The choice of a graph learning (GL) model (i.e., a GL algorithm and its hyperparameter settings) has a significant impact on the performance of downstream tasks. However, selecting the right GL model becomes increasingly difficult and time consuming as more and more GL models are developed. Accordingly, it is of great significance and practical value to equip users of GL with the ability to perform a near-instantaneous selection of an effective GL model without manual intervention. Despite the recent attempts to tackle this important problem, there has been no comprehensive benchmark environment to evaluate the performance of GL model selection methods. To bridge this gap, we present GLEMOS in this work, a comprehensive benchmark for instantaneous GL model selection that makes the following contributions. (i) GLEMOS provides extensive benchmark data for fundamental GL tasks, i.e., link prediction and node classification, including the performances of 366 models on 457 graphs on these tasks. (ii) GLEMOS designs multiple evaluation settings, and assesses how effectively representative model selection techniques perform in these different settings. (iii) GLEMOS is designed to be easily extended with new models, new graphs, and new performance records. (iv) Based on the experimental results, we discuss the limitations of existing approaches and highlight future research directions. To promote research on this significant problem, we make the benchmark data and code publicly available at https://github.com/facebookresearch/glemos.
Effective collaboration among heterogeneous clients in a decentralized setting is a rather unexplored avenue in the literature. To structurally address this, we introduce Model Agnostic Peer-to-peer Learning (coined as MAPL) a novel approach to simultaneously learn heterogeneous personalized models as well as a collaboration graph through peer-to-peer communication among neighboring clients. MAPL is comprised of two main modules: (i) local-level Personalized Model Learning (PML), leveraging a combination of intra- and inter-client contrastive losses; (ii) network-wide decentralized Collaborative Graph Learning (CGL) dynamically refining collaboration weights in a privacy-preserving manner based on local task similarities. Our extensive experimentation demonstrates the efficacy of MAPL and its competitive (or, in most cases, superior) performance compared to its centralized model-agnostic counterparts, without relying on any central server. Our code is available and can be accessed here: https://github.com/SayakMukherjee/MAPL
Effective agent coordination is crucial in cooperative Multi-Agent Reinforcement Learning (MARL). While agent cooperation can be represented by graph structures, prevailing graph learning methods in MARL are limited. They rely solely on one-step observations, neglecting crucial historical experiences, leading to deficient graphs that foster redundant or detrimental information exchanges. Additionally, high computational demands for action-pair calculations in dense graphs impede scalability. To address these challenges, we propose inferring a Latent Temporal Sparse Coordination Graph (LTS-CG) for MARL. The LTS-CG leverages agents' historical observations to calculate an agent-pair probability matrix, where a sparse graph is sampled from and used for knowledge exchange between agents, thereby simultaneously capturing agent dependencies and relation uncertainty. The computational complexity of this procedure is only related to the number of agents. This graph learning process is further augmented by two innovative characteristics: Predict-Future, which enables agents to foresee upcoming observations, and Infer-Present, ensuring a thorough grasp of the environmental context from limited data. These features allow LTS-CG to construct temporal graphs from historical and real-time information, promoting knowledge exchange during policy learning and effective collaboration. Graph learning and agent training occur simultaneously in an end-to-end manner. Our demonstrated results on the StarCraft II benchmark underscore LTS-CG's superior performance.
In the context of multi-view clustering, graph learning is recognized as a crucial technique, which generally involves constructing an adaptive neighbor graph based on probabilistic neighbors, and then learning a consensus graph to for clustering. However, they are confronted with two limitations. Firstly, they often rely on Euclidean distance to measure similarity when constructing the adaptive neighbor graph, which proves inadequate in capturing the intrinsic structure among data points in practice. Secondly, most of these methods focus solely on consensus graph, ignoring unique information from each view. Although a few graph-based studies have considered using specific information as well, the modelling approach employed does not exclude the noise impact from the specific component. To this end, we propose a novel tensor-based multi-view graph learning framework that simultaneously considers consistency and specificity, while effectively eliminating the influence of noise. Specifically, we calculate similarity distance on the Stiefel manifold to preserve the intrinsic properties of data. By making an assumption that the learned neighbor graph of each view comprises a consistent part, a specific part, and a noise part, we formulate a new tensor-based target graph learning paradigm for noise-free graph fusion. Owing to the benefits of tensor singular value decomposition (t-SVD) in uncovering high-order correlations, this model is capable of achieving a complete understanding of the target graph. Furthermore, we derive an algorithm to address the optimization problem. Experiments on six datasets have demonstrated the superiority of our method. We have released the source code on https://github.com/lshi91/CSTGL-Code.
