Mateusz Kania | Searcharxiv

arXiv2024

Propagation of weakly advantageous mutations in cancer cell population

Research into somatic mutations in cancer cell DNA and their role in tumour growth and progression between successive stages is crucial for improving our understanding of cancer evolution. Mathematical and computer modelling can provide valuable insights into the scenarios of cancer growth, the roles of somatic mutations, and the types and strengths of evolutionary forces they introduce. Previous studies have developed mathematical models of cancer evolution, incorporating driver and passenger somatic mutations. Driver mutations were assumed to have a strong advantageous effect on the growth of the cancer cell population, while passenger mutations were considered fully neutral or mildly deleterious. However, according to several studies, passenger mutations may have a weakly advantageous effect on tumour growth. In this paper, we develop models of cancer evolution with somatic mutations that introduce a weakly advantageous force to the evolution of cancer cells. The models used in this study can be classified into two categories: deterministic and stochastic. Deterministic models are based on systems of differential equations that balance the average number of cells and mutations during evolution. To verify the results of our deterministic modelling, we use a stochastic model based on the Gillespie algorithm. We compare the predictions of our modelling with some observational data on cancer evolution.

q-bio.PE↗

arXiv2020

Classification supporting COVID-19 diagnostics based on patient survey data

Distinguishing COVID-19 from other flu-like illnesses can be difficult due to ambiguous symptoms and still an initial experience of doctors. Whereas, it is crucial to filter out those sick patients who do not need to be tested for SARS-CoV-2 infection, especially in the event of the overwhelming increase in disease. As a part of the presented research, logistic regression and XGBoost classifiers, that allow for effective screening of patients for COVID-19, were generated. Each of the methods was tuned to achieve an assumed acceptable threshold of negative predictive values during classification. Additionally, an explanation of the obtained classification models was presented. The explanation enables the users to understand what was the basis of the decision made by the model. The obtained classification models provided the basis for the DECODE service (decode.polsl.pl), which can serve as support in screening patients with COVID-19 disease. Moreover, the data set constituting the basis for the analyses performed is made available to the research community. This data set consisting of more than 3,000 examples is based on questionnaires collected at a hospital in Poland.

cs.LG↗