Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.
Graph Neural Networks (GNNs) have been predominant for graph learning tasks; however, recent studies showed that a well-known graph algorithm, Label Propagation (LP), combined with a shallow neural network can achieve comparable performance to GNNs in semi-supervised node classification on graphs with high homophily. In this paper, we show that this approach falls short on graphs with low homophily, where nodes often connect to the nodes of the opposite classes. To overcome this, we carefully design a combination of a base predictor with LP algorithm that enjoys a closed-form solution as well as convergence guarantees. Our algorithm first learns the class compatibility matrix and then aggregates label predictions using LP algorithm weighted by class compatibilities. On a wide variety of benchmarks, we show that our approach achieves the leading performance on graphs with various levels of homophily. Meanwhile, it has orders of magnitude fewer parameters and requires less execution time. Empirical evaluations demonstrate that simple adaptations of LP can be competitive in semi-supervised node classification in both homophily and heterophily regimes.
MRI-based modeling of brain networks has been widely used to understand functional and structural interactions and connections among brain regions, and factors that affect them, such as brain development and disease. Graph mining on brain networks may facilitate the discovery of novel biomarkers for clinical phenotypes and neurodegenerative diseases. Since brain networks derived from functional and structural MRI describe the brain topology from different perspectives, exploring a representation that combines these cross-modality brain networks is non-trivial. Most current studies aim to extract a fused representation of the two types of brain network by projecting the structural network to the functional counterpart. Since the functional network is dynamic and the structural network is static, mapping a static object to a dynamic object is suboptimal. However, mapping in the opposite direction is not feasible due to the non-negativity requirement of current graph learning techniques. Here, we propose a novel graph learning framework, known as Deep Signed Brain Networks (DSBN), with a signed graph encoder that, from an opposite perspective, learns the cross-modality representations by projecting the functional network to the structural counterpart. We validate our framework on clinical phenotype and neurodegenerative disease prediction tasks using two independent, publicly available datasets (HCP and OASIS). The experimental results clearly demonstrate the advantages of our model compared to several state-of-the-art methods.
In this paper, we study the design and analysis of a class of efficient algorithms for computing the Gromov-Wasserstein (GW) distance tailored to large-scale graph learning tasks. Armed with the Luo-Tseng error bound condition~\citep{luo1992error}, two proposed algorithms, called Bregman Alternating Projected Gradient (BAPG) and hybrid Bregman Proximal Gradient (hBPG) enjoy the convergence guarantees. Upon task-specific properties, our analysis further provides novel theoretical insights to guide how to select the best-fit method. As a result, we are able to provide comprehensive experiments to validate the effectiveness of our methods on a host of tasks, including graph alignment, graph partition, and shape matching. In terms of both wall-clock time and modeling performance, the proposed methods achieve state-of-the-art results.
Graph neural networks (GNNs) have emerged as a series of competent graph learning methods for diverse real-world scenarios, ranging from daily applications like recommendation systems and question answering to cutting-edge technologies such as drug discovery in life sciences and n-body simulation in astrophysics. However, task performance is not the only requirement for GNNs. Performance-oriented GNNs have exhibited potential adverse effects like vulnerability to adversarial attacks, unexplainable discrimination against disadvantaged groups, or excessive resource consumption in edge computing environments. To avoid these unintentional harms, it is necessary to build competent GNNs characterised by trustworthiness. To this end, we propose a comprehensive roadmap to build trustworthy GNNs from the view of the various computing technologies involved. In this survey, we introduce basic concepts and comprehensively summarise existing efforts for trustworthy GNNs from six aspects, including robustness, explainability, privacy, fairness, accountability, and environmental well-being. Additionally, we highlight the intricate cross-aspect relations between the above six aspects of trustworthy GNNs. Finally, we present a thorough overview of trending directions for facilitating the research and industrialisation of trustworthy GNNs.
Graph neural networks (GNNs) mainly rely on the message-passing paradigm to propagate node features and build interactions, and different graph learning tasks require different ranges of node interactions. In this work, we explore the capacity of GNNs to capture interactions between nodes under contexts with different complexities. We discover that GNNs are usually unable to capture the most informative kinds of interaction styles for diverse graph learning tasks, and thus name this phenomenon as GNNs' representation bottleneck. As a response, we demonstrate that the inductive bias introduced by existing graph construction mechanisms can prevent GNNs from learning interactions of the most appropriate complexity, i.e., resulting in the representation bottleneck. To address that limitation, we propose a novel graph rewiring approach based on interaction patterns learned by GNNs to adjust the receptive fields of each node dynamically. Extensive experiments on both real-world and synthetic datasets prove the effectiveness of our algorithm to alleviate the representation bottleneck and its superiority to enhance the performance of GNNs over state-of-the-art graph rewiring baselines.
