Graph convolutional neural networks (GCNNs) are a powerful extension of deep learning techniques to graph-structured data problems. We empirically evaluate several pooling methods for GCNNs, and combinations of those graph pooling methods with three different architectures: GCN, TAGCN, and GraphSAGE. We confirm that graph pooling, especially DiffPool, improves classification accuracy on popular graph classification datasets and find that, on average, TAGCN achieves comparable or better accuracy than GCN and GraphSAGE, particularly for datasets with larger and sparser graph structures.
Graph-structured data arise in many scenarios. A fundamental problem is to quantify the similarities of graphs for tasks such as classification. R-convolution graph kernels are positive-semidefinite functions that decompose graphs into substructures and compare them. One problem in the effective implementation of this idea is that the substructures are not independent, which leads to high-dimensional feature space. In addition, graph kernels cannot capture the high-order complex interactions between vertices. To mitigate these two problems, we propose a framework called DeepMap to learn deep representations for graph feature maps. The learned deep representation for a graph is a dense and low-dimensional vector that captures complex high-order interactions in a vertex neighborhood. DeepMap extends Convolutional Neural Networks (CNNs) to arbitrary graphs by generating aligned vertex sequences and building the receptive field for each vertex. We empirically validate DeepMap on various graph classification benchmarks and demonstrate that it achieves state-of-the-art performance.
Graph convolution operators bring the advantages of deep learning to a variety of graph and mesh processing tasks previously deemed out of reach. With their continued success comes the desire to design more powerful architectures, often by adapting existing deep learning techniques to non-Euclidean data. In this paper, we argue geometry should remain the primary driving force behind innovation in the emerging field of geometric deep learning. We relate graph neural networks to widely successful computer graphics and data approximation models: radial basis functions (RBFs). We conjecture that, like RBFs, graph convolution layers would benefit from the addition of simple functions to the powerful convolution kernels. We introduce affine skip connections, a novel building block formed by combining a fully connected layer with any graph convolution operator. We experimentally demonstrate the effectiveness of our technique and show the improved performance is the consequence of more than the increased number of parameters. Operators equipped with the affine skip connection markedly outperform their base performance on every task we evaluated, i.e., shape reconstruction, dense shape correspondence, and graph classification. We hope our simple and effective approach will serve as a solid baseline and help ease future research in graph neural networks.
Graph Neural Networks (GNNs) have recently been used for node and graph classification tasks with great success, but GNNs model dependencies among the attributes of nearby neighboring nodes rather than dependencies among observed node labels. In this work, we consider the task of inductive node classification using GNNs in supervised and semi-supervised settings, with the goal of incorporating label dependencies. Because current GNNs are not universal (i.e., most-expressive) graph representations, we propose a general collective learning approach to increase the representation power of any existing GNN. Our framework combines ideas from collective classification with self-supervised learning, and uses a Monte Carlo approach to sampling embeddings for inductive learning across graphs. We evaluate performance on five real-world network datasets and demonstrate consistent, significant improvement in node classification accuracy, for a variety of state-of-the-art GNNs.
This paper aims at revisiting Graph Convolutional Neural Networks by bridging the gap between spectral and spatial design of graph convolutions. We theoretically demonstrate some equivalence of the graph convolution process regardless it is designed in the spatial or the spectral domain. The obtained general framework allows to lead a spectral analysis of the most popular ConvGNNs, explaining their performance and showing their limits. Moreover, the proposed framework is used to design new convolutions in spectral domain with a custom frequency profile while applying them in the spatial domain. We also propose a generalization of the depthwise separable convolution framework for graph convolutional networks, what allows to decrease the total number of trainable parameters by keeping the capacity of the model. To the best of our knowledge, such a framework has never been used in the GNNs literature. Our proposals are evaluated on both transductive and inductive graph learning problems. Obtained results show the relevance of the proposed method and provide one of the first experimental evidence of transferability of spectral filter coefficients from one graph to another. Our source codes are publicly available at: https://github.com/balcilar/Spectral-Designed-Graph-Convolutions
Graph Neural Networks (GNNs) have recently received significant research attention due to their superior performance on a variety of graph-related learning tasks. Most of the current works focus on either static or dynamic graph settings, addressing a single particular task, e.g., node/graph classification, link prediction. In this work, we investigate the question: can GNNs be applied to continuously learning a sequence of tasks? Towards that, we explore the Continual Graph Learning (CGL) paradigm and present the Experience Replay based framework ER-GNN for CGL to alleviate the catastrophic forgetting problem in existing GNNs. ER-GNN stores knowledge from previous tasks as experiences and replays them when learning new tasks to mitigate the catastrophic forgetting issue. We propose three experience node selection strategies: mean of feature, coverage maximization, and influence maximization, to guide the process of selecting experience nodes. Extensive experiments on three benchmark datasets demonstrate the effectiveness of our ER-GNN and shed light on the incremental graph (non-Euclidean) structure learning.
