A computational method based on the non-linear Gaussian process (GP), known as deep Gaussian processes (deep GPs) for uncertainty quantification & propagation in modelling of flow through heterogeneous porous media is presented. The method is also used for reducing dimensionality of model output and consequently emulating highly complex relationship between hydrogeological properties and reduced order fluid velocity field in a tractable manner. Deep GPs are multi-layer hierarchical generalisations of GPs with multiple, infinitely wide hidden layers that are very efficient models for deep learning and modelling of high-dimensional complex systems by tackling the complexity through several hidden layers connected with non-linear mappings. According to this approach, the hydrogeological data is modelled as the output of a multivariate GP whose inputs are governed by another GP such that each single layer is either a standard GP or the Gaussian process latent variable model. A variational approximation framework is used so that the posterior distribution of the model outputs associated to given inputs can be analytically approximated. In contrast to the other dimensionality reduction, methods that do not provide any information about the dimensionality of each hidden layer, the proposed method automatically selects the dimensionality of each hidden layer and it can be used to propagate uncertainty obtained in each layer across the hierarchy. Using this, dimensionality of the full input space consists of both geometrical parameters of modelling domain and stochastic hydrogeological parameters can be simultaneously reduced without the need for any simplifications generally being assumed for stochastic modelling of subsurface flow problems. It allows estimation of the flow statistics with greatly reduced computational efforts compared to other stochastic approaches such as Monte Carlo method.

We address the problem of building theoretical models that help elucidate the function of the visual brain at computational/algorithmic and structural/mechanistic levels. We seek to understand how the receptive fields and topographic maps found in visual cortical areas relate to underlying computational desiderata. We view the development of sensory systems from the popular perspective of probability density estimation; this is motivated by the notion that an effective internal representational scheme is likely to reflect the statistical structure of the environment in which an organism lives. We apply biologically based constraints on elements of the model. The thesis begins by surveying the relevant literature from the fields of neurobiology, theoretical neuroscience, and machine learning. After this review we present our main theoretical and algorithmic developments: we propose a class of probabilistic models, which we refer to as "energy-based models", and show equivalences between this framework and various other types of probabilistic model such as Markov random fields and factor graphs; we also develop and discuss approximate algorithms for performing maximum likelihood learning and inference in our energy based models. The rest of the thesis is then concerned with exploring specific instantiations of such models. By performing constrained optimisation of model parameters to maximise the likelihood of appropriate, naturalistic datasets we are able to qualitatively reproduce many of the receptive field and map properties found in vivo, whilst simultaneously learning about statistical regularities in the data.

While uncertainty estimation is a well-studied topic in deep learning, most such work focuses on marginal uncertainty estimates, i.e. the predictive mean and variance at individual input locations. But it is often more useful to estimate predictive correlations between the function values at different input locations. In this paper, we consider the problem of benchmarking how accurately Bayesian models can estimate predictive correlations. We first consider a downstream task which depends on posterior predictive correlations: transductive active learning (TAL). We find that TAL makes better use of models' uncertainty estimates than ordinary active learning, and recommend this as a benchmark for evaluating Bayesian models. Since TAL is too expensive and indirect to guide development of algorithms, we introduce two metrics which more directly evaluate the predictive correlations and which can be computed efficiently: meta-correlations (i.e. the correlations between the models correlation estimates and the true values), and cross-normalized likelihoods (XLL). We validate these metrics by demonstrating their consistency with TAL performance and obtain insights about the relative performance of current Bayesian neural net and Gaussian process models.

One of the main barriers to the broader adoption of algorithmic fairness in machine learning is the trade-off between fairness and performance of ML models: many practitioners are unwilling to sacrifice the performance of their ML model for fairness. In this paper, we show that this trade-off may not be necessary. If the algorithmic biases in an ML model are due to sampling biases in the training data, then enforcing algorithmic fairness may improve the performance of the ML model on unbiased test data. We study conditions under which enforcing algorithmic fairness helps practitioners learn the Bayes decision rule for (unbiased) test data from biased training data. We also demonstrate the practical implications of our theoretical results in real-world ML tasks.

