Recently, the paradigm of pre-training and fine-tuning graph neural networks has been intensively studied and applied in a wide range of graph mining tasks. Its success is generally attributed to the structural consistency between pre-training and downstream datasets, which, however, does not hold in many real-world scenarios. Existing works have shown that the structural divergence between pre-training and downstream graphs significantly limits the transferability when using the vanilla fine-tuning strategy. This divergence leads to model overfitting on pre-training graphs and causes difficulties in capturing the structural properties of the downstream graphs. In this paper, we identify the fundamental cause of structural divergence as the discrepancy of generative patterns between the pre-training and downstream graphs. Furthermore, we propose G-Tuning to preserve the generative patterns of downstream graphs. Given a downstream graph G, the core idea is to tune the pre-trained GNN so that it can reconstruct the generative patterns of G, the graphon W. However, the exact reconstruction of a graphon is known to be computationally expensive. To overcome this challenge, we provide a theoretical analysis that establishes the existence of a set of alternative graphons called graphon bases for any given graphon. By utilizing a linear combination of these graphon bases, we can efficiently approximate W. This theoretical finding forms the basis of our proposed model, as it enables effective learning of the graphon bases and their associated coefficients. Compared with existing algorithms, G-Tuning demonstrates an average improvement of 0.5% and 2.6% on in-domain and out-of-domain transfer learning experiments, respectively.
We present a novel edge-level ego-network encoding for learning on graphs that can boost Message Passing Graph Neural Networks (MP-GNNs) by providing additional node and edge features or extending message-passing formats. The proposed encoding is sufficient to distinguish Strongly Regular Graphs, a family of challenging 3-WL equivalent graphs. We show theoretically that such encoding is more expressive than node-based sub-graph MP-GNNs. In an empirical evaluation on four benchmarks with 10 graph datasets, our results match or improve previous baselines on expressivity, graph classification, graph regression, and proximity tasks -- while reducing memory usage by 18.1x in certain real-world settings.
Graph Neural Networks (GNNs) have displayed considerable promise in graph representation learning across various applications. The core learning process requires the initialization of model weight matrices within each GNN layer, which is typically accomplished via classic initialization methods such as Xavier initialization. However, these methods were originally motivated to stabilize the variance of hidden embeddings and gradients across layers of Feedforward Neural Networks (FNNs) and Convolutional Neural Networks (CNNs) to avoid vanishing gradients and maintain steady information flow. In contrast, within the GNN context classical initializations disregard the impact of the input graph structure and message passing on variance. In this paper, we analyze the variance of forward and backward propagation across GNN layers and show that the variance instability of GNN initializations comes from the combined effect of the activation function, hidden dimension, graph structure and message passing. To better account for these influence factors, we propose a new initialization method for Variance Instability Reduction within GNN Optimization (Virgo), which naturally tends to equate forward and backward variances across successive layers. We conduct comprehensive experiments on 15 datasets to show that Virgo can lead to superior model performance and more stable variance at initialization on node classification, link prediction and graph classification tasks. Codes are in https://github.com/LspongebobJH/virgo_icml2023.
Graph neural networks based on iterative one-hop message passing have been shown to struggle in harnessing the information from distant nodes effectively. Conversely, graph transformers allow each node to attend to all other nodes directly, but lack graph inductive bias and have to rely on ad-hoc positional encoding. In this paper, we propose a new architecture to reconcile these challenges. Our approach stems from the recent breakthroughs in long-range modeling provided by deep state-space models: for a given target node, our model aggregates other nodes by their shortest distances to the target and uses a linear RNN to encode the sequence of hop representations. The linear RNN is parameterized in a particular diagonal form for stable long-range signal propagation and is theoretically expressive enough to encode the neighborhood hierarchy. With no need for positional encoding, we empirically show that the performance of our model is comparable to or better than that of state-of-the-art graph transformers on various benchmarks, with a significantly reduced computational cost. Our code is open-source at https://github.com/skeletondyh/GRED.
