The dominant graph neural networks (GNNs) over-rely on the graph links, several serious performance problems with which have been witnessed already, e.g., suspended animation problem and over-smoothing problem. What's more, the inherently inter-connected nature precludes parallelization within the graph, which becomes critical for large-sized graph, as memory constraints limit batching across the nodes. In this paper, we will introduce a new graph neural network, namely GRAPH-BERT (Graph based BERT), solely based on the attention mechanism without any graph convolution or aggregation operators. Instead of feeding GRAPH-BERT with the complete large input graph, we propose to train GRAPH-BERT with sampled linkless subgraphs within their local contexts. GRAPH-BERT can be learned effectively in a standalone mode. Meanwhile, a pre-trained GRAPH-BERT can also be transferred to other application tasks directly or with necessary fine-tuning if any supervised label information or certain application oriented objective is available. We have tested the effectiveness of GRAPH-BERT on several graph benchmark datasets. Based the pre-trained GRAPH-BERT with the node attribute reconstruction and structure recovery tasks, we further fine-tune GRAPH-BERT on node classification and graph clustering tasks specifically. The experimental results have demonstrated that GRAPH-BERT can out-perform the existing GNNs in both the learning effectiveness and efficiency.
In this paper, we propose an end-to-end graph learning framework, namely Deep Iterative and Adaptive Learning for Graph Neural Networks (DIAL-GNN), for jointly learning the graph structure and graph embeddings simultaneously. We first cast the graph structure learning problem as a similarity metric learning problem and leverage an adapted graph regularization for controlling smoothness, connectivity and sparsity of the generated graph. We further propose a novel iterative method for searching for a hidden graph structure that augments the initial graph structure. Our iterative method dynamically stops when the learned graph structure approaches close enough to the optimal graph. Our extensive experiments demonstrate that the proposed DIAL-GNN model can consistently outperform or match state-of-the-art baselines in terms of both downstream task performance and computational time. The proposed approach can cope with both transductive learning and inductive learning.
Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.
We focus on developing a novel scalable graph-based semi-supervised learning (SSL) method for a small number of labeled data and a large amount of unlabeled data. Due to the lack of labeled data and the availability of large-scale unlabeled data, existing SSL methods usually encounter either suboptimal performance because of an improper graph or the high computational complexity of the large-scale optimization problem. In this paper, we propose to address both challenging problems by constructing a proper graph for graph-based SSL methods. Different from existing approaches, we simultaneously learn a small set of vertexes to characterize the high-dense regions of the input data and a graph to depict the relationships among these vertexes. A novel approach is then proposed to construct the graph of the input data from the learned graph of a small number of vertexes with some preferred properties. Without explicitly calculating the constructed graph of inputs, two transductive graph-based SSL approaches are presented with the computational complexity in linear with the number of input data. Extensive experiments on synthetic data and real datasets of varied sizes demonstrate that the proposed method is not only scalable for large-scale data, but also achieve good classification performance, especially for extremely small number of labels.
Generating graph structures is a challenging problem due to the diverse representations and complex dependencies among nodes. In this paper, we introduce Graph Variational Recurrent Neural Network (GraphVRNN), a probabilistic autoregressive model for graph generation. Through modeling the latent variables of graph data, GraphVRNN can capture the joint distributions of graph structures and the underlying node attributes. We conduct experiments on the proposed GraphVRNN in both graph structure learning and attribute generation tasks. The evaluation results show that the variational component allows our network to model complicated distributions, as well as generate plausible structures and node attributes.
Conversational machine comprehension (MC) has proven significantly more challenging compared to traditional MC since it requires better utilization of conversation history. However, most existing approaches do not effectively capture conversation history and thus have trouble handling questions involving coreference or ellipsis. Moreover, when reasoning over passage text, most of them simply treat it as a word sequence without exploring rich semantic relationships among words. In this paper, we first propose a simple yet effective graph structure learning technique to dynamically construct a question and conversation history aware context graph at each conversation turn. Then we propose a novel Recurrent Graph Neural Network, and based on that, we introduce a flow mechanism to model the temporal dependencies in a sequence of context graphs. The proposed GraphFlow model can effectively capture conversational flow in a dialog, and shows competitive performance compared to existing state-of-the-art methods on CoQA, QuAC and DoQA benchmarks. In addition, visualization experiments show that our proposed model can offer good interpretability for the reasoning process.
Processes such as disease propagation and information diffusion often spread over some latent network structure which must be learned from observation. Given a set of unlabeled training examples representing occurrences of an event type of interest (e.g., a disease outbreak), our goal is to learn a graph structure that can be used to accurately detect future events of that type. Motivated by new theoretical results on the consistency of constrained and unconstrained subset scans, we propose a novel framework for learning graph structure from unlabeled data by comparing the most anomalous subsets detected with and without the graph constraints. Our framework uses the mean normalized log-likelihood ratio score to measure the quality of a graph structure, and efficiently searches for the highest-scoring graph structure. Using simulated disease outbreaks injected into real-world Emergency Department data from Allegheny County, we show that our method learns a structure similar to the true underlying graph, but enables faster and more accurate detection.