstone for reducing overfitting in vision models, with methods like AutoAugment automating the design of task-specific augmentations. Recent advances in generative models, such as conditional diffusion and few-shot NeRFs, offer a new paradigm for data augmentation by synthesizing data with significantly greater diversity and realism. However, unlike traditional augmentations like cropping or rotation, these methods introduce substantial changes that enhance robustness but also risk degrading performance if the augmentations are poorly matched to the task. In this work, we present EvoAug, an automated augmentation learning pipeline, which leverages these generative models alongside an efficient evolutionary algorithm to learn optimal task-specific augmentations. Our pipeline introduces a novel approach to image augmentation that learns stochastic augmentation trees that hierarchically compose augmentations, enabling more structured and adaptive transformations. We demonstrate strong performance across fine-grained classification and few-shot learning tasks. Notably, our pipeline discovers augmentations that align with domain knowledge, even in low-data settings. These results highlight the potential of learned generative augmentations, unlocking new possibilities for robust model training.

The need to analyze graphs is ubiquitous across various fields, from social networks to biological research and recommendation systems. Therefore, enabling the ability of large language models (LLMs) to process graphs is an important step toward more advanced general intelligence. However, current LLM benchmarks on graph analysis require models to directly reason over the prompts describing graph topology, and are thus limited to small graphs with only a few dozens of nodes. In contrast, human experts typically write programs based on popular libraries for task solving, and can thus handle graphs with different scales. To this end, a question naturally arises: can LLMs analyze graphs like professionals? In this paper, we introduce ProGraph, a manually crafted benchmark containing 3 categories of graph tasks. The benchmark expects solutions based on programming instead of directly reasoning over raw inputs. Our findings reveal that the performance of current LLMs is unsatisfactory, with the best model achieving only 36% accuracy. To bridge this gap, we propose LLM4Graph datasets, which include crawled documents and auto-generated codes based on 6 widely used graph libraries. By augmenting closed-source LLMs with document retrieval and fine-tuning open-source ones on the codes, we show 11-32% absolute improvements in their accuracies. Our results underscore that the capabilities of LLMs in handling structured data are still under-explored, and show the effectiveness of LLM4Graph in enhancing LLMs' proficiency of graph analysis. The benchmark, datasets and enhanced open-source models are available at https://github.com/BUPT-GAMMA/ProGraph.

In this paper we propose a new approach to detect clusters in undirected graphs with attributed vertices. We incorporate structural and attribute similarities between the vertices in an augmented graph by creating additional vertices and edges as proposed in [1, 2]. The augmented graph is then embedded in a Euclidean space associated to its Laplacian and we cluster vertices via a modified K-means algorithm, using a new vector-valued distance in the embedding space. Main novelty of our method, which can be classified as an early fusion method, i.e., a method in which additional information on vertices are fused to the structure information before applying clustering, is the interpretation of attributes as new realizations of graph vertices, which can be dealt with as coordinate vectors in a related Euclidean space. This allows us to extend a scalable generalized spectral clustering procedure which substitutes graph Laplacian eigenvectors with some vectors, named algebraically smooth vectors, obtained by a linear-time complexity Algebraic MultiGrid (AMG) method. We discuss the performance of our proposed clustering method by comparison with recent literature approaches and public available results. Extensive experiments on different types of synthetic datasets and real-world attributed graphs show that our new algorithm, embedding attributes information in the clustering, outperforms structure-only-based methods, when the attributed network has an ambiguous structure. Furthermore, our new method largely outperforms the method which originally proposed the graph augmentation, showing that our embedding strategy and vector-valued distance are very effective in taking advantages from the augmented-graph representation.

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.

Data augmentation is a widely used strategy to improve model robustness and generalization by enriching training datasets with synthetic examples. While large language models (LLMs) have demonstrated strong generative capabilities for this purpose, their applications in high-stakes domains like healthcare present unique challenges due to the risk of generating clinically incorrect or misleading information. In this work, we propose a novel query-based model collaboration framework that integrates expert-level domain knowledge to guide the augmentation process to preserve critical medical information. Experiments on clinical prediction tasks demonstrate that our lightweight collaboration-based approach consistently outperforms existing LLM augmentation methods while improving safety through reduced factual errors. This framework addresses the gap between LLM augmentation potential and the safety requirements of specialized domains.

