Graph-based Retrieval-Augmented Generation (Graph-RAG) enhances large language models (LLMs) by structuring retrieval over an external corpus. However, existing approaches typically assume a static corpus, requiring expensive full-graph reconstruction whenever new documents arrive, limiting their scalability in dynamic, evolving environments. To address these limitations, we introduce EraRAG, a novel multi-layered Graph-RAG framework that supports efficient and scalable dynamic updates. Our method leverages hyperplane-based Locality-Sensitive Hashing (LSH) to partition and organize the original corpus into hierarchical graph structures, enabling efficient and localized insertions of new data without disrupting the existing topology. The design eliminates the need for retraining or costly recomputation while preserving high retrieval accuracy and low latency. Experiments on large-scale benchmarks demonstrate that EraRag achieves up to an order of magnitude reduction in update time and token consumption compared to existing Graph-RAG systems, while providing superior accuracy performance. This work offers a practical path forward for RAG systems that must operate over continually growing corpora, bridging the gap between retrieval efficiency and adaptability. Our code and data are available at https://github.com/EverM0re/EraRAG-Official.
Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic, low-dimensional and weakly nonlinear time-series data. To address these limitations, we present CausalDynamics, a large-scale benchmark and extensible data generation framework to advance the structural discovery of dynamical causal models. Our benchmark consists of true causal graphs derived from thousands of coupled ordinary and stochastic differential equations as well as two idealized climate models. We perform a comprehensive evaluation of state-of-the-art causal discovery algorithms for graph reconstruction on systems with noisy, confounded, and lagged dynamics. CausalDynamics consists of a plug-and-play, build-your-own coupling workflow that enables the construction of a hierarchy of physical systems. We anticipate that our framework will facilitate the development of robust causal discovery algorithms that are broadly applicable across domains while addressing their unique challenges. We provide a user-friendly implementation and documentation on https://kausable.github.io/CausalDynamics.
Federated learning claims to enable collaborative model training among multiple clients with data privacy by transmitting gradient updates instead of the actual client data. However, recent studies have shown the client privacy is still at risk due to the, so called, gradient inversion attacks which can precisely reconstruct clients' text and image data from the shared gradient updates. While these attacks demonstrate severe privacy risks for certain domains and architectures, the vulnerability of other commonly-used data types, such as graph-structured data, remain under-explored. To bridge this gap, we present GRAIN, the first exact gradient inversion attack on graph data in the honest-but-curious setting that recovers both the structure of the graph and the associated node features. Concretely, we focus on Graph Convolutional Networks (GCN) and Graph Attention Networks (GAT) -- two of the most widely used frameworks for learning on graphs. Our method first utilizes the low-rank structure of GNN gradients to efficiently reconstruct and filter the client subgraphs which are then joined to complete the input graph. We evaluate our approach on molecular, citation, and social network datasets using our novel metric. We show that GRAIN reconstructs up to 80% of all graphs exactly, significantly outperforming the baseline, which achieves up to 20% correctly positioned nodes.
We propose a novel machine learning approach for inferring causal variables of a target variable from observations. Our focus is on directly inferring a set of causal factors without requiring full causal graph reconstruction, which is computationally challenging in large-scale systems. The identified causal set consists of all potential regulators of the target variable under experimental settings, enabling efficient regulation when intervention costs and feasibility vary across variables. To achieve this, we train a neural network using supervised learning on simulated data to infer causality. By employing a local-inference strategy, our approach scales with linear complexity in the number of variables, efficiently scaling up to thousands of variables. Empirical results demonstrate superior performance in identifying causal relationships within large-scale gene regulatory networks, outperforming existing methods that emphasize full-graph discovery. We validate our model's generalization capability across out-of-distribution graph structures and generating mechanisms, including gene regulatory networks of E. coli and the human K562 cell line. Implementation codes are available at https://github.com/snu-mllab/Targeted-Cause-Discovery.
Evolving networks are complex data structures that emerge in a wide range of systems in science and engineering. Learning expressive representations for such networks that encode their structural connectivity and temporal evolution is essential for downstream data analytics and machine learning applications. In this study, we introduce a self-supervised method for learning representations of temporal networks and employ these representations in the dynamic link prediction task. While temporal networks are typically characterized as a sequence of interactions over the continuous time domain, our study focuses on their discrete-time versions. This enables us to balance the trade-off between computational complexity and precise modeling of the interactions. We propose a recurrent message-passing neural network architecture for modeling the information flow over time-respecting paths of temporal networks. The key feature of our method is the contrastive training objective of the model, which is a combination of three loss functions: link prediction, graph reconstruction, and contrastive predictive coding losses. The contrastive predictive coding objective is implemented using infoNCE losses at both local and global scales of the input graphs. We empirically show that the additional self-supervised losses enhance the training and improve the model's performance in the dynamic link prediction task. The proposed method is tested on Enron, COLAB, and Facebook datasets and exhibits superior results compared to existing models.
