Causal inference requires theory and prior knowledge to structure analyses, and is not usually thought of as an arena for the application of prediction modelling. However, contemporary causal inference methods, premised on counterfactual or potential outcomes approaches, often include processing steps before the final estimation step. The purposes of this paper are: (i) to overview the recent emergence of prediction underpinning steps in contemporary causal inference methods as a useful perspective on contemporary causal inference methods, and (ii) explore the role of machine learning (as one approach to'best prediction') in causal inference. Causal inference methods covered include propensity scores, inverse probability of treatment weights (IPTWs), G computation and targeted maximum likelihood estimation (TMLE). Machine learning has been used more for propensity scores and TMLE, and there is potential for increased use in G computation and estimation of IPTWs.

Mixtures-of-Experts (MoE) are conditional mixture models that have shown their performance in modeling heterogeneity in data in many statistical learning approaches for prediction, including regression and classification, as well as for clustering. Their estimation in high-dimensional problems is still however challenging. We consider the problem of parameter estimation and feature selection in MoE models with different generalized linear experts models, and propose a regularized maximum likelihood estimation that efficiently encourages sparse solutions for heterogeneous data with high-dimensional predictors. The developed proximal-Newton EM algorithm includes proximal Newton-type procedures to update the model parameter by monotonically maximizing the objective function and allows to perform efficient estimation and feature selection. An experimental study shows the good performance of the algorithms in terms of recovering the actual sparse solutions, parameter estimation, and clustering of heterogeneous regression data, compared to the main state-of-the art competitors.

Although deep neural networks have been widely applied in various domains [19, 25, 27], usually its parameters are learned via the principle of maximum likelihood, hence its success crucially hinges on the availability of large scale datasets. When training rich models on small datasets, explicit regularization techniques are crucial to alleviate overfitting. Previous works have explored various regularization [39] and data augmentation [19, 38] techniques to learn diversified representations. In this paper, we look into an alternative direction by proposing an adaptive and data-dependent regularization method to encourage neurons of the same layer to share statistical strength. The goal of our method is to prevent overfitting when training (large) networks on small dataset. Our key insight stems from the famous argument by Efron [8] in the literature of the empirical Bayes method: It is beneficial to learn from the experience of others. From an algorithmic perspective, we argue that the connection weights of neurons in the same layer (row/column vectors of the weight matrix) will be correlated with each other through the backpropagation learning. Hence, by learning the correlations of the weight matrix, a neuron can "borrow statistical strength" from other neurons in the same layer.

We present new techniques for automatically constructing probabilistic programs for data analysis, interpretation, and prediction. These techniques work with probabilistic domain-specific data modeling languages that capture key properties of a broad class of data generating processes, using Bayesian inference to synthesize probabilistic programs in these modeling languages given observed data. We provide a precise formulation of Bayesian synthesis for automatic data modeling that identifies sufficient conditions for the resulting synthesis procedure to be sound. We also derive a general class of synthesis algorithms for domain-specific languages specified by probabilistic context-free grammars and establish the soundness of our approach for these languages. We apply the techniques to automatically synthesize probabilistic programs for time series data and multivariate tabular data. We show how to analyze the structure of the synthesized programs to compute, for key qualitative properties of interest, the probability that the underlying data generating process exhibits each of these properties. Second, we translate probabilistic programs in the domain-specific language into probabilistic programs in Venture, a general-purpose probabilistic programming system. The translated Venture programs are then executed to obtain predictions of new time series data and new multivariate data records. Experimental results show that our techniques can accurately infer qualitative structure in multiple real-world data sets and outperform standard data analysis methods in forecasting and predicting new data.

Gaussian processes are used in machine learning to learn input-output mappings from observed data. Gaussian process regression is based on imposing a Gaussian process prior on the unknown regressor function and statistically conditioning it on the observed data. In system identification, Gaussian processes are used to form time series prediction models such as non-linear finite-impulse response (NFIR) models as well as non-linear autoregressive (NARX) models. Gaussian process state-space models (GPSS) can be used to learn the dynamic and measurement models for a state-space representation of the input-output data. Temporal and spatio-temporal Gaussian processes can be directly used to form regressor on the data in the time domain. The aim of this article is to briefly outline the main directions in system identification methods using Gaussian processes.

