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.
Typed entailment graphs try to learn the entailment relations between predicates from text and model them as edges between predicate nodes. The construction of entailment graphs usually suffers from severe sparsity and unreliability of distributional similarity. We propose a two-stage method, Entailment Graph with Textual Entailment and Transitivity (EGT2). EGT2 learns local entailment relations by recognizing possible textual entailment between template sentences formed by typed CCG-parsed predicates. Based on the generated local graph, EGT2 then uses three novel soft transitivity constraints to consider the logical transitivity in entailment structures. Experiments on benchmark datasets show that EGT2 can well model the transitivity in entailment graph to alleviate the sparsity issue, and lead to significant improvement over current state-of-the-art methods.
Graph structured data is ubiquitous in daily life and scientific areas and has attracted increasing attention. Graph Neural Networks (GNNs) have been proved to be effective in modeling graph structured data and many variants of GNN architectures have been proposed. However, much human effort is often needed to tune the architecture depending on different datasets. Researchers naturally adopt Automated Machine Learning on Graph Learning, aiming to reduce the human effort and achieve generally top-performing GNNs, but their methods focus more on the architecture search. To understand GNN practitioners' automated solutions, we organized AutoGraph Challenge at KDD Cup 2020, emphasizing on automated graph neural networks for node classification. We received top solutions especially from industrial tech companies like Meituan, Alibaba and Twitter, which are already open sourced on Github. After detailed comparisons with solutions from academia, we quantify the gaps between academia and industry on modeling scope, effectiveness and efficiency, and show that (1) academia AutoML for Graph solutions focus on GNN architecture search while industrial solutions, especially the winning ones in the KDD Cup, tend to obtain an overall solution (2) by neural architecture search only, academia solutions achieve on average 97.3% accuracy of industrial solutions (3) academia solutions are cheap to obtain with several GPU hours while industrial solutions take a few months' labors. Academic solutions also contain much fewer parameters.
Graph learning algorithms have attained state-of-the-art performance on many graph analysis tasks such as node classification, link prediction, and clustering. It has, however, become hard to track the field's burgeoning progress. One reason is due to the very small number of datasets used in practice to benchmark the performance of graph learning algorithms. This shockingly small sample size (~10) allows for only limited scientific insight into the problem. In this work, we aim to address this deficiency. We propose to generate synthetic graphs, and study the behaviour of graph learning algorithms in a controlled scenario. We develop a fully-featured synthetic graph generator that allows deep inspection of different models. We argue that synthetic graph generations allows for thorough investigation of algorithms and provides more insights than overfitting on three citation datasets. In the case study, we show how our framework provides insight into unsupervised and supervised graph neural network models.
We present a novel method for classification of Synthetic Aperture Radar (SAR) data by combining ideas from graph-based learning and neural network methods within an active learning framework. Graph-based methods in machine learning are based on a similarity graph constructed from the data. When the data consists of raw images composed of scenes, extraneous information can make the classification task more difficult. In recent years, neural network methods have been shown to provide a promising framework for extracting patterns from SAR images. These methods, however, require ample training data to avoid overfitting. At the same time, such training data are often unavailable for applications of interest, such as automatic target recognition (ATR) and SAR data. We use a Convolutional Neural Network Variational Autoencoder (CNNVAE) to embed SAR data into a feature space, and then construct a similarity graph from the embedded data and apply graph-based semi-supervised learning techniques. The CNNVAE feature embedding and graph construction requires no labeled data, which reduces overfitting and improves the generalization performance of graph learning at low label rates. Furthermore, the method easily incorporates a human-in-the-loop for active learning in the data-labeling process. We present promising results and compare them to other standard machine learning methods on the Moving and Stationary Target Acquisition and Recognition (MSTAR) dataset for ATR with small amounts of labeled data.
As a powerful tool for modeling complex relationships, hypergraphs are gaining popularity from the graph learning community. However, commonly used frameworks in deep hypergraph learning focus on hypergraphs with edge-independent vertex weights (EIVWs), without considering hypergraphs with edge-dependent vertex weights (EDVWs) that have more modeling power. To compensate for this, we present General Hypergraph Spectral Convolution (GHSC), a general learning framework that not only handles EDVW and EIVW hypergraphs, but more importantly, enables theoretically explicitly utilizing the existing powerful Graph Convolutional Neural Networks (GCNNs) such that largely ease the design of Hypergraph Neural Networks. In this framework, the graph Laplacian of the given undirected GCNNs is replaced with a unified hypergraph Laplacian that incorporates vertex weight information from a random walk perspective by equating our defined generalized hypergraphs with simple undirected graphs. Extensive experiments from various domains including social network analysis, visual objective classification, and protein learning demonstrate the state-of-the-art performance of the proposed framework.
