相关论文: Phase Transition in Distance-Based Phylogeny Recon…

Quickly growing computing facilities and an increasing number of extragalactic observations encourage the application of data-driven approaches to uncover hidden relations from astronomical data. In this work we raise the problem of…

We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…

DNA sequencing is the basic workhorse of modern day biology and medicine. Shotgun sequencing is the dominant technique used: many randomly located short fragments called reads are extracted from the DNA sequence, and these reads are…

This paper introduces a new way to define a genome rearrangement distance, using the concept of mean first passage time from probability theory. Crucially, this distance estimate provides a genuine metric on genome space. We develop the…

Phase retrieval is an ill-posed inverse problem in which classical and deep learning-based methods struggle to jointly achieve measurement fidelity and perceptual realism. We propose a novel framework for phase retrieval that leverages…

Time-frequency audio source separation is usually achieved by estimating the short-time Fourier transform (STFT) magnitude of each source, and then applying a phase recovery algorithm to retrieve time-domain signals. In particular, the…

Let x and y be two length n DNA sequences, and suppose we would like to estimate the divergence time T. A well known simple but crude estimate of T is p := d(x,y)/n, the fraction of mutated sites (the p-distance). We establish a posterior…

We study the inference of communities in stochastic block models with a growing number of communities. For block models with $n$ vertices and a fixed number of communities $q$, it was predicted in Decelle et al. (2011) that there are…

Most DNA sequencing technologies are based on the shotgun paradigm: many short reads are obtained from random unknown locations in the DNA sequence. A fundamental question, studied in arXiv:1203.6233, is what read length and coverage depth…

Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…

Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…

We present a Machine Learning-based method for tomographic reconstruction of dense layered objects, with range of projection angles limited to $\pm $10$^\circ$. Whereas previous approaches to phase tomography generally require two steps,…

We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…

We consider the problem of distance estimation under the TKF91 model of sequence evolution by insertions, deletions and substitutions on a phylogeny. In an asymptotic regime where the expected sequence lengths tend to infinity, we show that…

Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…

Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolution snapshots of lineage ancestries from digital…

CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…

An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…