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

Data augmentation has been established as an efficacious approach to supplement useful information for low-resource datasets. Traditional augmentation techniques such as noise injection and image transformations have been widely used. In addition, generative data augmentation (GDA) has been shown to produce more diverse and flexible data. While generative adversarial networks (GANs) have been frequently used for GDA, they lack diversity and controllability compared to text-to-image diffusion models. In this paper, we propose TTIDA (Text-to-Text-to-Image Data Augmentation) to leverage the capabilities of large-scale pre-trained Text-to-Text (T2T) and Text-to-Image (T2I) generative models for data augmentation. By conditioning the T2I model on detailed descriptions produced by T2T models, we are able to generate photo-realistic labeled images in a flexible and controllable manner. Experiments on in-domain classification, cross-domain classification, and image captioning tasks show consistent improvements over other data augmentation baselines. Analytical studies in varied settings, including few-shot, long-tail, and adversarial, further reinforce the effectiveness of TTIDA in enhancing performance and increasing robustness.

We present Deep Graph Infomax (DGI), a general approach for learning node representations within graph-structured data in an unsupervised manner. DGI relies on maximizing mutual information between patch representations and corresponding high-level summaries of graphs---both derived using established graph convolutional network architectures. The learnt patch representations summarize subgraphs centered around nodes of interest, and can thus be reused for downstream node-wise learning tasks. In contrast to most prior approaches to unsupervised learning with GCNs, DGI does not rely on random walk objectives, and is readily applicable to both transductive and inductive learning setups. We demonstrate competitive performance on a variety of node classification benchmarks, which at times even exceeds the performance of supervised learning.

Large language models (LLMs) have demonstrated remarkable in-context reasoning capabilities across a wide range of tasks, particularly with unstructured inputs such as language or images. However, LLMs struggle to handle structured data, such as graphs, due to their lack of understanding of non-Euclidean structures. As a result, without additional fine-tuning, their performance significantly lags behind that of graph neural networks (GNNs) in graph learning tasks. In this paper, we show that learning on graph data can be conceptualized as a retrieval-augmented generation (RAG) process, where specific instances (e.g., nodes or edges) act as queries, and the graph itself serves as the retrieved context. Building on this insight, we propose a series of RAG frameworks to enhance the in-context learning capabilities of LLMs for graph learning tasks. Comprehensive evaluations demonstrate that our proposed RAG frameworks significantly improve LLM performance on graph-based tasks, particularly in scenarios where a pretrained LLM must be used without modification or accessed via an API.

Knowledge graphs are useful tools to organize, recommend and sort data. Hierarchies in knowledge graphs provide significant benefit in improving understanding and compartmentalization of the data within a knowledge graph. This work leverages large language models to generate and augment hierarchies in an existing knowledge graph. For small (<100,000 node) domain-specific KGs, we find that a combination of few-shot prompting with one-shot generation works well, while larger KG may require cyclical generation. We present techniques for augmenting hierarchies, which led to coverage increase by 98% for intents and 99% for colors in our knowledge graph.

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.

Graph Retrieval Augmented Generation (GraphRAG) effectively enhances external knowledge integration capabilities by explicitly modeling knowledge relationships, thereby improving the factual accuracy and generation quality of Large Language Models (LLMs) in specialized domains. However, existing methods suffer from two inherent limitations: 1) Inefficient Information Aggregation: They rely on a single agent and fixed iterative patterns, making it difficult to adaptively capture multi-level textual, structural, and degree information within graph data. 2) Rigid Reasoning Mechanism: They employ preset reasoning schemes, which cannot dynamically adjust reasoning depth nor achieve precise semantic correction. To overcome these limitations, we propose Graph Counselor, an GraphRAG method based on multi-agent collaboration. This method uses the Adaptive Graph Information Extraction Module (AGIEM), where Planning, Thought, and Execution Agents work together to precisely model complex graph structures and dynamically adjust information extraction strategies, addressing the challenges of multi-level dependency modeling and adaptive reasoning depth. Additionally, the Self-Reflection with Multiple Perspectives (SR) module improves the accuracy and semantic consistency of reasoning results through self-reflection and backward reasoning mechanisms. Experiments demonstrate that Graph Counselor outperforms existing methods in multiple graph reasoning tasks, exhibiting higher reasoning accuracy and generalization ability. Our code is available at https://github.com/gjq100/Graph-Counselor.git.

