Characterizing the separation power of graph neural networks (GNNs) provides an understanding of their limitations for graph learning tasks. Results regarding separation power are, however, usually geared at specific GNN architectures, and tools for understanding arbitrary GNN architectures are generally lacking. We provide an elegant way to easily obtain bounds on the separation power of GNNs in terms of the Weisfeiler-Leman (WL) tests, which have become the yardstick to measure the separation power of GNNs. The crux is to view GNNs as expressions in a procedural tensor language describing the computations in the layers of the GNNs. Then, by a simple analysis of the obtained expressions, in terms of the number of indexes and the nesting depth of summations, bounds on the separation power in terms of the WL-tests readily follow. We use tensor language to define Higher-Order Message-Passing Neural Networks (or k-MPNNs), a natural extension of MPNNs. Furthermore, the tensor language point of view allows for the derivation of universality results for classes of GNNs in a natural way. Our approach provides a toolbox with which GNN architecture designers can analyze the separation power of their GNNs, without needing to know the intricacies of the WL-tests. We also provide insights in what is needed to boost the separation power of GNNs.
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.
In recent years, the prevalent online services generate a sheer volume of user activity data. Service providers collect these data in order to perform client behavior analysis, and offer better and more customized services. Majority of these data can be modeled and stored as graph, such as the social graph in Facebook, user-video interaction graph in Youtube. These graphs need to evolve over time to capture the dynamics in the real world, leading to the invention of dynamic graphs. However, the temporal information embedded in the dynamic graphs brings new challenges in analyzing and deploying them. Events staleness, temporal information learning and explicit time dimension usage are some example challenges in dynamic graph learning. In order to offer a convenient reference to both the industry and academia, this survey presents the Three Stages Recurrent Temporal Learning Framework based on dynamic graph evolution theories, so as to interpret the learning of temporal information with a generalized framework. Under this framework, this survey categories and reviews different learnable encoder-decoder architectures for supervised dynamic graph learning. We believe that this survey could supply useful guidelines to researchers and engineers in finding suitable graph structures for their dynamic learning tasks.
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.
Series photo selection (SPS) is an important branch of the image aesthetics quality assessment, which focuses on finding the best one from a series of nearly identical photos. While a great progress has been observed, most of the existing SPS approaches concentrate solely on extracting features from the original image, neglecting that multiple views, e.g, saturation level, color histogram and depth of field of the image, will be of benefit to successfully reflecting the subtle aesthetic changes. Taken multi-view into consideration, we leverage a graph neural network to construct the relationships between multi-view features. Besides, multiple views are aggregated with an adaptive-weight self-attention module to verify the significance of each view. Finally, a siamese network is proposed to select the best one from a series of nearly identical photos. Experimental results demonstrate that our model accomplish the highest success rates compared with competitive methods.
In this work, we study the applications of differential privacy (DP) in the context of graph-structured data. We discuss the formulations of DP applicable to the publication of graphs and their associated statistics as well as machine learning on graph-based data, including graph neural networks (GNNs). The formulation of DP in the context of graph-structured data is difficult, as individual data points are interconnected (often non-linearly or sparsely). This connectivity complicates the computation of individual privacy loss in differentially private learning. The problem is exacerbated by an absence of a single, well-established formulation of DP in graph settings. This issue extends to the domain of GNNs, rendering private machine learning on graph-structured data a challenging task. A lack of prior systematisation work motivated us to study graph-based learning from a privacy perspective. In this work, we systematise different formulations of DP on graphs, discuss challenges and promising applications, including the GNN domain. We compare and separate works into graph analysis tasks and graph learning tasks with GNNs. Finally, we conclude our work with a discussion of open questions and potential directions for further research in this area.
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.
Social learning algorithms provide models for the formation of opinions over social networks resulting from local reasoning and peer-to-peer exchanges. Interactions occur over an underlying graph topology, which describes the flow of information among the agents. To account for drifting conditions in the environment, this work adopts an adaptive social learning strategy, which is able to track variations in the underlying signal statistics. Among other results, we propose a technique that addresses questions of explainability and interpretability of the results when the graph is hidden. Given observations of the evolution of the beliefs over time, we aim to infer the underlying graph topology, discover pairwise influences between the agents, and identify significant trajectories in the network. The proposed framework is online in nature and can adapt dynamically to changes in the graph topology or the true hypothesis.
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.
Few-shot learning (FSL), purposing to resolve the problem of data-scarce, has attracted considerable attention in recent years. A popular FSL framework contains two phases: (i) the pre-train phase employs the base data to train a CNN-based feature extractor. (ii) the meta-test phase applies the frozen feature extractor to novel data (novel data has different categories from base data) and designs a classifier for recognition. To correct few-shot data distribution, researchers propose Semi-Supervised Few-Shot Learning (SSFSL) by introducing unlabeled data. Although SSFSL has been proved to achieve outstanding performances in the FSL community, there still exists a fundamental problem: the pre-trained feature extractor can not adapt to the novel data flawlessly due to the cross-category setting. Usually, large amounts of noises are introduced to the novel feature. We dub it as Feature-Extractor-Maladaptive (FEM) problem. To tackle FEM, we make two efforts in this paper. First, we propose a novel label prediction method, Isolated Graph Learning (IGL). IGL introduces the Laplacian operator to encode the raw data to graph space, which helps reduce the dependence on features when classifying, and then project graph representation to label space for prediction. The key point is that: IGL can weaken the negative influence of noise from the feature representation perspective, and is also flexible to independently complete training and testing procedures, which is suitable for SSFSL. Second, we propose Graph Co-Training (GCT) to tackle this challenge from a multi-modal fusion perspective by extending the proposed IGL to the co-training framework. GCT is a semi-supervised method that exploits the unlabeled samples with two modal features to crossly strengthen the IGL classifier.
Graphs are ubiquitous in encoding relational information of real-world objects in many domains. Graph generation, whose purpose is to generate new graphs from a distribution similar to the observed graphs, has received increasing attention thanks to the recent advances of deep learning models. In this paper, we conduct a comprehensive review on the existing literature of deep graph generation from a variety of emerging methods to its wide application areas. Specifically, we first formulate the problem of deep graph generation and discuss its difference with several related graph learning tasks. Secondly, we divide the state-of-the-art methods into three categories based on model architectures and summarize their generation strategies. Thirdly, we introduce three key application areas of deep graph generation. Lastly, we highlight challenges and opportunities in the future study of deep graph generation. We hope that our survey will be useful for researchers and practitioners who are interested in this exciting and rapidly-developing field.
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.