Graph representation learning based on graph neural networks (GNNs) can greatly improve the performance of downstream tasks, such as node and graph classification. However, the general GNN models do not aggregate node information in a hierarchical manner, and can miss key higher-order structural features of many graphs. The hierarchical aggregation also enables the graph representations to be explainable. In addition, supervised graph representation learning requires labeled data, which is expensive and error-prone. To address these issues, we present an unsupervised graph representation learning method, Unsupervised Hierarchical Graph Representation (UHGR), which can generate hierarchical representations of graphs. Our method focuses on maximizing mutual information between "local" and high-level "global" representations, which enables us to learn the node embeddings and graph embeddings without any labeled data. To demonstrate the effectiveness of the proposed method, we perform the node and graph classification using the learned node and graph embeddings. The results show that the proposed method achieves comparable results to state-of-the-art supervised methods on several benchmarks. In addition, our visualization of hierarchical representations indicates that our method can capture meaningful and interpretable clusters.
Graph classification aims to extract accurate information from graph-structured data for classification and is becoming more and more important in graph learning community. Although Graph Neural Networks (GNNs) have been successfully applied to graph classification tasks, most of them overlook the scarcity of labeled graph data in many applications. For example, in bioinformatics, obtaining protein graph labels usually needs laborious experiments. Recently, few-shot learning has been explored to alleviate this problem with only given a few labeled graph samples of test classes. The shared sub-structures between training classes and test classes are essential in few-shot graph classification. Exiting methods assume that the test classes belong to the same set of super-classes clustered from training classes. However, according to our observations, the label spaces of training classes and test classes usually do not overlap in real-world scenario. As a result, the existing methods don't well capture the local structures of unseen test classes. To overcome the limitation, in this paper, we propose a direct method to capture the sub-structures with well initialized meta-learner within a few adaptation steps. More specifically, (1) we propose a novel framework consisting of a graph meta-learner, which uses GNNs based modules for fast adaptation on graph data, and a step controller for the robustness and generalization of meta-learner; (2) we provide quantitative analysis for the framework and give a graph-dependent upper bound of the generalization error based on our framework; (3) the extensive experiments on real-world datasets demonstrate that our framework gets state-of-the-art results on several few-shot graph classification tasks compared to baselines.
In this work we produce a framework for constructing universal function approximators on graph isomorphism classes. We prove how this framework comes with a collection of theoretically desirable properties and enables novel analysis. We show how this allows us to achieve state-of-the-art performance on four different well-known datasets in graph classification and separate classes of graphs that other graph-learning methods cannot. Our approach is inspired by persistent homology, dependency parsing for NLP, and multivalued functions. The complexity of the underlying algorithm is O(#edges x #nodes) and code is publicly available (https://github.com/bruel-gabrielsson/universal-function-approximation-on-graphs).
We propose a novel method for comparing non-aligned graphs of different sizes, based on the Wasserstein distance between graph signal distributions induced by the respective graph Laplacian matrices. Specifically, we cast a new formulation for the one-to-many graph alignment problem, which aims at matching a node in the smaller graph with one or more nodes in the larger graph. By integrating optimal transport in our graph comparison framework, we generate both a structurally-meaningful graph distance, and a signal transportation plan that models the structure of graph data. The resulting alignment problem is solved with stochastic gradient descent, where we use a novel Dykstra operator to ensure that the solution is a one-to-many (soft) assignment matrix. We demonstrate the performance of our novel framework on graph alignment and graph classification, and we show that our method leads to significant improvements with respect to the state-of-the-art algorithms for each of these tasks.
