Federated graph learning collaboratively learns a global graph neural network with distributed graphs, where the non-independent and identically distributed property is one of the major challenges. Most relative arts focus on traditional distributed tasks like images and voices, incapable of graph structures. This paper firstly reveals that local client distortion is brought by both node-level semantics and graph-level structure. First, for node-level semantics, we find that contrasting nodes from distinct classes is beneficial to provide a well-performing discrimination. We pull the local node towards the global node of the same class and push it away from the global node of different classes. Second, we postulate that a well-structural graph neural network possesses similarity for neighbors due to the inherent adjacency relationships. However, aligning each node with adjacent nodes hinders discrimination due to the potential class inconsistency. We transform the adjacency relationships into the similarity distribution and leverage the global model to distill the relation knowledge into the local model, which preserves the structural information and discriminability of the local model. Empirical results on three graph datasets manifest the superiority of the proposed method over its counterparts.
In this paper, we present the Fast Optimizer Benchmark (FOB), a tool designed for evaluating deep learning optimizers during their development. The benchmark supports tasks from multiple domains such as computer vision, natural language processing, and graph learning. The focus is on convenient usage, featuring human-readable YAML configurations, SLURM integration, and plotting utilities. FOB can be used together with existing hyperparameter optimization (HPO) tools as it handles training and resuming of runs. The modular design enables integration into custom pipelines, using it simply as a collection of tasks. We showcase an optimizer comparison as a usage example of our tool. FOB can be found on GitHub: https://github.com/automl/FOB.
In our recent research, we have developed a framework called GraphSnapShot, which has been proven an useful tool for graph learning acceleration. GraphSnapShot is a framework for fast cache, storage, retrieval and computation for graph learning. It can quickly store and update the local topology of graph structure and allows us to track patterns in the structure of graph networks, just like take snapshots of the graphs. In experiments, GraphSnapShot shows efficiency, it can achieve up to 30% training acceleration and 73% memory reduction for lossless graph ML training compared to current baselines such as dgl.This technique is particular useful for large dynamic graph learning tasks such as social media analysis and recommendation systems to process complex relationships between entities. The code for GraphSnapShot is publicly available at https://github.com/NoakLiu/GraphSnapShot.
In recent years, Graph Neural Networks (GNNs) have become the de facto tool for learning node and graph representations. Most GNNs typically consist of a sequence of neighborhood aggregation (a.k.a., message-passing) layers, within which the representation of each node is updated based on those of its neighbors. The most expressive message-passing GNNs can be obtained through the use of the sum aggregator and of MLPs for feature transformation, thanks to their universal approximation capabilities. However, the limitations of MLPs recently motivated the introduction of another family of universal approximators, called Kolmogorov-Arnold Networks (KANs) which rely on a different representation theorem. In this work, we compare the performance of KANs against that of MLPs on graph learning tasks. We evaluate two different implementations of KANs using two distinct base families of functions, namely B-splines and radial basis functions. We perform extensive experiments on node classification, graph classification and graph regression datasets. Our results indicate that KANs are on-par with or better than MLPs on all studied tasks, making them viable alternatives, at the cost of some computational complexity. Code is available at https: //github.com/RomanBresson/KAGNN.
This paper introduces novel methodologies, the Distance Recomputator and Topology Reconstructor, aimed at enhancing Graph Neural Networks (GNNs). The Distance Recomputator dynamically recalibrates node distances within k-hop neighborhoods using a dynamic encoding scheme, thereby improving the accuracy and adaptability of node representations. Concurrently, the Topology Reconstructor adjusts local graph structures based on computed "similarity distances," optimizing network configurations for improved learning outcomes. These methods address the limitations of static node representations and fixed aggregation schemes in traditional GNNs, offering a more nuanced approach to modeling complex and dynamic graph topologies. Furthermore, our experimental evaluations demonstrate significant performance advantages over existing methods across various benchmark datasets. The proposed Distance Recomputator and Topology Reconstructor not only enhance node relationship modeling accuracy but also optimize information aggregation efficiency through an asynchronous aggregation mechanism. This approach proves particularly effective in scenarios involving dynamic or large-scale graphs, showcasing the methods' robustness and applicability in real-world graph learning tasks.
