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In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
This paper is placed at the intersection-point between the study of theoretical computational models aimed at capturing the essence of genetic regulatory networks and the field of Artificial Embryology (or Computational Development). A…
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…
Determining the trajectories of cells and their lineages or ancestries in live-cell experiments are fundamental to the understanding of how cells behave and divide. This paper proposes novel online algorithms for jointly tracking and…
We describe a percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Tissues are considered as structures made of regular healthy,…
The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and…
The interactions between diffusing molecules and membrane-bound receptors drive numerous cellular processes. In this work, we develop a spatial model of molecular interactions with membrane receptors by homogenizing the cell membrane and…
Cells exert traction forces on compliant substrates and can induce surface instabilities that appear as characteristic wrinkling patterns. Here, we develop a mechanical description of cell-induced wrinkling on soft substrates using a thin…
Modern biology and biomedicine are undergoing a big-data explosion needing advanced computational algorithms to extract mechanistic insights on the physiological state of living cells. We present the motivation for the Cell Physiome: a…
Cell segmentation is a fundamental task in microscopy image analysis. Several foundation models for cell segmentation have been introduced, virtually all of them are extensions of Segment Anything Model (SAM), improving it for microscopy…
Spatial distributions of morphogens provide positional information in developing systems, but how the distributions are established and maintained remains an open problem. Transport by diffusion has been the traditional mechanism, but…
We discuss the so-called "simplifying assumption" of conditional copulas in a general framework. We introduce several tests of the latter assumption for non- and semiparametric copula models. Some related test procedures based on…
Large contingency tables summarizing categorical variables arise in many areas. For example in biology when a large number of biomarkers are cross-tabulated according to their discrete expression level. Interactions of the variables are…
We present numerical procedures for analyzing the properties of periodic structures and associated couplers based upon time domain simulation. Simple post processing procedures are given for determining Brillouin diagrams and complex field…
Some generative models for sequences such as music and text allow us to edit only subsequences, given surrounding context sequences, which plays an important part in steering generation interactively. However, editing subsequences mainly…
The evolution of symbolic communication is a longstanding open research question in biology. While some theories suggest that it originated from sub-symbolic communication (i.e., iconic or indexical), little experimental evidence exists on…
In this paper, we present a compositional methodology for constructing symbolic models of nonlinear interconnected impulsive systems. Our approach relies on the concept of "alternating simulation function" to establish a relationship…
Biological cells can exchange messages through soluble molecules or membrane-bound receptors. In particular in the latter case, the interaction is usually located in specific regions of the interacting cells and may depend on or induce…
Nearly all cell models explicitly or implicitly deal with the biophysical constraints that must be respected for life to persist. Despite this, there is almost no systematicity in how these constraints are implemented, and we lack a…
Electrical signals in excitable cells involve spatially localized ionic fluxes through ion channels and pumps on cellular lipid membranes. Common approaches to understand how these localized fluxes spread assume that the membrane and the…