Graph convolutional networks are becoming indispensable for deep learning from graph-structured data. Most of the existing graph convolutional networks share two big shortcomings. First, they are essentially low-pass filters, thus the potentially useful middle and high frequency band of graph signals are ignored. Second, the bandwidth of existing graph convolutional filters is fixed. Parameters of a graph convolutional filter only transform the graph inputs without changing the curvature of a graph convolutional filter function. In reality, we are uncertain about whether we should retain or cut off the frequency at a certain point unless we have expert domain knowledge. In this paper, we propose Automatic Graph Convolutional Networks (AutoGCN) to capture the full spectrum of graph signals and automatically update the bandwidth of graph convolutional filters. While it is based on graph spectral theory, our AutoGCN is also localized in space and has a spatial form. Experimental results show that AutoGCN achieves significant improvement over baseline methods which only work as low-pass filters.

We study many-class few-shot (MCFS) problem in both supervised learning and meta-learning settings. Compared to the well-studied many-class many-shot and few-class few-shot problems, the MCFS problem commonly occurs in practical applications but has been rarely studied in previous literature. It brings new challenges of distinguishing between many classes given only a few training samples per class. In this article, we leverage the class hierarchy as a prior knowledge to train a coarse-to-fine classifier that can produce accurate predictions for MCFS problem in both settings. The propose model, “memory-augmented hierarchical-classification network (MahiNet)”, performs coarse-to-fine classification where each coarse class can cover multiple fine classes. Since it is challenging to directly distinguish a variety of fine classes given few-shot data per class, MahiNet starts from learning a classifier over coarse-classes with more training data whose labels are much cheaper to obtain. The coarse classifier reduces the searching range over the fine classes and thus alleviates the challenges from “many classes”. On architecture, MahiNet first deploys a convolutional neural network (CNN) to extract features. It then integrates a memory-augmented attention module and a multi-layer perceptron (MLP) together to produce the probabilities over coarse and fine classes. While the MLP extends the linear classifier, the attention module extends the KNN classifier, both together targeting the “few-shot” problem. We design several training strategies of MahiNet for supervised learning and meta-learning. In addition, we propose two novel benchmark datasets “mcfsImageNet” (as a subset of ImageNet) and “mcfsOmniglot” (re-splitted Omniglot) specially designed for MCFS problem. In experiments, we show that MahiNet outperforms several state-of-the-art models (e.g., prototypical networks and relation networks) on MCFS problems in both supervised learning and meta-learning.

Sequential diagnosis prediction on the Electronic Health Record (EHR) has been proven crucial for predictive analytics in the medical domain. EHR data, sequential records of a patient’s interactions with healthcare systems, has numerous inherent characteristics of temporality, irregularity and data insufficiency. Some recent works train healthcare predictive models by making use of sequential information in EHR data, but they are vulnerable to irregular, temporal EHR data with the states of admission/discharge from hospital, and insufficient data. To mitigate this, we propose an end-to-end robust transformer-based model called SETOR, which exploits neural ordinary differential equation to handle both irregular intervals between a patient’s visits with admitted timestamps and length of stay in each visit, to alleviate the limitation of insufficient data by integrating medical ontology, and to capture the dependencies between the patient’s visits by employing multi-layer transformer blocks. Experiments conducted on two real-world healthcare datasets show that, our sequential diagnoses prediction model SETOR not only achieves better predictive results than previous state-of-the-art approaches, irrespective of sufficient or insufficient training data, but also derives more interpretable embeddings of medical codes. The experimental codes are available at the GitHub repository1.1Github repository: https://github.com/Xueping/SETOR

Electronic health records (EHRs) are longitudinal records of a patient's interactions with healthcare systems. A patient's EHR data is organized as a three-level hierarchy from top to bottom: patient journey - all the experiences of diagnoses and treatments over a period of time; individual visit - a set of medical codes in a particular visit; and medical code - a specific record in the form of medical codes. As EHRs begin to amass in millions, the potential benefits, which these data might hold for medical research and medical outcome prediction, are staggering - including, for example, predicting future admissions to hospitals, diagnosing illnesses or determining the efficacy of medical treatments. Each of these analytics tasks requires a domain knowledge extraction method to transform the hierarchical patient journey into a vector representation for further prediction procedure. The representations should embed a sequence of visits and a set of medical codes with a specific timestamp, which are crucial to any downstream prediction tasks. Hence, expressively powerful representations are appealing to boost learning performance. To this end, we propose a novel self-attention mechanism that captures the contextual dependency and temporal relationships within a patient's healthcare journey. An end-to-end bidirectional temporal encoder network (BiteNet) then learns representations of the patient's journeys, based solely on the proposed attention mechanism. We have evaluated the effectiveness of our methods on two supervised prediction and two unsupervised clustering tasks with a real-world EHR dataset. The empirical results demonstrate the proposed BiteNet model produces higher-quality representations than state-of-the-art baseline methods.