In case law, the precedents are the relevant cases that are used to support the decisions made by the judges and the opinions of lawyers towards a given case. This relevance is referred to as the case-to-case reference relation. To efficiently find relevant cases from a large case pool, retrieval tools are widely used by legal practitioners. Existing legal case retrieval models mainly work by comparing the text representations of individual cases. Although they obtain a decent retrieval accuracy, the intrinsic case connectivity relationships among cases have not been well exploited for case encoding, therefore limiting the further improvement of retrieval performance. In a case pool, there are three types of case connectivity relationships: the case reference relationship, the case semantic relationship, and the case legal charge relationship. Due to the inductive manner in the task of legal case retrieval, using case reference as input is not applicable for testing. Thus, in this paper, a CaseLink model based on inductive graph learning is proposed to utilise the intrinsic case connectivity for legal case retrieval, a novel Global Case Graph is incorporated to represent both the case semantic relationship and the case legal charge relationship. A novel contrastive objective with a regularisation on the degree of case nodes is proposed to leverage the information carried by the case reference relationship to optimise the model. Extensive experiments have been conducted on two benchmark datasets, which demonstrate the state-of-the-art performance of CaseLink. The code has been released on https://github.com/yanran-tang/CaseLink.
Under circumstances of heterophily, where nodes with different labels tend to be connected based on semantic meanings, Graph Neural Networks (GNNs) often exhibit suboptimal performance. Current studies on graph heterophily mainly focus on aggregation calibration or neighbor extension and address the heterophily issue by utilizing node features or structural information to improve GNN representations. In this paper, we propose and demonstrate that the valuable semantic information inherent in heterophily can be utilized effectively in graph learning by investigating the distribution of neighbors for each individual node within the graph. The theoretical analysis is carried out to demonstrate the efficacy of the idea in enhancing graph learning. Based on this analysis, we propose HiGNN, an innovative approach that constructs an additional new graph structure, that integrates heterophilous information by leveraging node distribution to enhance connectivity between nodes that share similar semantic characteristics. We conduct empirical assessments on node classification tasks using both homophilous and heterophilous benchmark datasets and compare HiGNN to popular GNN baselines and SoTA methods, confirming the effectiveness in improving graph representations. In addition, by incorporating heterophilous information, we demonstrate a notable enhancement in existing GNN-based approaches, and the homophily degree across real-world datasets, thus affirming the efficacy of our approach.
We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.
Graph transformer has been proven as an effective graph learning method for its adoption of attention mechanism that is capable of capturing expressive representations from complex topological and feature information of graphs. Graph transformer conventionally performs dense attention (or global attention) for every pair of nodes to learn node representation vectors, resulting in quadratic computational costs that are unaffordable for large-scale graph data. Therefore, mini-batch training for graph transformers is a promising direction, but limited samples in each mini-batch can not support effective dense attention to encode informative representations. Facing this bottleneck, (1) we start by assigning each node a token list that is sampled by personalized PageRank (PPR) and then apply standard multi-head self-attention only on this list to compute its node representations. This PPR tokenization method decouples model training from complex graph topological information and makes heavy feature engineering offline and independent, such that mini-batch training of graph transformers is possible by loading each node's token list in batches. We further prove this PPR tokenization is viable as a graph convolution network with a fixed polynomial filter and jumping knowledge. However, only using personalized PageRank may limit information carried by a token list, which could not support different graph inductive biases for model training. To this end, (2) we rewire graphs by introducing multiple types of virtual connections through structure- and content-based super nodes that enable PPR tokenization to encode local and global contexts, long-range interaction, and heterophilous information into each node's token list, and then formalize our Virtual Connection Ranking based Graph Transformer (VCR-Graphormer).
