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The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

A community reveals the features and connections of its members that are different from those in other communities in a network. Detecting communities is of great significance in network analysis. Despite the classical spectral clustering and statistical inference methods, we notice a significant development of deep learning techniques for community detection in recent years with their advantages in handling high dimensional network data. Hence, a comprehensive overview of community detection's latest progress through deep learning is timely to both academics and practitioners. This survey devises and proposes a new taxonomy covering different categories of the state-of-the-art methods, including deep learning-based models upon deep neural networks, deep nonnegative matrix factorization and deep sparse filtering. The main category, i.e., deep neural networks, is further divided into convolutional networks, graph attention networks, generative adversarial networks and autoencoders. The survey also summarizes the popular benchmark data sets, model evaluation metrics, and open-source implementations to address experimentation settings. We then discuss the practical applications of community detection in various domains and point to implementation scenarios. Finally, we outline future directions by suggesting challenging topics in this fast-growing deep learning field.

Recently, deep multiagent reinforcement learning (MARL) has become a highly active research area as many real-world problems can be inherently viewed as multiagent systems. A particularly interesting and widely applicable class of problems is the partially observable cooperative multiagent setting, in which a team of agents learns to coordinate their behaviors conditioning on their private observations and commonly shared global reward signals. One natural solution is to resort to the centralized training and decentralized execution paradigm. During centralized training, one key challenge is the multiagent credit assignment: how to allocate the global rewards for individual agent policies for better coordination towards maximizing system-level's benefits. In this paper, we propose a new method called Q-value Path Decomposition (QPD) to decompose the system's global Q-values into individual agents' Q-values. Unlike previous works which restrict the representation relation of the individual Q-values and the global one, we leverage the integrated gradient attribution technique into deep MARL to directly decompose global Q-values along trajectory paths to assign credits for agents. We evaluate QPD on the challenging StarCraft II micromanagement tasks and show that QPD achieves the state-of-the-art performance in both homogeneous and heterogeneous multiagent scenarios compared with existing cooperative MARL algorithms.

Knowledge graph embedding, which aims to represent entities and relations as low dimensional vectors (or matrices, tensors, etc.), has been shown to be a powerful technique for predicting missing links in knowledge graphs. Existing knowledge graph embedding models mainly focus on modeling relation patterns such as symmetry/antisymmetry, inversion, and composition. However, many existing approaches fail to model semantic hierarchies, which are common in real-world applications. To address this challenge, we propose a novel knowledge graph embedding model---namely, Hierarchy-Aware Knowledge Graph Embedding (HAKE)---which maps entities into the polar coordinate system. HAKE is inspired by the fact that concentric circles in the polar coordinate system can naturally reflect the hierarchy. Specifically, the radial coordinate aims to model entities at different levels of the hierarchy, and entities with smaller radii are expected to be at higher levels; the angular coordinate aims to distinguish entities at the same level of the hierarchy, and these entities are expected to have roughly the same radii but different angles. Experiments demonstrate that HAKE can effectively model the semantic hierarchies in knowledge graphs, and significantly outperforms existing state-of-the-art methods on benchmark datasets for the link prediction task.

Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph neural network architectures. HGP-SL incorporates graph pooling and structure learning into a unified module to generate hierarchical representations of graphs. More specifically, the graph pooling operation adaptively selects a subset of nodes to form an induced subgraph for the subsequent layers. To preserve the integrity of graph's topological information, we further introduce a structure learning mechanism to learn a refined graph structure for the pooled graph at each layer. By combining HGP-SL operator with graph neural networks, we perform graph level representation learning with focus on graph classification task. Experimental results on six widely used benchmarks demonstrate the effectiveness of our proposed model.

This paper focuses on two fundamental tasks of graph analysis: community detection and node representation learning, which capture the global and local structures of graphs, respectively. In the current literature, these two tasks are usually independently studied while they are actually highly correlated. We propose a probabilistic generative model called vGraph to learn community membership and node representation collaboratively. Specifically, we assume that each node can be represented as a mixture of communities, and each community is defined as a multinomial distribution over nodes. Both the mixing coefficients and the community distribution are parameterized by the low-dimensional representations of the nodes and communities. We designed an effective variational inference algorithm which regularizes the community membership of neighboring nodes to be similar in the latent space. Experimental results on multiple real-world graphs show that vGraph is very effective in both community detection and node representation learning, outperforming many competitive baselines in both tasks. We show that the framework of vGraph is quite flexible and can be easily extended to detect hierarchical communities.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.

Object detection is considered as one of the most challenging problems in computer vision, since it requires correct prediction of both classes and locations of objects in images. In this study, we define a more difficult scenario, namely zero-shot object detection (ZSD) where no visual training data is available for some of the target object classes. We present a novel approach to tackle this ZSD problem, where a convex combination of embeddings are used in conjunction with a detection framework. For evaluation of ZSD methods, we propose a simple dataset constructed from Fashion-MNIST images and also a custom zero-shot split for the Pascal VOC detection challenge. The experimental results suggest that our method yields promising results for ZSD.