Related papers: Phylogeny-informed fitness estimation
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
The large number of exact fitness function evaluations makes evolutionary algorithms to have computational cost. In some real-world problems, reducing number of these evaluations is much more valuable even by increasing computational…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
In an extant population, how much information do extant individuals provide on the pedigree of their ancestors? Recent work by Kim, Mossel, Ramnarayan and Turner (2020) studied this question under a number of simplifying assumptions,…
We propose a new approach for building recommender systems by adapting surrogate-assisted interactive genetic algorithms. A pool of user-evaluated items is used to construct an approximative model which serves as a surrogate fitness…
In this paper, we introduce, MultiGA, an optimization framework which applies genetic algorithm principles to address complex natural language tasks and reasoning problems by sampling from a diverse population of LLMs to initialize the…
In evolutionary algorithms, a preselection operator aims to select the promising offspring solutions from a candidate offspring set. It is usually based on the estimated or real objective values of the candidate offspring solutions. In a…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
The genotype-fitness map plays a fundamental role in shaping the dynamics of evolution. However, it is difficult to directly measure a fitness landscape in practice, because the number of possible genotypes is astronomical. One approach is…
During the last two decades, ecological speciation has been a major research theme in evolutionary biology. Ecological speciation occurs when reproductive isolation between populations evolves as a result of niche differentiation.…
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…
In this paper we introduce the phylogenetic scan test (PhyloScan) for investigating cross-group differences in microbiome compositions using the Dirichlet-tree multinomial (DTM) model. DTM models the microbiome data through a cascade of…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Optimal subset selection is an important task that has numerous algorithms designed for it and has many application areas. STPGA contains a special genetic algorithm supplemented with a tabu memory property (that keeps track of previously…
A significant challenge in nature-inspired algorithmics is the identification of specific characteristics of problems that make them harder (or easier) to solve using specific methods. The hope is that, by identifying these characteristics,…
Inspired by natural evolution, evolutionary search algorithms have proven remarkably capable due to their dual abilities to radiantly explore through diverse populations and to converge to adaptive pressures. A large part of this behavior…
Optimization is ubiquitous in our daily lives. In the past, (sub-)optimal solutions to any problem have been derived by trial and error, sheer luck, or the expertise of knowledgeable individuals. In our contemporary age, there thankfully…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Given a sample of genome sequences from an asexual population, can one predict its evolutionary future? Here we demonstrate that the branching patterns of reconstructed genealogical trees contains information about the relative fitness of…