The success of deep learning has revolutionized many fields of research including areas of computer vision, text and speech processing. Enormous research efforts have led to numerous methods that are capable of efficiently analyzing data, especially in the Euclidean space. However, many problems are posed in non-Euclidean domains modeled as general graphs with complex connection patterns. Increased problem complexity and computational power constraints have limited early approaches to static and small-sized graphs. In recent years, a rising interest in machine learning on graph-structured data has been accompanied by improved methods that overcome the limitations of their predecessors. These methods paved the way for dealing with large-scale and time-dynamic graphs. This work aims to provide an overview of early and modern graph neural network based machine learning methods for node-level prediction tasks. Under the umbrella of taxonomies already established in the literature, we explain the core concepts and provide detailed explanations for convolutional methods that have had strong impact. In addition, we introduce common benchmarks and present selected applications from various areas. Finally, we discuss open problems for further research.

In this paper, we propose embedding sparsity into the structure of deep neural networks, where model parameters can be exactly zero during training with the stochastic gradient descent. Thus, it can learn the sparsified structure and the weights of networks simultaneously. The proposed approach can learn structured as well as unstructured sparsity.

We describe a hybrid meta-architecture -- the CHAMELEON -- for session-based news recommendation that is able to leverage a variety of information types using Recurrent Neural Networks. We evaluated our approach on two public datasets, using a temporal evaluation protocol that simulates the dynamics of a news portal in a realistic way. Our results confirm the benefits of modeling the sequence of session clicks with RNNs and leveraging side information about users and articles, resulting in significantly higher recommendation accuracy and catalog coverage than other session-based algorithms.

Traffic forecasting has recently attracted increasing interest due to the popularity of online navigation services, ridesharing and smart city projects. Owing to the non-stationary nature of road traffic, forecasting accuracy is fundamentally limited by the lack of contextual information. To address this issue, we propose the Hybrid Spatio-Temporal Graph Convolutional Network (H-STGCN), which is able to "deduce" future travel time by exploiting the data of upcoming traffic volume. Specifically, we propose an algorithm to acquire the upcoming traffic volume from an online navigation engine. Taking advantage of the piecewise-linear flow-density relationship, a novel transformer structure converts the upcoming volume into its equivalent in travel time. We combine this signal with the commonly-utilized travel-time signal, and then apply graph convolution to capture the spatial dependency. Particularly, we construct a compound adjacency matrix which reflects the innate traffic proximity. We conduct extensive experiments on real-world datasets. The results show that H-STGCN remarkably outperforms state-of-the-art methods in various metrics, especially for the prediction of non-recurring congestion.

The James-Stein (JS) shrinkage estimator is a biased estimator that captures the mean of Gaussian random vectors.While it has a desirable statistical property of dominance over the maximum likelihood estimator (MLE) in terms of mean squared error (MSE), not much progress has been made on extending the estimator onto manifold-valued data. We propose C-SURE, a novel Stein's unbiased risk estimate (SURE) of the JS estimator on the manifold of complex-valued data with a theoretically proven optimum over MLE. Adapting the architecture of the complex-valued SurReal classifier, we further incorporate C-SURE into a prototype convolutional neural network (CNN) classifier. We compare C-SURE with SurReal and a real-valued baseline on complex-valued MSTAR and RadioML datasets. C-SURE is more accurate and robust than SurReal, and the shrinkage estimator is always better than MLE for the same prototype classifier. Like SurReal, C-SURE is much smaller, outperforming the real-valued baseline on MSTAR (RadioML) with less than 1 percent (3 percent) of the baseline size

Background: The expanding research in the field of long non-coding RNAs(lncRNAs) showed abnormal expression of lncRNAs in many complex diseases. Accurately identifying lncRNA-disease association is essential in understanding lncRNA functionality and disease mechanism. There are many machine learning techniques involved in the prediction of lncRNA-disease association which use different biological interaction networks and associated features. Feature learning from the network structured data is one of the limiting factors of machine learning-based methods. Graph neural network based techniques solve this limitation by unsupervised feature learning. Deep belief networks (DBN) are recently used in biological network analysis to learn the latent representations of network features. Method: In this paper, we propose a DBN based lncRNA-disease association prediction model (DBNLDA) from lncRNA, disease and miRNA interactions. The architecture contains three major modules-network construction, DBN based feature learning and neural network-based prediction. First, we constructed three heterogeneous networks such as lncRNA-miRNA similarity (LMS), disease-miRNA similarity (DMS) and lncRNA-disease association (LDA) network. From the node embedding matrices of similarity networks, lncRNA-disease representations were learned separately by two DBN based subnetworks. The joint representation of lncRNA-disease was learned by a third DBN from outputs of the two subnetworks mentioned. This joint feature representation was used to predict the association score by an ANN classifier. Result: The proposed method obtained AUC of 0.96 and AUPR of 0.967 when tested against standard dataset used by the state-of-the-art methods. Analysis on breast, lung and stomach cancer cases also affirmed the effectiveness of DBNLDA in predicting significant lncRNA-disease associations.