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.

Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning. In the research community, implementing and benchmarking various advanced tasks are still painful and time-consuming with existing libraries. To facilitate graph deep learning research, we introduce DIG: Dive into Graphs, a turnkey library that provides a unified testbed for higher level, research-oriented graph deep learning tasks. Currently, we consider graph generation, self-supervised learning on graphs, explainability of graph neural networks, and deep learning on 3D graphs. For each direction, we provide unified implementations of data interfaces, common algorithms, and evaluation metrics. Altogether, DIG is an extensible, open-source, and turnkey library for researchers to develop new methods and effortlessly compare with common baselines using widely used datasets and evaluation metrics. Source code is available at https://github.com/divelab/DIG.

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.

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.

Every hour, huge amounts of visual contents are posted on social media and user-generated content platforms. To find relevant videos by means of a natural language query, text-video retrieval methods have received increased attention over the past few years. Data augmentation techniques were introduced to increase the performance on unseen test examples by creating new training samples with the application of semantics-preserving techniques, such as color space or geometric transformations on images. Yet, these techniques are usually applied on raw data, leading to more resource-demanding solutions and also requiring the shareability of the raw data, which may not always be true, e.g. copyright issues with clips from movies or TV series. To address this shortcoming, we propose a multimodal data augmentation technique which works in the feature space and creates new videos and captions by mixing semantically similar samples. We experiment our solution on a large scale public dataset, EPIC-Kitchens-100, and achieve considerable improvements over a baseline method, improved state-of-the-art performance, while at the same time performing multiple ablation studies. We release code and pretrained models on Github at https://github.com/aranciokov/FSMMDA_VideoRetrieval.

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.

The standard approach to tackling computer vision problems is to train deep convolutional neural network (CNN) models using large-scale image datasets which are representative of the target task. However, in many scenarios, it is often challenging to obtain sufficient image data for the target task. Data augmentation is a way to mitigate this challenge. A common practice is to explicitly transform existing images in desired ways so as to create the required volume and variability of training data necessary to achieve good generalization performance. In situations where data for the target domain is not accessible, a viable workaround is to synthesize training data from scratch--i.e., synthetic data augmentation. This paper presents an extensive review of synthetic data augmentation techniques. It covers data synthesis approaches based on realistic 3D graphics modeling, neural style transfer (NST), differential neural rendering, and generative artificial intelligence (AI) techniques such as generative adversarial networks (GANs) and variational autoencoders (VAEs). For each of these classes of methods, we focus on the important data generation and augmentation techniques, general scope of application and specific use-cases, as well as existing limitations and possible workarounds. Additionally, we provide a summary of common synthetic datasets for training computer vision models, highlighting the main features, application domains and supported tasks. Finally, we discuss the effectiveness of synthetic data augmentation methods. Since this is the first paper to explore synthetic data augmentation methods in great detail, we are hoping to equip readers with the necessary background information and in-depth knowledge of existing methods and their attendant issues.

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

Graph 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.

GraphRAG extends retrieval-augmented generation by organizing corpora as explicit knowledge graphs, enabling graph-based retrieval for complex question answering. However, existing frameworks extract entities and relations within individual chunks, leaving cross-chunk relations -- those whose evidence spans multiple passages -- systematically absent from the index. Exhaustive LLM-based recovery of such relations is impractical due to the combinatorial explosion of chunk combinations. We present CrossAug, a GNN-guided CROSS-Chunk Graph AUGmentation method that enriches GraphRAG indices with cross-chunk relational structure as an offline step before query-time retrieval. CrossAug derives training supervision through self-supervised graph corruption, uses a topology-aware GNN to score subgraphs for missingness, and applies evidence-grounded LLM completion only to selected high-scoring regions. Experiments on three LLM-based GraphRAG frameworks across four multi-hop and long-document QA benchmarks demonstrate that CrossAug consistently improves performance, confirming the benefit of cross-chunk graph augmentation for retrieval-based question answering. Our code is available at https://github.com/DonFinliani/CrossAug.

