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One of the fundamental challenges found throughout the data sciences is to explain why things happen in specific ways, or through which mechanisms a certain variable $X$ exerts influences over another variable $Y$. In statistics and machine learning, significant efforts have been put into developing machinery to estimate correlations across variables efficiently. In causal inference, a large body of literature is concerned with the decomposition of causal effects under the rubric of mediation analysis. However, many variations are spurious in nature, including different phenomena throughout the applied sciences. Despite the statistical power to estimate correlations and the identification power to decompose causal effects, there is still little understanding of the properties of spurious associations and how they can be decomposed in terms of the underlying causal mechanisms. In this manuscript, we develop formal tools for decomposing spurious variations in both Markovian and Semi-Markovian models. We prove the first results that allow a non-parametric decomposition of spurious effects and provide sufficient conditions for the identification of such decompositions. The described approach has several applications, ranging from explainable and fair AI to questions in epidemiology and medicine, and we empirically demonstrate its use on a real-world dataset.

This paper presents a novel approach to Bayesian nonparametric spectral analysis of stationary multivariate time series. Starting with a parametric vector-autoregressive model, the parametric likelihood is nonparametrically adjusted in the frequency domain to account for potential deviations from parametric assumptions. We show mutual contiguity of the nonparametrically corrected likelihood, the multivariate Whittle likelihood approximation and the exact likelihood for Gaussian time series. A multivariate extension of the nonparametric Bernstein-Dirichlet process prior for univariate spectral densities to the space of Hermitian positive definite spectral density matrices is specified directly on the correction matrices. An infinite series representation of this prior is then used to develop a Markov chain Monte Carlo algorithm to sample from the posterior distribution. The code is made publicly available for ease of use and reproducibility. With this novel approach we provide a generalization of the multivariate Whittle-likelihood-based method of Meier et al. (2020) as well as an extension of the nonparametrically corrected likelihood for univariate stationary time series of Kirch et al. (2019) to the multivariate case. We demonstrate that the nonparametrically corrected likelihood combines the efficiencies of a parametric with the robustness of a nonparametric model. Its numerical accuracy is illustrated in a comprehensive simulation study. We illustrate its practical advantages by a spectral analysis of two environmental time series data sets: a bivariate time series of the Southern Oscillation Index and fish recruitment and time series of windspeed data at six locations in California.

Long-term outcomes of experimental evaluations are necessarily observed after long delays. We develop semiparametric methods for combining the short-term outcomes of experiments with observational measurements of short-term and long-term outcomes, in order to estimate long-term treatment effects. We characterize semiparametric efficiency bounds for various instances of this problem. These calculations facilitate the construction of several estimators. We analyze the finite-sample performance of these estimators with a simulation calibrated to data from an evaluation of the long-term effects of a poverty alleviation program.

Health policy decisions are often informed by estimates of long-term survival based primarily on short-term data. A range of methods are available to include longer-term information, but there has previously been no comprehensive and accessible tool for implementing these. This paper introduces a novel model and software package for parametric survival modelling of individual-level, right-censored data, optionally combined with summary survival data on one or more time periods. It could be used to estimate long-term survival based on short-term data from a clinical trial, combined with longer-term disease registry or population data, or elicited judgements. All data sources are represented jointly in a Bayesian model. The hazard is modelled as an M-spline function, which can represent potential changes in the hazard trajectory at any time. Through Bayesian estimation, the model automatically adapts to fit the available data, and acknowledges uncertainty where the data are weak. Therefore long-term estimates are only confident if there are strong long-term data, and inferences do not rely on extrapolating parametric functions learned from short-term data. The effects of treatment or other explanatory variables can be estimated through proportional hazards or with a flexible non-proportional hazards model. Some commonly-used mechanisms for survival can also be assumed: cure models, additive hazards models with known background mortality, and models where the effect of a treatment wanes over time. All of these features are provided for the first time in an R package, $\texttt{survextrap}$, in which models can be fitted using standard R survival modelling syntax. This paper explains the model, and demonstrates the use of the package to fit a range of models to common forms of survival data used in health technology assessments.

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.

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.

The potential of graph convolutional neural networks for the task of zero-shot learning has been demonstrated recently. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing generalization to new classes when faced with a lack of data. However, knowledge from distant nodes can get diluted when propagating through intermediate nodes, because current approaches to zero-shot learning use graph propagation schemes that perform Laplacian smoothing at each layer. We show that extensive smoothing does not help the task of regressing classifier weights in zero-shot learning. In order to still incorporate information from distant nodes and utilize the graph structure, we propose an Attentive Dense Graph Propagation Module (ADGPM). ADGPM allows us to exploit the hierarchical graph structure of the knowledge graph through additional connections. These connections are added based on a node's relationship to its ancestors and descendants and an attention scheme is further used to weigh their contribution depending on the distance to the node. Finally, we illustrate that finetuning of the feature representation after training the ADGPM leads to considerable improvements. Our method achieves competitive results, outperforming previous zero-shot learning approaches.

Recently, deep learning has achieved very promising results in visual object tracking. Deep neural networks in existing tracking methods require a lot of training data to learn a large number of parameters. However, training data is not sufficient for visual object tracking as annotations of a target object are only available in the first frame of a test sequence. In this paper, we propose to learn hierarchical features for visual object tracking by using tree structure based Recursive Neural Networks (RNN), which have fewer parameters than other deep neural networks, e.g. Convolutional Neural Networks (CNN). First, we learn RNN parameters to discriminate between the target object and background in the first frame of a test sequence. Tree structure over local patches of an exemplar region is randomly generated by using a bottom-up greedy search strategy. Given the learned RNN parameters, we create two dictionaries regarding target regions and corresponding local patches based on the learned hierarchical features from both top and leaf nodes of multiple random trees. In each of the subsequent frames, we conduct sparse dictionary coding on all candidates to select the best candidate as the new target location. In addition, we online update two dictionaries to handle appearance changes of target objects. Experimental results demonstrate that our feature learning algorithm can significantly improve tracking performance on benchmark datasets.