CT-based bronchial tree analysis plays an important role in the computer-aided diagnosis for respiratory diseases, as it could provide structured information for clinicians. The basis of airway analysis is bronchial tree reconstruction, which consists of bronchus segmentation and classification. However, there remains a challenge for accurate bronchial analysis due to the individual variations and the severe class imbalance. In this paper, we propose a region and structure prior embedded framework named BronchusNet to achieve accurate segmentation and classification of bronchial regions in CT images. For bronchus segmentation, we propose an adaptive hard region-aware UNet that incorporates multi-level prior guidance of hard pixel-wise samples in the general Unet segmentation network to achieve better hierarchical feature learning. For the classification of bronchial branches, we propose a hybrid point-voxel graph learning module to fully exploit bronchial structure priors and to support simultaneous feature interactions across different branches. To facilitate the study of bronchial analysis, we contribute~\textbf{BRSC}: an open-access benchmark of \textbf{BR}onchus imaging analysis with high-quality pixel-wise \textbf{S}egmentation masks and the \textbf{C}lass of bronchial segments. Experimental results on BRSC show that our proposed method not only achieves the state-of-the-art performance for binary segmentation of bronchial region but also exceeds the best existing method on bronchial branches classification by 6.9\%.
Hyperdimensional Computing (HDC) developed by Kanerva is a computational model for machine learning inspired by neuroscience. HDC exploits characteristics of biological neural systems such as high-dimensionality, randomness and a holographic representation of information to achieve a good balance between accuracy, efficiency and robustness. HDC models have already been proven to be useful in different learning applications, especially in resource-limited settings such as the increasingly popular Internet of Things (IoT). One class of learning tasks that is missing from the current body of work on HDC is graph classification. Graphs are among the most important forms of information representation, yet, to this day, HDC algorithms have not been applied to the graph learning problem in a general sense. Moreover, graph learning in IoT and sensor networks, with limited compute capabilities, introduce challenges to the overall design methodology. In this paper, we present GraphHD$-$a baseline approach for graph classification with HDC. We evaluate GraphHD on real-world graph classification problems. Our results show that when compared to the state-of-the-art Graph Neural Networks (GNNs) the proposed model achieves comparable accuracy, while training and inference times are on average 14.6$\times$ and 2.0$\times$ faster, respectively.
Attributed graph clustering or community detection which learns to cluster the nodes of a graph is a challenging task in graph analysis. In this paper, we introduce a contrastive learning framework for learning clustering-friendly node embedding. Although graph contrastive learning has shown outstanding performance in self-supervised graph learning, using it for graph clustering is not well explored. We propose Gaussian mixture information maximization (GMIM) which utilizes a mutual information maximization approach for node embedding. Meanwhile, it assumes that the representation space follows a Mixture of Gaussians (MoG) distribution. The clustering part of our objective tries to fit a Gaussian distribution to each community. The node embedding is jointly optimized with the parameters of MoG in a unified framework. Experiments on real-world datasets demonstrate the effectiveness of our method in community detection.
While hyper-parameters (HPs) are important for knowledge graph (KG) learning, existing methods fail to search them efficiently. To solve this problem, we first analyze the properties of different HPs and measure the transfer ability from small subgraph to the full graph. Based on the analysis, we propose an efficient two-stage search algorithm KGTuner, which efficiently explores HP configurations on small subgraph at the first stage and transfers the top-performed configurations for fine-tuning on the large full graph at the second stage. Experiments show that our method can consistently find better HPs than the baseline algorithms within the same time budget, which achieves {9.1\%} average relative improvement for four embedding models on the large-scale KGs in open graph benchmark.
Recently, industrial recommendation services have been boosted by the continual upgrade of deep learning methods. However, they still face de-biasing challenges such as exposure bias and cold-start problem, where circulations of machine learning training on human interaction history leads algorithms to repeatedly suggest exposed items while ignoring less-active ones. Additional problems exist in multi-scenario platforms, e.g. appropriate data fusion from subsidiary scenarios, which we observe could be alleviated through graph structured data integration via message passing. In this paper, we present a multi-graph structured multi-scenario recommendation solution, which encapsulates interaction data across scenarios with multi-graph and obtains representation via graph learning. Extensive offline and online experiments on real-world datasets are conducted where the proposed method demonstrates an increase of 0.63% and 0.71% in CTR and Video Views per capita on new users over deployed set of baselines and outperforms regular method in increasing the number of outer-scenario videos by 25% and video watches by 116%, validating its superiority in activating cold videos and enriching target recommendation.
