Predicting node labels on a given graph is a widely studied problem with many applications, including community detection and molecular graph prediction. This paper considers predicting multiple node labeling functions on graphs simultaneously and revisits this problem from a multitask learning perspective. For a concrete example, consider overlapping community detection: each community membership is a binary node classification task. Due to complex overlapping patterns, we find that negative transfer is prevalent when we apply naive multitask learning to multiple community detection, as task relationships are highly nonlinear across different node labeling. To address the challenge, we develop an algorithm to cluster tasks into groups based on a higher-order task affinity measure. We then fit a multitask model on each task group, resulting in a boosting procedure on top of the baseline model. We estimate the higher-order task affinity measure between two tasks as the prediction loss of one task in the presence of another task and a random subset of other tasks. Then, we use spectral clustering on the affinity score matrix to identify task grouping. We design several speedup techniques to compute the higher-order affinity scores efficiently and show that they can predict negative transfers more accurately than pairwise task affinities. We validate our procedure using various community detection and molecular graph prediction data sets, showing favorable results compared with existing methods. Lastly, we provide a theoretical analysis to show that under a planted block model of tasks on graphs, our affinity scores can provably separate tasks into groups.
Geometric deep learning (GDL) models have demonstrated a great potential for the analysis of non-Euclidian data. They are developed to incorporate the geometric and topological information of non-Euclidian data into the end-to-end deep learning architectures. Motivated by the recent success of discrete Ricci curvature in graph neural network (GNNs), we propose TorGNN, an analytic Torsion enhanced Graph Neural Network model. The essential idea is to characterize graph local structures with an analytic torsion based weight formula. Mathematically, analytic torsion is a topological invariant that can distinguish spaces which are homotopy equivalent but not homeomorphic. In our TorGNN, for each edge, a corresponding local simplicial complex is identified, then the analytic torsion (for this local simplicial complex) is calculated, and further used as a weight (for this edge) in message-passing process. Our TorGNN model is validated on link prediction tasks from sixteen different types of networks and node classification tasks from three types of networks. It has been found that our TorGNN can achieve superior performance on both tasks, and outperform various state-of-the-art models. This demonstrates that analytic torsion is a highly efficient topological invariant in the characterization of graph structures and can significantly boost the performance of GNNs.
Hypergraphs are a powerful abstraction for representing higher-order interactions between entities of interest. To exploit these relationships in making downstream predictions, a variety of hypergraph neural network architectures have recently been proposed, in large part building upon precursors from the more traditional graph neural network (GNN) literature. Somewhat differently, in this paper we begin by presenting an expressive family of parameterized, hypergraph-regularized energy functions. We then demonstrate how minimizers of these energies effectively serve as node embeddings that, when paired with a parameterized classifier, can be trained end-to-end via a supervised bilevel optimization process. Later, we draw parallels between the implicit architecture of the predictive models emerging from the proposed bilevel hypergraph optimization, and existing GNN architectures in common use. Empirically, we demonstrate state-of-the-art results on various hypergraph node classification benchmarks. Code is available at https://github.com/yxzwang/PhenomNN.
Class imbalance is the phenomenon that some classes have much fewer instances than others, which is ubiquitous in real-world graph-structured scenarios. Recent studies find that off-the-shelf Graph Neural Networks (GNNs) would under-represent minor class samples. We investigate this phenomenon and discover that the subspaces of minor classes being squeezed by those of the major ones in the latent space is the main cause of this failure. We are naturally inspired to enlarge the decision boundaries of minor classes and propose a general framework GraphSHA by Synthesizing HArder minor samples. Furthermore, to avoid the enlarged minor boundary violating the subspaces of neighbor classes, we also propose a module called SemiMixup to transmit enlarged boundary information to the interior of the minor classes while blocking information propagation from minor classes to neighbor classes. Empirically, GraphSHA shows its effectiveness in enlarging the decision boundaries of minor classes, as it outperforms various baseline methods in class-imbalanced node classification with different GNN backbone encoders over seven public benchmark datasets. Code is avilable at https://github.com/wenzhilics/GraphSHA.
