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We describe a novel approach to statistical learning from particles tracked while moving in a random environment. The problem consists in inferring properties of the environment from recorded snapshots. We consider here the case of a fluid…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
The repton model is a simple model of the "reptation" motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of two types of particles with hard-sphere…
Compartmental models like the Susceptible-Infected-Recovered (SIR)\cite{Kermack1927} and its extensions such as the Susceptible-Exposed-Infected-Recovered (SEIRS)\cite{Ottar2020,Ignazio2021,Grimm2021,Paoluzzi2021} are commonly used to model…
We introduce a use of the \(M\)-cover (or \(M\)-layer) transform for machine learning. The method replicates a model \(M\) times, but instead of coupling the copies through parameter averaging or an explicit attractive force, as in…
Human mobility and activity patterns mediate contagion on many levels, including the spatial spread of infectious diseases, diffusion of rumors, and emergence of consensus. These patterns however are often dominated by specific locations…
Estimating individualized treatment rules (ITRs) is fundamental to precision medicine, where the goal is to tailor treatment decisions to individual patient characteristics. While numerous methods have been developed for ITR estimation,…
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation…
In this paper, we utilize weight gradients from backpropagation to characterize the representation space learned by deep learning algorithms. We demonstrate the utility of such gradients in applications including perceptual image quality…
The spread of PM2.5 pollutants that endanger health is difficult to predict because it involves many atmospheric variables. These micron particles can spread rapidly from their source to residential areas, increasing the risk of respiratory…
We introduce a reduced order model (ROM) methodology for inverse electromagnetic wave scattering in layered lossy media, using data gathered by an antenna which generates a probing wave and measures the time resolved reflected wave. We…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
Spatial transcriptomics data analysis integrates cellular transcriptional activity with spatial coordinates to identify spatial domains, infer cell-type dynamics, and characterize gene expression patterns within tissues. Despite recent…
Inverse problems arise in a multitude of applications, where the goal is to recover a clean signal from noisy and possibly (non)linear observations. The difficulty of a reconstruction problem depends on multiple factors, such as the ground…
Aggregation and fragmentation of single molecules in the cell environment lead to a spectrum of diffusivities and to statistical laws of movement very different from typical Brownian motion. Current models of intracellular transport do not…
The transport of particles in cells is influenced by the properties of intracellular networks they traverse while searching for localized target regions or reaction partners. Moreover, given the rapid turnover in many intracellular…
Monte Carlo (MC) simulations of transport in random porous networks indicate that for high variances of the log-normal permeability distribution, the transport of a passive tracer is non-Fickian. Here we model this non-Fickian dispersion in…
We introduce a novel algorithm to perform event-driven simulations of hard rigid bodies of arbitrary shape, that relies on the evaluation of the geometric distance. In the case of a monodisperse system of uniaxial hard ellipsoids,we perform…
A new dynamic system approach to the problem of radiative transfer inside scattering and absorbing media is presented, directly based on firsthand physical principles. This method, the Dynamic Radiative Transfer System (DRTS), calculates…