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The approximation of the Feynman-Kac semigroups by systems of interacting particles is a very active research field, with applications in many different areas. In this paper, we study the parallelization of such approximations. The total…
The detection of molecular signatures of selection is one of the major concerns of modern population genetics. A widely used strategy in this context is to compare samples from several populations, and to look for genomic regions with…
Artificial biological pacemakers were developed and tested in canine ventricles. Next steps will require obtaining oscillations sensitive to external regulations, and robust with respect to long term drifts of expression levels of pacemaker…
Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…
Bone marrow stromal cells (BMSC) -- which include skeletal stem cells -- are a promising tool in regenerative medicine. However, their heterogeneous and unpredictable in vivo behaviour remains a critical barrier preventing the development…
Among the different computational approaches modelling the dynamics of isogenic cell populations, discrete stochastic models can describe with sufficient accuracy the evolution of small size populations. However, for a systematic and…
We build networks of genetic similarity in which the nodes are organisms sampled from biological populations. The procedure is illustrated by constructing networks from genetic data of a marine clonal plant. An important feature in the…
We propose a computational approach to modeling the collective dynamics of populations of coupled heterogeneous biological oscillators. In contrast to Monte Carlo simulation, this approach utilizes generalized Polynomial Chaos (gPC) to…
Common cluster models for multi-type point processes model the aggregation of points of the same type. In complete contrast, in the study of Anglo-Saxon settlements it is hypothesized that administrative clusters involving complementary…
There has been much recent interest in modelling epidemics on networks, particularly in the presence of substantial clustering. Here, we develop pairwise methods to answer questions that are often addressed using epidemic models, in…
Several biological and social contagion phenomena, such as superspreading events or social reinforcement, are the results of multi-body interactions, for which hypergraphs offer a natural mathematical description. In this paper, we develop…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
We develop a model the dynamics of human mesenchymal stem cells (hMSCs) and chondrocytes evolving in a nonwoven polyethylene terephtalate (PET) scaffold impregnated with hyaluron and supplied with a differentiation medium. The scaffold and…
Microbial ecosystems are remarkably diverse, stable, and often consist of a balanced mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real…
In most biological studies and processes, cell proliferation and population dynamics play an essential role. Due to this ubiquity, a multitude of mathematical models has been developed to describe these processes. While the simplest models…
Deep clustering methods improve the performance of clustering tasks by jointly optimizing deep representation learning and clustering. While numerous deep clustering algorithms have been proposed, most of them rely on artificially…
A simplified model of clonal plant growth is formulated, motivated by observations of spatial structures in Posidonia oceanica meadows in the Mediterranean Sea. Two levels of approximation are considered for the scale-dependent feedback…
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry,…
Modern clustering approaches often trade interpretability for performance, particularly in deep learning-based methods. We present Generative Kernel Spectral Clustering (GenKSC), a novel model combining kernel spectral clustering with…
In ecology, species can mitigate their extinction risks in uncertain environments by diversifying individual phenotypes. This observation is quantified by the theory of bet-hedging, which provides a reason for the degree of phenotypic…