Click-through-rate (CTR) prediction has an essential impact on improving user experience and revenue in e-commerce search. With the development of deep learning, graph-based methods are well exploited to utilize graph structure extracted from user behaviors and other information to help embedding learning. However, most of the previous graph-based methods mainly focus on recommendation scenarios, and therefore their graph structures highly depend on item's sequential information from user behaviors, ignoring query's sequential signal and query-item correlation. In this paper, we propose a new approach named Light-weight End-to-End Graph Interest Network (EGIN) to effectively mine users' search interests and tackle previous challenges. (i) EGIN utilizes query and item's correlation and sequential information from the search system to build a heterogeneous graph for better CTR prediction in e-commerce search. (ii) EGIN's graph embedding learning shares the same training input and is jointly trained with CTR prediction, making the end-to-end framework effortless to deploy in large-scale search systems. The proposed EGIN is composed of three parts: query-item heterogeneous graph, light-weight graph sampling, and multi-interest network. The query-item heterogeneous graph captures correlation and sequential information of query and item efficiently by the proposed light-weight graph sampling. The multi-interest network is well designed to utilize graph embedding to capture various similarity relationships between query and item to enhance the final CTR prediction. We conduct extensive experiments on both public and industrial datasets to demonstrate the effectiveness of the proposed EGIN. At the same time, the training cost of graph learning is relatively low compared with the main CTR prediction task, ensuring efficiency in practical applications.
Message-Passing Neural Networks (MPNNs) are extensively employed in graph learning tasks but suffer from limitations such as the restricted scope of information exchange, by being confined to neighboring nodes during each round of message passing. Various strategies have been proposed to address these limitations, including incorporating virtual nodes to facilitate global information exchange. In this study, we introduce the Hierarchical Support Graph (HSG), an extension of the virtual node concept created through recursive coarsening of the original graph. This approach provides a flexible framework for enhancing information flow in graphs, independent of the specific MPNN layers utilized. We present a theoretical analysis of HSGs, investigate their empirical performance, and demonstrate that HSGs can surpass other methods augmented with virtual nodes, achieving state-of-the-art results across multiple datasets.
Graph Neural Networks (GNNs) are widely applied to graph learning problems such as node classification. When scaling up the underlying graphs of GNNs to a larger size, we are forced to either train on the complete graph and keep the full graph adjacency and node embeddings in memory (which is often infeasible) or mini-batch sample the graph (which results in exponentially growing computational complexities with respect to the number of GNN layers). Various sampling-based and historical-embedding-based methods are proposed to avoid this exponential growth of complexities. However, none of these solutions eliminates the linear dependence on graph size. This paper proposes a sketch-based algorithm whose training time and memory grow sublinearly with respect to graph size by training GNNs atop a few compact sketches of graph adjacency and node embeddings. Based on polynomial tensor-sketch (PTS) theory, our framework provides a novel protocol for sketching non-linear activations and graph convolution matrices in GNNs, as opposed to existing methods that sketch linear weights or gradients in neural networks. In addition, we develop a locality-sensitive hashing (LSH) technique that can be trained to improve the quality of sketches. Experiments on large-graph benchmarks demonstrate the scalability and competitive performance of our Sketch-GNNs versus their full-size GNN counterparts.
