Integration and visualisation of clinical-omics datasets for medical knowledge discovery

In recent decades, the rise of various omics fields has flooded life sciences with unprecedented amounts of high-throughput data, which have transformed the way biomedical research is conducted. This trend will only intensify in the coming decades, as the cost of data acquisition will continue to decrease. Therefore, there is a pressing need to find novel ways to turn this ocean of raw data into waves of information and finally distil those into drops of translational medical knowledge. This is particularly challenging because of the incredible richness of these datasets, the humbling complexity of biological systems and the growing abundance of clinical metadata, which makes the integration of disparate data sources even more difficult. Data integration has proven to be a promising avenue for knowledge discovery in biomedical research. Multi-omics studies allow us to examine a biological problem through different lenses using more than one analytical platform. These studies not only present tremendous opportunities for the deep and systematic understanding of health and disease, but they also pose new statistical and computational challenges. The work presented in this thesis aims to alleviate this problem with a novel pipeline for omics data integration. Modern omics datasets are extremely feature rich and in multi-omics studies this complexity is compounded by a second or even third dataset. However, many of these features might be completely irrelevant to the studied biological problem or redundant in the context of others. Therefore, in this thesis, clinical metadata driven feature selection is proposed as a viable option for narrowing down the focus of analyses in biomedical research. Our visual cortex has been fine-tuned through millions of years to become an outstanding pattern recognition machine. To leverage this incredible resource of the human brain, we need to develop advanced visualisation software that enables researchers to explore these vast biological datasets through illuminating charts and interactivity. Accordingly, a substantial portion of this PhD was dedicated to implementing truly novel visualisation methods for multi-omics studies.Open Acces

Impact of Community Factors on the Donor Quality Score in Liver Transplantation

An increasing prevalence of metabolic syndrome and obesity has been linked to the rise in transplant indication for cryptogenic cirrhosis and nonalcoholic fatty liver disease (NAFLD), creating a growing challenge to public health. NAFLD liver transplant (LT) candidates are listed with low priority, and their waiting mortality is high. The impact of community/geographic factors on donor risk models is unknown. The purpose of this study was to develop a parsimonious donor risk-adjusted model tailored to NAFLD recipients by assessing the impact of donor, recipient, transplant, and external factors on graft survival. The theoretical framework was the social ecological model. Secondary data were collected from 3,165 consecutive recipients from the Scientific Registry of Transplant Recipients and Community Health Scores, a proxy of community health disparities derived from the Robert Wood Johnson Foundation\u27s community health rankings. Data were examined using univariate and multivariate analyses. The donor risk-adjusted model was developed using donor-only factors and supplemented with recipient and transplant factors, classifying donors as low, medium, and high risk. NAFLD residents in high-risk counties had increased likelihood of liver graft failure. Findings may be used to allocate high-risk donors to a subset of NAFLD with excellent outcomes, increasing the donor pool and decreasing mortality on the wait list

Untangling hotel industry’s inefficiency: An SFA approach applied to a renowned Portuguese hotel chain

The present paper explores the technical efficiency of four hotels from Teixeira Duarte Group - a renowned Portuguese hotel chain. An efficiency ranking is established from these four hotel units located in Portugal using Stochastic Frontier Analysis. This methodology allows to discriminate between measurement error and systematic inefficiencies in the estimation process enabling to investigate the main inefficiency causes. Several suggestions concerning efficiency improvement are undertaken for each hotel studied.info:eu-repo/semantics/publishedVersio

The impact of macroeconomic leading indicators on inventory management

Forecasting tactical sales is important for long term decisions such as procurement and informing lower level inventory management decisions. Macroeconomic indicators have been shown to improve the forecast accuracy at tactical level, as these indicators can provide early warnings of changing markets while at the same time tactical sales are sufficiently aggregated to facilitate the identification of useful leading indicators. Past research has shown that we can achieve significant gains by incorporating such information. However, at lower levels, that inventory decisions are taken, this is often not feasible due to the level of noise in the data. To take advantage of macroeconomic leading indicators at this level we need to translate the tactical forecasts into operational level ones. In this research we investigate how to best assimilate top level forecasts that incorporate such exogenous information with bottom level (at Stock Keeping Unit level) extrapolative forecasts. The aim is to demonstrate whether incorporating these variables has a positive impact on bottom level planning and eventually inventory levels. We construct appropriate hierarchies of sales and use that structure to reconcile the forecasts, and in turn the different available information, across levels. We are interested both at the point forecast and the prediction intervals, as the latter inform safety stock decisions. Therefore the contribution of this research is twofold. We investigate the usefulness of macroeconomic leading indicators for SKU level forecasts and alternative ways to estimate the variance of hierarchically reconciled forecasts. We provide evidence using a real case study

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods

A comparison of the CAR and DAGAR spatial random effects models with an application to diabetics rate estimation in Belgium

When hierarchically modelling an epidemiological phenomenon on a finite collection of sites in space, one must always take a latent spatial effect into account in order to capture the correlation structure that links the phenomenon to the territory. In this work, we compare two autoregressive spatial models that can be used for this purpose: the classical CAR model and the more recent DAGAR model. Differently from the former, the latter has a desirable property: its ρ parameter can be naturally interpreted as the average neighbor pair correlation and, in addition, this parameter can be directly estimated when the effect is modelled using a DAGAR rather than a CAR structure. As an application, we model the diabetics rate in Belgium in 2014 and show the adequacy of these models in predicting the response variable when no covariates are available

Multivariate discretization of continuous valued attributes.

The area of Knowledge discovery and data mining is growing rapidly. Feature Discretization is a crucial issue in Knowledge Discovery in Databases (KDD), or Data Mining because most data sets used in real world applications have features with continuously values. Discretization is performed as a preprocessing step of the data mining to make data mining techniques useful for these data sets. This thesis addresses discretization issue by proposing a multivariate discretization (MVD) algorithm. It begins withal number of common discretization algorithms like Equal width discretization, Equal frequency discretization, Naïve; Entropy based discretization, Chi square discretization, and orthogonal hyper planes. After that comparing the results achieved by the multivariate discretization (MVD) algorithm with the accuracy results of other algorithms. This thesis is divided into six chapters, covering a few common discretization algorithms and tests these algorithms on a real world datasets which varying in size and complexity, and shows how data visualization techniques will be effective in determining the degree of complexity of the given data set. We have examined the multivariate discretization (MVD) algorithm with the same data sets. After that we have classified discrete data using artificial neural network single layer perceptron and multilayer perceptron with back propagation algorithm. We have trained the Classifier using the training data set, and tested its accuracy using the testing data set. Our experiments lead to better accuracy results with some data sets and low accuracy results with other data sets, and this is subject ot the degree of data complexity then we have compared the accuracy results of multivariate discretization (MVD) algorithm with the results achieved by other discretization algorithms. We have found that multivariate discretization (MVD) algorithm produces good accuracy results in comparing with the other discretization algorithm