We present a novel framework to overcome the limitations of equivariant architectures in learning functions with group symmetries. In contrary to equivariant architectures, we use an arbitrary base model such as an MLP or a transformer and symmetrize it to be equivariant to the given group by employing a small equivariant network that parameterizes the probabilistic distribution underlying the symmetrization. The distribution is end-to-end trained with the base model which can maximize performance while reducing sample complexity of symmetrization. We show that this approach ensures not only equivariance to given group but also universal approximation capability in expectation. We implement our method on various base models, including patch-based transformers that can be initialized from pretrained vision transformers, and test them for a wide range of symmetry groups including permutation and Euclidean groups and their combinations. Empirical tests show competitive results against tailored equivariant architectures, suggesting the potential for learning equivariant functions for diverse groups using a non-equivariant universal base architecture. We further show evidence of enhanced learning in symmetric modalities, like graphs, when pretrained from non-symmetric modalities, like vision. Code is available at https://github.com/jw9730/lps.
Our work combines aspects of three promising paradigms in machine learning, namely, attention mechanism, energy-based models, and associative memory. Attention is the power-house driving modern deep learning successes, but it lacks clear theoretical foundations. Energy-based models allow a principled approach to discriminative and generative tasks, but the design of the energy functional is not straightforward. At the same time, Dense Associative Memory models or Modern Hopfield Networks have a well-established theoretical foundation, and allow an intuitive design of the energy function. We propose a novel architecture, called the Energy Transformer (or ET for short), that uses a sequence of attention layers that are purposely designed to minimize a specifically engineered energy function, which is responsible for representing the relationships between the tokens. In this work, we introduce the theoretical foundations of ET, explore its empirical capabilities using the image completion task, and obtain strong quantitative results on the graph anomaly detection and graph classification tasks.
While graph neural networks have achieved state-of-the-art performances in many real-world tasks including graph classification and node classification, recent works have demonstrated they are also extremely vulnerable to adversarial attacks. Most previous works have focused on attacking node classification networks under impractical white-box scenarios. In this work, we will propose a non-targeted Hard Label Black Box Node Injection Attack on Graph Neural Networks, which to the best of our knowledge, is the first of its kind. Under this setting, more real world tasks can be studied because our attack assumes no prior knowledge about (1): the model architecture of the GNN we are attacking; (2): the model's gradients; (3): the output logits of the target GNN model. Our attack is based on an existing edge perturbation attack, from which we restrict the optimization process to formulate a node injection attack. In the work, we will evaluate the performance of the attack using three datasets, COIL-DEL, IMDB-BINARY, and NCI1.
Graph Neural Networks (GNNs) are powerful in learning semantics of graph data. Recently, a new paradigm "pre-train and prompt" has shown promising results in adapting GNNs to various tasks with less supervised data. The success of such paradigm can be attributed to the more consistent objectives of pre-training and task-oriented prompt tuning, where the pre-trained knowledge can be effectively transferred to downstream tasks. Most existing methods are based on the class prototype vector framework. However, in the few-shot scenarios, given few labeled data, class prototype vectors are difficult to be accurately constructed or learned. Meanwhile, the structure information of graph is usually exploited during pre-training for learning node representations, while neglected in the prompt tuning stage for learning more accurate prototype vectors. In addition, they generally ignore the impact of heterophilous neighborhoods on node representation and are not suitable for heterophilous graphs. To bridge these gaps, we propose a novel pre-training and structure prompt tuning framework for GNNs, namely PSP, which consistently exploits structure information in both pre-training and prompt tuning stages. In particular, PSP 1) employs a dual-view contrastive learning to align the latent semantic spaces of node attributes and graph structure, and 2) incorporates structure information in prompted graph to construct more accurate prototype vectors and elicit more pre-trained knowledge in prompt tuning. We conduct extensive experiments on node classification and graph classification tasks to evaluate the effectiveness of PSP. We show that PSP can lead to superior performance in few-shot scenarios on both homophilous and heterophilous graphs. The implemented code is available at https://github.com/gqq1210/PSP.
