Related papers: Gene tree species tree reconciliation with gene co…

Crossover and mutation are the two main operators that lead to new solutions in evolutionary approaches. In this article, a new method of performing the crossover phase is presented. The problem of choice is evolutionary decision tree…

Evolutionary multitasking has recently emerged as a novel paradigm that enables the similarities and/or latent complementarities (if present) between distinct optimization tasks to be exploited in an autonomous manner simply by solving them…

We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…

Program synthesis aims to {\it automatically} find programs from an underlying programming language that satisfy a given specification. While this has the potential to revolutionize computing, how to search over the vast space of programs…

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…

In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…

Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…

Genetic programming is a powerful heuristic search technique that is used for a number of real world applications to solve among others regression, classification, and time-series forecasting problems. A lot of progress towards a theoretic…

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…

We propose a novel method for automatic program synthesis. P-Tree Programming represents the program search space through a single probabilistic prototype tree. From this prototype tree we form program instances which we evaluate on a given…

Gene expression programming is an evolutionary optimization algorithm with the potential to generate interpretable and easily implementable equations for regression problems. Despite knowledge gained from previous optimizations being…

Modern software systems are increasingly designed to be highly configurable, which increases flexibility but can make programs harder to develop, test, and analyze, e.g., how configuration options are set to reach certain locations, what…

Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…

This paper characterizes and discusses devolutionary genetic algorithms and evaluates their performances in solving the minimum labeling Steiner tree (MLST) problem. We define devolutionary algorithms as the process of reaching a feasible…

Many common sequential data sources, such as source code and natural language, have a natural tree-structured representation. These trees can be generated by fitting a sequence to a grammar, yielding a hierarchical ordering of the tokens in…

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…

This paper describes a methodology for analyzing the evolutionary dynamics of genetic programming (GP) using genealogical information, diversity measures and information about the fitness variation from parent to offspring. We introduce a…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

In Search Based Software Engineering, Genetic Programming has been used for bug fixing, performance improvement and parallelisation of programs through the modification of source code. Where an evolutionary computation algorithm, such as…

Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…