Intent modeling has attracted widespread attention in recommender systems. As the core motivation behind user selection of items, intent is crucial for elucidating recommendation results. The current mainstream modeling method is to abstract the intent into unknowable but learnable shared or non-shared parameters. Despite considerable progress, we argue that it still confronts the following challenges: firstly, these methods only capture the coarse-grained aspects of intent, ignoring the fact that user-item interactions will be affected by collective and individual factors (e.g., a user may choose a movie because of its high box office or because of his own unique preferences); secondly, modeling believable intent is severely hampered by implicit feedback, which is incredibly sparse and devoid of true semantics. To address these challenges, we propose a novel recommendation framework designated as Bilateral Intent-guided Graph Collaborative Filtering (BIGCF). Specifically, we take a closer look at user-item interactions from a causal perspective and put forth the concepts of individual intent-which signifies private preferences-and collective intent-which denotes overall awareness. To counter the sparsity of implicit feedback, the feature distributions of users and items are encoded via a Gaussian-based graph generation strategy, and we implement the recommendation process through bilateral intent-guided graph reconstruction re-sampling. Finally, we propose graph contrastive regularization for both interaction and intent spaces to uniformize users, items, intents, and interactions in a self-supervised and non-augmented paradigm. Experimental results on three real-world datasets demonstrate the effectiveness of BIGCF compared with existing solutions.
Graph pooling compresses graph information into a compact representation. State-of-the-art graph pooling methods follow a hierarchical approach, which reduces the graph size step-by-step. These methods must balance memory efficiency with preserving node information, depending on whether they use node dropping or node clustering. Additionally, fixed pooling ratios or numbers of pooling layers are predefined for all graphs, which prevents personalized pooling structures from being captured for each individual graph. In this work, inspired by bottom-up grammar induction, we propose an efficient graph parsing algorithm to infer the pooling structure, which then drives graph pooling. The resulting Graph Parsing Network (GPN) adaptively learns personalized pooling structure for each individual graph. GPN benefits from the discrete assignments generated by the graph parsing algorithm, allowing good memory efficiency while preserving node information intact. Experimental results on standard benchmarks demonstrate that GPN outperforms state-of-the-art graph pooling methods in graph classification tasks while being able to achieve competitive performance in node classification tasks. We also conduct a graph reconstruction task to show GPN's ability to preserve node information and measure both memory and time efficiency through relevant tests.
Traffic forecasting is crucial for intelligent transportation systems (ITS), aiding in efficient resource allocation and effective traffic control. However, its effectiveness often relies heavily on abundant traffic data, while many cities lack sufficient data due to limited device support, posing a significant challenge for traffic forecasting. Recognizing this challenge, we have made a noteworthy observation: traffic patterns exhibit similarities across diverse cities. Building on this key insight, we propose a solution for the cross-city few-shot traffic forecasting problem called Multi-scale Traffic Pattern Bank (MTPB). Primarily, MTPB initiates its learning process by leveraging data-rich source cities, effectively acquiring comprehensive traffic knowledge through a spatial-temporal-aware pre-training process. Subsequently, the framework employs advanced clustering techniques to systematically generate a multi-scale traffic pattern bank derived from the learned knowledge. Next, the traffic data of the data-scarce target city could query the traffic pattern bank, facilitating the aggregation of meta-knowledge. This meta-knowledge, in turn, assumes a pivotal role as a robust guide in subsequent processes involving graph reconstruction and forecasting. Empirical assessments conducted on real-world traffic datasets affirm the superior performance of MTPB, surpassing existing methods across various categories and exhibiting numerous attributes conducive to the advancement of cross-city few-shot forecasting methodologies. The code is available in https://github.com/zhyliu00/MTPB.
