Related papers: A condition for the genotype-phenotype mapping: Ca…
Inspired by Fisher's geometric approach to study beneficial mutations, we analyse probabilities of beneficial mutation and crossover recombination of strings in a general Hamming space with arbitrary finite alphabet. Mutations and…
Surrogate models are a well established approach to reduce the number of expensive function evaluations in continuous optimization. In the context of genetic programming, surrogate modeling still poses a challenge, due to the complex…
In this article, we propose the definition of specific mutation operators for testing Geographic Information Systems. We describe the process for applying the operators and generating mutants, and present a case study where these mutation…
We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…
How can we identify causal genetic mechanisms that govern bacterial traits? Initial efforts entrusting machine learning models to handle the task of predicting phenotype from genotype return high accuracy scores. However, attempts to…
Exploring search spaces is one of the most unpredictable challenges that has attracted the interest of researchers for decades. One way to handle unpredictability is to characterise the search spaces and take actions accordingly. A…
A decision-maker must consider cofounding bias when attempting to apply machine learning prediction, and, while feature selection is widely recognized as important process in data-analysis, it could cause cofounding bias. A causal Bayesian…
Biological evolution can be conceptualized as a search process in the space of gene sequences guided by the fitness landscape, a mapping that assigns a measure of reproductive value to each genotype. Here we discuss probabilistic models of…
Identifying and characterizing mutational paths is an important issue in evolutionary biology and in bioengineering. We here introduce a generic description of mutational paths in terms of the goodness of sequences and of the mutational…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Functional effects of different mutations are known to combine to the total effect in highly nontrivial ways. For the trait under evolutionary selection (`fitness'), measured values over all possible combinations of a set of mutations yield…
Speciation is often associated with geographical barriers that limit gene flow. However, species can also emerge in continuous homogeneous environments through isolation by distance. When the environment is not homogeneous, natural…
This paper presents two different efficiency-enhancement techniques for probabilistic model building genetic algorithms. The first technique proposes the use of a mutation operator which performs local search in the sub-solution…
Coupling probability measures lies at the core of many problems in statistics and machine learning, from domain adaptation to transfer learning and causal inference. Yet, even when restricted to deterministic transports, such couplings are…
Mutational signatures describe the pattern of mutations over the different mutation types. Each mutation type is determined by a base substitution and the flanking nucleotides to the left and right of that base substitution. Due to the…
Genetic algorithms are a powerful tool in optimization for single and multi-modal functions. This paper provides an overview of their fundamentals with some analytical examples. In addition, we explore how they can be used as a parameter…
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions…
Understanding the evolution of complexity is an important topic in a wide variety of academic fields. Implications of better understanding complexity include increased knowledge of major evolutionary transitions and the properties of living…
In this paper, we explore the theory and expand upon the practice of fitness landscape analysis for optimization problems over the space of permutations. Many of the computational and analytical tools for fitness landscape analysis, such as…
Cartesian Genetic Programming is often used with a point mutation as the sole genetic operator. In this paper, we propose two phenotypic mutation techniques and take a step towards advanced phenotypic mutations in Cartesian Genetic…