相关论文: Maximum principle and mutation thresholds for four…

Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…

We present a new method for proving lower bounds on the expected running time of evolutionary algorithms. It is based on fitness-level partitions and an additional condition on transition probabilities between fitness levels. The method is…

This work presents a population genetic model of evolution, which includes haploid selection, mutation, recombination, and drift. The mutation-selection equilibrium can be expressed exactly in closed form for arbitrary fitness functions…

In the Minimum Description Length (MDL) principle, learning from the data is equivalent to an optimal coding problem. We show that the codes that achieve optimal compression in MDL are critical in a very precise sense. First, when they are…

We consider a periodic extension of the classical Kingman non-linear model (Kingman, 1978) for the balance between selection and mutation in a large population. In the original model, the fitness distribution of the population is modeled by…

The tree reconstruction problem is to collect and analyze massive data at the $n$th level of the tree, to identify whether there is non-vanishing information of the root, as $n$ goes to infinity. Its connection to the clustering problem in…

The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…

One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…

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…

We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…

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…

We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…

The ability of organisms to accurately sense their environment and respond accordingly is critical for evolutionary success. However, exactly how the sensory ability influences fitness is a topic of active research, while the necessity of a…

Maximum distance profile codes are characterized by the property that two trajectories which start at the same state and proceed to a different state will have the maximum possible distance from each other relative to any other…

We consider the Moran process with two populations competing under an iterated Prisoners' Dilemma in the presence of mutation, and concentrate on the case where there are multiple Evolutionarily Stable Strategies. We perform a complete…

We consider the evolution of an asexually reproducing population in an uncorrelated random fitness landscape in the limit of infinite genome size, which implies that each mutation generates a new fitness value drawn from a probability…

We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system…

Genetic fitness optimization using small populations or small population updates across generations generally suffers from randomly diverging evolutions. We propose a notion of highly probable fitness optimization through feasible…

Machine learning has been successfully applied to identify phases and phase transitions in condensed matter systems. However, quantitative characterization of the critical fluctuations near phase transitions is lacking. In this study we…

We twice modify the Penna model for biological ageing. First we introduce back (good) mutations and a memory for them into the model. It allows us to observe an improvement of the species fitness over long time scales as well as punctuated…