Related papers: Probability that a chromosome is lost without trac…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
The advent of modern genome sequencing techniques allows for a more stringent test of the neutrality hypothesis of Darwinian evolution, where all individuals have the same fitness. Using the individual based model of Wright and Fisher, we…
The discrete time risk model with two seasons and dependent claims is considered. An algorithm is created for computing the values of the ultimate ruin probability. Theoretical results are illustrated with numerical examples.
Motivation: Recombination rates vary considerably at the fine scale within mammalian genomes, with the majority of recombination occurring within hotspots of ~2 kb in width. We present a method for inferring the location of recombination…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
We give a method for proactively identifying small, plausible shifts in distribution which lead to large differences in model performance. These shifts are defined via parametric changes in the causal mechanisms of observed variables, where…
For a tree Markov random field non-reconstruction is said to hold if as the depth of the tree goes to infinity the information that a typical configuration at the leaves gives about the value at the root goes to zero. The distribution of…
We initiate a systematic investigation of distribution testing in the framework of algorithmic replicability. Specifically, given independent samples from a collection of probability distributions, the goal is to characterize the sample…
The paper describes a new class of capture-recapture models for closed populations when individual covariates are available. The novelty consists in combining a latent class model for the distribution of the capture history, where the class…
We propose a variation of the GMS model of evolution of species. In this version, as in the GMS model, at each birth, the new species in the system is labeled with a random fitness mark, but in our variation, to each extinction event is…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
Conformal prediction constructs a confidence set for an unobserved response of a feature vector based on previous identically distributed and exchangeable observations of responses and features. It has a coverage guarantee at any nominal…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
We study moment-based estimation with two sequentially collected variables subject to non-monotone missingness. The commonly used Missing at Random (MAR) assumption requiring all missingness mechanisms to depend on the same fully observed…
Conformal prediction is a non-parametric technique for constructing prediction intervals or sets from arbitrary predictive models under the assumption that the data is exchangeable. It is popular as it comes with theoretical guarantees on…
We report numerical and analytical studies of the donor-acceptor recombination in compensated semiconductors. Our calculations take into account random electric fields of charged impurities which are important in non zero compensation case.…
We investigate a neutral model for speciation and extinction, the constant rate birth-death process. The process is conditioned to have $n$ extant species today, we look at the tree distribution of the reconstructed trees-- i.e. the trees…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…