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Stol, Madelon (author)Understanding the role of genes and genetic variants is a key challenge in unraveling the driving mechanisms of Alzheimer's disease (AD). Single-cell RNA sequencing is a technique that quantifies gene expression at the cell (type) level enabling investigation of the roles of different cell types in disease. We analyzed changes in gene (co-...master thesis 2023
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Engel, Friso (author)Introduction<br/>In the era of growing antimicrobial resistance, early detection and immediate treatment of antibiotic-resistant infections are crucial to ensuring successful outcomes in critically ill patients. The aim of this study is to apply machine learning (ML) to create classifiers that predict antibiotic resistance in postoperative...master thesis 2023
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de Vries, Chiel (author)Alzheimer's disease (AD) is becoming more prevalent as the world population gets older. The formation of Amyloid-beta (\AB) plaques is one of the pathologies related to AD. Recent work has shown that the \ab load in brain tissue has a negative correlation with cognitive performance in cognitively healthy centenarians. <br/>This work aims to...master thesis 2023
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Borges Carioca Moreno Rodrigues, Inês (author)Tacrolimus is an immunosuppressive drug given to kidney transplant patients. A low concentration of this drug can lead to kidney rejection, but to our knowledge no research has been done to causally connect the two. This paper investigates the causal effect of tacrolimus concentration on kidney rejection occurrence using predictive analysis and...master thesis 2023
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Verlaan, Timo (author)Identifying key genes in Alzheimer’s Disease (AD) is important in increasing understanding about its pathogenesis, and discovering potential therapeutic targets. Recent advances in single-cell RNA sequencing (scRNAseq) technology have provided unprecedented opportunities to study the molecular mechanisms underlying AD at the cellular level. In...master thesis 2023
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Katz, Roy (author)Federated learning enables the construction of machine learning models, while adhering to privacy constraints and without sharing data between different devices. It is achieved by creating a machine learning model on each device that contains data, and then combining these models through an aggregation algorithm without sharing the data....bachelor thesis 2023
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Golik, Bartek (author)Analysing single-cell RNA sequencing data is becoming an increasingly tedious task as the size of data sets grows. As a proposed solution, recent discoveries suggest that these data sets can be binarized without losing much information. This in turn should allow for memory and time efficient methods of storage and computation. Numerous analyses...bachelor thesis 2023
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de Koning, Milan (author)As single-cell RNA sequencing techniques improve and more cells are measured in individual experiments, cell clustering procedures become increasingly more computationally intensive. This paper studies the runtime performance impact of a specialized clustering algorithm for data converted to a binary format, in order to reduce computational...bachelor thesis 2023
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Verigo, Pavel (author)The rapid increase in the size of single-cell RNAseq datasets presents significant performance challenges when conducting evaluations and extracting information. We research an alternative input data format that utilizes binarization. Our main focus is an analysis of peak memory usage. An in-depth exploration of the solution’s design and...bachelor thesis 2023
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Theunisz, Jurriën (author)Single-cell RNA sequencing data clustering is a valuable technique for demonstrating cell-to-cell heterogeneity and revealing cell dynamics within and amongst groups. Large up-scaling of scRNA-seq datasets in recent years pose computational challenges for existing state-of-the-art clustering techniques. A possible solution to tackle these...bachelor thesis 2023
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Beekhuizen, Michael (author)Cardiovascular diseases are one of the primary causes of mortality worldwide. Paroxysmal atrial fibrillation is a specific type that is difficult to detect and diagnose in a short time frame. To overcome this, we investigated if long-term wearable data can be used for the detection of heart diseases. The BigIdeasLab_STEP dataset and long-term...master thesis 2023
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Schouten, Janno (author)Patients who are admitted to the Intensive Care Unit (ICU) are extremely ill and at high risk of organ failure and death. Being admitted to the ICU is known to cause long lasting physical, cognitive, and physiological symptoms, which is called Post-Intensive Care syndrome (PICS). To provide better management of PICS, early recognition and...master thesis 2023
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Vlekke, Jimmy (author)Global warming causes coral bleaching which threatens the health and existence of coral reefs and therefore also the future of a lot of species, including human beings. Efforts to automate coral reef monitoring using annotated coral images to detect coral bleaching are hindered by the lack of a complete dataset that specifies the health and...master thesis 2022
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Biharie, Kirti (author)Knowing the relation between cell types is crucial for translating experimental results from mice to humans. Establishing cell type matches, however, is hindered by the biological differences between the species. A substantial amount of evolutionary information between genes that could be used to align the species, is discarded by most of the...master thesis 2022
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Khan, Abdul Rehman (author)Transformers have dominated the field of natural language processing due to their competency in learning complex relationships within a sequence. Reusing a pre-trained transformer for a downstream task is known as Trans-fer learning. Transfer learning restricts the transformer to a fixed vocabulary; modification in transformer implementation...master thesis 2022
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Lucas, Francesca (author)Motivation: Alzheimer’s disease (AD) is a highly prevalent disease whose genetic risk factors remain largely unknown. One potential genetic risk factor is tandem repeat expansions, which have been associated with over 40 diseases, most of which affect the nervous system. Detecting VNTRs from short-read data is a challenging task, leaving many...master thesis 2021
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Smit, Jim (author)Background: The covid-19 pandemic has overwhelmed hospitals worldwide and clinical prediction models may assist in timely identification of covid-19 patients at risk for clinical deterioration, i.e. `early warning'. In this article, we report on the development and validation of a new early warning model that predicts unplanned ICU admission or...master thesis 2021
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Darbari, Shubhankar (author)The expansion of the Internet and wireless access has led to a widespread increase of Internet of Things applications. These smart devices are becoming a daily aspect of our lives. All the convenient and automated services provided by smart devices come from a centralized service provider. This service provider has access to all the personal...bachelor thesis 2021
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van Ruyven, Noor (author)In 1997 it was discovered that fragments of DNA circulate freely in the blood plasma and, in the case of pregnancy, this DNA consists of DNA belonging to both the mother and the fetus. This circulating free DNA has made it possible to test for chromosomal aberration in the fetus through non-invasive methods, thereby avoiding the 1 in 100 chance...master thesis 2021
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Michielsen, Lieke (author)Since the revolution of single-cell RNA-sequencing, the number of available datasets has increased enormously. In these datasets, cell identification is mainly done manually, which is subjective and time-consuming. As a consequence, most datasets are annotated at a different resolution. This is not surprising as cell types form a hierarchy, but...master thesis 2020