This paper proposes a novel fixed inducing points online Bayesian calibration (FIPO-BC) algorithm to efficiently learn the model parameters using a benchmark database. The standard Bayesian calibration (STD-BC) algorithm provides a statistical method to calibrate the parameters of computationally expensive models. However, the STD-BC algorithm scales very badly with the number of data points and lacks online learning capability. The proposed FIPO-BC algorithm greatly improves the computational efficiency and enables the online calibration by executing the calibration on a set of predefined inducing points. To demonstrate the procedure of the FIPO-BC algorithm, two tests are performed, finding the optimal value and exploring the posterior distribution of 1) the parameter in a simple function, and 2) the high-wave number damping factor in a scale-resolving turbulence model (SAS-SST). The results (such as the calibrated model parameter and its posterior distribution) of FIPO-BC with different inducing points are compared to those of STD-BC. It is found that FIPO-BC and STD-BC can provide very similar results, once the predefined set of inducing point in FIPO-BC is sufficiently fine. But, the FIPO-BC algorithm is at least ten times faster than the STD-BC algorithm. Meanwhile, the online feature of the FIPO-BC allows continuous updating of the calibration outputs and potentially reduces the workload on generating the database.

This thesis focuses on the research and development of the Hemodynamic Tissue Signature (HTS) method: an unsupervised machine learning approach to describe the vascular heterogeneity of glioblastomas by means of perfusion MRI analysis. The HTS builds on the concept of habitats. An habitat is defined as a sub-region of the lesion with a particular MRI profile describing a specific physiological behavior. The HTS method delineates four habitats within the glioblastoma: the High Angiogenic Tumor (HAT) habitat, as the most perfused region of the enhancing tumor; the Low Angiogenic Tumor (LAT) habitat, as the region of the enhancing tumor with a lower angiogenic profile; the potentially Infiltrated Peripheral Edema (IPE) habitat, as the non-enhancing region adjacent to the tumor with elevated perfusion indexes; and the Vasogenic Peripheral Edema (VPE) habitat, as the remaining edema of the lesion with the lowest perfusion profile. The results of this thesis have been published in ten scientific contributions, including top-ranked journals and conferences in the areas of Medical Informatics, Statistics and Probability, Radiology & Nuclear Medicine, Machine Learning and Data Mining and Biomedical Engineering. An industrial patent registered in Spain (ES201431289A), Europe (EP3190542A1) and EEUU (US20170287133A1) was also issued, summarizing the efforts of the thesis to generate tangible assets besides the academic revenue obtained from research publications. Finally, the methods, technologies and original ideas conceived in this thesis led to the foundation of ONCOANALYTICS CDX, a company framed into the business model of companion diagnostics for pharmaceutical compounds, thought as a vehicle to facilitate the industrialization of the ONCOhabitats technology.

Independent sociological polls are forbidden in Belarus. Online polls performed without sound scientific rigour do not yield representative results. Yet, both inside and outside Belarus it is of great importance to obtain precise estimates of the ratings of all candidates. These ratings could function as reliable proxies for the election's outcomes. We conduct an independent poll based on the combination of the data collected via Viber and on the streets of Belarus. The Viber and the street data samples consist of almost 45000 and 1150 unique observations respectively. Bayesian regressions with poststratification were build to estimate ratings of the candidates and rates of early voting turnout for the population as a whole and within various focus subgroups. We show that both the officially announced results of the election and early voting rates are highly improbable. With a probability of at least 95%, Sviatlana Tikhanouskaya's rating lies between 75% and 80%, whereas Aliaksandr Lukashenka's rating lies between 13% and 18% and early voting rate predicted by the method ranges from 9% to 13% of those who took part in the election. These results contradict the officially announced outcomes, which are 10.12%, 80.11%, and 49.54% respectively and lie far outside even the 99.9% credible intervals predicted by our model. The only marginal groups of people where the upper bounds of the 99.9% credible intervals of the rating of Lukashenka are above 50% are people older than 60 and uneducated people. For all other marginal subgroups, including rural residents, even the upper bounds of 99.9% credible intervals for Lukashenka are far below 50%. The same is true for the population as a whole. Thus, with a probability of at least 99.9% Lukashenka could not have had enough electoral support to win the 2020 presidential election in Belarus.

A COVID-19 vaccine is our best bet for mitigating the ongoing onslaught of the pandemic. However, vaccine is also expected to be a limited resource. An optimal allocation strategy, especially in countries with access inequities and a temporal separation of hot-spots might be an effective way of halting the disease spread. We approach this problem by proposing a novel pipeline VacSIM that dovetails Actor-Critic using Kronecker-Factored Trust Region (ACKTR) model into a Contextual Bandits approach for optimizing the distribution of COVID-19 vaccine. Whereas the ACKTR model suggests better actions and rewards, Contextual Bandits allow online modifications that may need to be implemented on a day-to-day basis in the real world scenario. We evaluate this framework against a naive allocation approach of distributing vaccine proportional to the incidence of COVID-19 cases in five different States across India and demonstrate up to 100,000 additional lives potentially saved and a five-fold increase in the efficacy of limiting the spread over a period of 30 days through the VacSIM approach. We also propose novel evaluation strategies including a standard compartmental model based projections and a causality preserving evaluation of our model. Finally, we contribute a new Open-AI environment meant for the vaccine distribution scenario, and open-source VacSIM for wide testing and applications across the globe.