Node classification is one of the hottest tasks in graph analysis. Though existing studies have explored various node representations in directed and undirected graphs, they have overlooked the distinctions of their capabilities to capture the information of graphs. To tackle the limitation, we investigate various combinations of node representations (aggregated features vs. adjacency lists) and edge direction awareness within an input graph (directed vs. undirected). We address the first empirical study to benchmark the performance of various GNNs that use either combination of node representations and edge direction awareness. Our experiments demonstrate that no single combination stably achieves state-of-the-art results across datasets, which indicates that we need to select appropriate combinations depending on the dataset characteristics. In response, we propose a simple yet holistic classification method A2DUG which leverages all combinations of node representations in directed and undirected graphs. We demonstrate that A2DUG stably performs well on various datasets and improves the accuracy up to 11.29 compared with the state-of-the-art methods. To spur the development of new methods, we publicly release our complete codebase under the MIT license.
When training a Neural Network, it is optimized using the available training data with the hope that it generalizes well to new or unseen testing data. At the same absolute value, a flat minimum in the loss landscape is presumed to generalize better than a sharp minimum. Methods for determining flat minima have been mostly researched for independent and identically distributed (i. i. d.) data such as images. Graphs are inherently non-i. i. d. since the vertices are edge-connected. We investigate flat minima methods and combinations of those methods for training graph neural networks (GNNs). We use GCN and GAT as well as extend Graph-MLP to work with more layers and larger graphs. We conduct experiments on small and large citation, co-purchase, and protein datasets with different train-test splits in both the transductive and inductive training procedure. Results show that flat minima methods can improve the performance of GNN models by over 2 points, if the train-test split is randomized. Following Shchur et al., randomized splits are essential for a fair evaluation of GNNs, as other (fixed) splits like 'Planetoid' are biased. Overall, we provide important insights for improving and fairly evaluating flat minima methods on GNNs. We recommend practitioners to always use weight averaging techniques, in particular EWA when using early stopping. While weight averaging techniques are only sometimes the best performing method, they are less sensitive to hyperparameters, need no additional training, and keep the original model unchanged. All source code is available in https://github.com/Foisunt/FMMs-in-GNNs.
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.
Graph neural networks have been extensively studied for learning with inter-connected data. Despite this, recent evidence has revealed GNNs' deficiencies related to over-squashing, heterophily, handling long-range dependencies, edge incompleteness and particularly, the absence of graphs altogether. While a plausible solution is to learn new adaptive topology for message passing, issues concerning quadratic complexity hinder simultaneous guarantees for scalability and precision in large networks. In this paper, we introduce a novel all-pair message passing scheme for efficiently propagating node signals between arbitrary nodes, as an important building block for a pioneering Transformer-style network for node classification on large graphs, dubbed as \textsc{NodeFormer}. Specifically, the efficient computation is enabled by a kernerlized Gumbel-Softmax operator that reduces the algorithmic complexity to linearity w.r.t. node numbers for learning latent graph structures from large, potentially fully-connected graphs in a differentiable manner. We also provide accompanying theory as justification for our design. Extensive experiments demonstrate the promising efficacy of the method in various tasks including node classification on graphs (with up to 2M nodes) and graph-enhanced applications (e.g., image classification) where input graphs are missing.
Fairness in graph neural networks has been actively studied recently. However, existing works often do not explicitly consider the role of message passing in introducing or amplifying the bias. In this paper, we first investigate the problem of bias amplification in message passing. We empirically and theoretically demonstrate that message passing could amplify the bias when the 1-hop neighbors from different demographic groups are unbalanced. Guided by such analyses, we propose BeMap, a fair message passing method, that leverages a balance-aware sampling strategy to balance the number of the 1-hop neighbors of each node among different demographic groups. Extensive experiments on node classification demonstrate the efficacy of BeMap in mitigating bias while maintaining classification accuracy. The code is available at https://github.com/xiaolin-cs/BeMap.
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.
