Related papers: PhaTYP: Predicting the lifestyle for bacteriophage…
Pretrained Language Models (PLMs) harbor inherent social biases that can result in harmful real-world implications. Such social biases are measured through the probability values that PLMs output for different social groups and attributes…
The chemotactic pathway allows bacteria to respond and adapt to environmental changes, by tuning the tumbling and running motions that are due to clockwise and counterclockwise rotations of their flagella. The pathway is tightly regulated…
Diabetes is a prevalent chronic disease with significant health and economic burdens worldwide. Early prediction and diagnosis can aid in effective management and prevention of complications. This study explores the use of machine learning…
Phase-type distributions (PHDs), which are defined as the distribution of the lifetime up to the absorption in an absorbent Markov chain, are an appropriate candidate to model the lifetime of any system, since any non-negative probability…
Background: Phage therapy shows promise for treating antibiotic-resistant Klebsiella infections. Identifying phage depolymerases that target Klebsiella capsular polysaccharides is crucial, as these capsules contribute to biofilm formation…
Genetic association analyses often involve data from multiple potentially-heterogeneous subgroups. The expected amount of heterogeneity can vary from modest (e.g., a typical meta-analysis) to large (e.g., a strong gene--environment…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Phenotypic heterogeneity is a most fascinating property of a population of cells, which shows the differences among individuals even with the same genetic background and extracellular environmental conditions. However, the lack of…
Phage display is a powerful laboratory technique used to study the interactions between proteins and other molecules, whether other proteins, peptides, DNA or RNA. The under-utilisation of this data in conjunction with deep learning models…
Frailty models are essential tools in survival analysis for addressing unobserved heterogeneity and random effects in the data. These models incorporate a random effect, the frailty, which is assumed to impact the hazard rate…
Studying phenotype-gene association can uncover mechanism of diseases and develop efficient treatments. In complex disease where multiple phenotypes are available and correlated, analyzing and interpreting associated genes for each…
When an infection spreads in a community, an individual's probability of becoming infected depends on both her susceptibility and exposure to the contagion through contact with others. While one often has knowledge regarding an individual's…
Despite being similar in structure, functioning, and size viral pathogens enjoy very different mostly well-defined ways of life. They occupy their hosts for a few days (influenza), for a few weeks (measles), or even lifelong (HCV), which…
A person's passage of time perception (POTP) is strongly linked to their mental state and stress response, and can therefore provide an easily quantifiable means of continuous mental health monitoring. In this work, we develop a custom…
Personalized models of the gut microbiome are valuable for disease prevention and treatment. For this, one requires a mathematical model that predicts microbial community composition and the emergent behavior of microbial communities. We…
In the era of precision medicine, more and more clinical trials are now driven or guided by biomarkers, which are patient characteristics objectively measured and evaluated as indicators of normal biological processes, pathogenic processes,…
Vital sign measurement using cameras presents opportunities for comfortable, ubiquitous health monitoring. Remote photoplethysmography (rPPG), a foundational technology, enables cardiac measurement through minute changes in light reflected…
Objective: Endophenotypes such as brain age and fluid intelligence are important biomarkers of disease status. However, brain imaging studies to identify these biomarkers often encounter limited numbers of subjects and high dimensional…
Gut microbial composition has been linked to multiple health outcomes. Yet, temporal analysis of this composition had been limited to deterministic models. In this paper, we introduce a probabilistic model for the dynamics of intestinal…