Related papers: Refining genetically inferred relationships using …

There has been recent interest in improving performance of simple models for multiple reasons such as interpretability, robust learning from small data, deployment in memory constrained settings as well as environmental considerations. In…

In observational surveys, post-stratification is used to reduce bias resulting from differences between the survey population and the population under investigation. However, this can lead to inflated post-stratification weights and,…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…

In this paper, we consider the problem of estimating the covariance kernel and its eigenvalues and eigenfunctions from sparse, irregularly observed, noise corrupted and (possibly) correlated functional data. We present a method based on…

Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…

Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R…

Gradients play a pivotal role in neural networks explanation. The inherent high dimensionality and structural complexity of neural networks result in the original gradients containing a significant amount of noise. While several approaches…

We consider the problem of estimating a sparse multi-response regression function, with an application to expression quantitative trait locus (eQTL) mapping, where the goal is to discover genetic variations that influence gene-expression…

We consider the problem of state estimation in general state-space models using variational inference. For a generic variational family defined using the same backward decomposition as the actual joint smoothing distribution, we establish…

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…

Exploring the genetic basis of heritable traits remains one of the central challenges in biomedical research. In simple cases, single polymorphic loci explain a significant fraction of the phenotype variability. However, many traits of…

Tree shape statistics, particularly measures of tree (im)balance, play an important role in the analysis of the shape of phylogenetic trees. With applications ranging from testing evolutionary models to studying the impact of fertility…

We offer a survey of recent results on covariance estimation for heavy-tailed distributions. By unifying ideas scattered in the literature, we propose user-friendly methods that facilitate practical implementation. Specifically, we…

Change-plane regression identifies subpopulations through an interpretable linear threshold rule, but likelihood-based inference for the hard-threshold boundary is nonregular: objectives are non-smooth, the boundary is weakly identified…

We investigate an simple evolutionary game of sequences and demonstrate on this example the structure of fitness landscapes in discrete problems. We show the smoothing action of the genotype-phenotype mapping which still makes it feasible…

Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…

Research data sets are growing to unprecedented sizes and network modeling is commonly used to extract complex relationships in diverse domains, such as genetic interactions involved in disease, logistics, and social communities. As the…

It is now well documented that genetic covariance between functionally related traits leads to an uneven distribution of genetic variation across multivariate trait combinations, and possibly a large part of phenotype-space that is…

Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…

Quantitative genetic studies that model complex, multivariate phenotypes are important for both evolutionary prediction and artificial selection. For example, changes in gene expression can provide insight into developmental and…