Graph machine learning has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To tackle the challenge, automated graph machine learning, which aims at discovering the best hyper-parameter and neural architecture configuration for different graph tasks/data without manual design, is gaining an increasing number of attentions from the research community. In this paper, we extensively discuss automated graph machine learning approaches, covering hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We briefly overview existing libraries designed for either graph machine learning or automated machine learning respectively, and further in depth introduce AutoGL, our dedicated and the world's first open-source library for automated graph machine learning. Also, we describe a tailored benchmark that supports unified, reproducible, and efficient evaluations. Last but not least, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive discussion of approaches, libraries as well as directions for automated graph machine learning.
Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional graph representations. Graph neural networks (GNNs) are currently the most popular model in graph embedding approaches. However, standard GNNs in the neighborhood aggregation paradigm suffer from limited discriminative power in distinguishing \emph{high-order} graph structures as opposed to \emph{low-order} structures. To capture high-order structures, researchers have resorted to motifs and developed motif-based GNNs. However, existing motif-based GNNs still often suffer from less discriminative power on high-order structures. To overcome the above limitations, we propose Motif Graph Neural Network (MGNN), a novel framework to better capture high-order structures, hinging on our proposed motif redundancy minimization operator and injective motif combination. First, MGNN produces a set of node representations w.r.t. each motif. The next phase is our proposed redundancy minimization among motifs which compares the motifs with each other and distills the features unique to each motif. Finally, MGNN performs the updating of node representations by combining multiple representations from different motifs. In particular, to enhance the discriminative power, MGNN utilizes an injective function to combine the representations w.r.t. different motifs. We further show that our proposed architecture increases the expressive power of GNNs with a theoretical analysis. We demonstrate that MGNN outperforms state-of-the-art methods on seven public benchmarks on both node classification and graph classification tasks.
Graph Convolutional Networks (GCNs) have emerged as the state-of-the-art graph learning model. However, it can be notoriously challenging to inference GCNs over large graph datasets, limiting their application to large real-world graphs and hindering the exploration of deeper and more sophisticated GCN graphs. This is because real-world graphs can be extremely large and sparse. Furthermore, the node degree of GCNs tends to follow the power-law distribution and therefore have highly irregular adjacency matrices, resulting in prohibitive inefficiencies in both data processing and movement and thus substantially limiting the achievable GCN acceleration efficiency. To this end, this paper proposes a GCN algorithm and accelerator Co-Design framework dubbed GCoD which can largely alleviate the aforementioned GCN irregularity and boost GCNs' inference efficiency. Specifically, on the algorithm level, GCoD integrates a split and conquer GCN training strategy that polarizes the graphs to be either denser or sparser in local neighborhoods without compromising the model accuracy, resulting in graph adjacency matrices that (mostly) have merely two levels of workload and enjoys largely enhanced regularity and thus ease of acceleration. On the hardware level, we further develop a dedicated two-pronged accelerator with a separated engine to process each of the aforementioned denser and sparser workloads, further boosting the overall utilization and acceleration efficiency. Extensive experiments and ablation studies validate that our GCoD consistently reduces the number of off-chip accesses, leading to speedups of 15286x, 294x, 7.8x, and 2.5x as compared to CPUs, GPUs, and prior-art GCN accelerators including HyGCN and AWB-GCN, respectively, while maintaining or even improving the task accuracy. Codes are available at https://github.com/RICE-EIC/GCoD.
Bi-type multi-relational heterogeneous graph (BMHG) is one of the most common graphs in practice, for example, academic networks, e-commerce user behavior graph and enterprise knowledge graph. It is a critical and challenge problem on how to learn the numerical representation for each node to characterize subtle structures. However, most previous studies treat all node relations in BMHG as the same class of relation without distinguishing the different characteristics between the intra-class relations and inter-class relations of the bi-typed nodes, causing the loss of significant structure information. To address this issue, we propose a novel Dual Hierarchical Attention Networks (DHAN) based on the bi-typed multi-relational heterogeneous graphs to learn comprehensive node representations with the intra-class and inter-class attention-based encoder under a hierarchical mechanism. Specifically, the former encoder aggregates information from the same type of nodes, while the latter aggregates node representations from its different types of neighbors. Moreover, to sufficiently model node multi-relational information in BMHG, we adopt a newly proposed hierarchical mechanism. By doing so, the proposed dual hierarchical attention operations enable our model to fully capture the complex structures of the bi-typed multi-relational heterogeneous graphs. Experimental results on various tasks against the state-of-the-arts sufficiently confirm the capability of DHAN in learning node representations on the BMHGs.