Self-attention architectures, which are rapidly pushing the frontier in natural language processing, demonstrate a surprising depth-inefficient behavior: Empirical signals indicate that increasing the internal representation (network width) is just as useful as increasing the number of self-attention layers (network depth). In this paper, we theoretically study the interplay between depth and width in self-attention, and shed light on the root of the above phenomenon. We invalidate the seemingly plausible hypothesis by which widening is as effective as deepening for self-attention, and show that in fact stacking self-attention layers is so effective that it quickly saturates a capacity of the network width. Specifically, we pinpoint a "depth threshold" that is logarithmic in $d_x$, the network width: $L_{\textrm{th}}=\log_{3}(d_x)$. For networks of depth that is below the threshold, we establish a double-exponential depth-efficiency of the self-attention operation, while for depths over the threshold we show that depth-inefficiency kicks in. Our predictions strongly accord with extensive empirical ablations in Kaplan et al. (2020), accounting for the different behaviors in the two depth-(in)efficiency regimes. By identifying network width as a limiting factor, our analysis indicates that solutions for dramatically increasing the width can facilitate the next leap in self-attention expressivity.

In active learning, sampling bias could pose a serious inconsistency problem and hinder the algorithm from finding the optimal hypothesis. However, many methods for neural networks are hypothesis space agnostic and do not address this problem. We examine active learning with convolutional neural networks through the principled lens of version space reduction. We identify the connection between two approaches---prior mass reduction and diameter reduction---and propose a new diameter-based querying method---the minimum Gibbs-vote disagreement. By estimating version space diameter and bias, we illustrate how version space of neural networks evolves and examine the realizability assumption. With experiments on MNIST, Fashion-MNIST, SVHN and STL-10 datasets, we demonstrate that diameter reduction methods reduce the version space more effectively and perform better than prior mass reduction and other baselines, and that the Gibbs vote disagreement is on par with the best query method.

In the absence of large labelled datasets, self-supervised learning techniques can boost performance by learning useful representations from unlabelled data, which is often more readily available. However, there is often a domain shift between the unlabelled collection and the downstream target problem data. We show that by learning Bayesian instance weights for the unlabelled data, we can improve the downstream classification accuracy by prioritising the most useful instances. Additionally, we show that the training time can be reduced by discarding unnecessary datapoints. Our method, BetaDataWeighter is evaluated using the popular self-supervised rotation prediction task on STL-10 and Visual Decathlon. We compare to related instance weighting schemes, both hand-designed heuristics and meta-learning, as well as conventional self-supervised learning. BetaDataWeighter achieves both the highest average accuracy and rank across datasets, and on STL-10 it prunes up to 78% of unlabelled images without significant loss in accuracy, corresponding to over 50% reduction in training time.

Empowered by expressive function approximators such as neural networks, deep reinforcement learning (DRL) achieves tremendous empirical successes. However, learning expressive function approximators requires collecting a large dataset (interventional data) by interacting with the environment. Such a lack of sample efficiency prohibits the application of DRL to critical scenarios, e.g., autonomous driving and personalized medicine, since trial and error in the online setting is often unsafe and even unethical. In this paper, we study how to incorporate the dataset (observational data) collected offline, which is often abundantly available in practice, to improve the sample efficiency in the online setting. To incorporate the possibly confounded observational data, we propose the deconfounded optimistic value iteration (DOVI) algorithm, which incorporates the confounded observational data in a provably efficient manner. More specifically, DOVI explicitly adjusts for the confounding bias in the observational data, where the confounders are partially observed or unobserved. In both cases, such adjustments allow us to construct the bonus based on a notion of information gain, which takes into account the amount of information acquired from the offline setting. In particular, we prove that the regret of DOVI is smaller than the optimal regret achievable in the pure online setting by a multiplicative factor, which decreases towards zero when the confounded observational data are more informative upon the adjustments. Our algorithm and analysis serve as a step towards causal reinforcement learning.