Related papers: A Weighted Exact Test for Mutually Exclusive Mutat…
Mutation analysis assesses a test suite's adequacy by measuring its ability to detect small artificial faults, systematically seeded into the tested program. Mutation analysis is considered one of the strongest test-adequacy criteria.…
We consider two minimal mathematical models for cancer dynamics and self-adaptation. We aim to capture the interplay between the rapid progression of cancer growth and the possibility to leverage and enhance self-adaptive defense mechanisms…
Survival outcomes are common in comparative effectiveness studies and require unique handling because they are usually incompletely observed due to right-censoring. A ``once for all'' approach for causal inference with survival outcomes…
We introduce a new test for conditional independence which is based on what we call the weighted generalised covariance measure (WGCM). It is an extension of the recently introduced generalised covariance measure (GCM). To test the null…
In mutation testing the question whether a mutant is equivalent to its program is important in order to compute the correct mutation score. Unfortunately, answering this question is not always possible and can hardly be obtained just by…
Large variability between cell lines brings a difficult optimization problem of drug selection for cancer therapy. Standard approaches use prediction of value for this purpose, corresponding e.g. to expected value of their distribution.…
We study a structured permutation scheme for two-sample testing that restricts permutations to single cross-swaps between block-selected representatives. Our analysis yields three main results. First, we provide an exact validity…
Clinical machine learning applications are often plagued with confounders that are clinically irrelevant, but can still artificially boost the predictive performance of the algorithms. Confounding is especially problematic in mobile health…
Accurate screening of cancer types is crucial for effective cancer detection and precise treatment selection. However, the association between gene expression profiles and tumors is often limited to a small number of biomarker genes. While…
Quantifying the dynamics of tumor burden reveals useful information about cancer evolution concerning treatment effects and drug resistance, which play a crucial role in advancing model-informed drug developments (MIDD) towards personalized…
We propose a permutation-based method for testing a large collection of hypotheses simultaneously. Our method provides lower bounds for the number of true discoveries in any selected subset of hypotheses. These bounds are simultaneously…
In nonstandard testing environments, researchers often derive ad hoc tests with correct (asymptotic) size, but their optimality properties are typically unknown a priori and difficult to assess. This paper develops a numerical framework for…
Despite advances in methods to interrogate tumor biology, the observational and population-based approach of classical cancer research and clinical oncology does not enable anticipation of tumor outcomes to hasten the discovery of cancer…
The recent advances in cancer immunotherapy boosted the development of tumor-immune system models aiming to provide mechanistic understanding and indicate more efficient treatment regimes. However, the complexity of such models, their…
Recent works have stressed the important role that random mutations have in the development of cancer phenotype. We challenge this current view by means of bioinformatic data analysis and computational modelling approaches. Not all the…
The essence of precision oncology lies in its commitment to tailor targeted treatments and care measures to each patient based on the individual characteristics of the tumor. The inherent heterogeneity of tumors necessitates gathering…
Aims Late diagnosis of Oral Squamous Cell Carcinoma (OSCC) contributes significantly to its high global mortality rate, with over 50\% of cases detected at advanced stages and a 5-year survival rate below 50\% according to WHO statistics.…
Genetic studies have identified associations between gene mutations and clear cell renal cell carcinoma (ccRCC). Because the complete gene mutational landscape cannot be characterized through biopsy and sequencing assays for each patient,…
While the inverse probability of treatment weighting (IPTW) is a commonly used approach for treatment comparisons in observational data, the resulting estimates may be subject to bias and excessively large variance when there is lack of…
Statistics in ranked lists is important in analyzing molecular biology measurement data, such as ChIP-seq, which yields ranked lists of genomic sequences. State of the art methods study fixed motifs in ranked lists. More flexible models…