Related papers: An accurate model for genetic hitch-hiking
We study biological evolution in a high-dimensional genotype space in the regime of rare mutations and strong selection. The population performs an uphill walk which terminates at local fitness maxima. Assigning fitness randomly to…
Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The number of…
Affected relatives are essential for pedigree linkage analysis, however, they cause a violation of the independent sample assumption in case-control association studies. To avoid the correlation between samples, a common practice is to take…
We consider a stochastic model describing a constant size $N$ population that may be seen as a directed polymer in random medium with $N$ sites in the transverse direction. The population dynamics is governed by a noisy traveling wave…
When mutations are rampant, quasispecies theory or Eigen's model predicts that the fittest type in a population may not dominate. Beyond a critical mutation rate, the population may even be delocalized completely from the peak of the…
We develop a new sampling strategy that uses the hit-and-run algorithm within level sets of the target density. Our method can be applied to any quasi-concave density, which covers a broad class of models. Our sampler performs well in…
Computing the optimal transport distance between statistical distributions is a fundamental task in machine learning. One remarkable recent advancement is entropic regularization and the Sinkhorn algorithm, which utilizes only matrix…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
In this paper, we propose a hybrid model combining genetic algorithm and hill climbing algorithm for optimizing Convolutional Neural Networks (CNNs) on the CIFAR-100 dataset. The proposed model utilizes a population of chromosomes that…
The distribution and heritability of many traits depends on numerous loci in the genome. In general, the astronomical number of possible genotypes makes the system with large numbers of loci difficult to describe. Multilocus evolution,…
When testing for the association of a single SNP with a phenotypic response, one usually considers an additive genetic model, assuming that the mean of of the response for the heterozygous state is the average of the means for the two…
Muller's ratchet, in its prototype version, models a haploid, asexual population whose size~$N$ is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying…
We are interested in modelling Darwinian evolution, resulting from the interplay of phenotypic variation and natural selection through ecological interactions. Our models are rooted in the microscopic, stochastic description of a population…
In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can…
The site frequency spectrum (SFS) is a widely used summary statistic of genomic data. Motivated by recent evidence for the role of neutral evolution in cancer, we investigate the SFS of neutral mutations in an exponentially growing…
While generic competitive systems exhibit mixtures of hierarchy and cycles, real-world systems are predominantly hierarchical. We demonstrate and extend a mechanism for hierarchy; systems with similar agents approach perfect hierarchy in…
Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele…
The challenges posed by complex stochastic models used in computational ecology, biology and genetics have stimulated the development of approximate approaches to statistical inference. Here we focus on Synthetic Likelihood (SL), a…
A steady influx of a single deleterious multilocus genotype will impose genetic load on the resident population and leave multiple descendants carrying various numbers of the foreign alleles. Provided that the foreign types are rare at…
In this paper we consider the two-type Moran model with $N$ individuals. Each individual is assigned a resampling rate, drawn independently from a probability distribution ${\mathbb P}$ on ${\mathbb R}_+$, and a type, either $1$ or $0$.…