We propose a new method that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Our approach seems to be the first that is able to estimate more than one haplotype given such data. Even the accuracy of experimentally obtained allele frequencies can be improved by Read more…

Random Forests (RF) are at the cutting edge of supervised machine learning in terms of prediction performance, especially in genomics. Iterative Random Forests (iRF) use a tree ensemble from iteratively modified RF to obtain predictive and stable non-linear high-order Boolean interactions of features. They have shown great promise for high-order biological interaction discovery that is Read more…

Detecting epistatic drivers of human phenotypes remains a challenge. Traditional approaches use regression to sequentially test multiplicative interaction terms involving single pairs of genetic variants. For higher-order interactions and genome-wide large-scale data, this strategy is computationally intractable. Moreover, multiplicative terms used in regression modeling may not capture the form of biological interactions. Building on the Read more…

We introduce a new methodology for analyzing serial data by quantile regression assuming that the underlying quantile function consists of constant segments. The procedure does not rely on any distributional assumption besides serial independence. It is based on a multiscale statistic, which allows to control the (finite sample) prob- ability for selecting the correct number Read more…

We provide a minimax optimal estimation procedure for F and W in matrix valued linear models Y = F W + Z where the parameter matrix W and the design matrix F are unknown but the latter takes values in a known finite set. The proposed finite alphabet linear model is justified in a variety Read more…

Tree structures, showing hierarchical relationships and the latent structures between samples, are ubiquitous in genomic and biomedical sciences. A common question in many studies is whether there is an association between a response variable measured on each sample and the latent group structure represented by some given tree. Currently, this is addressed on an ad Read more…

We provide a new methodology for statistical recovery of single linear mixtures of piecewise constant signals (sources) with unknown mixing weights and change points in a multiscale fashion. We show exact recovery within an ε-neighborhood of the mixture when the sources take only values in a known finite alphabet. Based on this we provide the Read more…

We give under weak assumptions a complete combinatorial characterization of identifiability for linear mixtures of finite alphabet sources, with unknown mixing weights and unknown source signals, but known alphabet. This is based on a detailed treatment of the case of a single linear mixture. Notably, our identifiability analysis applies also to the case of unknown Read more…