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Optimal model reduction for large-scale linear dynamical systems is studied. In contrast to most existing works, the systems under consideration are not required to be stable, neither in discrete nor in continuous time. As a consequence, the underlying rational transfer functions are allowed to have poles in general domains in the complex plane. In particular, this covers the case of specific conservative partial differential equations such as the linear Schr\"odinger and the undamped linear wave equation with spectra on the imaginary axis. By an appropriate modification of the classical continuous time Hardy space $\mathcal{H}_2$, a new $\mathcal{H}_2$ like optimal model reduction problem is introduced and first order optimality conditions are derived. As in the classical $\mathcal{H}_2$ case, these conditions exhibit a rational Hermite interpolation structure for which an iterative model reduction algorithm is proposed. Numerical examples demonstrate the effectiveness of the new method.

The decreasing cost and improved sensor and monitoring system technology (e.g. fiber optics and strain gauges) have led to more measurements in close proximity to each other. When using such spatially dense measurement data in Bayesian system identification strategies, the correlation in the model prediction error can become significant. The widely adopted assumption of uncorrelated Gaussian error may lead to inaccurate parameter estimation and overconfident predictions, which may lead to sub-optimal decisions. This paper addresses the challenges of performing Bayesian system identification for structures when large datasets are used, considering both spatial and temporal dependencies in the model uncertainty. We present an approach to efficiently evaluate the log-likelihood function, and we utilize nested sampling to compute the evidence for Bayesian model selection. The approach is first demonstrated on a synthetic case and then applied to a (measured) real-world steel bridge. The results show that the assumption of dependence in the model prediction uncertainties is decisively supported by the data. The proposed developments enable the use of large datasets and accounting for the dependency when performing Bayesian system identification, even when a relatively large number of uncertain parameters is inferred.

We propose a posterior for Bayesian Likelihood-Free Inference (LFI) based on generalized Bayesian inference. To define the posterior, we use Scoring Rules (SRs), which evaluate probabilistic models given an observation. In LFI, we can sample from the model but not evaluate the likelihood; hence, we employ SRs which admit unbiased empirical estimates. We use the Energy and Kernel SRs, for which our posterior enjoys consistency in a well-specified setting and outlier robustness. We perform inference with pseudo-marginal (PM) Markov Chain Monte Carlo (MCMC) or stochastic-gradient (SG) MCMC. While PM-MCMC works satisfactorily for simple setups, it mixes poorly for concentrated targets. Conversely, SG-MCMC requires differentiating the simulator model but improves performance over PM-MCMC when both work and scales to higher-dimensional setups as it is rejection-free. Although both techniques target the SR posterior approximately, the error diminishes as the number of model simulations at each MCMC step increases. In our simulations, we employ automatic differentiation to effortlessly differentiate the simulator model. We compare our posterior with related approaches on standard benchmarks and a chaotic dynamical system from meteorology, for which SG-MCMC allows inferring the parameters of a neural network used to parametrize a part of the update equations of the dynamical system.

Assessing causal effects in the presence of unmeasured confounding is a challenging problem. Although auxiliary variables, such as instrumental variables, are commonly used to identify causal effects, they are often unavailable in practice due to stringent and untestable conditions. To address this issue, previous researches have utilized linear structural equation models to show that the causal effect can be identifiable when noise variables of the treatment and outcome are both non-Gaussian. In this paper, we investigate the problem of identifying the causal effect using auxiliary covariates and non-Gaussianity from the treatment. Our key idea is to characterize the impact of unmeasured confounders using an observed covariate, assuming they are all Gaussian. The auxiliary covariate can be an invalid instrument or an invalid proxy variable. We demonstrate that the causal effect can be identified using this measured covariate, even when the only source of non-Gaussianity comes from the treatment. We then extend the identification results to the multi-treatment setting and provide sufficient conditions for identification. Based on our identification results, we propose a simple and efficient procedure for calculating causal effects and show the $\sqrt{n}$-consistency of the proposed estimator. Finally, we evaluate the performance of our estimator through simulation studies and an application.