Graph machine learning has made significant strides in recent years, yet the integration of visual information with graph structure and its potential for improving performance in downstream tasks remains an underexplored area. To address this critical gap, we introduce the Multimodal Graph Benchmark (MM-GRAPH), a pioneering benchmark that incorporates both visual and textual information into graph learning tasks. MM-GRAPH extends beyond existing text-attributed graph benchmarks, offering a more comprehensive evaluation framework for multimodal graph learning Our benchmark comprises seven diverse datasets of varying scales (ranging from thousands to millions of edges), designed to assess algorithms across different tasks in real-world scenarios. These datasets feature rich multimodal node attributes, including visual data, which enables a more holistic evaluation of various graph learning frameworks in complex, multimodal environments. To support advancements in this emerging field, we provide an extensive empirical study on various graph learning frameworks when presented with features from multiple modalities, particularly emphasizing the impact of visual information. This study offers valuable insights into the challenges and opportunities of integrating visual data into graph learning.
Graph Convolutional Networks (GCNs) have been widely studied. The core of GCNs is the definition of convolution operators on graphs. However, existing Graph Convolution (GC) operators are mainly defined on adjacency matrix and node features and generally focus on obtaining effective node embeddings which cannot be utilized to address the graphs with (high-dimensional) edge features. To address this problem, by leveraging tensor contraction representation and tensor product graph diffusion theories, this paper analogously defines an effective convolution operator on graphs with edge features which is named as Tensor Product Graph Convolution (TPGC). The proposed TPGC aims to obtain effective edge embeddings. It provides a complementary model to traditional graph convolutions (GCs) to address the more general graph data analysis with both node and edge features. Experimental results on several graph learning tasks demonstrate the effectiveness of the proposed TPGC.
Graph deep learning (GDL) has demonstrated impressive performance in predicting population-based brain disorders (BDs) through the integration of both imaging and non-imaging data. However, the effectiveness of GDL based methods heavily depends on the quality of modeling the multi-modal population graphs and tends to degrade as the graph scale increases. Furthermore, these methods often constrain interactions between imaging and non-imaging data to node-edge interactions within the graph, overlooking complex inter-modal correlations, leading to suboptimal outcomes. To overcome these challenges, we propose MM-GTUNets, an end-to-end graph transformer based multi-modal graph deep learning (MMGDL) framework designed for brain disorders prediction at large scale. Specifically, to effectively leverage rich multi-modal information related to diseases, we introduce Modality Reward Representation Learning (MRRL) which adaptively constructs population graphs using a reward system. Additionally, we employ variational autoencoder to reconstruct latent representations of non-imaging features aligned with imaging features. Based on this, we propose Adaptive Cross-Modal Graph Learning (ACMGL), which captures critical modality-specific and modality-shared features through a unified GTUNet encoder taking advantages of Graph UNet and Graph Transformer, and feature fusion module. We validated our method on two public multi-modal datasets ABIDE and ADHD-200, demonstrating its superior performance in diagnosing BDs. Our code is available at https://github.com/NZWANG/MM-GTUNets.
Graph Neural Networks (GNNs) have shown impressive performance in graph representation learning, but they face challenges in capturing long-range dependencies due to their limited expressive power. To address this, Graph Transformers (GTs) were introduced, utilizing self-attention mechanism to effectively model pairwise node relationships. Despite their advantages, GTs suffer from quadratic complexity w.r.t. the number of nodes in the graph, hindering their applicability to large graphs. In this work, we present Graph-Enhanced Contextual Operator (GECO), a scalable and effective alternative to GTs that leverages neighborhood propagation and global convolutions to effectively capture local and global dependencies in quasilinear time. Our study on synthetic datasets reveals that GECO reaches 169x speedup on a graph with 2M nodes w.r.t. optimized attention. Further evaluations on diverse range of benchmarks showcase that GECO scales to large graphs where traditional GTs often face memory and time limitations. Notably, GECO consistently achieves comparable or superior quality compared to baselines, improving the SOTA up to 4.5%, and offering a scalable and effective solution for large-scale graph learning.
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.