We propose SAM-Road, an adaptation of the Segment Anything Model (SAM) for extracting large-scale, vectorized road network graphs from satellite imagery. To predict graph geometry, we formulate it as a dense semantic segmentation task, leveraging the inherent strengths of SAM. The image encoder of SAM is fine-tuned to produce probability masks for roads and intersections, from which the graph vertices are extracted via simple non-maximum suppression. To predict graph topology, we designed a lightweight transformer-based graph neural network, which leverages the SAM image embeddings to estimate the edge existence probabilities between vertices. Our approach directly predicts the graph vertices and edges for large regions without expensive and complex post-processing heuristics, and is capable of building complete road network graphs spanning multiple square kilometers in a matter of seconds. With its simple, straightforward, and minimalist design, SAM-Road achieves comparable accuracy with the state-of-the-art method RNGDet++, while being 40 times faster on the City-scale dataset. We thus demonstrate the power of a foundational vision model when applied to a graph learning task. The code is available at https://github.com/htcr/sam_road.
Spatial-Temporal Graph (STG) data is characterized as dynamic, heterogenous, and non-stationary, leading to the continuous challenge of spatial-temporal graph learning. In the past few years, various GNN-based methods have been proposed to solely focus on mimicking the relationships among node individuals of the STG network, ignoring the significance of modeling the intrinsic features that exist in STG system over time. In contrast, modern Selective State Space Models (SSSMs) present a new approach which treat STG Network as a system, and meticulously explore the STG system's dynamic state evolution across temporal dimension. In this work, we introduce Spatial-Temporal Graph Mamba (STG-Mamba) as the first exploration of leveraging the powerful selective state space models for STG learning by treating STG Network as a system, and employing the Spatial-Temporal Selective State Space Module (ST-S3M) to precisely focus on the selected STG latent features. Furthermore, to strengthen GNN's ability of modeling STG data under the setting of selective state space models, we propose Kalman Filtering Graph Neural Networks (KFGN) for dynamically integrate and upgrade the STG embeddings from different temporal granularities through a learnable Kalman Filtering statistical theory-based approach. Extensive empirical studies are conducted on three benchmark STG forecasting datasets, demonstrating the performance superiority and computational efficiency of STG-Mamba. It not only surpasses existing state-of-the-art methods in terms of STG forecasting performance, but also effectively alleviate the computational bottleneck of large-scale graph networks in reducing the computational cost of FLOPs and test inference time. The implementation code is available at: \url{https://github.com/LincanLi98/STG-Mamba}.
Graph neural networks (GNNs) have achieved remarkable success across a wide range of applications, such as recommendation, drug discovery, and question answering. Behind the success of GNNs lies the backpropagation (BP) algorithm, which is the de facto standard for training deep neural networks (NNs). However, despite its effectiveness, BP imposes several constraints, which are not only biologically implausible, but also limit the scalability, parallelism, and flexibility in learning NNs. Examples of such constraints include storage of neural activities computed in the forward pass for use in the subsequent backward pass, and the dependence of parameter updates on non-local signals. To address these limitations, the forward-forward algorithm (FF) was recently proposed as an alternative to BP in the image classification domain, which trains NNs by performing two forward passes over positive and negative data. Inspired by this advance, we propose ForwardGNN in this work, a new forward learning procedure for GNNs, which avoids the constraints imposed by BP via an effective layer-wise local forward training. ForwardGNN extends the original FF to deal with graph data and GNNs, and makes it possible to operate without generating negative inputs (hence no longer forward-forward). Further, ForwardGNN enables each layer to learn from both the bottom-up and top-down signals without relying on the backpropagation of errors. Extensive experiments on real-world datasets show the effectiveness and generality of the proposed forward graph learning framework. We release our code at https://github.com/facebookresearch/forwardgnn.