We present Geo2DR (Geometric to Distributed Representations), a GPU ready Python library for unsupervised learning on graph-structured data using discrete substructure patterns and neural language models. It contains efficient implementations of popular graph decomposition algorithms and neural language models in PyTorch which can be combined to learn representations of graphs using the distributive hypothesis. Furthermore, Geo2DR comes with general data processing and loading methods to bring substantial speed-up in the training of the neural language models. Through this we provide a modular set of tools and methods to quickly construct systems capable of learning distributed representations of graphs. This is useful for replication of existing methods, modification, or development of completely new methods. This paper serves to present the Geo2DR library and perform a comprehensive comparative analysis of existing methods re-implemented using Geo2DR across widely used graph classification benchmarks. Geo2DR displays a high reproducibility of results in published methods and interoperability with other libraries useful for distributive language modelling.
We introduce a family of multilayer graph kernels and establish new links between graph convolutional neural networks and kernel methods. Our approach generalizes convolutional kernel networks to graph-structured data, by representing graphs as a sequence of kernel feature maps, where each node carries information about local graph substructures. On the one hand, the kernel point of view offers an unsupervised, expressive, and easy-to-regularize data representation, which is useful when limited samples are available. On the other hand, our model can also be trained end-to-end on large-scale data, leading to new types of graph convolutional neural networks. We show that our method achieves competitive performance on several graph classification benchmarks, while offering simple model interpretation. Our code is freely available at https://github.com/claying/GCKN.
We present Karate Club a Python framework combining more than 30 state-of-the-art graph mining algorithms which can solve unsupervised machine learning tasks. The primary goal of the package is to make community detection, node and whole graph embedding available to a wide audience of machine learning researchers and practitioners. We designed Karate Club with an emphasis on a consistent application interface, scalability, ease of use, sensible out of the box model behaviour, standardized dataset ingestion, and output generation. This paper discusses the design principles behind this framework with practical examples. We show Karate Club's efficiency with respect to learning performance on a wide range of real world clustering problems, classification tasks and support evidence with regards to its competitive speed.
We introduce COPT, a novel distance metric between graphs defined via an optimization routine, computing a coordinated pair of optimal transport maps simultaneously. This gives an unsupervised way to learn general-purpose graph representation, applicable to both graph sketching and graph comparison. COPT involves simultaneously optimizing dual transport plans, one between the vertices of two graphs, and another between graph signal probability distributions. We show theoretically that our method preserves important global structural information on graphs, in particular spectral information, and analyze connections to existing studies. Empirically, COPT outperforms state of the art methods in graph classification on both synthetic and real datasets.
In the last few years, graph neural networks (GNNs) have become the standard toolkit for analyzing and learning from data on graphs. This emerging field has witnessed an extensive growth of promising techniques that have been applied with success to computer science, mathematics, biology, physics and chemistry. But for any successful field to become mainstream and reliable, benchmarks must be developed to quantify progress. This led us in March 2020 to release a benchmark framework that i) comprises of a diverse collection of mathematical and real-world graphs, ii) enables fair model comparison with the same parameter budget to identify key architectures, iii) has an open-source, easy-to-use and reproducible code infrastructure, and iv) is flexible for researchers to experiment with new theoretical ideas. As of December 2022, the GitHub repository has reached 2,000 stars and 380 forks, which demonstrates the utility of the proposed open-source framework through the wide usage by the GNN community. In this paper, we present an updated version of our benchmark with a concise presentation of the aforementioned framework characteristics, an additional medium-sized molecular dataset AQSOL, similar to the popular ZINC, but with a real-world measured chemical target, and discuss how this framework can be leveraged to explore new GNN designs and insights. As a proof of value of our benchmark, we study the case of graph positional encoding (PE) in GNNs, which was introduced with this benchmark and has since spurred interest of exploring more powerful PE for Transformers and GNNs in a robust experimental setting.