Inspired by the extensive success of deep learning, graph neural networks (GNNs) have been proposed to learn expressive node representations and demonstrated promising performance in various graph learning tasks. However, existing endeavors predominately focus on the conventional semi-supervised setting where relatively abundant gold-labeled nodes are provided. While it is often impractical due to the fact that data labeling is unbearably laborious and requires intensive domain knowledge, especially when considering the heterogeneity of graph-structured data. Under the few-shot semi-supervised setting, the performance of most of the existing GNNs is inevitably undermined by the overfitting and oversmoothing issues, largely owing to the shortage of labeled data. In this paper, we propose a decoupled network architecture equipped with a novel meta-learning algorithm to solve this problem. In essence, our framework Meta-PN infers high-quality pseudo labels on unlabeled nodes via a meta-learned label propagation strategy, which effectively augments the scarce labeled data while enabling large receptive fields during training. Extensive experiments demonstrate that our approach offers easy and substantial performance gains compared to existing techniques on various benchmark datasets.
Lifelong graph learning deals with the problem of continually adapting graph neural network (GNN) models to changes in evolving graphs. We address two critical challenges of lifelong graph learning in this work: dealing with new classes and tackling imbalanced class distributions. The combination of these two challenges is particularly relevant since newly emerging classes typically resemble only a tiny fraction of the data, adding to the already skewed class distribution. We make several contributions: First, we show that the amount of unlabeled data does not influence the results, which is an essential prerequisite for lifelong learning on a sequence of tasks. Second, we experiment with different label rates and show that our methods can perform well with only a tiny fraction of annotated nodes. Third, we propose the gDOC method to detect new classes under the constraint of having an imbalanced class distribution. The critical ingredient is a weighted binary cross-entropy loss function to account for the class imbalance. Moreover, we demonstrate combinations of gDOC with various base GNN models such as GraphSAGE, Simplified Graph Convolution, and Graph Attention Networks. Lastly, our k-neighborhood time difference measure provably normalizes the temporal changes across different graph datasets. With extensive experimentation, we find that the proposed gDOC method is consistently better than a naive adaption of DOC to graphs. Specifically, in experiments using the smallest history size, the out-of-distribution detection score of gDOC is 0.09 compared to 0.01 for DOC. Furthermore, gDOC achieves an Open-F1 score, a combined measure of in-distribution classification and out-of-distribution detection, of 0.33 compared to 0.25 of DOC (32% increase).
Multivariate time series (MTS) forecasting has attracted much attention in many intelligent applications. It is not a trivial task, as we need to consider both intra-variable dependencies and inter-variable dependencies. However, existing works are designed for specific scenarios, and require much domain knowledge and expert efforts, which is difficult to transfer between different scenarios. In this paper, we propose a scale-aware neural architecture search framework for MTS forecasting (SNAS4MTF). A multi-scale decomposition module transforms raw time series into multi-scale sub-series, which can preserve multi-scale temporal patterns. An adaptive graph learning module infers the different inter-variable dependencies under different time scales without any prior knowledge. For MTS forecasting, a search space is designed to capture both intra-variable dependencies and inter-variable dependencies at each time scale. The multi-scale decomposition, adaptive graph learning, and neural architecture search modules are jointly learned in an end-to-end framework. Extensive experiments on two real-world datasets demonstrate that SNAS4MTF achieves a promising performance compared with the state-of-the-art methods.
Simplicial neural networks (SNN) have recently emerged as the newest direction in graph learning which expands the idea of convolutional architectures from node space to simplicial complexes on graphs. Instead of pre-dominantly assessing pairwise relations among nodes as in the current practice, simplicial complexes allow us to describe higher-order interactions and multi-node graph structures. By building upon connection between the convolution operation and the new block Hodge-Laplacian, we propose the first SNN for link prediction. Our new Block Simplicial Complex Neural Networks (BScNets) model generalizes the existing graph convolutional network (GCN) frameworks by systematically incorporating salient interactions among multiple higher-order graph structures of different dimensions. We discuss theoretical foundations behind BScNets and illustrate its utility for link prediction on eight real-world and synthetic datasets. Our experiments indicate that BScNets outperforms the state-of-the-art models by a significant margin while maintaining low computation costs. Finally, we show utility of BScNets as the new promising alternative for tracking spread of infectious diseases such as COVID-19 and measuring the effectiveness of the healthcare risk mitigation strategies.