The opioid crisis has been one of the most critical society concerns in the United States. Although the medication assisted treatment (MAT) is recognized as the most effective treatment for opioid misuse and addiction, the various side effects can trigger opioid relapse. In addition to MAT, the dietary nutrition intervention has been demonstrated its importance in opioid misuse prevention and recovery. However, research on the alarming connections between dietary patterns and opioid misuse remain under-explored. In response to this gap, in this paper, we first establish a large-scale multifaceted dietary benchmark dataset related to opioid users at the first attempt and then develop a novel framework - i.e., namely Opioid Misuse Detection with Interpretable Dietary Patterns (Diet-ODIN) - to bridge heterogeneous graph (HG) and large language model (LLM) for the identification of users with opioid misuse and the interpretation of their associated dietary patterns. Specifically, in Diet-ODIN, we first construct an HG to comprehensively incorporate both dietary and health-related information, and then we devise a holistic graph learning framework with noise reduction to fully capitalize both users' individual dietary habits and shared dietary patterns for the detection of users with opioid misuse. To further delve into the intricate correlations between dietary patterns and opioid misuse, we exploit an LLM by utilizing the knowledge obtained from the graph learning model for interpretation. The extensive experimental results based on our established benchmark with quantitative and qualitative measures demonstrate the outstanding performance of Diet-ODIN in exploring the complex interplay between opioid misuse and dietary patterns, by comparison with state-of-the-art baseline methods.
Fair graph learning plays a pivotal role in numerous practical applications. Recently, many fair graph learning methods have been proposed; however, their evaluation often relies on poorly constructed semi-synthetic datasets or substandard real-world datasets. In such cases, even a basic Multilayer Perceptron (MLP) can outperform Graph Neural Networks (GNNs) in both utility and fairness. In this work, we illustrate that many datasets fail to provide meaningful information in the edges, which may challenge the necessity of using graph structures in these problems. To address these issues, we develop and introduce a collection of synthetic, semi-synthetic, and real-world datasets that fulfill a broad spectrum of requirements. These datasets are thoughtfully designed to include relevant graph structures and bias information crucial for the fair evaluation of models. The proposed synthetic and semi-synthetic datasets offer the flexibility to create data with controllable bias parameters, thereby enabling the generation of desired datasets with user-defined bias values with ease. Moreover, we conduct systematic evaluations of these proposed datasets and establish a unified evaluation approach for fair graph learning models. Our extensive experimental results with fair graph learning methods across our datasets demonstrate their effectiveness in benchmarking the performance of these methods. Our datasets and the code for reproducing our experiments are available at https://github.com/XweiQ/Benchmark-GraphFairness.
Bilevel optimization refers to scenarios whereby the optimal solution of a lower-level energy function serves as input features to an upper-level objective of interest. These optimal features typically depend on tunable parameters of the lower-level energy in such a way that the entire bilevel pipeline can be trained end-to-end. Although not generally presented as such, this paper demonstrates how a variety of graph learning techniques can be recast as special cases of bilevel optimization or simplifications thereof. In brief, building on prior work we first derive a more flexible class of energy functions that, when paired with various descent steps (e.g., gradient descent, proximal methods, momentum, etc.), form graph neural network (GNN) message-passing layers; critically, we also carefully unpack where any residual approximation error lies with respect to the underlying constituent message-passing functions. We then probe several simplifications of this framework to derive close connections with non-GNN-based graph learning approaches, including knowledge graph embeddings, various forms of label propagation, and efficient graph-regularized MLP models. And finally, we present supporting empirical results that demonstrate the versatility of the proposed bilevel lens, which we refer to as BloomGML, referencing that BiLevel Optimization Offers More Graph Machine Learning. Our code is available at https://github.com/amberyzheng/BloomGML. Let graph ML bloom.
In representation learning on graph-structured data, many popular graph neural networks (GNNs) fail to capture long-range dependencies, leading to performance degradation. Furthermore, this weakness is magnified when the concerned graph is characterized by heterophily (low homophily). To solve this issue, this paper proposes a novel graph learning framework called the graph convolutional network with self-attention (GCN-SA). The proposed scheme exhibits an exceptional generalization capability in node-level representation learning. The proposed GCN-SA contains two enhancements corresponding to edges and node features. For edges, we utilize a self-attention mechanism to design a stable and effective graph-structure-learning module that can capture the internal correlation between any pair of nodes. This graph-structure-learning module can identify reliable neighbors for each node from the entire graph. Regarding the node features, we modify the transformer block to make it more applicable to enable GCN to fuse valuable information from the entire graph. These two enhancements work in distinct ways to help our GCN-SA capture long-range dependencies, enabling it to perform representation learning on graphs with varying levels of homophily. The experimental results on benchmark datasets demonstrate the effectiveness of the proposed GCN-SA. Compared to other outstanding GNN counterparts, the proposed GCN-SA is competitive.