This paper proposes a new eXplanation framework, called OrphicX, for generating causal explanations for any graph neural networks (GNNs) based on learned latent causal factors. Specifically, we construct a distinct generative model and design an objective function that encourages the generative model to produce causal, compact, and faithful explanations. This is achieved by isolating the causal factors in the latent space of graphs by maximizing the information flow measurements. We theoretically analyze the cause-effect relationships in the proposed causal graph, identify node attributes as confounders between graphs and GNN predictions, and circumvent such confounder effect by leveraging the backdoor adjustment formula. Our framework is compatible with any GNNs, and it does not require access to the process by which the target GNN produces its predictions. In addition, it does not rely on the linear-independence assumption of the explained features, nor require prior knowledge on the graph learning tasks. We show a proof-of-concept of OrphicX on canonical classification problems on graph data. In particular, we analyze the explanatory subgraphs obtained from explanations for molecular graphs (i.e., Mutag) and quantitatively evaluate the explanation performance with frequently occurring subgraph patterns. Empirically, we show that OrphicX can effectively identify the causal semantics for generating causal explanations, significantly outperforming its alternatives.
Contrastive self-supervised learning has recently benefited fMRI classification with inductive biases. Its weak label reliance prevents overfitting on small medical datasets and tackles the high intraclass variances. Nonetheless, existing contrastive methods generate resemblant pairs only on pixel-level features of 3D medical images, while the functional connectivity that reveals critical cognitive information is under-explored. Additionally, existing methods predict labels on individual contrastive representation without recognizing neighbouring information in the patient group, whereas interpatient contrast can act as a similarity measure suitable for population-based classification. We hereby proposed contrastive functional connectivity graph learning for population-based fMRI classification. Representations on the functional connectivity graphs are "repelled" for heterogeneous patient pairs meanwhile homogeneous pairs "attract" each other. Then a dynamic population graph that strengthens the connections between similar patients is updated for classification. Experiments on a multi-site dataset ADHD200 validate the superiority of the proposed method on various metrics. We initially visualize the population relationships and exploit potential subtypes.
Semi-supervised learning (SSL) has recently received increased attention from machine learning researchers. By enabling effective propagation of known labels in graph-based deep learning (GDL) algorithms, SSL is poised to become an increasingly used technique in GDL in the coming years. However, there are currently few explorations in the graph-based SSL literature on exploiting classical dimensionality reduction techniques for improved label propagation. In this work, we investigate the use of dimensionality reduction techniques such as PCA, t-SNE, and UMAP to see their effect on the performance of graph neural networks (GNNs) designed for semi-supervised propagation of node labels. Our study makes use of benchmark semi-supervised GDL datasets such as the Cora and Citeseer datasets to allow meaningful comparisons of the representations learned by each algorithm when paired with a dimensionality reduction technique. Our comprehensive benchmarks and clustering visualizations quantitatively and qualitatively demonstrate that, under certain conditions, employing a priori and a posteriori dimensionality reduction to GNN inputs and outputs, respectively, can simultaneously improve the effectiveness of semi-supervised node label propagation and node clustering. Our source code is freely available on GitHub.
The identification of drug-target binding affinity (DTA) has attracted increasing attention in the drug discovery process due to the more specific interpretation than binary interaction prediction. Recently, numerous deep learning-based computational methods have been proposed to predict the binding affinities between drugs and targets benefiting from their satisfactory performance. However, the previous works mainly focus on encoding biological features and chemical structures of drugs and targets, with a lack of exploiting the essential topological information from the drug-target affinity network. In this paper, we propose a novel hierarchical graph representation learning model for the drug-target binding affinity prediction, namely HGRL-DTA. The main contribution of our model is to establish a hierarchical graph learning architecture to incorporate the intrinsic properties of drug/target molecules and the topological affinities of drug-target pairs. In this architecture, we adopt a message broadcasting mechanism to integrate the hierarchical representations learned from the global-level affinity graph and the local-level molecular graph. Besides, we design a similarity-based embedding map to solve the cold start problem of inferring representations for unseen drugs and targets. Comprehensive experimental results under different scenarios indicate that HGRL-DTA significantly outperforms the state-of-the-art models and shows better model generalization among all the scenarios.
Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world applications. Current studies use existing techniques, such as weight constraint, representation constraint, which are derived from images or text data, to transfer the invariant knowledge from the pre-train stage to fine-tuning stage. However, these methods failed to preserve invariances from graph structure and Graph Neural Network (GNN) style models. In this paper, we present a novel optimal transport-based fine-tuning framework called GTOT-Tuning, namely, Graph Topology induced Optimal Transport fine-Tuning, for GNN style backbones. GTOT-Tuning is required to utilize the property of graph data to enhance the preservation of representation produced by fine-tuned networks. Toward this goal, we formulate graph local knowledge transfer as an Optimal Transport (OT) problem with a structural prior and construct the GTOT regularizer to constrain the fine-tuned model behaviors. By using the adjacency relationship amongst nodes, the GTOT regularizer achieves node-level optimal transport procedures and reduces redundant transport procedures, resulting in efficient knowledge transfer from the pre-trained models. We evaluate GTOT-Tuning on eight downstream tasks with various GNN backbones and demonstrate that it achieves state-of-the-art fine-tuning performance for GNNs.
