Related papers: A Weighted Exact Test for Mutually Exclusive Mutat…
We consider finite-sample inference for a single regression coefficient in the fixed-design linear model $Y = Z\beta + bX + \varepsilon$, where $\varepsilon\in\mathbb{R}^n$ may exhibit complex dependence or heterogeneity. We develop a group…
In this thesis we develop minimal models of the relationship between motility, growth, and evolution of cancer cells. We utilise simple simulations of a population of individual cells in space to examine how changes in mechanical properties…
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in…
We investigate the dynamics of cancer initiation in a mathematical model with one driver mutation and several passenger mutations. Our analysis is based on a multi type branching process: We model individual cells which can either divide or…
We consider the problems of weighted constrained sampling and weighted model counting, where we are given a propositional formula and a weight for each world. The first problem consists of sampling worlds with a probability proportional to…
Cancer genomes exhibit a large number of different alterations that affect many genes in a diverse manner. It is widely believed that these alterations follow combinatorial patterns that have a strong connection with the underlying…
One of the mechanisms that ensure cancer robustness is tumor heterogeneity, and its effects on tumor cells dynamics have to be taken into account when studying cancer progression. There is no unifying theoretical framework in mathematical…
Mutation testing is an approach to check the robustness of test suites. The program code is slightly changed by mutations to inject errors. A test suite is robust enough if it finds such errors. Tools for mutation testing usually integrate…
The comparison of different medical treatments from observational studies or across different clinical studies is often biased by confounding factors such as systematic differences in patient demographics or in the inclusion criteria for…
Recently, Ainsworth et al. showed that using weight matching (WM) to minimize the $L^2$ distance in a permutation search of model parameters effectively identifies permutations that satisfy linear mode connectivity (LMC), where the loss…
Tumor protein P53 is believed to be involved in over half of human cancers cases, the prediction of malignancies plays essential roles not only in advance detection for cancer, but also in discovering effective prevention and treatment of…
In our study, we introduce a novel hybrid ensemble model that synergistically combines LSTM, BiLSTM, CNN, GRU, and GloVe embeddings for the classification of gene mutations in cancer. This model was rigorously tested using Kaggle's…
The emergence of acquired drug resistance in cancer represents a major barrier to treatment success. While research has traditionally focused on genetic sources of resistance, recent findings suggest that cancer cells can acquire transient…
Metastatic prostate cancer is one of the most common cancers in men. In the advanced stages of prostate cancer, tumours can metastasise to other tissues in the body, which is fatal. In this thesis, we performed a genetic analysis of…
Model-based mutation testing uses altered test models to derive test cases that are able to reveal whether a modelled fault has been implemented. This requires conformance checking between the original and the mutated model. This paper…
Cancer is one of the leading cause of death, worldwide. Many believe that genomic data will enable us to better predict the survival time of these patients, which will lead to better, more personalized treatment options and patient care. As…
Advancement in sequencing technology enables the study of association between complex disorders and rare variants with low minor allele frequencies. One of the major challenges in rare variant testing is lack of statistical power of…
When software evolves, opportunities for introducing faults appear. Therefore, it is important to test the evolved program behaviors during each evolution cycle. We conduct an exploratory study to investigate the properties of…
Estimating software testability can crucially assist software managers to optimize test budgets and software quality. In this paper, we propose a new approach that radically differs from the traditional approach of pursuing testability…
In this paper we consider continuous mathematical models of tumour growth and invasion based on the model introduced by Chaplain and Lolas \cite{Chaplain&Lolas2006}, for the case of one space dimension. The models consist of a system of…