We consider the problem of inferring the conditional independence graph (CIG) of a high-dimensional stationary multivariate Gaussian time series. In a time series graph, each component of the vector series is represented by distinct node, and associations between components are represented by edges between the corresponding nodes. We formulate the problem as one of multi-attribute graph estimation for random vectors where a vector is associated with each node of the graph. At each node, the associated random vector consists of a time series component and its delayed copies. We present an alternating direction method of multipliers (ADMM) solution to minimize a sparse-group lasso penalized negative pseudo log-likelihood objective function to estimate the precision matrix of the random vector associated with the entire multi-attribute graph. The time series CIG is then inferred from the estimated precision matrix. A theoretical analysis is provided. Numerical results illustrate the proposed approach which outperforms existing frequency-domain approaches in correctly detecting the graph edges.
Scalability is an important consideration for deep graph neural networks. Inspired by the conventional pooling layers in CNNs, many recent graph learning approaches have introduced the pooling strategy to reduce the size of graphs for learning, such that the scalability and efficiency can be improved. However, these pooling-based methods are mainly tailored to a single graph-level task and pay more attention to local information, limiting their performance in multi-task settings which often require task-specific global information. In this paper, departure from these pooling-based efforts, we design a new approach called DOTIN (\underline{D}r\underline{o}pping \underline{T}ask-\underline{I}rrelevant \underline{N}odes) to reduce the size of graphs. Specifically, by introducing $K$ learnable virtual nodes to represent the graph embeddings targeted to $K$ different graph-level tasks, respectively, up to 90\% raw nodes with low attentiveness with an attention model -- a transformer in this paper, can be adaptively dropped without notable performance decreasing. Achieving almost the same accuracy, our method speeds up GAT by about 50\% on graph-level tasks including graph classification and graph edit distance (GED) with about 60\% less memory, on D\&D dataset. Code will be made publicly available in https://github.com/Sherrylone/DOTIN.
The design automation of analog circuits is a longstanding challenge. This paper presents a reinforcement learning method enhanced by graph learning to automate the analog circuit parameter optimization at the pre-layout stage, i.e., finding device parameters to fulfill desired circuit specifications. Unlike all prior methods, our approach is inspired by human experts who rely on domain knowledge of analog circuit design (e.g., circuit topology and couplings between circuit specifications) to tackle the problem. By originally incorporating such key domain knowledge into policy training with a multimodal network, the method best learns the complex relations between circuit parameters and design targets, enabling optimal decisions in the optimization process. Experimental results on exemplary circuits show it achieves human-level design accuracy (99%) 1.5X efficiency of existing best-performing methods. Our method also shows better generalization ability to unseen specifications and optimality in circuit performance optimization. Moreover, it applies to design radio-frequency circuits on emerging semiconductor technologies, breaking the limitations of prior learning methods in designing conventional analog circuits.
We propose Graph Tree Networks (GTNets), a deep graph learning architecture with a new general message passing scheme that originates from the tree representation of graphs. In the tree representation, messages propagate upward from the leaf nodes to the root node, and each node preserves its initial information prior to receiving information from its child nodes (neighbors). We formulate a general propagation rule following the nature of message passing in the tree to update a node's feature by aggregating its initial feature and its neighbor nodes' updated features. Two graph representation learning models are proposed within this GTNet architecture - Graph Tree Attention Network (GTAN) and Graph Tree Convolution Network (GTCN), with experimentally demonstrated state-of-the-art performance on several popular benchmark datasets. Unlike the vanilla Graph Attention Network (GAT) and Graph Convolution Network (GCN) which have the "over-smoothing" issue, the proposed GTAN and GTCN models can go deep as demonstrated by comprehensive experiments and rigorous theoretical analysis.
