Graph neural networks (GNNs) have been used effectively in different applications involving the processing of signals on irregular structures modeled by graphs. Relying on the use of shift-invariant graph filters, GNNs extend the operation of convolution to graphs. However, the operations of pooling and sampling are still not clearly defined and the approaches proposed in the literature either modify the graph structure in a way that does not preserve its spectral properties, or require defining a policy for selecting which nodes to keep. In this work, we propose a new strategy for pooling and sampling on GNNs using graphons which preserves the spectral properties of the graph. To do so, we consider the graph layers in a GNN as elements of a sequence of graphs that converge to a graphon. In this way we have no ambiguity in the node labeling when mapping signals from one layer to the other and a spectral representation that is consistent throughout the layers. We evaluate this strategy in a synthetic and a real-world numerical experiment where we show that graphon pooling GNNs are less prone to overfitting and improve upon other pooling techniques, especially when the dimensionality reduction ratios between layers is large.
University of Pennsylvania（宾夕法尼亚大学）；Dept. of Electrical and Systems Eng.（电气与系统工程系）；Philadelphia, PA 19143（费城，PA 19143）
Graph neural networks (GNNs) rely on graph convolutions to extract local features from network data. These graph convolutions combine information from adjacent nodes using coefficients that are shared across all nodes. Since these coefficients are shared and do not depend on the graph, one can envision using the same coefficients to define a GNN on another graph. This motivates analyzing the transferability of GNNs across graphs. In this paper we introduce graphon NNs as limit objects of GNNs and prove a bound on the difference between the output of a GNN and its limit graphon-NN. This bound v…
Graph neural networks (GNNs) are learning architectures that rely on knowledge of the graph structure to generate meaningful representations of large-scale network data. GNN stability is thus important as in real-world scenarios there are typically uncertainties associated with the graph. We analyze GNN stability using kernel objects called graphons. Graphons are both limits of convergent graph sequences and generating models for deterministic and stochastic graphs. Building upon the theory of graphon signal processing, we define graphon neural networks and analyze their stability to graphon p…
In this work, we propose to train a graph neural network via resampling from a graphon estimate obtained from the underlying network data. More specifically, the graphon or the link probability matrix of the underlying network is first obtained from which a new network will be resampled and used during the training process at each layer. Due to the uncertainty induced from the resampling, it helps mitigate the well-known issue of over-smoothing in a graph neural network (GNN) model. Our framework is general, computationally efficient, and conceptually simple. Another appealing feature of our m…
Technical University of Munich（慕尼黑工业大学）；IMPRS-IS, University of Tübingen（图宾根大学）；University of Tübingen（图宾根大学）
Network-valued data are encountered in a wide range of applications and pose challenges in learning due to their complex structure and absence of vertex correspondence. Typical examples of such problems include classification or grouping of protein structures and social networks. Various methods, ranging from graph kernels to graph neural networks, have been proposed that achieve some success in graph classification problems. However, most methods have limited theoretical justification, and their applicability beyond classification remains unexplored. In this work, we propose methods for clust…
LMU Munich（慕尼黑大学）；Technion - Israel Institute of Technology（以色列理工学院）；University of Tromsø（特罗姆瑟大学）
We study spectral graph convolutional neural networks (GCNNs), where filters are defined as continuous functions of the graph shift operator (GSO) through functional calculus. A spectral GCNN is not tailored to one specific graph and can be transferred between different graphs. It is hence important to study the GCNN transferability: the capacity of the network to have approximately the same repercussion on different graphs that represent the same phenomenon. Transferability ensures that GCNNs trained on certain graphs generalize if the graphs in the test set represent the same phenomena as th…
fortiss GmbH（fortiss有限公司）；An-Institut Technische Universität München（慕尼黑工业大学附属研究所）
Graph Neural Network (GNN) research has concentrated on improving convolutional layers, with little attention paid to developing graph pooling layers. Yet pooling layers can enable GNNs to reason over abstracted groups of nodes instead of single nodes. To close this gap, we propose a graph pooling layer relying on the notion of edge contraction: EdgePool learns a localized and sparse hard pooling transform. We show that EdgePool outperforms alternative pooling methods, can be easily integrated into most GNN models, and improves performance on both node and graph classification.