Knowledge graph embedding models (KGEMs) have gained considerable traction in recent years. These models learn a vector representation of knowledge graph entities and relations, a.k.a. knowledge graph embeddings (KGEs). Learning versatile KGEs is desirable as it makes them useful for a broad range of tasks. However, KGEMs are usually trained for a specific task, which makes their embeddings task-dependent. In parallel, the widespread assumption that KGEMs actually create a semantic representation of the underlying entities and relations (e.g., project similar entities closer than dissimilar ones) has been challenged. In this work, we design heuristics for generating protographs -- small, modified versions of a KG that leverage RDF/S information. The learnt protograph-based embeddings are meant to encapsulate the semantics of a KG, and can be leveraged in learning KGEs that, in turn, also better capture semantics. Extensive experiments on various evaluation benchmarks demonstrate the soundness of this approach, which we call Modular and Agnostic SCHema-based Integration of protograph Embeddings (MASCHInE). In particular, MASCHInE helps produce more versatile KGEs that yield substantially better performance for entity clustering and node classification tasks. For link prediction, using MASCHinE substantially increases the number of semantically valid predictions with equivalent rank-based performance.
Graph neural networks (GNNs) have achieved remarkable advances in graph-oriented tasks. However, real-world graphs invariably contain a certain proportion of heterophilous nodes, challenging the homophily assumption of traditional GNNs and hindering their performance. Most existing studies continue to design generic models with shared weights between heterophilous and homophilous nodes. Despite the incorporation of high-order messages or multi-channel architectures, these efforts often fall short. A minority of studies attempt to train different node groups separately but suffer from inappropriate separation metrics and low efficiency. In this paper, we first propose a new metric, termed Neighborhood Confusion (NC), to facilitate a more reliable separation of nodes. We observe that node groups with different levels of NC values exhibit certain differences in intra-group accuracy and visualized embeddings. These pave the way for Neighborhood Confusion-guided Graph Convolutional Network (NCGCN), in which nodes are grouped by their NC values and accept intra-group weight sharing and message passing. Extensive experiments on both homophilous and heterophilous benchmarks demonstrate that our framework can effectively separate nodes and yield significant performance improvement compared to the latest methods. The source code will be available in https://github.com/GISec-Team/NCGNN.
Graph neural networks (GNNs) learn the representation of graph-structured data, and their expressiveness can be further enhanced by inferring node relations for propagation. Attention-based GNNs infer neighbor importance to manipulate the weight of its propagation. Despite their popularity, the discussion on deep graph attention and its unique challenges has been limited. In this work, we investigate some problematic phenomena related to deep graph attention, including vulnerability to over-smoothed features and smooth cumulative attention. Through theoretical and empirical analyses, we show that various attention-based GNNs suffer from these problems. Motivated by our findings, we propose AEROGNN, a novel GNN architecture designed for deep graph attention. AERO-GNN provably mitigates the proposed problems of deep graph attention, which is further empirically demonstrated with (a) its adaptive and less smooth attention functions and (b) higher performance at deep layers (up to 64). On 9 out of 12 node classification benchmarks, AERO-GNN outperforms the baseline GNNs, highlighting the advantages of deep graph attention. Our code is available at https://github.com/syleeheal/AERO-GNN.
Heterogeneous Graph Neural Networks (HGNNs) have gained significant popularity in various heterogeneous graph learning tasks. However, most existing HGNNs rely on spatial domain-based methods to aggregate information, i.e., manually selected meta-paths or some heuristic modules, lacking theoretical guarantees. Furthermore, these methods cannot learn arbitrary valid heterogeneous graph filters within the spectral domain, which have limited expressiveness. To tackle these issues, we present a positive spectral heterogeneous graph convolution via positive noncommutative polynomials. Then, using this convolution, we propose PSHGCN, a novel Positive Spectral Heterogeneous Graph Convolutional Network. PSHGCN offers a simple yet effective method for learning valid heterogeneous graph filters. Moreover, we demonstrate the rationale of PSHGCN in the graph optimization framework. We conducted an extensive experimental study to show that PSHGCN can learn diverse heterogeneous graph filters and outperform all baselines on open benchmarks. Notably, PSHGCN exhibits remarkable scalability, efficiently handling large real-world graphs comprising millions of nodes and edges. Our codes are available at https://github.com/ivam-he/PSHGCN.
Node classifiers are required to comprehensively reduce prediction errors, training resources, and inference latency in the industry. However, most graph neural networks (GNN) concentrate only on one or two of them. The compromised aspects thus are the shortest boards on the bucket, hindering their practical deployments for industrial-level tasks. This work proposes a novel semi-supervised learning method termed Graph Entropy Minimization (GEM) to resolve the three issues simultaneously. GEM benefits its one-hop aggregation from massive uncategorized nodes, making its prediction accuracy comparable to GNNs with two or more hops message passing. It can be decomposed to support stochastic training with mini-batches of independent edge samples, achieving extremely fast sampling and space-saving training. While its one-hop aggregation is faster in inference than deep GNNs, GEM can be further accelerated to an extreme by deriving a non-hop classifier via online knowledge distillation. Thus, GEM can be a handy choice for latency-restricted and error-sensitive services running on resource-constraint hardware. Code is available at https://github.com/cf020031308/GEM.