Graph Neural Networks (GNNs) are widely deployed in vast fields, but they often struggle to maintain accurate representations as graphs evolve. We theoretically establish a lower bound, proving that under mild conditions, representation distortion inevitably occurs over time. To estimate the temporal distortion without human annotation after deployment, one naive approach is to pre-train a recurrent model (e.g., RNN) before deployment and use this model afterwards, but the estimation is far from satisfactory. In this paper, we analyze the representation distortion from an information theory perspective, and attribute it primarily to inaccurate feature extraction during evolution. Consequently, we introduce Smart, a straightforward and effective baseline enhanced by an adaptive feature extractor through self-supervised graph reconstruction. In synthetic random graphs, we further refine the former lower bound to show the inevitable distortion over time and empirically observe that Smart achieves good estimation performance. Moreover, we observe that Smart consistently shows outstanding generalization estimation on four real-world evolving graphs. The ablation studies underscore the necessity of graph reconstruction. For example, on OGB-arXiv dataset, the estimation metric MAPE deteriorates from 2.19% to 8.00% without reconstruction.

Text augmentation is a technique for constructing synthetic data from an under-resourced corpus to improve predictive performance. Synthetic data generation is common in numerous domains. However, recently text augmentation has emerged in natural language processing (NLP) to improve downstream tasks. One of the current state-of-the-art text augmentation techniques is easy data augmentation (EDA), which augments the training data by injecting and replacing synonyms and randomly permuting sentences. One major obstacle with EDA is the need for versatile and complete synonym dictionaries, which cannot be easily found in low-resource languages. To improve the utility of EDA, we propose two extensions, easy distributional data augmentation (EDDA) and type specific similar word replacement (TSSR), which uses semantic word context information and part-of-speech tags for word replacement and augmentation. In an extensive empirical evaluation, we show the utility of the proposed methods, measured by F1 score, on two representative datasets in Swedish as an example of a low-resource language. With the proposed methods, we show that augmented data improve classification performances in low-resource settings.

The era of foundation models has revolutionized AI research, yet Graph Foundation Models (GFMs) remain constrained by the scarcity of large-scale graph corpora. Traditional graph data synthesis techniques primarily focus on simplistic structural operations, lacking the capacity to generate semantically rich nodes with meaningful textual attributes: a critical limitation for real-world applications. While large language models (LLMs) demonstrate exceptional text generation capabilities, their direct application to graph synthesis is impeded by context window limitations, hallucination phenomena, and structural consistency challenges. To address these issues, we introduce GraphMaster, the first multi-agent framework specifically designed for graph data synthesis in data-limited environments. GraphMaster orchestrates four specialized LLM agents (Manager, Perception, Enhancement, and Evaluation) that collaboratively optimize the synthesis process through iterative refinement, ensuring both semantic coherence and structural integrity. To rigorously evaluate our approach, we create new data-limited "Sub" variants of six standard graph benchmarks, specifically designed to test synthesis capabilities under realistic constraints. Additionally, we develop a novel interpretability assessment framework that combines human evaluation with a principled Grassmannian manifold-based analysis, providing both qualitative and quantitative measures of semantic coherence. Experimental results demonstrate that GraphMaster significantly outperforms traditional synthesis methods across multiple datasets, establishing a strong foundation for advancing GFMs in data-scarce environments.

Message-passing Graph Neural Networks (GNNs) are often criticized for their limited expressiveness, issues like over-smoothing and over-squashing, and challenges in capturing long-range dependencies. Conversely, Graph Transformers (GTs) are regarded as superior due to their employment of global attention mechanisms, which potentially mitigate these challenges. Literature frequently suggests that GTs outperform GNNs in graph-level tasks, especially for graph classification and regression on small molecular graphs. In this study, we explore the untapped potential of GNNs through an enhanced framework, GNN+, which integrates six widely used techniques: edge feature integration, normalization, dropout, residual connections, feed-forward networks, and positional encoding, to effectively tackle graph-level tasks. We conduct a systematic re-evaluation of three classic GNNs (GCN, GIN, and GatedGCN) enhanced by the GNN+ framework across 14 well-known graph-level datasets. Our results reveal that, contrary to prevailing beliefs, these classic GNNs consistently match or surpass the performance of GTs, securing top-three rankings across all datasets and achieving first place in eight. Furthermore, they demonstrate greater efficiency, running several times faster than GTs on many datasets. This highlights the potential of simple GNN architectures, challenging the notion that complex mechanisms in GTs are essential for superior graph-level performance. Our source code is available at https://github.com/LUOyk1999/GNNPlus.

