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Clusters of genes that have evolved by repeated segmental duplication present difficult challenges throughout genomic analysis, from sequence assembly to functional analysis. Improved understanding of these clusters is of utmost importance,…
Homologous recombination is an important operator in the evolution of biological organisms. However, there is still no clear, generally accepted understanding of why it exists and under what circumstances it is useful. In this paper we…
The implementation of deep learning algorithms has brought new perspectives to plankton ecology. Emerging as an alternative approach to established methods, deep learning offers objective schemes to investigate plankton organisms in diverse…
The potentially beneficial interaction between learning and evolution, the Baldwin effect, has long been established. This paper considers their interaction within a coevolutionary scenario, ie, where the adaptations of one species…
In quantum adiabatic evolution algorithms, the quantum computer follows the ground state of a slowly varying Hamiltonian. The ground state of the initial Hamiltonian is easy to construct; the ground state of the final Hamiltonian encodes…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
New approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, enforced by new crossover operators, especially worked out for…
I consider the many ways in which evolved information-flows are restricted and metabolic resources protected and hidden -- the thesis of living phenomena as evolutionary cryptosystems. I present the information theory of secrecy systems and…
A new implementation of an adiabatically-trained ensemble model is derived that shows significant improvements over classical methods. In particular, empirical results of this new algorithm show that it offers not just higher performance,…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
Using a bit string model, we show that asexual reproduction for diploids is more efficient than for haploids: it improves genetic material producing new individuals with less deleterious mutations. We also see that in a system where…
An inductive learning algorithm takes a set of data as input and generates a hypothesis as output. A set of data is typically consistent with an infinite number of hypotheses; therefore, there must be factors other than the data that…
Meta-learning models, or models that learn to learn, have been a long-desired target for their ability to quickly solve new tasks. Traditional meta-learning methods can require expensive inner and outer loops, thus there is demand for…
This paper develops a quasispecies model where cells can adopt a two-cell survival strategy. Within this strategy, pairs of cells join together, at which point one of the cells sacrifices its own replicative ability for the sake of the…
The intertwined processes of learning and evolution in complex environmental niches have resulted in a remarkable diversity of morphological forms. Moreover, many aspects of animal intelligence are deeply embodied in these evolved…
We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution---a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an…
Evolution sculpts both the body plans and nervous systems of agents together over time. In contrast, in AI and robotics, a robot's body plan is usually designed by hand, and control policies are then optimized for that fixed design. The…
The idea of the inheritance of biological processes, such as the developmental process or the life cycle of an organism, has been discussed in the biology literature, but formal mathematical descriptions and plausible data analysis…
A key question in biological systems is whether genetic diversity persists in the long run under evolutionary competition or whether a single dominant genotype emerges. Classic work by Kalmus in 1945 has established that even in simple…
We discuss two different ways of chromosomes' and genomes' evolution. Purifying selection dominates in large panmictic populations, where Mendelian law of independent gene assortment is valid. If the populations are small, recombination…