In the graph node embedding problem, embedding spaces can vary significantly for different data types, leading to the need for different GNN model types. In this paper, we model the embedding update of a node feature as a Hamiltonian orbit over time. Since the Hamiltonian orbits generalize the exponential maps, this approach allows us to learn the underlying manifold of the graph in training, in contrast to most of the existing literature that assumes a fixed graph embedding manifold with a closed exponential map solution. Our proposed node embedding strategy can automatically learn, without extensive tuning, the underlying geometry of any given graph dataset even if it has diverse geometries. We test Hamiltonian functions of different forms and verify the performance of our approach on two graph node embedding downstream tasks: node classification and link prediction. Numerical experiments demonstrate that our approach adapts better to different types of graph datasets than popular state-of-the-art graph node embedding GNNs. The code is available at \url{https://github.com/zknus/Hamiltonian-GNN}.
Although Graph Neural Networks (GNNs) have been successful in node classification tasks, their performance heavily relies on the availability of a sufficient number of labeled nodes per class. In real-world situations, not all classes have many labeled nodes and there may be instances where the model needs to classify new classes, making manual labeling difficult. To solve this problem, it is important for GNNs to be able to classify nodes with a limited number of labeled nodes, known as few-shot node classification. Previous episodic meta-learning based methods have demonstrated success in few-shot node classification, but our findings suggest that optimal performance can only be achieved with a substantial amount of diverse training meta-tasks. To address this challenge of meta-learning based few-shot learning (FSL), we propose a new approach, the Task-Equivariant Graph few-shot learning (TEG) framework. Our TEG framework enables the model to learn transferable task-adaptation strategies using a limited number of training meta-tasks, allowing it to acquire meta-knowledge for a wide range of meta-tasks. By incorporating equivariant neural networks, TEG can utilize their strong generalization abilities to learn highly adaptable task-specific strategies. As a result, TEG achieves state-of-the-art performance with limited training meta-tasks. Our experiments on various benchmark datasets demonstrate TEG's superiority in terms of accuracy and generalization ability, even when using minimal meta-training data, highlighting the effectiveness of our proposed approach in addressing the challenges of meta-learning based few-shot node classification. Our code is available at the following link: https://github.com/sung-won-kim/TEG
Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.
Graph neural networks (GNNs) have shown promising results across various graph learning tasks, but they often assume homophily, which can result in poor performance on heterophilic graphs. The connected nodes are likely to be from different classes or have dissimilar features on heterophilic graphs. In this paper, we propose a novel GNN that incorporates the principle of heterophily by modeling the flow of information on nodes using the convection-diffusion equation (CDE). This allows the CDE to take into account both the diffusion of information due to homophily and the ``convection'' of information due to heterophily. We conduct extensive experiments, which suggest that our framework can achieve competitive performance on node classification tasks for heterophilic graphs, compared to the state-of-the-art methods. The code is available at \url{https://github.com/zknus/Graph-Diffusion-CDE}.
This paper investigates a missing feature imputation problem for graph learning tasks. Several methods have previously addressed learning tasks on graphs with missing features. However, in cases of high rates of missing features, they were unable to avoid significant performance degradation. To overcome this limitation, we introduce a novel concept of channel-wise confidence in a node feature, which is assigned to each imputed channel feature of a node for reflecting certainty of the imputation. We then design pseudo-confidence using the channel-wise shortest path distance between a missing-feature node and its nearest known-feature node to replace unavailable true confidence in an actual learning process. Based on the pseudo-confidence, we propose a novel feature imputation scheme that performs channel-wise inter-node diffusion and node-wise inter-channel propagation. The scheme can endure even at an exceedingly high missing rate (e.g., 99.5\%) and it achieves state-of-the-art accuracy for both semi-supervised node classification and link prediction on various datasets containing a high rate of missing features. Codes are available at https://github.com/daehoum1/pcfi.