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

Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\cal…

In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…

We prove that in a large collection of naturally defined sets of permutations of fixed length, the numbers of permutations at Ulam distance k from the identity form a log-concave sequence in k.

Optical phase contains key information for biomedical and astronomical imaging. However, it is often obscured by layers of heterogeneous and scattering media, which render optical phase imaging at different depths an utmost challenge.…

Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…

The ancestral sequence reconstruction problem is the inference, back in time, of the properties of common sequence ancestors from measured properties of contemporary populations. Standard algorithms for this problem assume independent…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Genomic datasets generated with massively parallel sequencing methods have the potential to propel systematics in new and exciting directions, but selecting appropriate markers and methods is not straightforward. We applied two approaches…

We consider the phase retrieval problem of reconstructing a $n$-dimensional real or complex signal $\mathbf{X}^{\star}$ from $m$ (possibly noisy) observations $Y_\mu = | \sum_{i=1}^n \Phi_{\mu i} X^{\star}_i/\sqrt{n}|$, for a large class of…

In this paper, we analyze the scalability of a recent Wasserstein-distance approach for training stochastic neural networks (SNNs) to reconstruct multidimensional random field models. We prove a generalization error bound for reconstructing…

We propose a technique for learning representations of parser states in transition-based dependency parsers. Our primary innovation is a new control structure for sequence-to-sequence neural networks---the stack LSTM. Like the conventional…

We consider the limiting behaviour of the point processes associated with a branching random walk with supercritical branching mechanism and balanced regularly varying step size. Assuming that the underlying branching process satisfies…

A distance-based method to reconstruct a phylogenetic tree with $n$ leaves takes a distance matrix, $n \times n$ symmetric matrix with $0$s in the diagonal, as its input and reconstructs a tree with $n$ leaves using tools in combinatorics.…

In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…

Trace reconstruction considers the task of recovering an unknown string $x \in \{0,1\}^n$ given a number of independent "traces", i.e., subsequences of $x$ obtained by randomly and independently deleting every symbol of $x$ with some…

Next-generation accelerator concepts which hinge on the precise shaping of beam distributions, demand equally precise diagnostic methods capable of reconstructing beam distributions within 6-dimensional position-momentum spaces. However,…