In complex networks, nodes that share similar structural characteristics often exhibit similar roles (e.g type of users in a social network or the hierarchical position of employees in a company). In order to leverage this relationship, a growing literature proposed latent representations that identify structurally equivalent nodes. However, most of the existing methods require high time and space complexity. In this paper, we propose VNEstruct, a simple approach for generating low-dimensional structural node embeddings, that is both time efficient and robust to perturbations of the graph structure. The proposed approach focuses on the local neighborhood of each node and employs the Von Neumann entropy, an information-theoretic tool, to extract features that capture the neighborhood's topology. Moreover, on graph classification tasks, we suggest the utilization of the generated structural embeddings for the transformation of an attributed graph structure into a set of augmented node attributes. Empirically, we observe that the proposed approach exhibits robustness on structural role identification tasks and state-of-the-art performance on graph classification tasks, while maintaining very high computational speed.
A novel kernel-based support vector machine (SVM) for graph classification is proposed. The SVM feature space mapping consists of a sequence of graph convolutional layers, which generates a vector space representation for each vertex, followed by a pooling layer which generates a reproducing kernel Hilbert space (RKHS) representation for the graph. The use of a RKHS offers the ability to implicitly operate in this space using a kernel function without the computational complexity of explicitly mapping into it. The proposed model is trained in a supervised end-to-end manner whereby the convolutional layers, the kernel function and SVM parameters are jointly optimized with respect to a regularized classification loss. This approach is distinct from existing kernel-based graph classification models which instead either use feature engineering or unsupervised learning to define the kernel function. Experimental results demonstrate that the proposed model outperforms existing deep learning baseline models on a number of datasets.
We propose to study the problem of few shot graph classification in graph neural networks (GNNs) to recognize unseen classes, given limited labeled graph examples. Despite several interesting GNN variants being proposed recently for node and graph classification tasks, when faced with scarce labeled examples in the few shot setting, these GNNs exhibit significant loss in classification performance. Here, we present an approach where a probability measure is assigned to each graph based on the spectrum of the graphs normalized Laplacian. This enables us to accordingly cluster the graph base labels associated with each graph into super classes, where the Lp Wasserstein distance serves as our underlying distance metric. Subsequently, a super graph constructed based on the super classes is then fed to our proposed GNN framework which exploits the latent inter class relationships made explicit by the super graph to achieve better class label separation among the graphs. We conduct exhaustive empirical evaluations of our proposed method and show that it outperforms both the adaptation of state of the art graph classification methods to few shot scenario and our naive baseline GNNs. Additionally, we also extend and study the behavior of our method to semi supervised and active learning scenarios.
Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph. We also introduce two new networks based on this layer: memory-based GNN (MemGNN) and graph memory network (GMN) that can learn hierarchical graph representations. The experimental results shows that the proposed models achieve state-of-the-art results in eight out of nine graph classification and regression benchmarks. We also show that the learned representations could correspond to chemical features in the molecule data. Code and reference implementations are released at: https://github.com/amirkhas/GraphMemoryNet
Graph distance metric learning serves as the foundation for many graph learning problems, e.g., graph clustering, graph classification and graph matching. Existing research works on graph distance metric (or graph kernels) learning fail to maintain the basic properties of such metrics, e.g., non-negative, identity of indiscernibles, symmetry and triangle inequality, respectively. In this paper, we will introduce a new graph neural network based distance metric learning approaches, namely GB-DISTANCE (GRAPH-BERT based Neural Distance). Solely based on the attention mechanism, GB-DISTANCE can learn graph instance representations effectively based on a pre-trained GRAPH-BERT model. Different from the existing supervised/unsupervised metrics, GB-DISTANCE can be learned effectively in a semi-supervised manner. In addition, GB-DISTANCE can also maintain the distance metric basic properties mentioned above. Extensive experiments have been done on several benchmark graph datasets, and the results demonstrate that GB-DISTANCE can out-perform the existing baseline methods, especially the recent graph neural network model based graph metrics, with a significant gap in computing the graph distance.