Theoretical results from discrete geometry suggest that normed spaces can abstractly embed finite metric spaces with surprisingly low theoretical bounds on distortion in low dimensions. In this paper, inspired by this theoretical insight, we highlight normed spaces as a more flexible and computationally efficient alternative to several popular Riemannian manifolds for learning graph embeddings. Normed space embeddings significantly outperform several popular manifolds on a large range of synthetic and real-world graph reconstruction benchmark datasets while requiring significantly fewer computational resources. We also empirically verify the superiority of normed space embeddings on growing families of graphs associated with negative, zero, and positive curvature, further reinforcing the flexibility of normed spaces in capturing diverse graph structures as graph sizes increase. Lastly, we demonstrate the utility of normed space embeddings on two applied graph embedding tasks, namely, link prediction and recommender systems. Our work highlights the potential of normed spaces for geometric graph representation learning, raises new research questions, and offers a valuable tool for experimental mathematics in the field of finite metric space embeddings. We make our code and data publically available.
By treating users' interactions as a user-item graph, graph learning models have been widely deployed in Collaborative Filtering(CF) based recommendation. Recently, researchers have introduced Graph Contrastive Learning(GCL) techniques into CF to alleviate the sparse supervision issue, which first constructs contrastive views by data augmentations and then provides self-supervised signals by maximizing the mutual information between contrastive views. Despite the effectiveness, we argue that current GCL-based recommendation models are still limited as current data augmentation techniques, either structure augmentation or feature augmentation. First, structure augmentation randomly dropout nodes or edges, which is easy to destroy the intrinsic nature of the user-item graph. Second, feature augmentation imposes the same scale noise augmentation on each node, which neglects the unique characteristics of nodes on the graph. To tackle the above limitations, we propose a novel Variational Graph Generative-Contrastive Learning(VGCL) framework for recommendation. Specifically, we leverage variational graph reconstruction to estimate a Gaussian distribution of each node, then generate multiple contrastive views through multiple samplings from the estimated distributions, which builds a bridge between generative and contrastive learning. Besides, the estimated variances are tailored to each node, which regulates the scale of contrastive loss for each node on optimization. Considering the similarity of the estimated distributions, we propose a cluster-aware twofold contrastive learning, a node-level to encourage consistency of a node's contrastive views and a cluster-level to encourage consistency of nodes in a cluster. Finally, extensive experimental results on three public datasets clearly demonstrate the effectiveness of the proposed model.
Although powerful graph neural networks (GNNs) have boosted numerous real-world applications, the potential privacy risk is still underexplored. To close this gap, we perform the first comprehensive study of graph reconstruction attack that aims to reconstruct the adjacency of nodes. We show that a range of factors in GNNs can lead to the surprising leakage of private links. Especially by taking GNNs as a Markov chain and attacking GNNs via a flexible chain approximation, we systematically explore the underneath principles of graph reconstruction attack, and propose two information theory-guided mechanisms: (1) the chain-based attack method with adaptive designs for extracting more private information; (2) the chain-based defense method that sharply reduces the attack fidelity with moderate accuracy loss. Such two objectives disclose a critical belief that to recover better in attack, you must extract more multi-aspect knowledge from the trained GNN; while to learn safer for defense, you must forget more link-sensitive information in training GNNs. Empirically, we achieve state-of-the-art results on six datasets and three common GNNs. The code is publicly available at: https://github.com/tmlr-group/MC-GRA.
Network embedding, a graph representation learning method illustrating network topology by mapping nodes into lower-dimension vectors, is challenging to accommodate the ever-changing dynamic graphs in practice. Existing research is mainly based on node-by-node embedding modifications, which falls into the dilemma of efficient calculation and accuracy. Observing that the embedding dimensions are usually much smaller than the number of nodes, we break this dilemma with a novel dynamic network embedding paradigm that rotates and scales the axes of embedding space instead of a node-by-node update. Specifically, we propose the Dynamic Adjacency Matrix Factorization (DAMF) algorithm, which achieves an efficient and accurate dynamic network embedding by rotating and scaling the coordinate system where the network embedding resides with no more than the number of edge modifications changes of node embeddings. Moreover, a dynamic Personalized PageRank is applied to the obtained network embeddings to enhance node embeddings and capture higher-order neighbor information dynamically. Experiments of node classification, link prediction, and graph reconstruction on different-sized dynamic graphs suggest that DAMF advances dynamic network embedding. Further, we unprecedentedly expand dynamic network embedding experiments to billion-edge graphs, where DAMF updates billion-level parameters in less than 10ms.