Calibrated estimates of uncertainty are critical for many real-world computer vision applications of deep learning. While there are several widely-used uncertainty estimation methods, dropout inference stands out for its simplicity and efficacy. This technique, however, requires multiple forward passes through the network during inference and therefore can be too resource-intensive to be deployed in real-time applications. We propose a simple, easy-to-optimize distillation method for learning the conditional predictive distribution of a pre-trained dropout model for fast, sample-free uncertainty estimation in computer vision tasks. We empirically test the effectiveness of the proposed method on both semantic segmentation and depth estimation tasks and demonstrate our method can significantly reduce the inference time, enabling real-time uncertainty quantification, while achieving improved quality of both the uncertainty estimates and predictive performance over the regular dropout model.

We develop a Bregman proximal gradient method for structure learning on linear structural causal models. While the problem is non-convex, has high curvature and is in fact NP-hard, Bregman gradient methods allow us to neutralize at least part of the impact of curvature by measuring smoothness against a highly nonlinear kernel. This allows the method to make longer steps and significantly improves convergence. Each iteration requires solving a Bregman proximal step which is convex and efficiently solvable for our particular choice of kernel. We test our method on various synthetic and real data sets.

In this paper we provide a new efficient algorithm for approximately computing the profile maximum likelihood (PML) distribution, a prominent quantity in symmetric property estimation. We provide an algorithm which matches the previous best known efficient algorithms for computing approximate PML distributions and improves when the number of distinct observed frequencies in the given instance is small. We achieve this result by exploiting new sparsity structure in approximate PML distributions and providing a new matrix rounding algorithm, of independent interest. Leveraging this result, we obtain the first provable computationally efficient implementation of PseudoPML, a general framework for estimating a broad class of symmetric properties. Additionally, we obtain efficient PML-based estimators for distributions with small profile entropy, a natural instance-based complexity measure. Further, we provide a simpler and more practical PseudoPML implementation that matches the best-known theoretical guarantees of such an estimator and evaluate this method empirically.

While deep neural networks provide good performance for a range of challenging tasks, calibration and uncertainty estimation remain major challenges. In this paper, we propose the amortized conditional normalized maximum likelihood (ACNML) method as a scalable general-purpose approach for uncertainty estimation, calibration, and out-of-distribution robustness with deep networks. Our algorithm builds on the conditional normalized maximum likelihood (CNML) coding scheme, which has minimax optimal properties according to the minimum description length principle, but is computationally intractable to evaluate exactly for all but the simplest of model classes. We propose to use approximate Bayesian inference technqiues to produce a tractable approximation to the CNML distribution. Our approach can be combined with any approximate inference algorithm that provides tractable posterior densities over model parameters. We demonstrate that ACNML compares favorably to a number of prior techniques for uncertainty estimation in terms of calibration on out-of-distribution inputs.

Loss functions are a cornerstone of machine learning and the starting point of most algorithms. Statistics and Bayesian decision theory have contributed, via properness, to elicit over the past decades a wide set of admissible losses in supervised learning, to which most popular choices belong (logistic, square, Matsushita, etc.). Rather than making a potentially biased ad hoc choice of the loss, there has recently been a boost in efforts to fit the loss to the domain at hand while training the model itself. The key approaches fit a canonical link, a function which monotonically relates the closed unit interval to R and can provide a proper loss via integration. In this paper, we rely on a broader view of proper composite losses and a recent construct from information geometry, source functions, whose fitting alleviates constraints faced by canonical links. We introduce a trick on squared Gaussian Processes to obtain a random process whose paths are compliant source functions with many desirable properties in the context of link estimation. Experimental results demonstrate substantial improvements over the state of the art.

The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting data obtained from high-throughput experiments or meta-scale information from public databases. Most existing prediction tools are targeted at predicting protein functions that are described in the gene ontology (GO). However, in many cases biologists wish to discover functionally related genes for which GO terms are inadequate. In this paper, we introduce a rich set of features and use them in conjunction with semisupervised learning approaches in order to expand an initial set of seed genes to a larger cluster of functionally related genes. Among all the semi-supervised methods that were evaluated, the framework of learning with positive and unlabeled examples (LPU) is shown to be especially appropriate for mining functionally related genes. When evaluated on experimentally validated benchmark data, the LPU approaches1 significantly outperform a standard supervised learning algorithm as well as an established state-of-the-art method. Given an initial set of seed genes, our best performing approach could be used to mine functionally related genes in a wide range of organisms.