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Social contexts -- such as families, schools, and neighborhoods -- shape life outcomes. The key question is not simply whether they matter, but rather for whom and under what conditions. Here, we argue that prediction gaps -- differences in…
Phagocytosis and receptor-mediated endocytosis are vitally important particle uptake mechanisms in many cell types, ranging from single-cell organisms to immune cells. In both processes, engulfment by the cell depends critically on both…
We explore the role of cellular life cycles for viruses and host cells in an infection process. For this purpose, we derive a generalized version of the basic model of virus dynamics (Nowak, M.A., Bangham, C.R.M., 1996. Population dynamics…
Estimating heterogeneous treatment effect (HTE) for survival outcomes has gained increasing attention, as it captures the variation in treatment efficacy across patients or subgroups in delaying disease progression. However, most existing…
Over the past decade, machine learning has revolutionized computers' ability to analyze text through flexible computational models. Due to their structural similarity to written language, transformer-based architectures have also shown…
Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Finetuning can significantly modify the behavior of large language models, including introducing harmful or unsafe behaviors. To study these risks, researchers develop model organisms: models finetuned to exhibit specific known behaviors…
The relationship between the design and functionality of molecular networks is now a key issue in biology. Comparison of regulatory networks performing similar tasks can give insights into how network architecture is constrained by the…
Acyclic phase-type (PH) distributions have been a popular tool in survival analysis, thanks to their natural interpretation in terms of ageing towards its inevitable absorption. In this paper, we consider an extension to the bivariate…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Deep learning models for survival analysis have gained significant attention in the literature, but they suffer from severe performance deficits when the dataset contains many irrelevant features. We give empirical evidence for this problem…
One of the main goals of mathematical modeling in systems medicine related to medical applications is to obtain patient-specific parameterizations and model predictions. In clinical practice, however, the number of available measurements…
Bacteriophages are promising alternative antimicrobial agents due to their high specificity for host bacteria and minimal immunogenicity in humans. However, their therapeutic application is limited by their nature as biological entities,…
A rapid, cost-effective and easy method that allows on-site determination of the concentration of live and dead bacterial cells using a fibre-based spectroscopic device (the optrode system) is proposed and demonstrated. Identification of…
Single-cell lineage tracking strategies enabled by recent experimental technologies have produced significant insights into cell fate decisions, but lack the quantitative framework necessary for rigorous statistical analysis of mechanistic…
We present a novel learning-based method that achieves state-of-the-art performance on several heart rate estimation benchmarks extracted from photoplethysmography signals (PPG). We consider the evolution of the heart rate in the context of…
Preliminary diagnosis of fungal infections can rely on microscopic examination. However, in many cases, it does not allow unambiguous identification of the species by microbiologist due to their visual similarity. Therefore, it is usually…
The development of molecular diagnostic tools to achieve individualized medicine requires identifying predictive biomarkers associated with subgroups of individuals who might receive beneficial or harmful effects from different available…
Clinical notes contain an extensive record of a patient's health status, such as smoking status or the presence of heart conditions. However, this detail is not replicated within the structured data of electronic health systems.…