Related papers: KATKA: A KRAKEN-like tool with $k$ given at query …
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
Compact Genetic Algorithms (cGAs) are condensed variants of classical Genetic Algorithms (GAs) that use a probability vector representation of the population instead of the complete population. cGAs have been shown to significantly reduce…
Random Indexing (RI) K-tree is the combination of two algorithms for clustering. Many large scale problems exist in document clustering. RI K-tree scales well with large inputs due to its low complexity. It also exhibits features that are…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Tree structures are very often used data structures. Among ordered types of trees there are many variants whose basic operations such as insert, delete, search, delete-min are characterized by logarithmic time complexity. In the article I…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Background. The supertree problem, i.e., the task of finding a common refinement of a set of rooted trees is an important topic in mathematical phylogenetics. The special case of a common leaf set $L$ is known to be solvable in linear time.…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
In this paper, we propose the distributed tree kernels (DTK) as a novel method to reduce time and space complexity of tree kernels. Using a linear complexity algorithm to compute vectors for trees, we embed feature spaces of tree fragments…
We define a new problem in comparative genomics, denoted PQ-Tree Search, that takes as input a PQ-tree $T$ representing the known gene orders of a gene cluster of interest, a gene-to-gene substitution scoring function $h$, integer…
A simple and elementary proof of Butcher's theorem on the order conditions of Runge-Kutta methods is presented. It is based on a recursive definition of rooted trees and avoids combinatorial tools such as labelings and Faa di Bruno's…
Tree path minimum query problem is a fundamental problem while processing trees, and is used widely in minimum spanning tree verification and randomized minimum spanning tree algorithms. In this paper, we study the possibility of building…
The third-generation long reads sequencing technologies, such as PacBio and Nanopore, have great advantages over second-generation Illumina sequencing in de novo assembly studies. However, due to the inherent low base accuracy,…
This paper introduces the Cartesian Merkle Tree, a deterministic data structure that combines the properties of a Binary Search Tree, a Heap, and a Merkle tree. The Cartesian Merkle Tree supports insertions, updates, and removals of…
Background. Large scale metagenomic projects aim to extract biodiversity knowledge between different environmental conditions. Current methods for comparing microbial communities face important limitations. Those based on taxonomical or…
Thin spanning trees lie at the intersection of graph theory, approximation algorithms, and combinatorial optimization. They are central to the long-standing \emph{thin tree conjecture}, which asks whether every $k$-edge-connected graph…
Frequencies of $k$-mers in sequences are sometimes used as a basis for inferring phylogenetic trees without first obtaining a multiple sequence alignment. We show that a standard approach of using the squared-Euclidean distance between…
The minimum spanning tree clustering algorithm is capable of detecting clusters with irregular boundaries. In this paper we propose two minimum spanning trees based clustering algorithm. The first algorithm produces k clusters with center…
A $k$-decision tree $t$ (or $k$-tree) is a recursive partition of a matrix (2D-signal) into $k\geq 1$ block matrices (axis-parallel rectangles, leaves) where each rectangle is assigned a real label. Its regression or classification loss to…