Graph embedding has shown its effectiveness to represent graph information and capture deep relationships in graph data. Most recent graph embedding methods focus on attributed graphs, since they preserve both structure and content information in the network. However, corruption can exist in the graph structure as well as the node content of the graph, and both can lead to inferior embedding results. Unfortunately, few existing graph embedding algorithms have considered the corruption problem, and to the best of our knowledge, none has studied structural corruption in attributed graphs, including missing and redundant edges. This field is difficult for previous methods, mainly due to two challenges: (1) the existence of various corruption causes has made it difficult to recognize corruptions in graphs, and (2) the complexity of graph-structured data has increased the difficulty of handling corruption therein for graph embedding methods. These facts lead us here to propose a novel autoencoder-based graph embedding approach, which is robust against structural corruption. Our idea comes from the recent discovery of memorization effects in deep learning. Namely, deep neural networks prefer to fit clean data first, before they over-fit corrupted data. Specifically, we train two autoencoders simultaneously and let them learn the reliability of the edges in the graph from each other. The two autoencoders would evaluate the edges according to their reconstructed structure and manipulate this by devaluing those distrusted edges to update the structure information. The updated structure would be used further in the next iteration as the ground-truth of its peer-network. Experiments on different versions of real-world graphs show state-of-the-art results and demonstrate the robustness of our model against structural corruption.

Modeling multivariate time series has long been a subject that has attracted researchers from a diverse range of fields including economics, finance, and traffic. A basic assumption behind multivariate time series forecasting is that its variables depend on one another but, upon looking closely, it is fair to say that existing methods fail to fully exploit latent spatial dependencies between pairs of variables. In recent years, meanwhile, graph neural networks (GNNs) have shown high capability in handling relational dependencies. GNNs require well-defined graph structures for information propagation which means they cannot be applied directly for multivariate time series where the dependencies are not known in advance. In this paper, we propose a general graph neural network framework designed specifically for multivariate time series data. Our approach automatically extracts the uni-directed relations among variables through a graph learning module, into which external knowledge like variable attributes can be easily integrated. A novel mix-hop propagation layer and a dilated inception layer are further proposed to capture the spatial and temporal dependencies within the time series. The graph learning, graph convolution, and temporal convolution modules are jointly learned in an end-to-end framework. Experimental results show that our proposed model outperforms the state-of-the-art baseline methods on 3 of 4 benchmark datasets and achieves on-par performance with other approaches on two traffic datasets which provide extra structural information.

In longitudinal electronic health records (EHRs), the event records of a patient are distributed over a long period of time and the temporal relations between the events reflect sufficient domain knowledge to benefit prediction tasks such as the rate of inpatient mortality. Medical concept embedding as a feature extraction method that transforms a set of medical concepts with a specific time stamp into a vector, which will be fed into a supervised learning algorithm. The quality of the embedding significantly determines the learning performance over the medical data. In this paper, we propose a medical concept embedding method based on applying a self-attention mechanism to represent each medical concept. We propose a novel attention mechanism which captures the contextual information and temporal relationships between medical concepts. A light-weight neural net, "Temporal Self-Attention Network (TeSAN)", is then proposed to learn medical concept embedding based solely on the proposed attention mechanism. To test the effectiveness of our proposed methods, we have conducted clustering and prediction tasks on two public EHRs datasets comparing TeSAN against five state-of-the-art embedding methods. The experimental results demonstrate that the proposed TeSAN model is superior to all the compared methods. To the best of our knowledge, this work is the first to exploit temporal self-attentive relations between medical events.

Numerous network representation-based algorithms for network classification have emerged in recent years, but many suffer from two limitations. First, they separate the network representation learning and node classification in networks into two steps, which may result in sub-optimal results because the node representation may not fit the classification model well, and vice versa. Second, they are mostly shallow methods that can only capture the linear and simple relationships in the data. In this paper, we propose an effective deep learning model, Graph Ladder Networks (GLN), for node classification in networks. Our model learns a ladder network which unifies the representation learning and network classification into one single framework by exploiting both labeled and unlabeled nodes in a network. To integrate both structure and node content information in the networks, the most recently developed graph convolution network, is further employed. The experiments on the most popular academic network dataset, Citeseer, demonstrate that our approach reaches outstanding performance compared to other state-of-the-art algorithms.

Graph clustering aims to discovercommunity structures in networks, the task being fundamentally challenging mainly because the topology structure and the content of the graphs are difficult to represent for clustering analysis. Recently, graph clustering has moved from traditional shallow methods to deep learning approaches, thanks to the unique feature representation learning capability of deep learning. However, existing deep approaches for graph clustering can only exploit the structure information, while ignoring the content information associated with the nodes in a graph. In this paper, we propose a novel marginalized graph autoencoder (MGAE) algorithm for graph clustering. The key innovation of MGAE is that it advances the autoencoder to the graph domain, so graph representation learning can be carried out not only in a purely unsupervised setting by leveraging structure and content information, it can also be stacked in a deep fashion to learn effective representation. From a technical viewpoint, we propose a marginalized graph convolutional network to corrupt network node content, allowing node content to interact with network features, and marginalizes the corrupted features in a graph autoencoder context to learn graph feature representations. The learned features are fed into the spectral clustering algorithm for graph clustering. Experimental results on benchmark datasets demonstrate the superior performance of MGAE, compared to numerous baselines.