Graph Neural Networks (GNNs) have shown remarkable merit in performing various learning-based tasks in complex networks. The superior performance of GNNs often correlates with the availability and quality of node-level features in the input networks. However, for many network applications, such node-level information may be missing or unreliable, thereby limiting the applicability and efficacy of GNNs. To address this limitation, we present a novel approach denoted as Ego-centric Spectral subGraph Embedding Augmentation (ESGEA), which aims to enhance and design node features, particularly in scenarios where information is lacking. Our method leverages the topological structure of the local subgraph to create topology-aware node features. The subgraph features are generated using an efficient spectral graph embedding technique, and they serve as node features that capture the local topological organization of the network. The explicit node features, if present, are then enhanced with the subgraph embeddings in order to improve the overall performance. ESGEA is compatible with any GNN-based architecture and is effective even in the absence of node features. We evaluate the proposed method in a social network graph classification task where node attributes are unavailable, as well as in a node classification task where node features are corrupted or even absent. The evaluation results on seven datasets and eight baseline models indicate up to a 10% improvement in AUC and a 7% improvement in accuracy for graph and node classification tasks, respectively.
GNNs, like other deep learning models, are data and computation hungry. There is a pressing need to scale training of GNNs on large datasets to enable their usage on low-resource environments. Graph distillation is an effort in that direction with the aim to construct a smaller synthetic training set from the original training data without significantly compromising model performance. While initial efforts are promising, this work is motivated by two key observations: (1) Existing graph distillation algorithms themselves rely on training with the full dataset, which undermines the very premise of graph distillation. (2) The distillation process is specific to the target GNN architecture and hyper-parameters and thus not robust to changes in the modeling pipeline. We circumvent these limitations by designing a distillation algorithm called Mirage for graph classification. Mirage is built on the insight that a message-passing GNN decomposes the input graph into a multiset of computation trees. Furthermore, the frequency distribution of computation trees is often skewed in nature, enabling us to condense this data into a concise distilled summary. By compressing the computation data itself, as opposed to emulating gradient flows on the original training set-a prevalent approach to date-Mirage transforms into an unsupervised and architecture-agnostic distillation algorithm. Extensive benchmarking on real-world datasets underscores Mirage's superiority, showcasing enhanced generalization accuracy, data compression, and distillation efficiency when compared to state-of-the-art baselines.
Designing a single model to address multiple tasks has been a long-standing objective in artificial intelligence. Recently, large language models have demonstrated exceptional capability in solving different tasks within the language domain. However, a unified model for various graph tasks remains underexplored, primarily due to the challenges unique to the graph learning domain. First, graph data from different areas carry distinct attributes and follow different distributions. Such discrepancy makes it hard to represent graphs in a single representation space. Second, tasks on graphs diversify into node, link, and graph tasks, requiring distinct embedding strategies. Finally, an appropriate graph prompting paradigm for in-context learning is unclear. We propose \textbf{One for All (OFA)}, the first general framework that can use a single graph model to address the above challenges. Specifically, OFA proposes text-attributed graphs to unify different graph data by describing nodes and edges with natural language and uses language models to encode the diverse and possibly cross-domain text attributes to feature vectors in the same embedding space. Furthermore, OFA introduces the concept of nodes-of-interest to standardize different tasks with a single task representation. For in-context learning on graphs, OFA introduces a novel graph prompting paradigm that appends prompting substructures to the input graph, which enables it to address varied tasks without fine-tuning. We train the OFA model using graph data from multiple domains (including citation networks, molecular graphs, knowledge graphs, etc.) simultaneously and evaluate its ability in supervised, few-shot, and zero-shot learning scenarios. OFA performs well across different tasks, making it the first general-purpose across-domains classification model on graphs.
Joint-Embedding Predictive Architectures (JEPAs) have recently emerged as a novel and powerful technique for self-supervised representation learning. They aim to learn an energy-based model by predicting the latent representation of a target signal y from the latent representation of a context signal x. JEPAs bypass the need for negative and positive samples, traditionally required by contrastive learning while avoiding the overfitting issues associated with generative pretraining. In this paper, we show that graph-level representations can be effectively modeled using this paradigm by proposing a Graph Joint-Embedding Predictive Architecture (Graph-JEPA). In particular, we employ masked modeling and focus on predicting the latent representations of masked subgraphs starting from the latent representation of a context subgraph. To endow the representations with the implicit hierarchy that is often present in graph-level concepts, we devise an alternative prediction objective that consists of predicting the coordinates of the encoded subgraphs on the unit hyperbola in the 2D plane. Through multiple experimental evaluations, we show that Graph-JEPA can learn highly semantic and expressive representations, as shown by the downstream performance in graph classification, regression, and distinguishing non-isomorphic graphs. The code is available at https://github.com/geriskenderi/graph-jepa.
