Related papers: Simulation based estimation of branching models fo…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
Fitting generative models to sequential data typically involves two recursive computations through time, one forward and one backward. The latter could be a computation of the loss gradient (as in backpropagation through time), or an…
This work presents a model reduction approach for problems with coherent structures that propagate over time such as convection-dominated flows and wave-type phenomena. Traditional model reduction methods have difficulties with these…
This paper presents DDTracking, a novel deep generative framework for diffusion MRI tractography that formulates streamline propagation as a conditional denoising diffusion process. In DDTracking, we introduce a dual-pathway encoding…
We analyze damage propagation modeling of turbo-engines in a data-driven approach. We investigate subspace tracking assuming a low dimensional manifold structure and a static behavior during the healthy state of the machines. Our damage…
This paper presents a novel virus propagation model using NetLogo. The model allows agents to move across multiple sites using different routes. Routes can be configured, enabled for mobility and (un)locked down independently. Similarly,…
We propose a continuous model for evolutionary rate variation across sites and over the tree and derive exact transition probabilities under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in…
RNA design shows growing applications in synthetic biology and therapeutics, driven by the crucial role of RNA in various biological processes. A fundamental challenge is to find functional RNA sequences that satisfy given structural…
We are interested in the comparison of transcript boundaries from cells which originated in different environments. The goal is to assess whether this phenomenon, called differential splicing, is used to modify the transcription of the…
We study the spreading of viruses, such as SARS-CoV-2, by airborne aerosols, via a new first-passage-time problem for Lagrangian tracers that are advected by a turbulent flow: By direct numerical simulations of the three-dimensional (3D)…
Plant phenotyping (Guo et al. 2021; Pieruschka et al. 2019) focuses on studying the diverse traits of plants related to the plants' growth. To be more specific, by accurately measuring the plant's anatomical, ontogenetical, physiological…
We present a general theoretical framework to discuss mechanisms of morphogen transport and gradient formation in a cell layer. Trafficking events on the cellular scale lead to transport on larger scales. We discuss in particular the case…
In this work we approach cell migration under a large-scale assumption, so that the system reduces to a particle in motion. Unlike classical particle models, the cell displacement results from its internal activity: the cell velocity is a…
Ray tracing is a widely used deterministic method for radio propagation simulations, capable of producing physically accurate multipath components. The accuracy depends on the quality of the environment model and its electromagnetic…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
In non-destructive and biomedical imaging, spatial patterns inside a sample are imaged without destroying it. Therefore, propagating waves, including electromagnetic or ultrasonic signals, or even diffuse heat are generated or modified by…
The use of network theory to model disease propagation on populations introduces important elements of reality to the classical epidemiological models. The use of random geometric graphs (RGG) is one of such network models that allows for…
We study a model for the spread of an infectious disease which incorporates spatial and temporal effects. The model is a delayed multi-type branching process in which types represent geographic regions while infected individuals reproduce…
Computationally expensive Radiative Transfer Models (RTMs) are widely used} to realistically reproduce the light interaction with the Earth surface and atmosphere. Because these models take long processing time, the common practice is to…
Accurate modeling of ultrasound wave propagation is essential for high-fidelity simulation and imaging in ultrasonic testing. A primary challenge lies in characterizing the excitation source, particularly for transducers with large…