Related papers: Fast Computation of the Kinship Coefficients
The compact genetic algorithm is an Estimation of Distribution Algorithm for binary optimisation problems. Unlike the standard Genetic Algorithm, no cross-over or mutation is involved. Instead, the compact Genetic Algorithm uses a virtual…
Genome-to-genome comparisons require designating anchor points, which are given by Maximum Exact Matches (MEMs) between their sequences. For large genomes this is a challenging problem and the performance of existing solutions, even in…
Family history is a major risk factor for many types of cancer. Mendelian risk prediction models translate family histories into cancer risk predictions based on knowledge of cancer susceptibility genes. These models are widely used in…
Efficiently computing low discrepancy colorings of various set systems, has been studied extensively since the breakthrough work by Bansal (FOCS 2010), who gave the first polynomial time algorithms for several important settings, including…
Early methods used face representations in kinship verification, which are less accurate than joint representations of parents' and children's facial images learned from scratch. We propose an approach featuring graph neural network…
The evolutionary edit distance between two individuals in a population, i.e., the amount of applications of any genetic operator it would take the evolutionary process to generate one individual starting from the other, seems like a…
We construct fast algorithms for evaluating transforms associated with families of functions which satisfy recurrence relations. These include algorithms both for computing the coefficients in linear combinations of the functions, given the…
We connect the problem of properly PAC learning decision trees to the parameterized Nearest Codeword Problem ($k$-NCP). Despite significant effort by the respective communities, algorithmic progress on both problems has been stuck: the…
Motivated by genome-wide association studies, we consider a standard linear model with one additional random effect in situations where many predictors have been collected on the same subjects and each predictor is analyzed separately.…
Evolutionary graph theory studies the evolutionary dynamics in a population structure given as a connected graph. Each node of the graph represents an individual of the population, and edges determine how offspring are placed. We consider…
Pedigree GWAS (Option 29) in the current version of the Mendel software is an optimized subroutine for performing large scale genome-wide QTL analysis. This analysis (a) works for random sample data, pedigree data, or a mix of both, (b) is…
Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables…
We extend the herding algorithm to continuous spaces by using the kernel trick. The resulting "kernel herding" algorithm is an infinite memory deterministic process that learns to approximate a PDF with a collection of samples. We show that…
We study coalescent processes conditional on the population pedigree under the exchangeable diploid bi-parental population model of \citet{BirknerEtAl2018}. While classical coalescent models average over all reproductive histories, thereby…
Herding and kernel herding are deterministic methods of choosing samples which summarise a probability distribution. A related task is choosing samples for estimating integrals using Bayesian quadrature. We show that the criterion minimised…
Herding and kernel herding are deterministic methods of choosing samples which summarise a probability distribution. A related task is choosing samples for estimating integrals using Bayesian quadrature. We show that the criterion minimised…
Personalized community detection aims to generate communities associated with user need on graphs, which benefits many downstream tasks such as node recommendation and link prediction for users, etc. It is of great importance but lack of…
This paper gives drastically faster gossip algorithms to compute exact and approximate quantiles. Gossip algorithms, which allow each node to contact a uniformly random other node in each round, have been intensely studied and been adopted…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Associated to a finite measure on the real line with finite moments are recurrence coefficients in a three-term formula for orthogonal polynomials with respect to this measure. These recurrence coefficients are frequently inputs to modern…