Video self-supervised learning is a challenging task, which requires significant expressive power from the model to leverage rich spatial-temporal knowledge and generate effective supervisory signals from large amounts of unlabeled videos. However, existing methods fail to increase the temporal diversity of unlabeled videos and ignore elaborately modeling multi-scale temporal dependencies in an explicit way. To overcome these limitations, we take advantage of the multi-scale temporal dependencies within videos and proposes a novel video self-supervised learning framework named Temporal Contrastive Graph Learning (TCGL), which jointly models the inter-snippet and intra-snippet temporal dependencies for temporal representation learning with a hybrid graph contrastive learning strategy. Specifically, a Spatial-Temporal Knowledge Discovering (STKD) module is first introduced to extract motion-enhanced spatial-temporal representations from videos based on the frequency domain analysis of discrete cosine transform. To explicitly model multi-scale temporal dependencies of unlabeled videos, our TCGL integrates the prior knowledge about the frame and snippet orders into graph structures, i.e., the intra-/inter- snippet Temporal Contrastive Graphs (TCG). Then, specific contrastive learning modules are designed to maximize the agreement between nodes in different graph views. To generate supervisory signals for unlabeled videos, we introduce an Adaptive Snippet Order Prediction (ASOP) module which leverages the relational knowledge among video snippets to learn the global context representation and recalibrate the channel-wise features adaptively. Experimental results demonstrate the superiority of our TCGL over the state-of-the-art methods on large-scale action recognition and video retrieval benchmarks.The code is publicly available at https://github.com/YangLiu9208/TCGL.
Multivariate time series forecasting is a challenging task because the data involves a mixture of long- and short-term patterns, with dynamic spatio-temporal dependencies among variables. Existing graph neural networks (GNN) typically model multivariate relationships with a pre-defined spatial graph or learned fixed adjacency graph. It limits the application of GNN and fails to handle the above challenges. In this paper, we propose a novel framework, namely static- and dynamic-graph learning-neural network (SDGL). The model acquires static and dynamic graph matrices from data to model long- and short-term patterns respectively. Static matric is developed to capture the fixed long-term association pattern via node embeddings, and we leverage graph regularity for controlling the quality of the learned static graph. To capture dynamic dependencies among variables, we propose dynamic graphs learning method to generate time-varying matrices based on changing node features and static node embeddings. And in the method, we integrate the learned static graph information as inductive bias to construct dynamic graphs and local spatio-temporal patterns better. Extensive experiments are conducted on two traffic datasets with extra structural information and four time series datasets, which show that our approach achieves state-of-the-art performance on almost all datasets. If the paper is accepted, I will open the source code on github.
Graph Neural Networks (GNNs) have achieved great success in processing graph data by extracting and propagating structure-aware features. Existing GNN research designs various propagation schemes to guide the aggregation of neighbor information. Recently the field has advanced from local propagation schemes that focus on local neighbors towards extended propagation schemes that can directly deal with extended neighbors consisting of both local and high-order neighbors. Despite the impressive performance, existing approaches are still insufficient to build an efficient and learnable extended propagation scheme that can adaptively adjust the influence of local and high-order neighbors. This paper proposes an efficient yet effective end-to-end framework, namely Contrastive Adaptive Propagation Graph Neural Networks (CAPGNN), to address these issues by combining Personalized PageRank and attention techniques. CAPGNN models the learnable extended propagation scheme with a polynomial of a sparse local affinity matrix, where the polynomial relies on Personalized PageRank to provide superior initial coefficients. In order to adaptively adjust the influence of both local and high-order neighbors, a coefficient-attention model is introduced to learn to adjust the coefficients of the polynomial. In addition, we leverage self-supervised learning techniques and design a negative-free entropy-aware contrastive loss to explicitly take advantage of unlabeled data for training. We implement CAPGNN as two different versions named CAPGCN and CAPGAT, which use static and dynamic sparse local affinity matrices, respectively. Experiments on graph benchmark datasets suggest that CAPGNN can consistently outperform or match state-of-the-art baselines. The source code is publicly available at https://github.com/hujunxianligong/CAPGNN.