Dynamic text-attributed graphs (DyTAGs) are prevalent in various real-world scenarios, where each node and edge are associated with text descriptions, and both the graph structure and text descriptions evolve over time. Despite their broad applicability, there is a notable scarcity of benchmark datasets tailored to DyTAGs, which hinders the potential advancement in many research fields. To address this gap, we introduce Dynamic Text-attributed Graph Benchmark (DTGB), a collection of large-scale, time-evolving graphs from diverse domains, with nodes and edges enriched by dynamically changing text attributes and categories. To facilitate the use of DTGB, we design standardized evaluation procedures based on four real-world use cases: future link prediction, destination node retrieval, edge classification, and textual relation generation. These tasks require models to understand both dynamic graph structures and natural language, highlighting the unique challenges posed by DyTAGs. Moreover, we conduct extensive benchmark experiments on DTGB, evaluating 7 popular dynamic graph learning algorithms and their variants of adapting to text attributes with LLM embeddings, along with 6 powerful large language models (LLMs). Our results show the limitations of existing models in handling DyTAGs. Our analysis also demonstrates the utility of DTGB in investigating the incorporation of structural and textual dynamics. The proposed DTGB fosters research on DyTAGs and their broad applications. It offers a comprehensive benchmark for evaluating and advancing models to handle the interplay between dynamic graph structures and natural language. The dataset and source code are available at https://github.com/zjs123/DTGB.
Federated Graph Learning (FGL) has emerged as a promising way to learn high-quality representations from distributed graph data with privacy preservation. Despite considerable efforts have been made for FGL under either cross-device or cross-silo paradigm, how to effectively capture graph knowledge in a more complicated cross-silo cross-device environment remains an under-explored problem. However, this task is challenging because of the inherent hierarchy and heterogeneity of decentralized clients, diversified privacy constraints in different clients, and the cross-client graph integrity requirement. To this end, in this paper, we propose a Hierarchical Federated Graph Learning (HiFGL) framework for cross-silo cross-device FGL. Specifically, we devise a unified hierarchical architecture to safeguard federated GNN training on heterogeneous clients while ensuring graph integrity. Moreover, we propose a Secret Message Passing (SecMP) scheme to shield unauthorized access to subgraph-level and node-level sensitive information simultaneously. Theoretical analysis proves that HiFGL achieves multi-level privacy preservation with complexity guarantees. Extensive experiments on real-world datasets validate the superiority of the proposed framework against several baselines. Furthermore, HiFGL's versatile nature allows for its application in either solely cross-silo or cross-device settings, further broadening its utility in real-world FGL applications.
Causal learning tackles the computationally demanding task of estimating causal graphs. This paper introduces a new divide-and-conquer approach for causal graph learning, called DCILP. In the divide phase, the Markov blanket MB($X_i$) of each variable $X_i$ is identified, and causal learning subproblems associated with each MB($X_i$) are independently addressed in parallel. This approach benefits from a more favorable ratio between the number of data samples and the number of variables considered. In counterpart, it can be adversely affected by the presence of hidden confounders, as variables external to MB($X_i$) might influence those within it. The reconciliation of the local causal graphs generated during the divide phase is a challenging combinatorial optimization problem, especially in large-scale applications. The main novelty of DCILP is an original formulation of this reconciliation as an integer linear programming (ILP) problem, which can be delegated and efficiently handled by an ILP solver. Through experiments on medium to large scale graphs, and comparisons with state-of-the-art methods, DCILP demonstrates significant improvements in terms of computational complexity, while preserving the learning accuracy on real-world problem and suffering at most a slight loss of accuracy on synthetic problems.