Incomplete multi-view clustering is a hot and emerging topic. It is well known that unavoidable data incompleteness greatly weakens the effective information of multi-view data. To date, existing incomplete multi-view clustering methods usually bypass unavailable views according to prior missing information, which is considered as a second-best scheme based on evasion. Other methods that attempt to recover missing information are mostly applicable to specific two-view datasets. To handle these problems, in this paper, we propose an information recovery-driven deep incomplete multi-view clustering network, termed as RecFormer. Concretely, a two-stage autoencoder network with the self-attention structure is built to synchronously extract high-level semantic representations of multiple views and recover the missing data. Besides, we develop a recurrent graph reconstruction mechanism that cleverly leverages the restored views to promote the representation learning and the further data reconstruction. Visualization of recovery results are given and sufficient experimental results confirm that our RecFormer has obvious advantages over other top methods.
Person re-identification (re-ID) via 3D skeleton data is an emerging topic with prominent advantages. Existing methods usually design skeleton descriptors with raw body joints or perform skeleton sequence representation learning. However, they typically cannot concurrently model different body-component relations, and rarely explore useful semantics from fine-grained representations of body joints. In this paper, we propose a generic Transformer-based Skeleton Graph prototype contrastive learning (TranSG) approach with structure-trajectory prompted reconstruction to fully capture skeletal relations and valuable spatial-temporal semantics from skeleton graphs for person re-ID. Specifically, we first devise the Skeleton Graph Transformer (SGT) to simultaneously learn body and motion relations within skeleton graphs, so as to aggregate key correlative node features into graph representations. Then, we propose the Graph Prototype Contrastive learning (GPC) to mine the most typical graph features (graph prototypes) of each identity, and contrast the inherent similarity between graph representations and different prototypes from both skeleton and sequence levels to learn discriminative graph representations. Last, a graph Structure-Trajectory Prompted Reconstruction (STPR) mechanism is proposed to exploit the spatial and temporal contexts of graph nodes to prompt skeleton graph reconstruction, which facilitates capturing more valuable patterns and graph semantics for person re-ID. Empirical evaluations demonstrate that TranSG significantly outperforms existing state-of-the-art methods. We further show its generality under different graph modeling, RGB-estimated skeletons, and unsupervised scenarios.
Computational discovery of ideal lead compounds is a critical process for modern drug discovery. It comprises multiple stages: hit screening, molecular property prediction, and molecule optimization. Current efforts are disparate, involving the establishment of models for each stage, followed by multi-stage multi-model integration. However, this is non-ideal, as clumsy integration of incompatible models increases research overheads, and may even reduce success rates in drug discovery. Facilitating compatibilities requires establishing inherent model consistencies across lead discovery stages. Towards that effect, we propose an open deep graph learning (DGL) based pipeline: generative adversarial feature subspace enhancement (GAFSE), which first unifies the modeling of these stages into one learning framework. GAFSE also offers standardized modular design and streamlined interfaces for future expansions and community support. GAFSE combines adversarial/generative learning, graph attention network, graph reconstruction network, and optimizes the classification/regression loss, adversarial/generative loss, and reconstruction loss simultaneously. Convergence analysis theoretically guarantees model generalization performance. Exhaustive benchmarking demonstrates that the GAFSE pipeline achieves excellent performance across almost all lead discovery stages, while also providing valuable model interpretability. Hence, we believe this tool will enhance the efficiency and productivity of drug discovery researchers.
Effective data imputation demands rich latent ``structure" discovery capabilities from ``plain" tabular data. Recent advances in graph neural networks-based data imputation solutions show their strong structure learning potential by directly translating tabular data as bipartite graphs. However, due to a lack of relations between samples, those solutions treat all samples equally which is against one important observation: ``similar sample should give more information about missing values." This paper presents a novel Iterative graph Generation and Reconstruction framework for Missing data imputation(IGRM). Instead of treating all samples equally, we introduce the concept: ``friend networks" to represent different relations among samples. To generate an accurate friend network with missing data, an end-to-end friend network reconstruction solution is designed to allow for continuous friend network optimization during imputation learning. The representation of the optimized friend network, in turn, is used to further optimize the data imputation process with differentiated message passing. Experiment results on eight benchmark datasets show that IGRM yields 39.13% lower mean absolute error compared with nine baselines and 9.04% lower than the second-best. Our code is available at https://github.com/G-AILab/IGRM.
