Related papers: Phylogeny-informed fitness estimation
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
The fitness level method is a widely used technique for estimating the mean hitting time of elitist evolutionary algorithms on level-based fitness functions. However, this paper identifies its main limitation: the linear lower bound derived…
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,…
Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…
In evolutionary algorithms, the fitness of a population increases with time by mutating and recombining individuals and by a biased selection of more fit individuals. The right selection pressure is critical in ensuring sufficient…
Existing genetic programming (GP) methods are typically designed based on a certain representation, such as tree-based or linear representations. These representations show various pros and cons in different domains. However, due to the…
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
This paper combines the idea of a hierarchical distributed genetic algorithm with different inter-agent partnering strategies. Cascading clusters of sub-populations are built from bottom up, with higher-level sub-populations optimising…
Historical linguistics aims at inferring the most likely language phylogenetic tree starting from information concerning the evolutionary relatedness of languages. The available information are typically lists of homologous (lexical,…
Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…
Phylogenetic comparative analysis is an approach to inferring evolutionary process from a combination of phylogenetic and phenotypic data. The last few years have seen increasingly sophisticated models employed in the evaluation of more and…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Decision trees are a crucial class of models offering robust predictive performance and inherent interpretability across various domains, including healthcare, finance, and logistics. However, current tree induction methods often face…
Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Phylogenetic analyses of gene expression have great potential for addressing a wide range of questions. These analyses will, for example, identify genes that have evolutionary shifts in expression that are correlated with evolutionary…
Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of…