In this paper we study the type IV Knorr Held space time models. Such models typically apply intrinsic Markov random fields and constraints are imposed for identifiability. INLA is an efficient inference tool for such models where constraints are dealt with through a conditioning by kriging approach. When the number of spatial and/or temporal time points become large, it becomes computationally expensive to fit such models, partly due to the number of constraints involved. We propose a new approach, HyMiK, dividing constraints into two separate sets where one part is treated through a mixed effect approach while the other one is approached by the standard conditioning by kriging method, resulting in a more efficient procedure for dealing with constraints. The new approach is easy to apply based on existing implementations of INLA. We run the model on simulated data, on a real data set containing dengue fever cases in Brazil and another real data set of confirmed positive test cases of Covid-19 in the counties of Norway. For all cases we get very similar results when comparing the new approach with the tradition one while at the same time obtaining a significant increase in computational speed, varying on a factor from 2 to 4, depending on the sizes of the data sets.

To estimate causal effects, analysts performing observational studies in health settings utilize several strategies to mitigate bias due to confounding by indication. There are two broad classes of approaches for these purposes: use of confounders and instrumental variables (IVs). Because such approaches are largely characterized by untestable assumptions, analysts must operate under an indefinite paradigm that these methods will work imperfectly. In this tutorial, we formalize a set of general principles and heuristics for estimating causal effects in the two approaches when the assumptions are potentially violated. This crucially requires reframing the process of observational studies as hypothesizing potential scenarios where the estimates from one approach are less inconsistent than the other. While most of our discussion of methodology centers around the linear setting, we touch upon complexities in non-linear settings and flexible procedures such as target minimum loss-based estimation (TMLE) and double machine learning (DML). To demonstrate the application of our principles, we investigate the use of donepezil off-label for mild cognitive impairment (MCI). We compare and contrast results from confounder and IV methods, traditional and flexible, within our analysis and to a similar observational study and clinical trial.

The Naive Bayesian classifier is a popular classification method employing the Bayesian paradigm. The concept of having conditional dependence among input variables sounds good in theory but can lead to a majority vote style behaviour. Achieving conditional independence is often difficult, and they introduce decision biases in the estimates. In Naive Bayes, certain features are called independent features as they have no conditional correlation or dependency when predicting a classification. In this paper, we focus on the optimal partition of features by proposing a novel technique called the Comonotone-Independence Classifier (CIBer) which is able to overcome the challenges posed by the Naive Bayes method. For different datasets, we clearly demonstrate the efficacy of our technique, where we achieve lower error rates and higher or equivalent accuracy compared to models such as Random Forests and XGBoost.

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.

Learning disentanglement aims at finding a low dimensional representation which consists of multiple explanatory and generative factors of the observational data. The framework of variational autoencoder (VAE) is commonly used to disentangle independent factors from observations. However, in real scenarios, factors with semantics are not necessarily independent. Instead, there might be an underlying causal structure which renders these factors dependent. We thus propose a new VAE based framework named CausalVAE, which includes a Causal Layer to transform independent exogenous factors into causal endogenous ones that correspond to causally related concepts in data. We further analyze the model identifiabitily, showing that the proposed model learned from observations recovers the true one up to a certain degree. Experiments are conducted on various datasets, including synthetic and real word benchmark CelebA. Results show that the causal representations learned by CausalVAE are semantically interpretable, and their causal relationship as a Directed Acyclic Graph (DAG) is identified with good accuracy. Furthermore, we demonstrate that the proposed CausalVAE model is able to generate counterfactual data through "do-operation" to the causal factors.

In structure learning, the output is generally a structure that is used as supervision information to achieve good performance. Considering the interpretation of deep learning models has raised extended attention these years, it will be beneficial if we can learn an interpretable structure from deep learning models. In this paper, we focus on Recurrent Neural Networks (RNNs) whose inner mechanism is still not clearly understood. We find that Finite State Automaton (FSA) that processes sequential data has more interpretable inner mechanism and can be learned from RNNs as the interpretable structure. We propose two methods to learn FSA from RNN based on two different clustering methods. We first give the graphical illustration of FSA for human beings to follow, which shows the interpretability. From the FSA's point of view, we then analyze how the performance of RNNs are affected by the number of gates, as well as the semantic meaning behind the transition of numerical hidden states. Our results suggest that RNNs with simple gated structure such as Minimal Gated Unit (MGU) is more desirable and the transitions in FSA leading to specific classification result are associated with corresponding words which are understandable by human beings.