The field of temporal graph learning aims to learn from evolving network data to forecast future interactions. Given a collection of observed temporal graphs, is it possible to predict the evolution of an unseen network from the same domain? To answer this question, we first present the Temporal Graph Scaling (TGS) dataset, a large collection of temporal graphs consisting of eighty-four ERC20 token transaction networks collected from 2017 to 2023. Next, we evaluate the transferability of Temporal Graph Neural Networks (TGNNs) for the temporal graph property prediction task by pre-training on a collection of up to sixty-four token transaction networks and then evaluating the downstream performance on twenty unseen token networks. We find that the neural scaling law observed in NLP and Computer Vision also applies in temporal graph learning, where pre-training on greater number of networks leads to improved downstream performance. To the best of our knowledge, this is the first empirical demonstration of the transferability of temporal graphs learning. On downstream token networks, the largest pre-trained model outperforms single model TGNNs on thirteen unseen test networks. Therefore, we believe that this is a promising first step towards building foundation models for temporal graphs.
Foundation models (FMs) are large-scale deep learning models trained on massive datasets, often using self-supervised learning techniques. These models serve as a versatile base for a wide range of downstream tasks, including those in medicine and healthcare. FMs have demonstrated remarkable success across multiple healthcare domains. However, existing surveys in this field do not comprehensively cover all areas where FMs have made significant strides. In this survey, we present a comprehensive review of FMs in medicine, focusing on their evolution, learning strategies, flagship models, applications, and associated challenges. We examine how prominent FMs, such as the BERT and GPT families, are transforming various aspects of healthcare, including clinical large language models, medical image analysis, and omics research. Additionally, we provide a detailed taxonomy of FM-enabled healthcare applications, spanning clinical natural language processing, medical computer vision, graph learning, and other biology- and omics- related tasks. Despite the transformative potentials of FMs, they also pose unique challenges. This survey delves into these challenges and highlights open research questions and lessons learned to guide researchers and practitioners. Our goal is to provide valuable insights into the capabilities of FMs in health, facilitating responsible deployment and mitigating associated risks.
Deep graph learning has gained grand popularity over the past years due to its versatility and success in representing graph data across a wide range of domains. However, the pervasive issue of imbalanced graph data distributions, where certain parts exhibit disproportionally abundant data while others remain sparse, undermines the efficacy of conventional graph learning algorithms, leading to biased outcomes. To address this challenge, Imbalanced Graph Learning (IGL) has garnered substantial attention, enabling more balanced data distributions and better task performance. Despite the proliferation of IGL algorithms, the absence of consistent experimental protocols and fair performance comparisons pose a significant barrier to comprehending advancements in this field. To bridge this gap, we introduce IGL-Bench, a foundational comprehensive benchmark for imbalanced graph learning, embarking on 16 diverse graph datasets and 24 distinct IGL algorithms with uniform data processing and splitting strategies. Specifically, IGL-Bench systematically investigates state-of-the-art IGL algorithms in terms of effectiveness, robustness, and efficiency on node-level and graph-level tasks, with the scope of class-imbalance and topology-imbalance. Extensive experiments demonstrate the potential benefits of IGL algorithms on various imbalanced conditions, offering insights and opportunities in the IGL field. Further, we have developed an open-sourced and unified package to facilitate reproducible evaluation and inspire further innovative research, which is available at https://github.com/RingBDStack/IGL-Bench.
Dataset condensation (DC) methods aim to learn a smaller synthesized dataset with informative data records to accelerate the training of machine learning models. Current distribution matching (DM) based DC methods learn a synthesized dataset by matching the mean of the latent embeddings between the synthetic and the real dataset. However two distributions with the same mean can still be vastly different. In this work we demonstrate the shortcomings of using Maximum Mean Discrepancy to match latent distributions i.e. the weak matching power and lack of outlier regularization. To alleviate these shortcomings we propose our new method: Latent Quantile Matching (LQM) which matches the quantiles of the latent embeddings to minimize the goodness of fit test statistic between two distributions. Empirical experiments on both image and graph-structured datasets show that LQM matches or outperforms previous state of the art in distribution matching based DC. Moreover we show that LQM improves the performance in continual graph learning (CGL) setting where memory efficiency and privacy can be important. Our work sheds light on the application of DM based DC for CGL.