In recent years, Cross-Domain Recommendation (CDR) has drawn significant attention, which utilizes user data from multiple domains to enhance the recommendation performance. However, current CDR methods require sharing user data across domains, thereby violating the General Data Protection Regulation (GDPR). Consequently, numerous approaches have been proposed for Federated Cross-Domain Recommendation (FedCDR). Nevertheless, the data heterogeneity across different domains inevitably influences the overall performance of federated learning. In this study, we propose FedHCDR, a novel Federated Cross-Domain Recommendation framework with Hypergraph signal decoupling. Specifically, to address the data heterogeneity across domains, we introduce an approach called hypergraph signal decoupling (HSD) to decouple the user features into domain-exclusive and domain-shared features. The approach employs high-pass and low-pass hypergraph filters to decouple domain-exclusive and domain-shared user representations, which are trained by the local-global bi-directional transfer algorithm. In addition, a hypergraph contrastive learning (HCL) module is devised to enhance the learning of domain-shared user relationship information by perturbing the user hypergraph. Extensive experiments conducted on three real-world scenarios demonstrate that FedHCDR outperforms existing baselines significantly.
We consider the problem of jointly learning row-wise and column-wise dependencies of matrix-variate observations, which are modelled separately by two precision matrices. Due to the complicated structure of Kronecker-product precision matrices in the commonly used matrix-variate Gaussian graphical models, a sparser Kronecker-sum structure was proposed recently based on the Cartesian product of graphs. However, existing methods for estimating Kronecker-sum structured precision matrices do not scale well to large scale datasets. In this paper, we introduce DNNLasso, a diagonally non-negative graphical lasso model for estimating the Kronecker-sum structured precision matrix, which outperforms the state-of-the-art methods by a large margin in both accuracy and computational time. Our code is available at https://github.com/YangjingZhang/DNNLasso.
Graph learning has become essential in various domains, including recommendation systems and social network analysis. Graph Neural Networks (GNNs) have emerged as promising techniques for encoding structural information and improving performance in tasks like link prediction and node classification. However, a key challenge remains: the difficulty of generalizing to unseen graph data with different properties. In this work, we propose a novel graph foundation model, called OpenGraph, to address this challenge. Our approach tackles several technical obstacles. Firstly, we enhance data augmentation using a large language model (LLM) to overcome data scarcity in real-world scenarios. Secondly, we introduce a unified graph tokenizer that enables the model to generalize effectively to diverse graph data, even when encountering unseen properties during training. Thirdly, our developed scalable graph transformer captures node-wise dependencies within the global topological context. Extensive experiments validate the effectiveness of our framework. By adapting OpenGraph to new graph characteristics and comprehending diverse graphs, our approach achieves remarkable zero-shot graph learning performance across various settings. We release the model implementation at https://github.com/HKUDS/OpenGraph.
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.
The traditional two-stage approach to causal inference first identifies a single causal model (or equivalence class of models), which is then used to answer causal queries. However, this neglects any epistemic model uncertainty. In contrast, Bayesian causal inference does incorporate epistemic uncertainty into query estimates via Bayesian marginalisation (posterior averaging) over all causal models. While principled, this marginalisation over entire causal models, i.e., both causal structures (graphs) and mechanisms, poses a tremendous computational challenge. In this work, we address this challenge by decomposing structure marginalisation into the marginalisation over (i) causal orders and (ii) directed acyclic graphs (DAGs) given an order. We can marginalise the latter in closed form by limiting the number of parents per variable and utilising Gaussian processes to model mechanisms. To marginalise over orders, we use a sampling-based approximation, for which we devise a novel auto-regressive distribution over causal orders (ARCO). Our method outperforms state-of-the-art in structure learning on simulated non-linear additive noise benchmarks, and yields competitive results on real-world data. Furthermore, we can accurately infer interventional distributions and average causal effects.