Privacy and interpretability are two important ingredients for achieving trustworthy machine learning. We study the interplay of these two aspects in graph machine learning through graph reconstruction attacks. The goal of the adversary here is to reconstruct the graph structure of the training data given access to model explanations. Based on the different kinds of auxiliary information available to the adversary, we propose several graph reconstruction attacks. We show that additional knowledge of post-hoc feature explanations substantially increases the success rate of these attacks. Further, we investigate in detail the differences between attack performance with respect to three different classes of explanation methods for graph neural networks: gradient-based, perturbation-based, and surrogate model-based methods. While gradient-based explanations reveal the most in terms of the graph structure, we find that these explanations do not always score high in utility. For the other two classes of explanations, privacy leakage increases with an increase in explanation utility. Finally, we propose a defense based on a randomized response mechanism for releasing the explanations, which substantially reduces the attack success rate. Our code is available at https://github.com/iyempissy/graph-stealing-attacks-with-explanation
Spatio-temporal graph learning is a key method for urban computing tasks, such as traffic flow, taxi demand and air quality forecasting. Due to the high cost of data collection, some developing cities have few available data, which makes it infeasible to train a well-performed model. To address this challenge, cross-city knowledge transfer has shown its promise, where the model learned from data-sufficient cities is leveraged to benefit the learning process of data-scarce cities. However, the spatio-temporal graphs among different cities show irregular structures and varied features, which limits the feasibility of existing Few-Shot Learning (\emph{FSL}) methods. Therefore, we propose a model-agnostic few-shot learning framework for spatio-temporal graph called ST-GFSL. Specifically, to enhance feature extraction by transfering cross-city knowledge, ST-GFSL proposes to generate non-shared parameters based on node-level meta knowledge. The nodes in target city transfer the knowledge via parameter matching, retrieving from similar spatio-temporal characteristics. Furthermore, we propose to reconstruct the graph structure during meta-learning. The graph reconstruction loss is defined to guide structure-aware learning, avoiding structure deviation among different datasets. We conduct comprehensive experiments on four traffic speed prediction benchmarks and the results demonstrate the effectiveness of ST-GFSL compared with state-of-the-art methods.
Graph Convolutional Networks (GCN) have achieved state-of-art results on single text classification tasks like sentiment analysis, emotion detection, etc. However, the performance is achieved by testing and reporting on resource-rich languages like English. Applying GCN for multi-task text classification is an unexplored area. Moreover, training a GCN or adopting an English GCN for Indian languages is often limited by data availability, rich morphological variation, syntax, and semantic differences. In this paper, we study the use of GCN for the Telugu language in single and multi-task settings for four natural language processing (NLP) tasks, viz. sentiment analysis (SA), emotion identification (EI), hate-speech (HS), and sarcasm detection (SAR). In order to evaluate the performance of GCN with one of the Indian languages, Telugu, we analyze the GCN based models with extensive experiments on four downstream tasks. In addition, we created an annotated Telugu dataset, TEL-NLP, for the four NLP tasks. Further, we propose a supervised graph reconstruction method, Multi-Task Text GCN (MT-Text GCN) on the Telugu that leverages to simultaneously (i) learn the low-dimensional word and sentence graph embeddings from word-sentence graph reconstruction using graph autoencoder (GAE) and (ii) perform multi-task text classification using these latent sentence graph embeddings. We argue that our proposed MT-Text GCN achieves significant improvements on TEL-NLP over existing Telugu pretrained word embeddings, and multilingual pretrained Transformer models: mBERT, and XLM-R. On TEL-NLP, we achieve a high F1-score for four NLP tasks: SA (0.84), EI (0.55), HS (0.83) and SAR (0.66). Finally, we show our model's quantitative and qualitative analysis on the four NLP tasks in Telugu.
Graph neural networks (GNNs) have drawn significant research attention recently, mostly under the setting of semi-supervised learning. When task-agnostic representations are preferred or supervision is simply unavailable, the auto-encoder framework comes in handy with a natural graph reconstruction objective for unsupervised GNN training. However, existing graph auto-encoders are designed to reconstruct the direct links, so GNNs trained in this way are only optimized towards proximity-oriented graph mining tasks, and will fall short when the topological structures matter. In this work, we revisit the graph encoding process of GNNs which essentially learns to encode the neighborhood information of each node into an embedding vector, and propose a novel graph decoder to reconstruct the entire neighborhood information regarding both proximity and structure via Neighborhood Wasserstein Reconstruction (NWR). Specifically, from the GNN embedding of each node, NWR jointly predicts its node degree and neighbor feature distribution, where the distribution prediction adopts an optimal-transport loss based on the Wasserstein distance. Extensive experiments on both synthetic and real-world network datasets show that the unsupervised node representations learned with NWR have much more advantageous in structure-oriented graph mining tasks, while also achieving competitive performance in proximity-oriented ones.