Use of high throughput sequencing to observe genome dynamics at a single cell level

With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions. Here, we sequenced several genomes of Escherichia coli from colonies obtained after chemical mutagenesis and observed a strikingly nonrandom distribution of the induced mutations. These include long stretches of exclusively G to A or C to T transitions along the genome and orders of magnitude intra- and inter-genomic differences in mutation density. Whereas most of these observations can be explained by the known features of enzymatic processes, the others could reflect stochasticity in the molecular processes at the single-cell level. Our results demonstrate how analysis of the molecular records left in the genomes of the descendants of an individual mutagenized cell allows for genome-scale observations of fixation and segregation of mutations, as well as recombination events, in the single genome of their progenitor.Comment: 22 pages, 9 figures (including 5 supplementary), one tabl

A Memetic Algorithm for the Generalized Traveling Salesman Problem

The generalized traveling salesman problem (GTSP) is an extension of the well-known traveling salesman problem. In GTSP, we are given a partition of cities into groups and we are required to find a minimum length tour that includes exactly one city from each group. The recent studies on this subject consider different variations of a memetic algorithm approach to the GTSP. The aim of this paper is to present a new memetic algorithm for GTSP with a powerful local search procedure. The experiments show that the proposed algorithm clearly outperforms all of the known heuristics with respect to both solution quality and running time. While the other memetic algorithms were designed only for the symmetric GTSP, our algorithm can solve both symmetric and asymmetric instances.Comment: 15 pages, to appear in Natural Computing, Springer, available online: http://www.springerlink.com/content/5v4568l492272865/?p=e1779dd02e4d4cbfa49d0d27b19b929f&pi=1

Tile Pattern KL-Divergence for Analysing and Evolving Game Levels

This paper provides a detailed investigation of using the Kullback-Leibler (KL) Divergence as a way to compare and analyse game-levels, and hence to use the measure as the objective function of an evolutionary algorithm to evolve new levels. We describe the benefits of its asymmetry for level analysis and demonstrate how (not surprisingly) the quality of the results depends on the features used. Here we use tile-patterns of various sizes as features. When using the measure for evolution-based level generation, we demonstrate that the choice of variation operator is critical in order to provide an efficient search process, and introduce a novel convolutional mutation operator to facilitate this. We compare the results with alternative generators, including evolving in the latent space of generative adversarial networks, and Wave Function Collapse. The results clearly show the proposed method to provide competitive performance, providing reasonable quality results with very fast training and reasonably fast generation.Comment: 8 pages plus references. Proceedings of GECCO 201

Genetic Optimization Using Derivatives: The rgenoud Package for R

genoud is an R function that combines evolutionary algorithm methods with a derivative-based (quasi-Newton) method to solve difficult optimization problems. genoud may also be used for optimization problems for which derivatives do not exist. genoud solves problems that are nonlinear or perhaps even discontinuous in the parameters of the function to be optimized. When the function to be optimized (for example, a log-likelihood) is nonlinear in the model's parameters, the function will generally not be globally concave and may have irregularities such as saddlepoints or discontinuities. Optimization methods that rely on derivatives of the objective function may be unable to find any optimum at all. Multiple local optima may exist, so that there is no guarantee that a derivative-based method will converge to the global optimum. On the other hand, algorithms that do not use derivative information (such as pure genetic algorithms) are for many problems needlessly poor at local hill climbing. Most statistical problems are regular in a neighborhood of the solution. Therefore, for some portion of the search space, derivative information is useful. The function supports parallel processing on multiple CPUs on a single machine or a cluster of computers.

Tracking moving optima using Kalman-based predictions

The dynamic optimization problem concerns finding an optimum in a changing environment. In the field of evolutionary algorithms, this implies dealing with a timechanging fitness landscape. In this paper we compare different techniques for integrating motion information into an evolutionary algorithm, in the case it has to follow a time-changing optimum, under the assumption that the changes follow a nonrandom law. Such a law can be estimated in order to improve the optimum tracking capabilities of the algorithm. In particular, we will focus on first order dynamical laws to track moving objects. A vision-based tracking robotic application is used as testbed for experimental comparison

Modular knowledge systems accelerate human migration in asymmetric random environments

Migration is a key mechanism for expansion of communities. In spatially heterogeneous environments, rapidly gaining knowledge about the local environment is key to the evolutionary success of a migrating population. For historical human migration, environmental heterogeneity was naturally asymmetric in the north-south (NS) and east-west (EW) directions. We here consider the human migration process in the Americas, modeled as random, asymmetric, modularly correlated environments. Knowledge about the environments determines the fitness of each individual. We present a phase diagram for asymmetry of migration as a function of carrying capacity and fitness threshold. We find that the speed of migration is proportional to the inverse complement of the spatial environmental gradient, and in particular we find that north-south migration rates are lower than east-west migration rates when the environmental gradient is higher in the north-south direction. Communication of knowledge between individuals can help to spread beneficial knowledge within the population. The speed of migration increases when communication transmits pieces of knowledge that contribute in a modular way to the fitness of individuals. The results for the dependence of migration rate on asymmetry and modularity are consistent with existing archaeological observations. The results for asymmetry of genetic divergence are consistent with patterns of human gene flow.Comment: 13 pages, 6 figures, 1 table in Proc. Roy. Soc. Interface 201