Related papers: Fast Computation of the Kinship Coefficients
Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze…
Study sample sizes in human genetics are growing rapidly, and in due course it will become routine to analyze samples with hundreds of thousands if not millions of individuals. In addition to posing computational challenges, such large…
Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract this information (at least partially) but they require sophisticated statistical techniques that have been made…
We introduce a stochastic model of a population with overlapping generations and arbitrary levels of self-fertilization versus outcrossing. We study how the global graph of reproductive relationships, or population pedigree, influences the…
We show that there is a polynomial space algorithm that counts the number of perfect matchings in an $n$-vertex graph in $O^*(2^{n/2})\subset O(1.415^n)$ time. ($O^*(f(n))$ suppresses functions polylogarithmic in $f(n)$).The previously…
Recruitment dynamics, or the distribution of the number of offspring among individuals, is central for understanding ecology and evolution. Sweepstakes reproduction (heavy right-tailed offspring number distribution) is central for…
An important problem in tree breeding is optimal selection from candidate pedigree members to produce the highest performance in seed orchards, while conserving essential genetic diversity. The most beneficial members should contribute as…
An efficient algorithm is presented to compute the characteristic polynomial of a threshold graph. Threshold graphs were introduced by Chv\'atal and Hammer, as well as by Henderson and Zalcstein in 1977. A threshold graph is obtained from a…
In this paper, we provide faster algorithms for computing various fundamental quantities associated with random walks on a directed graph, including the stationary distribution, personalized PageRank vectors, hitting times, and escape…
In evolutionary optimization, it is important to understand how fast evolutionary algorithms converge to the optimum per generation, or their convergence rate. This paper proposes a new measure of the convergence rate, called average…
Recent improvements in high-throughput genotyping and sequencing technologies have afforded the collection of massive, genome-wide datasets of DNA information from hundreds of thousands of individuals. These datasets, in turn, provide…
Kinship verification is an emerging task in computer vision with multiple potential applications. However, there's no large enough kinship dataset to train a representative and robust model, which is a limitation for achieving better…
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry…
Fast exact algorithms are known for Hamiltonian paths in undirected and directed bipartite graphs through elegant though involved algorithms that are quite different from each other. We devise algorithms that are simple and similar to each…
In both criminal cases and civil cases there is an increasing demand for the analysis of DNA mixtures involving relationships. The goal might be, for example, to identify the contributors to a DNA mixture where the donors may be related, or…
We introduce a general diploid population model with self-fertilization and possible overlapping generations, and study the genealogy of a sample of $n$ genes as the population size $N$ tends to infinity. Unlike traditional approach in…
The widespread use of quantile regression methods depends crucially on the existence of fast algorithms. Despite numerous algorithmic improvements, the computation time is still non-negligible because researchers often estimate many…
When an advantageous mutation occurs in a population, the favorable allele may spread to the entire population in a short time, an event known as a selective sweep. As a result, when we sample $n$ individuals from a population and trace…