Understanding the halo-galaxy connection is fundamental in order to improve our knowledge on the nature and properties of dark matter. In this work we build a model that infers the mass of a halo given the positions, velocities, stellar masses, and radii of the galaxies it hosts. In order to capture information from correlations among galaxy properties and their phase-space, we use Graph Neural Networks (GNNs), that are designed to work with irregular and sparse data. We train our models on galaxies from more than 2,000 state-of-the-art simulations from the Cosmology and Astrophysics with MachinE Learning Simulations (CAMELS) project. Our model, that accounts for cosmological and astrophysical uncertainties, is able to constrain the masses of the halos with a $\sim$0.2 dex accuracy. Furthermore, a GNN trained on a suite of simulations is able to preserve part of its accuracy when tested on simulations run with a different code that utilizes a distinct subgrid physics model, showing the robustness of our method. The PyTorch Geometric implementation of the GNN is publicly available on Github at https://github.com/PabloVD/HaloGraphNet
Many real-world relational systems, such as social networks and biological systems, contain dynamic interactions. When learning dynamic graph representation, it is essential to employ sequential temporal information and geometric structure. Mainstream work achieves topological embedding via message passing networks (e.g., GCN, GAT). The temporal evolution, on the other hand, is conventionally expressed via memory units (e.g., LSTM or GRU) that possess convenient information filtration in a gate mechanism. Though, such a design prevents large-scale input sequence due to the over-complicated encoding. This work learns from the philosophy of self-attention and proposes an efficient spectral-based neural unit that employs informative long-range temporal interaction. The developed spectral window unit (SWINIT) model predicts scalable dynamic graphs with assured efficiency. The architecture is assembled with a few simple effective computational blocks that constitute randomized SVD, MLP, and graph Framelet convolution. The SVD plus MLP module encodes the long-short-term feature evolution of the dynamic graph events. A fast framelet graph transform in the framelet convolution embeds the structural dynamics. Both strategies enhance the model's ability on scalable analysis. In particular, the iterative SVD approximation shrinks the computational complexity of attention to O(Nd\log(d)) for the dynamic graph with N edges and d edge features, and the multiscale transform of framelet convolution allows sufficient scalability in the network training. Our SWINIT achieves state-of-the-art performance on a variety of online continuous-time dynamic graph learning tasks, while compared to baseline methods, the number of its learnable parameters reduces by up to seven times.
Graph Convolutional Networks (GCNs) have fueled a surge of research interest due to their encouraging performance on graph learning tasks, but they are also shown vulnerability to adversarial attacks. In this paper, an effective graph structural attack is investigated to disrupt graph spectral filters in the Fourier domain, which are the theoretical foundation of GCNs. We define the notion of spectral distance based on the eigenvalues of graph Laplacian to measure the disruption of spectral filters. We realize the attack by maximizing the spectral distance and propose an efficient approximation to reduce the time complexity brought by eigen-decomposition. The experiments demonstrate the remarkable effectiveness of the proposed attack in both black-box and white-box settings for both test-time evasion attacks and training-time poisoning attacks. Our qualitative analysis suggests the connection between the imposed spectral changes in the Fourier domain and the attack behavior in the spatial domain, which provides empirical evidence that maximizing spectral distance is an effective way to change the graph structural property and thus disturb the frequency components for graph filters to affect the learning of GCNs.
Many widely used datasets for graph machine learning tasks have generally been homophilous, where nodes with similar labels connect to each other. Recently, new Graph Neural Networks (GNNs) have been developed that move beyond the homophily regime; however, their evaluation has often been conducted on small graphs with limited application domains. We collect and introduce diverse non-homophilous datasets from a variety of application areas that have up to 384x more nodes and 1398x more edges than prior datasets. We further show that existing scalable graph learning and graph minibatching techniques lead to performance degradation on these non-homophilous datasets, thus highlighting the need for further work on scalable non-homophilous methods. To address these concerns, we introduce LINKX -- a strong simple method that admits straightforward minibatch training and inference. Extensive experimental results with representative simple methods and GNNs across our proposed datasets show that LINKX achieves state-of-the-art performance for learning on non-homophilous graphs. Our codes and data are available at https://github.com/CUAI/Non-Homophily-Large-Scale.
Recent works reveal that feature or label smoothing lies at the core of Graph Neural Networks (GNNs). Concretely, they show feature smoothing combined with simple linear regression achieves comparable performance with the carefully designed GNNs, and a simple MLP model with label smoothing of its prediction can outperform the vanilla GCN. Though an interesting finding, smoothing has not been well understood, especially regarding how to control the extent of smoothness. Intuitively, too small or too large smoothing iterations may cause under-smoothing or over-smoothing and can lead to sub-optimal performance. Moreover, the extent of smoothness is node-specific, depending on its degree and local structure. To this end, we propose a novel algorithm called node-dependent local smoothing (NDLS), which aims to control the smoothness of every node by setting a node-specific smoothing iteration. Specifically, NDLS computes influence scores based on the adjacency matrix and selects the iteration number by setting a threshold on the scores. Once selected, the iteration number can be applied to both feature smoothing and label smoothing. Experimental results demonstrate that NDLS enjoys high accuracy -- state-of-the-art performance on node classifications tasks, flexibility -- can be incorporated with any models, scalability and efficiency -- can support large scale graphs with fast training.
