Related papers: Maximizing Phylogenetic Diversity under Time Press…
Phylogenetic diversity is a popular measure for quantifying the biodiversity of a collection $Y$ of species, while phylogenetic diversity indices provide a way to apportion phylogenetic diversity to individual species. Typically, for some…
Phylogenetic diversity indices such as the Fair Proportion (FP) index are frequently discussed as prioritization criteria in biodiversity conservation. They rank species according to their contribution to overall diversity by taking into…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
This paper explores the enhancement of solution diversity in evolutionary algorithms (EAs) for the maximum matching problem, concentrating on complete bipartite graphs and paths. We adopt binary string encoding for matchings and use Hamming…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
The problem Parsimony Haplotyping (PH) asks for the smallest set of haplotypes which can explain a given set of genotypes, and the problem Minimum Perfect Phylogeny Haplotyping (MPPH) asks for the smallest such set which also allows the…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
The Noah's Ark Problem (NAP) is an NP-Hard optimization problem with relevance to ecological conservation management. It asks to maximize the phylogenetic diversity (PD) of a set of taxa given a fixed budget, where each taxon is associated…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
Mathematical modeling is a standard approach to solve many real-world problems and {\em diversity} of solutions is an important issue, emerging in applying solutions obtained from mathematical models to real-world problems. Many studies…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
A number of methods have been developed to infer differential rates of species diversification through time and among clades using time-calibrated phylogenetic trees. However, we lack a general framework that can delineate and quantify…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Reinforcement Learning's high sensitivity to hyperparameters is a source of instability and inefficiency, creating significant challenges for practitioners. Hyperparameter Optimization (HPO) algorithms have been developed to address this…
In microbial ecology studies, the most commonly used ways of investigating alpha (within-sample) diversity are either to apply count-only measures such as Simpson's index to Operational Taxonomic Unit (OTU) groupings, or to use classical…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
To make machine learning (ML) sustainable and apt to run on the diverse devices where relevant data is, it is essential to compress ML models as needed, while still meeting the required learning quality and time performance. However, how…
Planning for the protection of species often involves difficult choices about which species to prioritize, given constrained resources. One way of prioritizing species is to consider their "evolutionary distinctiveness", i.e. their relative…