Graph Augmentation Learning (GAL) provides outstanding solutions for graph learning in handling incomplete data, noise data, etc. Numerous GAL methods have been proposed for graph-based applications such as social network analysis and traffic flow forecasting. However, the underlying reasons for the effectiveness of these GAL methods are still unclear. As a consequence, how to choose optimal graph augmentation strategy for a certain application scenario is still in black box. There is a lack of systematic, comprehensive, and experimentally validated guideline of GAL for scholars. Therefore, in this survey, we in-depth review GAL techniques from macro (graph), meso (subgraph), and micro (node/edge) levels. We further detailedly illustrate how GAL enhance the data quality and the model performance. The aggregation mechanism of augmentation strategies and graph learning models are also discussed by different application scenarios, i.e., data-specific, model-specific, and hybrid scenarios. To better show the outperformance of GAL, we experimentally validate the effectiveness and adaptability of different GAL strategies in different downstream tasks. Finally, we share our insights on several open issues of GAL, including heterogeneity, spatio-temporal dynamics, scalability, and generalization.
In order to advance the state of the art in graph learning algorithms, it is necessary to construct large real-world datasets. While there are many benchmark datasets for homogeneous graphs, only a few of them are available for heterogeneous graphs. Furthermore, the latter graphs are small in size rendering them insufficient to understand how graph learning algorithms perform in terms of classification metrics and computational resource utilization. We introduce, PDNS-Net, the largest public heterogeneous graph dataset containing 447K nodes and 897K edges for the malicious domain classification task. Compared to the popular heterogeneous datasets IMDB and DBLP, PDNS-Net is 38 and 17 times bigger respectively. We provide a detailed analysis of PDNS-Net including the data collection methodology, heterogeneous graph construction, descriptive statistics and preliminary graph classification performance. The dataset is publicly available at https://github.com/qcri/PDNS-Net. Our preliminary evaluation of both popular homogeneous and heterogeneous graph neural networks on PDNS-Net reveals that further research is required to improve the performance of these models on large heterogeneous graphs.
Graph neural networks (GNNs) have been widely adopted for semi-supervised learning on graphs. A recent study shows that the graph random neural network (GRAND) model can generate state-of-the-art performance for this problem. However, it is difficult for GRAND to handle large-scale graphs since its effectiveness relies on computationally expensive data augmentation procedures. In this work, we present a scalable and high-performance GNN framework GRAND+ for semi-supervised graph learning. To address the above issue, we develop a generalized forward push (GFPush) algorithm in GRAND+ to pre-compute a general propagation matrix and employ it to perform graph data augmentation in a mini-batch manner. We show that both the low time and space complexities of GFPush enable GRAND+ to efficiently scale to large graphs. Furthermore, we introduce a confidence-aware consistency loss into the model optimization of GRAND+, facilitating GRAND+'s generalization superiority. We conduct extensive experiments on seven public datasets of different sizes. The results demonstrate that GRAND+ 1) is able to scale to large graphs and costs less running time than existing scalable GNNs, and 2) can offer consistent accuracy improvements over both full-batch and scalable GNNs across all datasets.
Benefiting from the powerful expressive capability of graphs, graph-based approaches have been popularly applied to handle multi-modal medical data and achieved impressive performance in various biomedical applications. For disease prediction tasks, most existing graph-based methods tend to define the graph manually based on specified modality (e.g., demographic information), and then integrated other modalities to obtain the patient representation by Graph Representation Learning (GRL). However, constructing an appropriate graph in advance is not a simple matter for these methods. Meanwhile, the complex correlation between modalities is ignored. These factors inevitably yield the inadequacy of providing sufficient information about the patient's condition for a reliable diagnosis. To this end, we propose an end-to-end Multi-modal Graph Learning framework (MMGL) for disease prediction with multi-modality. To effectively exploit the rich information across multi-modality associated with the disease, modality-aware representation learning is proposed to aggregate the features of each modality by leveraging the correlation and complementarity between the modalities. Furthermore, instead of defining the graph manually, the latent graph structure is captured through an effective way of adaptive graph learning. It could be jointly optimized with the prediction model, thus revealing the intrinsic connections among samples. Our model is also applicable to the scenario of inductive learning for those unseen data. An extensive group of experiments on two disease prediction tasks demonstrates that the proposed MMGL achieves more favorable performance. The code of MMGL is available at \url{https://github.com/SsGood/MMGL}.