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.
In this paper, we propose a graph classification approach for automatically determining whether to use a monolithic or a decomposition-based solution method. In this approach, an optimization problem is represented as a graph that captures the structural and functional coupling among the variables and constraints of the problem via an appropriate set of features. Given this representation, a graph classifier is built to determine the best solution method for a given problem. The proposed approach is used to develop a classifier that determines whether a convex Mixed Integer Nonlinear Programming problem should be solved using branch and bound or the outer approximation algorithm. Finally, it is shown how the learned classifier can be incorporated into existing mixed integer optimization solvers.
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.
Graph Neural Networks (GNNs) require a large number of labeled graph samples to obtain good performance on the graph classification task. The performance of GNNs degrades significantly as the number of labeled graph samples decreases. To reduce the annotation cost, it is therefore important to develop graph augmentation methods that can generate new graph instances to increase the size and diversity of the limited set of available labeled graph samples. In this work, we propose a novel mixup-based graph augmentation method, Graph Dual Mixup (GDM), that leverages both functional and structural information of the graph instances to generate new labeled graph samples. GDM employs a graph structural auto-encoder to learn structural embeddings of the graph samples, and then applies mixup to the structural information of the graphs in the learned structural embedding space and generates new graph structures from the mixup structural embeddings. As for the functional information, GDM applies mixup directly to the input node features of the graph samples to generate functional node feature information for new mixup graph instances. Jointly, the generated input node features and graph structures yield new graph samples which can supplement the set of original labeled graphs. Furthermore, we propose two novel Balanced Graph Sampling methods to enhance the balanced difficulty and diversity for the generated graph samples. Experimental results on the benchmark datasets demonstrate that our proposed method substantially outperforms the state-of-the-art graph augmentation methods when the labeled graphs are scarce.
Node features bolster graph-based learning when exploited jointly with network structure. However, a lack of nodal attributes is prevalent in graph data. We present a framework to recover completely missing node features for a set of graphs, where we only know the signals of a subset of graphs. Our approach incorporates prior information from both graph topology and existing nodal values. We demonstrate an example implementation of our framework where we assume that node features depend on local graph structure. Missing nodal values are estimated by aggregating known features from the most similar nodes. Similarity is measured through a node embedding space that preserves local topological features, which we train using a Graph AutoEncoder. We empirically show not only the accuracy of our feature estimation approach but also its value for downstream graph classification. Our success embarks on and implies the need to emphasize the relationship between node features and graph structure in graph-based learning.
With the development of computational fluid dynamics, the requirements for the fluid simulation accuracy in industrial applications have also increased. The quality of the generated mesh directly affects the simulation accuracy. However, previous mesh quality metrics and models cannot evaluate meshes comprehensively and objectively. To this end, we propose MQENet, a structured mesh quality evaluation neural network based on dynamic graph attention. MQENet treats the mesh evaluation task as a graph classification task for classifying the quality of the input structured mesh. To make graphs generated from structured meshes more informative, MQENet introduces two novel structured mesh preprocessing algorithms. These two algorithms can also improve the conversion efficiency of structured mesh data. Experimental results on the benchmark structured mesh dataset NACA-Market show the effectiveness of MQENet in the mesh quality evaluation task.
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
Graph classification, aiming at learning the graph-level representations for effective class assignments, has received outstanding achievements, which heavily relies on high-quality datasets that have balanced class distribution. In fact, most real-world graph data naturally presents a long-tailed form, where the head classes occupy much more samples than the tail classes, it thus is essential to study the graph-level classification over long-tailed data while still remaining largely unexplored. However, most existing long-tailed learning methods in visions fail to jointly optimize the representation learning and classifier training, as well as neglect the mining of the hard-to-classify classes. Directly applying existing methods to graphs may lead to sub-optimal performance, since the model trained on graphs would be more sensitive to the long-tailed distribution due to the complex topological characteristics. Hence, in this paper, we propose a novel long-tailed graph-level classification framework via Collaborative Multi-expert Learning (CoMe) to tackle the problem. To equilibrate the contributions of head and tail classes, we first develop balanced contrastive learning from the view of representation learning, and then design an individual-expert classifier training based on hard class mining. In addition, we execute gated fusion and disentangled knowledge distillation among the multiple experts to promote the collaboration in a multi-expert framework. Comprehensive experiments are performed on seven widely-used benchmark datasets to demonstrate the superiority of our method CoMe over state-of-the-art baselines.
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.
This study introduced the use of Graph Neural Network (GNN) for predicting the weather and weekday of a day in London, from the dataset of Santander Cycles bike-sharing system as a graph classification task. The proposed GNN models newly introduced (i) a concatenation operator of graph features with trained node embeddings and (ii) a graph coarsening operator based on geographical contiguity, namely "Spatial Graph Coarsening". With the node features of land-use characteristics and number of households around the bike stations and graph features of temperatures in the city, our proposed models outperformed the baseline model in cross-entropy loss and accuracy of the validation dataset.
This study delves into the intricacies of emotional contagion and its impact on performance within dyadic interactions. Specifically, it focuses on the context of stereotype-based stress (SBS) during collaborative problem-solving tasks among female pairs. Through an exploration of emotional contagion, this study seeks to unveil its underlying mechanisms and effects. Leveraging EEG-based hyperscanning technology, we introduced an innovative approach known as the functional Graph Contrastive Learning (fGCL), which extracts subject-invariant representations of neural activity patterns from feedback trials. These representations are further subjected to analysis using the Dynamic Graph Classification (DGC) model, aimed at dissecting the process of emotional contagion along three independent temporal stages. The results underscore the substantial role of emotional contagion in shaping the trajectories of participants' performance during collaborative tasks in the presence of SBS conditions. Overall, our research contributes invaluable insights into the neural underpinnings of emotional contagion, thereby enriching our comprehension of the complexities underlying social interactions and emotional dynamics.
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.
We address catastrophic forgetting issues in graph learning as incoming data transits from one to another graph distribution. Whereas prior studies primarily tackle one setting of graph continual learning such as incremental node classification, we focus on a universal approach wherein each data point in a task can be a node or a graph, and the task varies from node to graph classification. We propose a novel method that enables graph neural networks to excel in this universal setting. Our approach perseveres knowledge about past tasks through a rehearsal mechanism that maintains local and global structure consistency across the graphs. We benchmark our method against various continual learning baselines in real-world graph datasets and achieve significant improvement in average performance and forgetting across tasks.
Graph Neural Networks (GNNs) are a powerful tool for handling structured graph data and addressing tasks such as node classification, graph classification, and clustering. However, the sparse nature of GNN computation poses new challenges for performance optimization compared to traditional deep neural networks. We address these challenges by providing a unified view of GNN computation, I/O, and memory. By analyzing the computational graphs of the Graph Convolutional Network (GCN) and Graph Attention (GAT) layers -- two widely used GNN layers -- we propose alternative computation strategies. We present adaptive operator reordering with caching, which achieves a speedup of up to 2.43x for GCN compared to the current state-of-the-art. Furthermore, an exploration of different caching schemes for GAT yields a speedup of up to 1.94x. The proposed optimizations save memory, are easily implemented across various hardware platforms, and have the potential to alleviate performance bottlenecks in training large-scale GNN models.
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.