This paper focuses on three critical problems on protein classification. Firstly, Carbohydrate-active enzyme (CAZyme) classification can help people to understand the properties of enzymes. However, one CAZyme may belong to several classes. This leads to Multi-label CAZyme classification. Secondly, to capture information from the secondary structure of protein, protein classification is modeled as graph classification problem. Thirdly, compound-protein interactions prediction employs graph learning for compound with sequential embedding for protein. This can be seen as classification task for compound-protein pairs. This paper proposes three models for protein classification. Firstly, this paper proposes a Multi-label CAZyme classification model using CNN-LSTM with Attention mechanism. Secondly, this paper proposes a variational graph autoencoder based subspace learning model for protein graph classification. Thirdly, this paper proposes graph isomorphism networks (GIN) and Attention-based CNN-LSTM for compound-protein interactions prediction, as well as comparing GIN with graph convolution networks (GCN) and graph attention networks (GAT) in this task. The proposed models are effective for protein classification. Source code and data are available at https://github.com/zshicode/GNN-AttCL-protein. Besides, this repository collects and collates the benchmark datasets with respect to above problems, including CAZyme classification, enzyme protein graph classification, compound-protein interactions prediction, drug-target affinities prediction and drug-drug interactions prediction. Hence, the usage for evaluation by benchmark datasets can be more conveniently.
Given entities and their interactions in the web data, which may have occurred at different time, how can we find communities of entities and track their evolution? In this paper, we approach this important task from graph clustering perspective. Recently, state-of-the-art clustering performance in various domains has been achieved by deep clustering methods. Especially, deep graph clustering (DGC) methods have successfully extended deep clustering to graph-structured data by learning node representations and cluster assignments in a joint optimization framework. Despite some differences in modeling choices (e.g., encoder architectures), existing DGC methods are mainly based on autoencoders and use the same clustering objective with relatively minor adaptations. Also, while many real-world graphs are dynamic, previous DGC methods considered only static graphs. In this work, we develop CGC, a novel end-to-end framework for graph clustering, which fundamentally differs from existing methods. CGC learns node embeddings and cluster assignments in a contrastive graph learning framework, where positive and negative samples are carefully selected in a multi-level scheme such that they reflect hierarchical community structures and network homophily. Also, we extend CGC for time-evolving data, where temporal graph clustering is performed in an incremental learning fashion, with the ability to detect change points. Extensive evaluation on real-world graphs demonstrates that the proposed CGC consistently outperforms existing methods.
Precise segmentation of teeth from intra-oral scanner images is an essential task in computer-aided orthodontic surgical planning. The state-of-the-art deep learning-based methods often simply concatenate the raw geometric attributes (i.e., coordinates and normal vectors) of mesh cells to train a single-stream network for automatic intra-oral scanner image segmentation. However, since different raw attributes reveal completely different geometric information, the naive concatenation of different raw attributes at the (low-level) input stage may bring unnecessary confusion in describing and differentiating between mesh cells, thus hampering the learning of high-level geometric representations for the segmentation task. To address this issue, we design a two-stream graph convolutional network (i.e., TSGCN), which can effectively handle inter-view confusion between different raw attributes to more effectively fuse their complementary information and learn discriminative multi-view geometric representations. Specifically, our TSGCN adopts two input-specific graph-learning streams to extract complementary high-level geometric representations from coordinates and normal vectors, respectively. Then, these single-view representations are further fused by a self-attention module to adaptively balance the contributions of different views in learning more discriminative multi-view representations for accurate and fully automatic tooth segmentation. We have evaluated our TSGCN on a real-patient dataset of dental (mesh) models acquired by 3D intraoral scanners. Experimental results show that our TSGCN significantly outperforms state-of-the-art methods in 3D tooth (surface) segmentation. Github: https://github.com/ZhangLingMing1/TSGCNet.
Despite significant progress, previous multi-view unsupervised feature selection methods mostly suffer from two limitations. First, they generally utilize either cluster structure or similarity structure to guide the feature selection, which neglect the possibility of a joint formulation with mutual benefits. Second, they often learn the similarity structure by either global structure learning or local structure learning, which lack the capability of graph learning with both global and local structural awareness. In light of this, this paper presents a joint multi-view unsupervised feature selection and graph learning (JMVFG) approach. Particularly, we formulate the multi-view feature selection with orthogonal decomposition, where each target matrix is decomposed into a view-specific basis matrix and a view-consistent cluster indicator. The cross-space locality preservation is incorporated to bridge the cluster structure learning in the projected space and the similarity learning (i.e., graph learning) in the original space. Further, a unified objective function is presented to enable the simultaneous learning of the cluster structure, the global and local similarity structures, and the multi-view consistency and inconsistency, upon which an alternating optimization algorithm is developed with theoretically proved convergence. Extensive experiments on a variety of real-world multi-view datasets demonstrate the superiority of our approach for both the multi-view feature selection and graph learning tasks. The code is available at https://github.com/huangdonghere/JMVFG.
The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at https://github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.