Bayesian Networks (BNs) have become a powerful technology for reasoning under uncertainty, particularly in areas that require causal assumptions that enable us to simulate the effect of intervention. The graphical structure of these models can be determined by causal knowledge, learnt from data, or a combination of both. While it seems plausible that the best approach in constructing a causal graph involves combining knowledge with machine learning, this approach remains underused in practice. We implement and evaluate 10 knowledge approaches with application to different case studies and BN structure learning algorithms available in the open-source Bayesys structure learning system. The approaches enable us to specify pre-existing knowledge that can be obtained from heterogeneous sources, to constrain or guide structure learning. Each approach is assessed in terms of structure learning effectiveness and efficiency, including graphical accuracy, model fitting, complexity, and runtime; making this the first paper that provides a comparative evaluation of a wide range of knowledge approaches for BN structure learning. Because the value of knowledge depends on what data are available, we illustrate the results both with limited and big data. While the overall results show that knowledge becomes less important with big data due to higher learning accuracy rendering knowledge less important, some of the knowledge approaches are actually found to be more important with big data. Amongst the main conclusions is the observation that reduced search space obtained from knowledge does not always imply reduced computational complexity, perhaps because the relationships implied by the data and knowledge are in tension.
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Agents that interact with other agents often do not know a priori what the other agents' strategies are, but have to maximise their own online return while interacting with and learning about others. The optimal adaptive behaviour under uncertainty over the other agents' strategies w.r.t. some prior can in principle be computed using the Interactive Bayesian Reinforcement Learning framework. Unfortunately, doing so is intractable in most settings, and existing approximation methods are restricted to small tasks. To overcome this, we propose to meta-learn approximate belief inference and Bayes-optimal behaviour for a given prior. To model beliefs over other agents, we combine sequential and hierarchical Variational Auto-Encoders, and meta-train this inference model alongside the policy. We show empirically that our approach outperforms existing methods that use a model-free approach, sample from the approximate posterior, maintain memory-free models of others, or do not fully utilise the known structure of the environment.
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.
Structural data well exists in Web applications, such as social networks in social media, citation networks in academic websites, and threads data in online forums. Due to the complex topology, it is difficult to process and make use of the rich information within such data. Graph Neural Networks (GNNs) have shown great advantages on learning representations for structural data. However, the non-transparency of the deep learning models makes it non-trivial to explain and interpret the predictions made by GNNs. Meanwhile, it is also a big challenge to evaluate the GNN explanations, since in many cases, the ground-truth explanations are unavailable. In this paper, we take insights of Counterfactual and Factual (CF^2) reasoning from causal inference theory, to solve both the learning and evaluation problems in explainable GNNs. For generating explanations, we propose a model-agnostic framework by formulating an optimization problem based on both of the two casual perspectives. This distinguishes CF^2 from previous explainable GNNs that only consider one of them. Another contribution of the work is the evaluation of GNN explanations. For quantitatively evaluating the generated explanations without the requirement of ground-truth, we design metrics based on Counterfactual and Factual reasoning to evaluate the necessity and sufficiency of the explanations. Experiments show that no matter ground-truth explanations are available or not, CF^2 generates better explanations than previous state-of-the-art methods on real-world datasets. Moreover, the statistic analysis justifies the correlation between the performance on ground-truth evaluation and our proposed metrics.
Graph Neural Networks (GNNs) have shown promising results on a broad spectrum of applications. Most empirical studies of GNNs directly take the observed graph as input, assuming the observed structure perfectly depicts the accurate and complete relations between nodes. However, graphs in the real world are inevitably noisy or incomplete, which could even exacerbate the quality of graph representations. In this work, we propose a novel Variational Information Bottleneck guided Graph Structure Learning framework, namely VIB-GSL, in the perspective of information theory. VIB-GSL advances the Information Bottleneck (IB) principle for graph structure learning, providing a more elegant and universal framework for mining underlying task-relevant relations. VIB-GSL learns an informative and compressive graph structure to distill the actionable information for specific downstream tasks. VIB-GSL deduces a variational approximation for irregular graph data to form a tractable IB objective function, which facilitates training stability. Extensive experimental results demonstrate that the superior effectiveness and robustness of VIB-GSL.
Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.
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.
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.
The goal of few-shot learning is to learn a classifier that generalizes well even when trained with a limited number of training instances per class. The recently introduced meta-learning approaches tackle this problem by learning a generic classifier across a large number of multiclass classification tasks and generalizing the model to a new task. Yet, even with such meta-learning, the low-data problem in the novel classification task still remains. In this paper, we propose Transductive Propagation Network (TPN), a novel meta-learning framework for transductive inference that classifies the entire test set at once to alleviate the low-data problem. Specifically, we propose to learn to propagate labels from labeled instances to unlabeled test instances, by learning a graph construction module that exploits the manifold structure in the data. TPN jointly learns both the parameters of feature embedding and the graph construction in an end-to-end manner. We validate TPN on multiple benchmark datasets, on which it largely outperforms existing few-shot learning approaches and achieves the state-of-the-art results.
Inferring missing links in knowledge graphs (KG) has attracted a lot of attention from the research community. In this paper, we tackle a practical query answering task involving predicting the relation of a given entity pair. We frame this prediction problem as an inference problem in a probabilistic graphical model and aim at resolving it from a variational inference perspective. In order to model the relation between the query entity pair, we assume that there exists an underlying latent variable (paths connecting two nodes) in the KG, which carries the equivalent semantics of their relations. However, due to the intractability of connections in large KGs, we propose to use variation inference to maximize the evidence lower bound. More specifically, our framework (\textsc{Diva}) is composed of three modules, i.e. a posterior approximator, a prior (path finder), and a likelihood (path reasoner). By using variational inference, we are able to incorporate them closely into a unified architecture and jointly optimize them to perform KG reasoning. With active interactions among these sub-modules, \textsc{Diva} is better at handling noise and coping with more complex reasoning scenarios. In order to evaluate our method, we conduct the experiment of the link prediction task on multiple datasets and achieve state-of-the-art performances on both datasets.
State-of-the-art recommendation algorithms -- especially the collaborative filtering (CF) based approaches with shallow or deep models -- usually work with various unstructured information sources for recommendation, such as textual reviews, visual images, and various implicit or explicit feedbacks. Though structured knowledge bases were considered in content-based approaches, they have been largely neglected recently due to the availability of vast amount of data, and the learning power of many complex models. However, structured knowledge bases exhibit unique advantages in personalized recommendation systems. When the explicit knowledge about users and items is considered for recommendation, the system could provide highly customized recommendations based on users' historical behaviors. A great challenge for using knowledge bases for recommendation is how to integrated large-scale structured and unstructured data, while taking advantage of collaborative filtering for highly accurate performance. Recent achievements on knowledge base embedding sheds light on this problem, which makes it possible to learn user and item representations while preserving the structure of their relationship with external knowledge. In this work, we propose to reason over knowledge base embeddings for personalized recommendation. Specifically, we propose a knowledge base representation learning approach to embed heterogeneous entities for recommendation. Experimental results on real-world dataset verified the superior performance of our approach compared with state-of-the-art baselines.
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