Related papers: Robust boundary formation in a morphogen gradient …

We investigate the effect of time-dependent noise on the shape of a morphogen gradient in a developing embryo. Perturbation theory is used to calculate the deviations from deterministic behavior in a simple reaction-diffusion model of…

The boundary element method (BEM) is an efficient numerical method for simulating harmonic wave propagation. It uses boundary integral formulations of the Helmholtz equation at the interfaces of piecewise homogeneous domains. The…

Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise…

This paper studies the problem of learning causal structures from observational data. We reformulate the Structural Equation Model (SEM) with additive noises in a form parameterized by binary graph adjacency matrix and show that, if the…

Cell polarity and movement are fundamental to many biological functions. Experimental and theoretically studies have indicated that interactions of certain proteins lead to the cell polarization which plays a key role in controlling the…

Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…

Here we characterized an information measure for cell polarity that applies to non-motile cells responding to a chemical gradient. The central idea is that polarization represents information about the direction of the gradient. We applied…

Robustness of machine learning models to various adversarial and non-adversarial corruptions continues to be of interest. In this paper, we introduce the notion of the boundary thickness of a classifier, and we describe its connection with…

Recent progress in image generation has sparked research into controlling these models through condition signals, with various methods addressing specific challenges in conditional generation. Instead of proposing another specialized…

This paper develops a smooth model identification and self-learning strategy for dynamic systems taking into account possible parameter variations and uncertainties. We have tried to solve the problem such that the model follows the changes…

One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not…

The aim of this paper is to propose a novel methodology to deal with micro-structural boundary conditions for the analysis of granular materials. The response of the granular assembly is modelled through the discrete element method (DEM),…

Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…

We propose a novel mesh refinement scheme based on signal processing for boundary integral simulations of inviscid droplet dynamics with axial symmetry. A key idea is to directly access the Fourier coefficients of a principal curvature as a…

The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…

In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be improved by nonlocal information, e.g.,…

The processes of gene expression are inherently stochastic, even for essential genes required for growth. How does the cell maximize fitness in light of noise? To answer this question, we build a mathematical model to explore the trade-off…

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…

Morphogen gradients play an essential role in the spatial regulation of cell patterning during early development. The classical mechanism of morphogen gradient formation involves the diffusion of morphogens away from a localized source…

We present CT-Bound, a robust and fast boundary detection method for very noisy images using a hybrid Convolution and Transformer neural network. The proposed architecture decomposes boundary estimation into two tasks: local detection and…