Existing approaches for classifying dynamic graphs either lift graph kernels to the temporal domain, or use graph neural networks (GNNs). However, current baselines have scalability issues, cannot handle a changing node set, or do not take edge weight information into account. We propose filtration surfaces, a novel method that is scalable and flexible, to alleviate said restrictions. We experimentally validate the efficacy of our model and show that filtration surfaces outperform previous state-of-the-art baselines on datasets that rely on edge weight information. Our method does so while being either completely parameter-free or having at most one parameter, and yielding the lowest overall standard deviation among similarly scalable methods.
Graph machine learning methods excel at leveraging pairwise relations present in the data. However, graphs are unable to fully capture the multi-way interactions inherent in many complex systems. An effective way to incorporate them is to model the data on higher-order combinatorial topological spaces, such as Simplicial Complexes (SCs) or Cell Complexes. For this reason, we introduce Generalized Simplicial Attention Neural Networks (GSANs), novel neural network architectures designed to process data living on simplicial complexes using masked self-attentional layers. Hinging on topological signal processing principles, we devise a series of principled self-attention mechanisms able to process data associated with simplices of various order, such as nodes, edges, triangles, and beyond. These schemes learn how to combine data associated with neighbor simplices of consecutive order in a task-oriented fashion, leveraging on the simplicial Dirac operator and its Dirac decomposition. We also prove that GSAN satisfies two fundamental properties: permutation equivariance and simplicial-awareness. Finally, we illustrate how our approach compares favorably with other simplicial and graph models when applied to several (inductive and transductive) tasks such as trajectory prediction, missing data imputation, graph classification, and simplex prediction.
Predictions over graphs play a crucial role in various domains, including social networks and medicine. Graph Neural Networks (GNNs) have emerged as the dominant approach for learning on graph data. Although a graph-structure is provided as input to the GNN, in some cases the best solution can be obtained by ignoring it. While GNNs have the ability to ignore the graph- structure in such cases, it is not clear that they will. In this work, we show that GNNs actually tend to overfit the given graph-structure. Namely, they use it even when a better solution can be obtained by ignoring it. We analyze the implicit bias of gradient-descent learning of GNNs and prove that when the ground truth function does not use the graphs, GNNs are not guaranteed to learn a solution that ignores the graph, even with infinite data. We examine this phenomenon with respect to different graph distributions and find that regular graphs are more robust to this over-fitting. We also prove that within the family of regular graphs, GNNs are guaranteed to extrapolate when learning with gradient descent. Finally, based on our empirical and theoretical findings, we demonstrate on real-data how regular graphs can be leveraged to reduce graph overfitting and enhance performance.
The recent Long-Range Graph Benchmark (LRGB, Dwivedi et al. 2022) introduced a set of graph learning tasks strongly dependent on long-range interaction between vertices. Empirical evidence suggests that on these tasks Graph Transformers significantly outperform Message Passing GNNs (MPGNNs). In this paper, we carefully reevaluate multiple MPGNN baselines as well as the Graph Transformer GPS (Ramp\'a\v{s}ek et al. 2022) on LRGB. Through a rigorous empirical analysis, we demonstrate that the reported performance gap is overestimated due to suboptimal hyperparameter choices. It is noteworthy that across multiple datasets the performance gap completely vanishes after basic hyperparameter optimization. In addition, we discuss the impact of lacking feature normalization for LRGB's vision datasets and highlight a spurious implementation of LRGB's link prediction metric. The principal aim of our paper is to establish a higher standard of empirical rigor within the graph machine learning community.
