Related papers: Fast phylogeny reconstruction through learning of …

Linear model trees are regression trees that incorporate linear models in the leaf nodes. This preserves the intuitive interpretation of decision trees and at the same time enables them to better capture linear relationships, which is hard…

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…

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…

The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random…

In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…

Given a threshold $L$ and a set $\mathcal{R} = \{R_1, \ldots, R_m\}$ of $m$ haplotype sequences, each having length $n$, the minimum segmentation problem for founder reconstruction is to partition the sequences into disjoint segments…

Reconstruction of PET images is an ill-posed inverse problem and often requires iterative algorithms to achieve good image quality for reliable clinical use in practice, at huge computational costs. In this paper, we consider the PET…

Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…

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…

This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…

Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…

Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on…

Convolutional Neural Network (CNN) has gained state-of-the-art results in many pattern recognition and computer vision tasks. However, most of the CNN structures are manually designed by experienced researchers. Therefore, auto- matically…

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…

Motivated by questions in social networks, distributed computing and probabilistic combinatorics, the last few years have seen increasing interest in network evolution models where new vertices entering the system need to make decisions…

We propose an approach to 3D reconstruction via inverse procedural modeling and investigate two variants of this approach. The first option consists in the fitting set of input parameters using a genetic algorithm. We demonstrate the…

The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…

A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…