Graph neural networks (GNNs) are powerful tools for conducting inference on graph data but are often seen as "black boxes" due to difficulty in extracting meaningful subnetworks driving predictive performance. Many interpretable GNN methods exist, but they cannot quantify uncertainty in edge weights and suffer in predictive accuracy when applied to challenging graph structures. In this work, we proposed BetaExplainer which addresses these issues by using a sparsity-inducing prior to mask unimportant edges during model training. To evaluate our approach, we examine various simulated data sets with diverse real-world characteristics. Not only does this implementation provide a notion of edge importance uncertainty, it also improves upon evaluation metrics for challenging datasets compared to state-of-the art explainer methods.
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Graph neural networks (GNNs) are a type of deep learning models that learning over graphs, and have been successfully applied in many domains. Despite the effectiveness of GNNs, it is still challenging for GNNs to efficiently scale to large graphs. As a remedy, distributed computing becomes a promising solution of training large-scale GNNs, since it is able to provide abundant computing resources. However, the dependency of graph structure increases the difficulty of achieving high-efficiency distributed GNN training, which suffers from the massive communication and workload imbalance. In recent years, many efforts have been made on distributed GNN training, and an array of training algorithms and systems have been proposed. Yet, there is a lack of systematic review on the optimization techniques from graph processing to distributed execution. In this survey, we analyze three major challenges in distributed GNN training that are massive feature communication, the loss of model accuracy and workload imbalance. Then we introduce a new taxonomy for the optimization techniques in distributed GNN training that address the above challenges. The new taxonomy classifies existing techniques into four categories that are GNN data partition, GNN batch generation, GNN execution model, and GNN communication protocol.We carefully discuss the techniques in each category. In the end, we summarize existing distributed GNN systems for multi-GPUs, GPU-clusters and CPU-clusters, respectively, and give a discussion about the future direction on scalable GNNs.
Interpretability methods are developed to understand the working mechanisms of black-box models, which is crucial to their responsible deployment. Fulfilling this goal requires both that the explanations generated by these methods are correct and that people can easily and reliably understand them. While the former has been addressed in prior work, the latter is often overlooked, resulting in informal model understanding derived from a handful of local explanations. In this paper, we introduce explanation summary (ExSum), a mathematical framework for quantifying model understanding, and propose metrics for its quality assessment. On two domains, ExSum highlights various limitations in the current practice, helps develop accurate model understanding, and reveals easily overlooked properties of the model. We also connect understandability to other properties of explanations such as human alignment, robustness, and counterfactual minimality and plausibility.
Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful prediction of molecule property by GNNs is the scarcity of labeled data. Though graph contrastive learning (GCL) methods have achieved extraordinary performance with insufficient labeled data, most focused on designing data augmentation schemes for general graphs. However, the fundamental property of a molecule could be altered with the augmentation method (like random perturbation) on molecular graphs. Whereas, the critical geometric information of molecules remains rarely explored under the current GNN and GCL architectures. To this end, we propose a novel graph contrastive learning method utilizing the geometry of the molecule across 2D and 3D views, which is named GeomGCL. Specifically, we first devise a dual-view geometric message passing network (GeomMPNN) to adaptively leverage the rich information of both 2D and 3D graphs of a molecule. The incorporation of geometric properties at different levels can greatly facilitate the molecular representation learning. Then a novel geometric graph contrastive scheme is designed to make both geometric views collaboratively supervise each other to improve the generalization ability of GeomMPNN. We evaluate GeomGCL on various downstream property prediction tasks via a finetune process. Experimental results on seven real-life molecular datasets demonstrate the effectiveness of our proposed GeomGCL against state-of-the-art baselines.
Normalization is known to help the optimization of deep neural networks. Curiously, different architectures require specialized normalization methods. In this paper, we study what normalization is effective for Graph Neural Networks (GNNs). First, we adapt and evaluate the existing methods from other domains to GNNs. Faster convergence is achieved with InstanceNorm compared to BatchNorm and LayerNorm. We provide an explanation by showing that InstanceNorm serves as a preconditioner for GNNs, but such preconditioning effect is weaker with BatchNorm due to the heavy batch noise in graph datasets. Second, we show that the shift operation in InstanceNorm results in an expressiveness degradation of GNNs for highly regular graphs. We address this issue by proposing GraphNorm with a learnable shift. Empirically, GNNs with GraphNorm converge faster compared to GNNs using other normalization. GraphNorm also improves the generalization of GNNs, achieving better performance on graph classification benchmarks.
A large number of real-world graphs or networks are inherently heterogeneous, involving a diversity of node types and relation types. Heterogeneous graph embedding is to embed rich structural and semantic information of a heterogeneous graph into low-dimensional node representations. Existing models usually define multiple metapaths in a heterogeneous graph to capture the composite relations and guide neighbor selection. However, these models either omit node content features, discard intermediate nodes along the metapath, or only consider one metapath. To address these three limitations, we propose a new model named Metapath Aggregated Graph Neural Network (MAGNN) to boost the final performance. Specifically, MAGNN employs three major components, i.e., the node content transformation to encapsulate input node attributes, the intra-metapath aggregation to incorporate intermediate semantic nodes, and the inter-metapath aggregation to combine messages from multiple metapaths. Extensive experiments on three real-world heterogeneous graph datasets for node classification, node clustering, and link prediction show that MAGNN achieves more accurate prediction results than state-of-the-art baselines.
