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

At the core of high throughput DNA sequencing platforms lies a bio-physical surface process that results in a random geometry of clusters of homogenous short DNA fragments typically hundreds of base pairs long - bridge amplification. The…

We propose a transition-based dependency parser using Recurrent Neural Networks with Long Short-Term Memory (LSTM) units. This extends the feedforward neural network parser of Chen and Manning (2014) and enables modelling of entire…

We study robust community detection in the context of node-corrupted stochastic block model, where an adversary can arbitrarily modify all the edges incident to a fraction of the $n$ vertices. We present the first polynomial-time algorithm…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

Hybrid evolution and horizontal gene transfer (HGT) are processes where evolutionary relationships may more accurately be described by a reticulated network than by a tree. In such a network, there will often be several paths between any…

Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…

A reconstruction method for recovering the initial conditions of the Universe starting from the present galaxy distribution is presented which guarantees uniqueness of solutions. We show how our method can be used to obtain the peculiar…

Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…

Light-field microscopy (LFM) enables single-shot capture of multi-angular information from biological samples, supporting real-time volumetric imaging. However, traditional physics-based algorithms often suffer from limited spatial…

Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…

Motivation: mtDNA distance matrices are standard inputs for distance-based phylogeny, but computing all pairwise alignments is costly. Missing entries can degrade inferred topology and branch lengths, and generic matrix-completion methods…

Existing frequency domain methods for bootstrapping time series have a limited range. Consider for instance the class of spectral mean statistics (also called integrated periodograms) which includes many important statistics in time series…

Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…

While the existing stochastic control theory is well equipped to handle dynamical systems with stochastic uncertainties, a paradigm shift using distance measure based decision making is required for the effective further exploration of the…

A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…

Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…

We propose a forward-backward splitting algorithm based on Bregman distances for composite minimization problems in general reflexive Banach spaces. The convergence is established using the notion of variable quasi-Bregman monotone…

With the rapid advancement of remote sensing technology, super-resolution image reconstruction is of great research and practical significance. Existing deep learning methods have made progress but still face limitations in handling complex…

Characterizing the phase space distribution of particle beams in accelerators is a central part of accelerator understanding and performance optimization. However, conventional reconstruction-based techniques either use simplifying…

A linear and thus convex phase retrieval algorithm for the application in phaseless near-field far-field transformations is presented. The formulation exploits locally known phase relations among sets of measurement samples, which can in…