Multiple Sclerosis (MS) is a severe neurological disease characterized by inflammatory lesions in the central nervous system. Hence, predicting inflammatory disease activity is crucial for disease assessment and treatment. However, MS lesions can occur throughout the brain and vary in shape, size and total count among patients. The high variance in lesion load and locations makes it challenging for machine learning methods to learn a globally effective representation of whole-brain MRI scans to assess and predict disease. Technically it is non-trivial to incorporate essential biomarkers such as lesion load or spatial proximity. Our work represents the first attempt to utilize graph neural networks (GNN) to aggregate these biomarkers for a novel global representation. We propose a two-stage MS inflammatory disease activity prediction approach. First, a 3D segmentation network detects lesions, and a self-supervised algorithm extracts their image features. Second, the detected lesions are used to build a patient graph. The lesions act as nodes in the graph and are initialized with image features extracted in the first stage. Finally, the lesions are connected based on their spatial proximity and the inflammatory disease activity prediction is formulated as a graph classification task. Furthermore, we propose a self-pruning strategy to auto-select the most critical lesions for prediction. Our proposed method outperforms the existing baseline by a large margin (AUCs of 0.67 vs. 0.61 and 0.66 vs. 0.60 for one-year and two-year inflammatory disease activity, respectively). Finally, our proposed method enjoys inherent explainability by assigning an importance score to each lesion for the overall prediction. Code is available at https://github.com/chinmay5/ms_ida.git
Over-squashing and over-smoothing are two critical issues, that limit the capabilities of graph neural networks (GNNs). While over-smoothing eliminates the differences between nodes making them indistinguishable, over-squashing refers to the inability of GNNs to propagate information over long distances, as exponentially many node states are squashed into fixed-size representations. Both phenomena share similar causes, as both are largely induced by the graph topology. To mitigate these problems in graph classification tasks, we propose CurvPool, a novel pooling method. CurvPool exploits the notion of curvature of a graph to adaptively identify structures responsible for both over-smoothing and over-squashing. By clustering nodes based on the Balanced Forman curvature, CurvPool constructs a graph with a more suitable structure, allowing deeper models and the combination of distant information. We compare it to other state-of-the-art pooling approaches and establish its competitiveness in terms of classification accuracy, computational complexity, and flexibility. CurvPool outperforms several comparable methods across all considered tasks. The most consistent results are achieved by pooling densely connected clusters using the sum aggregation, as this allows additional information about the size of each pool.
Graph Neural Networks (GNNs) have emerged as promising solutions for collaborative filtering (CF) through the modeling of user-item interaction graphs. The nucleus of existing GNN-based recommender systems involves recursive message passing along user-item interaction edges to refine encoded embeddings. Despite their demonstrated effectiveness, current GNN-based methods encounter challenges of limited receptive fields and the presence of noisy "interest-irrelevant" connections. In contrast, Transformer-based methods excel in aggregating information adaptively and globally. Nevertheless, their application to large-scale interaction graphs is hindered by inherent complexities and challenges in capturing intricate, entangled structural information. In this paper, we propose TransGNN, a novel model that integrates Transformer and GNN layers in an alternating fashion to mutually enhance their capabilities. Specifically, TransGNN leverages Transformer layers to broaden the receptive field and disentangle information aggregation from edges, which aggregates information from more relevant nodes, thereby enhancing the message passing of GNNs. Additionally, to capture graph structure information effectively, positional encoding is meticulously designed and integrated into GNN layers to encode such structural knowledge into node attributes, thus enhancing the Transformer's performance on graphs. Efficiency considerations are also alleviated by proposing the sampling of the most relevant nodes for the Transformer, along with two efficient sample update strategies to reduce complexity. Furthermore, theoretical analysis demonstrates that TransGNN offers increased expressiveness compared to GNNs, with only a marginal increase in linear complexity. Extensive experiments on five public datasets validate the effectiveness and efficiency of TransGNN.
Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current methods often fall short in capturing longer ranges, hierarchical structures, or community structures, which are common in various graphs such as molecules, social networks, and citation networks. This paper presents a Hierarchical Distance Structural Encoding (HDSE) method to model node distances in a graph, focusing on its multi-level, hierarchical nature. We introduce a novel framework to seamlessly integrate HDSE into the attention mechanism of existing graph transformers, allowing for simultaneous application with other positional encodings. To apply graph transformers with HDSE to large-scale graphs, we further propose a high-level HDSE that effectively biases the linear transformers towards graph hierarchies. We theoretically prove the superiority of HDSE over shortest path distances in terms of expressivity and generalization. Empirically, we demonstrate that graph transformers with HDSE excel in graph classification, regression on 7 graph-level datasets, and node classification on 11 large-scale graphs, including those with up to a billion nodes.