The design of deep graph models still remains to be investigated and the crucial part is how to explore and exploit the knowledge from different hops of neighbors in an efficient way. In this paper, we propose a novel RNN-like deep graph neural network architecture by incorporating AdaBoost into the computation of network; and the proposed graph convolutional network called AdaGCN~(AdaBoosting Graph Convolutional Network) has the ability to efficiently extract knowledge from high-order neighbors and integrate knowledge from different hops of neighbors into the network in an AdaBoost way. We also present the architectural difference between AdaGCN and existing graph convolutional methods to show the benefits of our proposal. Finally, extensive experiments demonstrate the state-of-the-art prediction performance and the computational advantage of our approach AdaGCN.
Graph convolutional networks (GCNs) have recently become one of the most powerful tools for graph analytics tasks in numerous applications, ranging from social networks and natural language processing to bioinformatics and chemoinformatics, thanks to their ability to capture the complex relationships between concepts. At present, the vast majority of GCNs use a neighborhood aggregation framework to learn a continuous and compact vector, then performing a pooling operation to generalize graph embedding for the classification task. These approaches have two disadvantages in the graph classification task: (1)when only the largest sub-graph structure ($k$-hop neighbor) is used for neighborhood aggregation, a large amount of early-stage information is lost during the graph convolution step; (2) simple average/sum pooling or max pooling utilized, which loses the characteristics of each node and the topology between nodes. In this paper, we propose a novel framework called, dual attention graph convolutional networks (DAGCN) to address these problems. DAGCN automatically learns the importance of neighbors at different hops using a novel attention graph convolution layer, and then employs a second attention component, a self-attention pooling layer, to generalize the graph representation from the various aspects of a matrix graph embedding. The dual attention network is trained in an end-to-end manner for the graph classification task. We compare our model with state-of-the-art graph kernels and other deep learning methods. The experimental results show that our framework not only outperforms other baselines but also achieves a better rate of convergence.
Distant supervision can effectively label data for relation extraction, but suffers from the noise labeling problem. Recent works mainly perform soft bag-level noise reduction strategies to find the relatively better samples in a sentence bag, which is suboptimal compared with making a hard decision of false positive samples in sentence level. In this paper, we introduce an adversarial learning framework, which we named DSGAN, to learn a sentence-level true-positive generator. Inspired by Generative Adversarial Networks, we regard the positive samples generated by the generator as the negative samples to train the discriminator. The optimal generator is obtained until the discrimination ability of the discriminator has the greatest decline. We adopt the generator to filter distant supervision training dataset and redistribute the false positive instances into the negative set, in which way to provide a cleaned dataset for relation classification. The experimental results show that the proposed strategy significantly improves the performance of distant supervision relation extraction comparing to state-of-the-art systems.
Recurrent neural nets (RNN) and convolutional neural nets (CNN) are widely used on NLP tasks to capture the long-term and local dependencies, respectively. Attention mechanisms have recently attracted enormous interest due to their highly parallelizable computation, significantly less training time, and flexibility in modeling dependencies. We propose a novel attention mechanism in which the attention between elements from input sequence(s) is directional and multi-dimensional (i.e., feature-wise). A light-weight neural net, "Directional Self-Attention Network (DiSAN)", is then proposed to learn sentence embedding, based solely on the proposed attention without any RNN/CNN structure. DiSAN is only composed of a directional self-attention with temporal order encoded, followed by a multi-dimensional attention that compresses the sequence into a vector representation. Despite its simple form, DiSAN outperforms complicated RNN models on both prediction quality and time efficiency. It achieves the best test accuracy among all sentence encoding methods and improves the most recent best result by 1.02% on the Stanford Natural Language Inference (SNLI) dataset, and shows state-of-the-art test accuracy on the Stanford Sentiment Treebank (SST), Multi-Genre natural language inference (MultiNLI), Sentences Involving Compositional Knowledge (SICK), Customer Review, MPQA, TREC question-type classification and Subjectivity (SUBJ) datasets.
Convolutional Neural Networks (CNNs) have gained significant traction in the field of machine learning, particularly due to their high accuracy in visual recognition. Recent works have pushed the performance of GPU implementations of CNNs to significantly improve their classification and training times. With these improvements, many frameworks have become available for implementing CNNs on both CPUs and GPUs, with no support for FPGA implementations. In this work we present a modified version of the popular CNN framework Caffe, with FPGA support. This allows for classification using CNN models and specialized FPGA implementations with the flexibility of reprogramming the device when necessary, seamless memory transactions between host and device, simple-to-use test benches, and the ability to create pipelined layer implementations. To validate the framework, we use the Xilinx SDAccel environment to implement an FPGA-based Winograd convolution engine and show that the FPGA layer can be used alongside other layers running on a host processor to run several popular CNNs (AlexNet, GoogleNet, VGG A, Overfeat). The results show that our framework achieves 50 GFLOPS across 3x3 convolutions in the benchmarks. This is achieved within a practical framework, which will aid in future development of FPGA-based CNNs.
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