The Gaussian process (GP) is a nonparametric prior distribution over functions indexed by time, space, or other high-dimensional index set. The GP is a flexible model yet its limitation is given by its very nature: it can only model Gaussian marginal distributions. To model non-Gaussian data, a GP can be warped by a nonlinear transformation (or warping) as performed by warped GPs (WGPs) and more computationally-demanding alternatives such as Bayesian WGPs and deep GPs. However, the WGP requires a numerical approximation of the inverse warping for prediction, which increases the computational complexity in practice. To sidestep this issue, we construct a novel class of warpings consisting of compositions of multiple elementary functions, for which the inverse is known explicitly. We then propose the compositionally-warped GP (CWGP), a non-Gaussian generative model whose expressiveness follows from its deep compositional architecture, and its computational efficiency is guaranteed by the analytical inverse warping. Experimental validation using synthetic and real-world datasets confirms that the proposed CWGP is robust to the choice of warpings and provides more accurate point predictions, better trained models and shorter computation times than WGP.

This paper considers the problem of estimating a low-rank matrix from the observation of all, or a subset, of its entries in the presence of Poisson noise. When we observe all the entries, this is a problem of matrix denoising; when we observe only a subset of the entries, this is a problem of matrix completion. In both cases, we exploit an assumption that the underlying matrix is low-rank. Specifically, we analyze several estimators, including a constrained nuclear-norm minimization program, nuclear-norm regularized least squares, and a nonconvex constrained low-rank optimization problem. We show that for all three estimators, with high probability, we have an upper error bound (in the Frobenius norm error metric) that depends on the matrix rank, the fraction of the elements observed, and maximal row and column sums of the true matrix. We furthermore show that the above results are minimax optimal (within a universal constant) in classes of matrices with low rank and bounded row and column sums. We also extend these results to handle the case of matrix multinomial denoising and completion.

We propose a new framework of XGBoost that predicts the entire conditional distribution of a univariate response variable. In particular, XGBoostLSS models all moments of a parametric distribution, i.e., mean, location, scale and shape (LSS), instead of the conditional mean only. Choosing from a wide range of continuous, discrete and mixed discrete-continuous distribution, modelling and predicting the entire conditional distribution greatly enhances the flexibility of XGBoost, as it allows to gain additional insight into the data generating process, as well as to create probabilistic forecasts from which prediction intervals and quantiles of interest can be derived. We present both a simulation study and real world examples that demonstrate the benefits of our approach.

We derive the functional form of mutual information (MI) from a set of design criteria and a principle of maximal sufficiency. The (MI) between two sets of propositions is a global quantifier of correlations and is implemented as a tool for ranking joint probability distributions with respect to said correlations. The derivation parallels the derivations of relative entropy with an emphasis on the behavior of independent variables. By constraining the functional $I$ according to special cases, we arrive at its general functional form and hence establish a clear meaning behind its definition. We also discuss the notion of sufficiency and offer a new definition which broadens its applicability.

The time series cluster kernel (TCK) provides a powerful tool for analysing multivariate time series subject to missing data. TCK is designed using an ensemble learning approach in which Bayesian mixture models form the base models. Because of the Bayesian approach, TCK can naturally deal with missing values without resorting to imputation and the ensemble strategy ensures robustness to hyperparameters, making it particularly well suited for unsupervised learning. However, TCK assumes missing at random and that the underlying missingness mechanism is ignorable, i.e. uninformative, an assumption that does not hold in many real-world applications, such as e.g. medicine. To overcome this limitation, we present a kernel capable of exploiting the potentially rich information in the missing values and patterns, as well as the information from the observed data. In our approach, we create a representation of the missing pattern, which is incorporated into mixed mode mixture models in such a way that the information provided by the missing patterns is effectively exploited. Moreover, we also propose a semi-supervised kernel, capable of taking advantage of incomplete label information to learn more accurate similarities. Experiments on benchmark data, as well as a real-world case study of patients described by longitudinal electronic health record data who potentially suffer from hospital-acquired infections, demonstrate the effectiveness of the proposed methods.