Graph Neural Networks (GNNs) are information processing architectures for signals supported on graphs. They are presented here as generalizations of convolutional neural networks (CNNs) in which individual layers contain banks of graph convolutional filters instead of banks of classical convolutional filters. Otherwise, GNNs operate as CNNs. Filters are composed with pointwise nonlinearities and stacked in layers. It is shown that GNN architectures exhibit equivariance to permutation and stability to graph deformations. These properties help explain the good performance of GNNs that can be obs…
NORCE, the Norwegian Research Centre（挪威研究中心NORCE）；Università della Svizzera italiana（意大利语区大学（瑞士））；Politecnico di Milano（米兰理工大学）
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem an…
Institute of Exact and Applied Sciences (EA7484), University of New Caledonia（精确与应用科学研究所（EA7484），新喀里多尼亚大学）；Big Data Institute, College of Computer Science and Software Engineering（大数据研究所，计算机科学与软件工程学院）；Shenzhen University, China（深圳大学，中国）
Michigan State University（密歇根州立大学）；Pennsylvania State University（宾夕法尼亚州立大学）；IBM T. J. Watson Research Center（IBM T·J·沃森研究中心）
Graph neural networks, which generalize deep neural network models to graph structured data, have attracted increasing attention in recent years. They usually learn node representations by transforming, propagating and aggregating node features and have been proven to improve the performance of many graph related tasks such as node classification and link prediction. To apply graph neural networks for the graph classification task, approaches to generate the \textit{graph representation} from node representations are demanded. A common way is to globally combine the node representations. Howev…
Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph n…
This work generalizes graph neural networks (GNNs) beyond those based on the Weisfeiler-Lehman (WL) algorithm, graph Laplacians, and diffusions. Our approach, denoted Relational Pooling (RP), draws from the theory of finite partial exchangeability to provide a framework with maximal representation power for graphs. RP can work with existing graph representation models and, somewhat counterintuitively, can make them even more powerful than the original WL isomorphism test. Additionally, RP allows architectures like Recurrent Neural Networks and Convolutional Neural Networks to be used in a theo…
Graph neural networks (GNNs) use graph convolutions to exploit network invariances and learn meaningful feature representations from network data. However, on large-scale graphs convolutions incur in high computational cost, leading to scalability limitations. Leveraging the graphon -- the limit object of a graph -- in this paper we consider the problem of learning a graphon neural network (WNN) -- the limit object of a GNN -- by training GNNs on graphs sampled from the graphon. Under smoothness conditions, we show that: (i) the expected distance between the learning steps on the GNN and on th…
Deep learning methods for graphs have seen rapid progress in recent years with much focus awarded to generalising Convolutional Neural Networks (CNN) to graph data. CNNs are typically realised by alternating convolutional and pooling layers where the pooling layers subsample the grid and exchange spatial or temporal resolution for increased feature dimensionality. Whereas the generalised convolution operator for graphs has been studied extensively and proven useful, hierarchical coarsening of graphs is still challenging since nodes in graphs have no spatial locality and no natural order. This …
Convolutional layers in graph neural networks are a fundamental type of layer which output a representation or embedding of each graph vertex. The representation typically encodes information about the vertex in question and its neighbourhood. If one wishes to perform a graph centric task, such as graph classification, this set of vertex representations must be integrated or pooled to form a graph representation. In this article we propose a novel pooling method which maps a set of vertex representations to a function space representation. This method is distinct from existing pooling methods …
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁大学医学院）；Facebook AI Research（Facebook人工智能研究院）
Understanding how certain brain regions relate to a specific neurological disorder has been an important area of neuroimaging research. A promising approach to identify the salient regions is using Graph Neural Networks (GNNs), which can be used to analyze graph structured data, e.g. brain networks constructed by functional magnetic resonance imaging (fMRI). We propose an interpretable GNN framework with a novel salient region selection mechanism to determine neurological brain biomarkers associated with disorders. Specifically, we design novel regularized pooling layers that highlight salient…
Physical Pooling Functions in Graph Neural Networks for Molecular Property Prediction
RWTH Aachen University（亚琛工业大学）；Delft University of Technology（代尔夫特理工大学）；Forschungszentrum Jülich GmbH（于利希研究中心）；JARA Center for Simulation and Data Science (CSD)（JARA模拟与数据科学中心）
Texas A&M University（德州农工大学）；University of Georgia（佐治亚大学）；Rice University（莱斯大学）