Due to advances in machine learning and artificial intelligence (AI), a new role is emerging for machines as intelligent assistants to radiologists in their clinical workflows. But what systematic clinical thought processes are these machines using? Are they similar enough to those of radiologists to be trusted as assistants? A live demonstration of such a technology was conducted at the 2016 Scientific Assembly and Annual Meeting of the Radiological Society of North America (RSNA). The demonstration was presented in the form of a question-answering system that took a radiology multiple choice question and a medical image as inputs. The AI system then demonstrated a cognitive workflow, involving text analysis, image analysis, and reasoning, to process the question and generate the most probable answer. A post demonstration survey was made available to the participants who experienced the demo and tested the question answering system. Of the reported 54,037 meeting registrants, 2,927 visited the demonstration booth, 1,991 experienced the demo, and 1,025 completed a post-demonstration survey. In this paper, the methodology of the survey is shown and a summary of its results are presented. The results of the survey show a very high level of receptiveness to cognitive computing technology and artificial intelligence among radiologists.

Plants are fundamentally important to life. Key research areas in plant science include plant species identification, weed classification using hyper spectral images, monitoring plant health and tracing leaf growth, and the semantic interpretation of leaf information. Botanists easily identify plant species by discriminating between the shape of the leaf, tip, base, leaf margin and leaf vein, as well as the texture of the leaf and the arrangement of leaflets of compound leaves. Because of the increasing demand for experts and calls for biodiversity, there is a need for intelligent systems that recognize and characterize leaves so as to scrutinize a particular species, the diseases that affect them, the pattern of leaf growth, and so on. We review several image processing methods in the feature extraction of leaves, given that feature extraction is a crucial technique in computer vision. As computers cannot comprehend images, they are required to be converted into features by individually analysing image shapes, colours, textures and moments. Images that look the same may deviate in terms of geometric and photometric variations. In our study, we also discuss certain machine learning classifiers for an analysis of different species of leaves.

This paper shows that dropout training in Generalized Linear Models is the minimax solution of a two-player, zero-sum game where an adversarial nature corrupts a statistician's covariates using a multiplicative nonparametric errors-in-variables model. In this game---known as a Distributionally Robust Optimization problem---nature's least favorable distribution is dropout noise, where nature independently deletes entries of the covariate vector with some fixed probability $\delta$. Our decision-theoretic analysis shows that dropout training---the statistician's minimax strategy in the game---indeed provides out-of-sample expected loss guarantees for distributions that arise from multiplicative perturbations of in-sample data. This paper also provides a novel, parallelizable, Unbiased Multi-Level Monte Carlo algorithm to speed-up the implementation of dropout training. Our algorithm has a much smaller computational cost compared to the naive implementation of dropout, provided the number of data points is much smaller than the dimension of the covariate vector.

Finite mixture models, typically Gaussian mixtures, are well known and widely used as model-based clustering. In practical situations, there are many non-Gaussian data that are heavy-tailed and/or asymmetric. Normal inverse Gaussian (NIG) distributions are normal-variance mean which mixing densities are inverse Gaussian distributions and can be used for both haavy-tail and asymmetry. For NIG mixture models, both expectation-maximization method and variational Bayesian (VB) algorithms have been proposed. However, the existing VB algorithm for NIG mixture have a disadvantage that the shape of the mixing density is limited. In this paper, we propose another VB algorithm for NIG mixture that improves on the shortcomings. We also propose an extension of Dirichlet process mixture models to overcome the difficulty in determining the number of clusters in finite mixture models. We evaluated the performance with artificial data and found that it outperformed Gaussian mixtures and existing implementations for NIG mixtures, especially for highly non-normative data.

In this work, we propose information laundering, a novel framework for enhancing model privacy. Unlike data privacy that concerns the protection of raw data information, model privacy aims to protect an already-learned model that is to be deployed for public use. The private model can be obtained from general learning methods, and its deployment means that it will return a deterministic or random response for a given input query. An informationlaundered model consists of probabilistic components that deliberately maneuver the intended input and output for queries to the model, so the model's adversarial acquisition is less likely. Under the proposed framework, we develop an information-theoretic principle to quantify the fundamental tradeoffs between model utility and privacy leakage and derive the optimal design. An emerging number of applications involve the following user-scenario. Alice developed a model that takes a specific query as input and calculates a response as output. The model is a stochastic black-box that may represent a novel type of ensemble models, a known deep neural network architecture with sophisticated parameter tuning, or a physical law described by stochastic differential equations.

The COVID-19 pandemic provides new motivation for a classic problem in epidemiology: estimating the empirical rate of transmission during an outbreak (formally, the time-varying reproduction number) from case counts. While standard methods exist, they work best at coarse-grained national or state scales with abundant data, and struggle to accommodate the partial observability and sparse data common at finer scales (e.g., individual schools or towns). For example, case counts may be sparse when only a small fraction of infections are caught by a testing program. Or, whether an infected individual tests positive may depend on the kind of test and the point in time when they are tested. We propose a Bayesian framework which accommodates partial observability in a principled manner. Our model places a Gaussian process prior over the unknown reproduction number at each time step and models observations sampled from the distribution of a specific testing program. For example, our framework can accommodate a variety of kinds of tests (viral RNA, antibody, antigen, etc.) and sampling schemes (e.g., longitudinal or cross-sectional screening). Inference in this framework is complicated by the presence of tens or hundreds of thousands of discrete latent variables. To address this challenge, we propose an efficient stochastic variational inference method which relies on a novel gradient estimator for the variational objective. Experimental results for an example motivated by COVID-19 show that our method produces an accurate and well-calibrated posterior, while standard methods for estimating the reproduction number can fail badly.