Graph Neural Networks (GNNs) have been widely studied in various graph data mining tasks. Most existingGNNs embed graph data into Euclidean space and thus are less effective to capture the ubiquitous hierarchical structures in real-world networks. Hyperbolic Graph Neural Networks(HGNNs) extend GNNs to hyperbolic space and thus are more effective to capture the hierarchical structures of graphs in node representation learning. In hyperbolic geometry, the graph hierarchical structure can be reflected by the curvatures of the hyperbolic space, and different curvatures can model different hierarchical structures of a graph. However, most existing HGNNs manually set the curvature to a fixed value for simplicity, which achieves a suboptimal performance of graph learning due to the complex and diverse hierarchical structures of the graphs. To resolve this problem, we propose an Adaptive Curvature Exploration Hyperbolic Graph NeuralNetwork named ACE-HGNN to adaptively learn the optimal curvature according to the input graph and downstream tasks. Specifically, ACE-HGNN exploits a multi-agent reinforcement learning framework and contains two agents, ACE-Agent andHGNN-Agent for learning the curvature and node representations, respectively. The two agents are updated by a NashQ-leaning algorithm collaboratively, seeking the optimal hyperbolic space indexed by the curvature. Extensive experiments on multiple real-world graph datasets demonstrate a significant and consistent performance improvement in model quality with competitive performance and good generalization ability.
We target open-world feature extrapolation problem where the feature space of input data goes through expansion and a model trained on partially observed features needs to handle new features in test data without further retraining. The problem is of much significance for dealing with features incrementally collected from different fields. To this end, we propose a new learning paradigm with graph representation and learning. Our framework contains two modules: 1) a backbone network (e.g., feedforward neural nets) as a lower model takes features as input and outputs predicted labels; 2) a graph neural network as an upper model learns to extrapolate embeddings for new features via message passing over a feature-data graph built from observed data. Based on our framework, we design two training strategies, a self-supervised approach and an inductive learning approach, to endow the model with extrapolation ability and alleviate feature-level over-fitting. We also provide theoretical analysis on the generalization error on test data with new features, which dissects the impact of training features and algorithms on generalization performance. Our experiments over several classification datasets and large-scale advertisement click prediction datasets demonstrate that our model can produce effective embeddings for unseen features and significantly outperforms baseline methods that adopt KNN and local aggregation.
Molecular property prediction is one of the fastest-growing applications of deep learning with critical real-world impacts. Including 3D molecular structure as input to learned models improves their performance for many molecular tasks. However, this information is infeasible to compute at the scale required by several real-world applications. We propose pre-training a model to reason about the geometry of molecules given only their 2D molecular graphs. Using methods from self-supervised learning, we maximize the mutual information between 3D summary vectors and the representations of a Graph Neural Network (GNN) such that they contain latent 3D information. During fine-tuning on molecules with unknown geometry, the GNN still generates implicit 3D information and can use it to improve downstream tasks. We show that 3D pre-training provides significant improvements for a wide range of properties, such as a 22% average MAE reduction on eight quantum mechanical properties. Moreover, the learned representations can be effectively transferred between datasets in different molecular spaces.
The application of light field data in salient object de-tection is becoming increasingly popular recently. The diffi-culty lies in how to effectively fuse the features within the fo-cal stack and how to cooperate them with the feature of theall-focus image. Previous methods usually fuse focal stackfeatures via convolution or ConvLSTM, which are both lesseffective and ill-posed. In this paper, we model the infor-mation fusion within focal stack via graph networks. Theyintroduce powerful context propagation from neighbouringnodes and also avoid ill-posed implementations. On the onehand, we construct local graph connections thus avoidingprohibitive computational costs of traditional graph net-works. On the other hand, instead of processing the twokinds of data separately, we build a novel dual graph modelto guide the focal stack fusion process using all-focus pat-terns. To handle the second difficulty, previous methods usu-ally implement one-shot fusion for focal stack and all-focusfeatures, hence lacking a thorough exploration of their sup-plements. We introduce a reciprocative guidance schemeand enable mutual guidance between these two kinds of in-formation at multiple steps. As such, both kinds of featurescan be enhanced iteratively, finally benefiting the saliencyprediction. Extensive experimental results show that theproposed models are all beneficial and we achieve signif-icantly better results than state-of-the-art methods.