Search · four archives
Search · four archives
11 papers · ranked by Valyu relevance
Ignacio A. Rodriguez-Brenes, Dominik Wodarz, Natalia L. Komarova
Spatial stochastic simulations of evolutionary processes are computationally expensive. Here, based on spatially explicit decoupling approximations (SEDA) introduced in [1], we derive a deterministic approximation to a spatial stochastic birth-death process in the presence of two types: the less advantageous resident…
Xiaoquan Wen, Yeji Lee
With the increasing availability of functional genomic data (4, 7, 1), incorporating genomic annotations into QTL mapping has become a standard analytical procedure. However, the existing analysis methods often lack rigor and/or computational efficiency. We present a novel algorithm to perform integrative multi-SNP QTL…
Tom Van Wouwe, Lena H. Ting, Friedl De Groote
Optimal control simulations have shown that both musculoskeletal dynamics and physiological noise are important determinants of movement. However, due to the limited efficiency of available computational tools, deterministic simulations of movement focus on accurately modelling the musculoskeletal system while…
Guillaume Martin, Lionel Roques
Various models describe asexual evolution by mutation, selection and drift. Some focus directly on fitness, typically modelling drift but ignoring or simplifying both epistasis and the distribution of mutation effects (travelling wave models). Others follow the dynamics of quantitative traits determining fitness…
Charles Mullon, Laurent Lehmann
Understanding selection on ecological interactions that take place in dispersal-limited communities is an important challenge for ecology and evolutionary biology. The problem is that local demographic stochasticity generates eco-evolutionary dynamics that are too complicated to make tractable analytical…
Loïc Marrec, Claudia Bank, Thibault Bertrand
Population growth is a fundamental process in ecology, evolution, and epidemiology. The population size dynamics during growth are often described by deterministic equations derived from kinetic models. Here, we simulate several population growth models and compare the size averaged over many stochastic realizations…
Elias Ventre, Thibault Espinasse, Charles-Edouard Bréhier, Vincent Calvez + 2 more
Differentiation is the process whereby a cell acquires a specific phenotype, by differential gene expression as a function of time. This is thought to result from the dynamical functioning of an underlying Gene Regulatory Network (GRN). The precise path from the stochastic GRN behavior to the resulting cell state is…
S. Gerber, L. Pospisil, M. Navandar, I. Horenko
Finding reliable discrete approximations of complex systems is a key prerequisite when applying many of the most popular modeling tools. Common discretization approaches (for example, the very popular K-means clustering) are crucially limited in terms of quality and cost. We introduce a low-cost improved-quality…
Mahdi Belbasi, Antonio Blanca, Robert S. Harris, David Koslicki + 1 more
Sketching is now widely used in bioinformatics to reduce data size and increase data processing speed. Sketching approaches entice with improved scalability but also carry the danger of decreased accuracy and added bias. In this paper, we investigate the minimizer sketch and its use to estimate the Jaccard similarity…
Sungho Shin, Ophelia Venturelli, Victor M. Zavala
We present a nonlinear programming (NLP) framework for the scalable solution of parameter estimation problems that arise in dynamic modeling of biological systems. Such problems are computationally challenging because they often involve highly nonlinear and stif differential equations as well as many experimental data…
Peter L. Bartlett, Chris Junchi Li, Jingfeng Wu, Bin Yu
In the field of optimization, developing accelerated methods for solving minimax and fixed-point problems remains a fundamental challenge. This paper presents a novel family of dual accelerated algorithms that achieve optimal convergence rates for both minimax and fixed-point problems. By exploring new anchoring…