This work develops \emph{mixup for graph data}. Mixup has shown superiority in improving the generalization and robustness of neural networks by interpolating features and labels between two random samples. Traditionally, Mixup can work on regular, grid-like, and Euclidean data such as image or tabular data. However, it is challenging to directly adopt Mixup to augment graph data because different graphs typically: 1) have different numbers of nodes; 2) are not readily aligned; and 3) have unique typologies in non-Euclidean space. To this end, we propose $\mathcal{G}$-Mixup to augment graphs f…
Graph neural networks have achieved great success in learning node representations for graph tasks such as node classification and link prediction. Graph representation learning requires graph pooling to obtain graph representations from node representations. It is challenging to develop graph pooling methods due to the variable sizes and isomorphic structures of graphs. In this work, we propose to use second-order pooling as graph pooling, which naturally solves the above challenges. In addition, compared to existing graph pooling methods, second-order pooling is able to use information from …
University of Pennsylvania（宾夕法尼亚大学）；Simons-Berkeley Institute（西蒙斯-伯克利研究所）
Graph Neural Networks (GNNs) rely on graph convolutions to exploit meaningful patterns in networked data. Based on matrix multiplications, convolutions incur in high computational costs leading to scalability limitations in practice. To overcome these limitations, proposed methods rely on training GNNs in smaller number of nodes, and then transferring the GNN to larger graphs. Even though these methods are able to bound the difference between the output of the GNN with different number of nodes, they do not provide guarantees against the optimal GNN on the very large graph. In this paper, we p…
Shanghai Jiao Tong University（上海交通大学）；École Polytechnique Fédérale de Lausanne (EPFL)（洛桑联邦理工学院（EPFL））
With the advent of data science, the analysis of network or graph data has become a very timely research problem. A variety of recent works have been proposed to generalize neural networks to graphs, either from a spectral graph theory or a spatial perspective. The majority of these works however focus on adapting the convolution operator to graph representation. At the same time, the pooling operator also plays an important role in distilling multiscale and hierarchical representations but it has been mostly overlooked so far. In this paper, we propose a parameter-free pooling operator, calle…
Geometry-Aware Edge Pooling for Graph Neural Networks
Helmholtz Munich（海德堡-穆恩大学）；Technical University of Munich（慕尼黑技术大学）；Université de Montréal（蒙特利尔大学）；Mila - Quebec AI Institute（魁北克人工智能研究所）；Université de Fribourg（弗里堡大学）
University of Pittsburgh（匹兹堡大学）；Intel Labs（英特尔实验室）
Recent years have witnessed the emergence and development of graph neural networks (GNNs), which have been shown as a powerful approach for graph representation learning in many tasks, such as node classification and graph classification. The research on the robustness of these models has also started to attract attentions in the machine learning field. However, most of the existing work in this area focus on the GNNs for node-level tasks, while little work has been done to study the robustness of the GNNs for the graph classification task. In this paper, we aim to explore the vulnerability of…
MaxCutPool: differentiable feature-aware Maxcut for pooling in graph neural networks
Alma Mater Studiorum - University of Bologna（博洛尼亚大学）；UiT the Arctic University of Norway（挪威北极大学）；Fondazione Istituto Italiano di Tecnologia（意大利技术研究院）；NORCE Norwegian Research Centre AS（NORCE挪威研究中心）
Hierarchical Representation Learning in Graph Neural Networks with Node Decimation Pooling
UiT the Arctic University of Norway（挪威北极大学）；NORCE, Norwegian Research Centre（挪威NORCE研究中心）；Università della Svizzera italiana（意大利语瑞士大学）；University of Manitoba（曼尼托巴大学）；University of Exeter（埃克塞特大学）；Politecnico di Milano（米兰理工大学）
Graph Neural Networks achieve state-of-the-art performance on a plethora of graph classification tasks, especially due to pooling operators, which aggregate learned node embeddings hierarchically into a final graph representation. However, they are not only questioned by recent work showing on par performance with random pooling, but also ignore completely higher-order connectivity patterns. To tackle this issue, we propose HoscPool, a clustering-based graph pooling operator that captures higher-order information hierarchically, leading to richer graph representations. In fact, we learn a prob…
Università della Svizzera italiana（瑞士意大利语大学）；UiT the Arctic University of Norway（挪威北极大学）；NORCE, The Norwegian Research Centre（挪威NORCE研究中心）；Politecnico di Milano（米兰理工大学）
Graph neural networks (GNN) extends deep learning to graph-structure dataset. Similar to Convolutional Neural Networks (CNN) using on image prediction, convolutional and pooling layers are the foundation to success for GNN on graph prediction tasks. In the initial PAN paper, it uses a path integral based graph neural networks for graph prediction. Specifically, it uses a convolution operation that involves every path linking the message sender and receiver with learnable weights depending on the path length, which corresponds to the maximal entropy random walk. It further generalizes such conv…
We propose PiNet, a generalised differentiable attention-based pooling mechanism for utilising graph convolution operations for graph level classification. We demonstrate high sample efficiency and superior performance over other graph neural networks in distinguishing isomorphic graph classes, as well as competitive results with state of the art methods on standard chemo-informatics datasets.