Text data augmentation is an effective strategy for overcoming the challenge of limited sample sizes in many natural language processing (NLP) tasks. This challenge is especially prominent in the few-shot learning scenario, where the data in the target domain is generally much scarcer and of lowered quality. A natural and widely-used strategy to mitigate such challenges is to perform data augmentation to better capture the data invariance and increase the sample size. However, current text data augmentation methods either can't ensure the correct labeling of the generated data (lacking faithfulness) or can't ensure sufficient diversity in the generated data (lacking compactness), or both. Inspired by the recent success of large language models, especially the development of ChatGPT, which demonstrated improved language comprehension abilities, in this work, we propose a text data augmentation approach based on ChatGPT (named AugGPT). AugGPT rephrases each sentence in the training samples into multiple conceptually similar but semantically different samples. The augmented samples can then be used in downstream model training. Experiment results on few-shot learning text classification tasks show the superior performance of the proposed AugGPT approach over state-of-the-art text data augmentation methods in terms of testing accuracy and distribution of the augmented samples.

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

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.

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.

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

NLP has achieved great progress in the past decade through the use of neural models and large labeled datasets. The dependence on abundant data prevents NLP models from being applied to low-resource settings or novel tasks where significant time, money, or expertise is required to label massive amounts of textual data. Recently, data augmentation methods have been explored as a means of improving data efficiency in NLP. To date, there has been no systematic empirical overview of data augmentation for NLP in the limited labeled data setting, making it difficult to understand which methods work in which settings. In this paper, we provide an empirical survey of recent progress on data augmentation for NLP in the limited labeled data setting, summarizing the landscape of methods (including token-level augmentations, sentence-level augmentations, adversarial augmentations, and hidden-space augmentations) and carrying out experiments on 11 datasets covering topics/news classification, inference tasks, paraphrasing tasks, and single-sentence tasks. Based on the results, we draw several conclusions to help practitioners choose appropriate augmentations in different settings and discuss the current challenges and future directions for limited data learning in NLP.

Graph Neural Networks (GNNs) are an effective framework for representation learning of graphs. GNNs follow a neighborhood aggregation scheme, where the representation vector of a node is computed by recursively aggregating and transforming representation vectors of its neighboring nodes. Many GNN variants have been proposed and have achieved state-of-the-art results on both node and graph classification tasks. However, despite GNNs revolutionizing graph representation learning, there is limited understanding of their representational properties and limitations. Here, we present a theoretical framework for analyzing the expressive power of GNNs to capture different graph structures. Our results characterize the discriminative power of popular GNN variants, such as Graph Convolutional Networks and GraphSAGE, and show that they cannot learn to distinguish certain simple graph structures. We then develop a simple architecture that is provably the most expressive among the class of GNNs and is as powerful as the Weisfeiler-Lehman graph isomorphism test. We empirically validate our theoretical findings on a number of graph classification benchmarks, and demonstrate that our model achieves state-of-the-art performance.

Graph Retrieval-Augmented Generation (GraphRAG) enhances factual reasoning in LLMs by structurally modeling knowledge through graph-based representations. However, existing GraphRAG approaches face two core limitations: shallow retrieval that fails to surface all critical evidence, and inefficient utilization of pre-constructed structural graph data, which hinders effective reasoning from complex queries. To address these challenges, we propose GraphSearch, a novel agentic deep searching workflow with dual-channel retrieval for GraphRAG. GraphSearch organizes the retrieval process into a modular framework comprising six modules, enabling multi-turn interactions and iterative reasoning. Furthermore, GraphSearch adopts a dual-channel retrieval strategy that issues semantic queries over chunk-based text data and relational queries over structural graph data, enabling comprehensive utilization of both modalities and their complementary strengths. Experimental results across six multi-hop RAG benchmarks demonstrate that GraphSearch consistently improves answer accuracy and generation quality over the traditional strategy, confirming GraphSearch as a promising direction for advancing graph retrieval-augmented generation.

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.

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.