McGill University（麦吉尔大学）；Université de Montréal（蒙特利尔大学）；HEC Montréal（蒙特利尔高等商学院）；Mila（米拉人工智能研究所）
Graph Neural Networks (GNNs) are attracting growing attention due to their effectiveness and flexibility in modeling a variety of graph-structured data. Exiting GNN architectures usually adopt simple pooling operations (eg. sum, average, max) when aggregating messages from a local neighborhood for updating node representation or pooling node representations from the entire graph to compute the graph representation. Though simple and effective, these linear operations do not model high-order non-linear interactions among nodes. We propose the Tensorized Graph Neural Network (tGNN), a highly exp…
Kim Jaechul Graduate School of AI（金在哲人工智能研究生院）；KAIST（韩国科学技术院）
Graph neural networks (GNNs) are one of the most popular approaches to using deep learning on graph-structured data, and they have shown state-of-the-art performances on a variety of tasks. However, according to a recent study, a careful choice of pooling functions, which are used for the aggregation and readout operations in GNNs, is crucial for enabling GNNs to extrapolate. Without proper choices of pooling functions, which varies across tasks, GNNs completely fail to generalize to out-of-distribution data, while the number of possible choices grows exponentially with the number of layers. I…
Aalto University（阿尔托大学）；Federal Institute of Ceará（塞阿拉联邦研究所）；University of Manchester（曼彻斯特大学）
Graph pooling is a central component of a myriad of graph neural network (GNN) architectures. As an inheritance from traditional CNNs, most approaches formulate graph pooling as a cluster assignment problem, extending the idea of local patches in regular grids to graphs. Despite the wide adherence to this design choice, no work has rigorously evaluated its influence on the success of GNNs. In this paper, we build upon representative GNNs and introduce variants that challenge the need for locality-preserving representations, either using randomization or clustering on the complement graph. Stri…
Nanjing Normal University（南京师范大学）；Universität Basel（巴塞尔大学）
Graph neural networks achieve high accuracy in link prediction by jointly leveraging graph topology and node attributes. Topology, however, is represented indirectly; state-of-the-art methods based on subgraph classification label nodes with distance to the target link, so that, although topological information is present, it is tempered by pooling. This makes it challenging to leverage features like loops and motifs associated with network formation mechanisms. We propose a link prediction algorithm based on a new pooling scheme called WalkPool. WalkPool combines the expressivity of topologic…
Although theoretical properties such as expressive power and over-smoothing of graph neural networks (GNN) have been extensively studied recently, its convergence property is a relatively new direction. In this paper, we investigate the convergence of one powerful GNN, Invariant Graph Network (IGN) over graphs sampled from graphons. We first prove the stability of linear layers for general $k$-IGN (of order $k$) based on a novel interpretation of linear equivariant layers. Building upon this result, we prove the convergence of $k$-IGN under the model of \citet{ruiz2020graphon}, where we access…
Princeton University（普林斯顿大学）；University of Technology Sydney（悉尼科技大学）；Max Planck Institute for Mathematics in the Sciences（马克斯·普朗克数学科学研究所）；University of New South Wales（新南威尔士大学）；Zhejiang Normal University（浙江师范大学）；University of Cambridge（剑桥大学）
Graph neural networks (GNNs) extends the functionality of traditional neural networks to graph-structured data. Similar to CNNs, an optimized design of graph convolution and pooling is key to success. Borrowing ideas from physics, we propose a path integral based graph neural networks (PAN) for classification and regression tasks on graphs. Specifically, we consider a convolution operation that involves every path linking the message sender and receiver with learnable weights depending on the path length, which corresponds to the maximal entropy random walk. It generalizes the graph Laplacian …
Hierarchical Pooling and Explainability in Graph Neural Networks for Tumor and Tissue-of-Origin Classification Using RNA-seq Data
Institute of Informatics（信息学院）；Universidade Federal do Rio Grande do Sul（鲁汶联邦大学）；Bioinformatics Core（生物信息学核心）；Hospital de Clínicas de Porto Alegre（波多利亚临床医院）
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Paradigm. Inc.（第四范式）；Department of Electronic Engineering, Tsinghua University（清华大学电子工程系）；Lenovo（联想）
Graph classification is an important problem with applications across many domains, like chemistry and bioinformatics, for which graph neural networks (GNNs) have been state-of-the-art (SOTA) methods. GNNs are designed to learn node-level representation based on neighborhood aggregation schemes, and to obtain graph-level representation, pooling methods are applied after the aggregation operation in existing GNN models to generate coarse-grained graphs. However,due to highly diverse applications of graph classification, and the performance of existing pooling methods vary on different graphs. I…