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility across various graph-related tasks. This survey provides an in-depth review of recent progress and challenges in graph transformer research. We begin with foundational concepts of graphs and transformers. We then explore design perspectives of graph transformers, focusing on how they integrate graph inductive biases and graph attention mechanisms into the transformer architecture. Furthermore, we propose a taxonomy classifying graph transformers based on depth, scalability, and pre-training strategies, summarizing key principles for effective development of graph transformer models. Beyond technical analysis, we discuss the applications of graph transformer models for node-level, edge-level, and graph-level tasks, exploring their potential in other application scenarios as well. Finally, we identify remaining challenges in the field, such as scalability and efficiency, generalization and robustness, interpretability and explainability, dynamic and complex graphs, as well as data quality and diversity, charting future directions for graph transformer research.

Text-Attributed Graphs (TAGs) enhance graph structures with natural language descriptions, enabling detailed representation of data and their relationships across a broad spectrum of real-world scenarios. Despite the potential for deeper insights, existing TAG representation learning primarily relies on supervised methods, necessitating extensive labeled data and limiting applicability across diverse contexts. This paper introduces a new self-supervised learning framework, Text-And-Graph Multi-View Alignment (TAGA), which overcomes these constraints by integrating TAGs' structural and semantic dimensions. TAGA constructs two complementary views: Text-of-Graph view, which organizes node texts into structured documents based on graph topology, and the Graph-of-Text view, which converts textual nodes and connections into graph data. By aligning representations from both views, TAGA captures joint textual and structural information. In addition, a novel structure-preserving random walk algorithm is proposed for efficient training on large-sized TAGs. Our framework demonstrates strong performance in zero-shot and few-shot scenarios across eight real-world datasets.

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

We study the problem of adversarially robust self-supervised learning on graphs. In the contrastive learning framework, we introduce a new method that increases the adversarial robustness of the learned representations through i) adversarial transformations and ii) transformations that not only remove but also insert edges. We evaluate the learned representations in a preliminary set of experiments, obtaining promising results. We believe this work takes an important step towards incorporating robustness as a viable auxiliary task in graph contrastive learning.

Retrieval-Augmented Generation (RAG) enhances the performance of LLMs across various tasks by retrieving relevant information from external sources, particularly on text-based data. For structured data, such as knowledge graphs, GraphRAG has been widely used to retrieve relevant information. However, recent studies have revealed that structuring implicit knowledge from text into graphs can benefit certain tasks, extending the application of GraphRAG from graph data to general text-based data. Despite their successful extensions, most applications of GraphRAG for text data have been designed for specific tasks and datasets, lacking a systematic evaluation and comparison between RAG and GraphRAG on widely used text-based benchmarks. In this paper, we systematically evaluate RAG and GraphRAG on well-established benchmark tasks, such as Question Answering and Query-based Summarization. Our results highlight the distinct strengths of RAG and GraphRAG across different tasks and evaluation perspectives. Inspired by these observations, we investigate strategies to integrate their strengths to improve downstream tasks. Additionally, we provide an in-depth discussion of the shortcomings of current GraphRAG approaches and outline directions for future research.

Retrieval-augmented generation (RAG) empowers large language models to access external and private corpus, enabling factually consistent responses in specific domains. By exploiting the inherent structure of the corpus, graph-based RAG methods further enrich this process by building a knowledge graph index and leveraging the structural nature of graphs. However, current graph-based RAG approaches seldom prioritize the design of graph structures. Inadequately designed graph not only impede the seamless integration of diverse graph algorithms but also result in workflow inconsistencies and degraded performance. To further unleash the potential of graph for RAG, we propose NodeRAG, a graph-centric framework introducing heterogeneous graph structures that enable the seamless and holistic integration of graph-based methodologies into the RAG workflow. By aligning closely with the capabilities of LLMs, this framework ensures a fully cohesive and efficient end-to-end process. Through extensive experiments, we demonstrate that NodeRAG exhibits performance advantages over previous methods, including GraphRAG and LightRAG, not only in indexing time, query time, and storage efficiency but also in delivering superior question-answering performance on multi-hop benchmarks and open-ended head-to-head evaluations with minimal retrieval tokens. Our GitHub repository could be seen at https://github.com/Terry-Xu-666/NodeRAG.