Inheritance-Based Diversity Measures for Explicit Convergence Control in Evolutionary Algorithms

Diversity is an important factor in evolutionary algorithms to prevent premature convergence towards a single local optimum. In order to maintain diversity throughout the process of evolution, various means exist in literature. We analyze approaches to diversity that (a) have an explicit and quantifiable influence on fitness at the individual level and (b) require no (or very little) additional domain knowledge such as domain-specific distance functions. We also introduce the concept of genealogical diversity in a broader study. We show that employing these approaches can help evolutionary algorithms for global optimization in many cases.Comment: GECCO '18: Genetic and Evolutionary Computation Conference, 2018, Kyoto, Japa

Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

Self-adaptive fitness in evolutionary processes

Most optimization algorithms or methods in artificial intelligence can be regarded as evolutionary processes. They start from (basically) random guesses and produce increasingly better results with respect to a given target function, which is defined by the process's designer. The value of the achieved results is communicated to the evolutionary process via a fitness function that is usually somewhat correlated with the target function but does not need to be exactly the same. When the values of the fitness function change purely for reasons intrinsic to the evolutionary process, i.e., even though the externally motivated goals (as represented by the target function) remain constant, we call that phenomenon self-adaptive fitness. We trace the phenomenon of self-adaptive fitness back to emergent goals in artificial chemistry systems, for which we develop a new variant based on neural networks. We perform an in-depth analysis of diversity-aware evolutionary algorithms as a prime example of how to effectively integrate self-adaptive fitness into evolutionary processes. We sketch the concept of productive fitness as a new tool to reason about the intrinsic goals of evolution. We introduce the pattern of scenario co-evolution, which we apply to a reinforcement learning agent competing against an evolutionary algorithm to improve performance and generate hard test cases and which we also consider as a more general pattern for software engineering based on a solid formal framework. Multiple connections to related topics in natural computing, quantum computing and artificial intelligence are discovered and may shape future research in the combined fields.Die meisten Optimierungsalgorithmen und die meisten Verfahren in Bereich künstlicher Intelligenz können als evolutionäre Prozesse aufgefasst werden. Diese beginnen mit (prinzipiell) zufällig geratenen Lösungskandidaten und erzeugen dann immer weiter verbesserte Ergebnisse für gegebene Zielfunktion, die der Designer des gesamten Prozesses definiert hat. Der Wert der erreichten Ergebnisse wird dem evolutionären Prozess durch eine Fitnessfunktion mitgeteilt, die normalerweise in gewissem Rahmen mit der Zielfunktion korreliert ist, aber auch nicht notwendigerweise mit dieser identisch sein muss. Wenn die Werte der Fitnessfunktion sich allein aus für den evolutionären Prozess intrinsischen Gründen ändern, d.h. auch dann, wenn die extern motivierten Ziele (repräsentiert durch die Zielfunktion) konstant bleiben, nennen wir dieses Phänomen selbst-adaptive Fitness. Wir verfolgen das Phänomen der selbst-adaptiven Fitness zurück bis zu künstlichen Chemiesystemen (artificial chemistry systems), für die wir eine neue Variante auf Basis neuronaler Netze entwickeln. Wir führen eine tiefgreifende Analyse diversitätsbewusster evolutionärer Algorithmen durch, welche wir als Paradebeispiel für die effektive Integration von selbst-adaptiver Fitness in evolutionäre Prozesse betrachten. Wir skizzieren das Konzept der produktiven Fitness als ein neues Werkzeug zur Untersuchung von intrinsischen Zielen der Evolution. Wir führen das Muster der Szenarien-Ko-Evolution (scenario co-evolution) ein und wenden es auf einen Agenten an, der mittels verstärkendem Lernen (reinforcement learning) mit einem evolutionären Algorithmus darum wetteifert, seine Leistung zu erhöhen bzw. härtere Testszenarien zu finden. Wir erkennen dieses Muster auch in einem generelleren Kontext als formale Methode in der Softwareentwicklung. Wir entdecken mehrere Verbindungen der besprochenen Phänomene zu Forschungsgebieten wie natural computing, quantum computing oder künstlicher Intelligenz, welche die zukünftige Forschung in den kombinierten Forschungsgebieten prägen könnten

Practice-oriented controversies and borrowed epistemic credibility in current evolutionary biology: phylogeography as a case study

Although there is increasing recognition that theory and practice in science are intimately intertwined, philosophy of science perspectives on scientific controversies have been historically focused on theory rather than practice. As a step in the construction of frameworks for understanding controversies linked to scientific practices, here we introduce the notion of borrowed epistemic credibility (BEC), to describe the situation in which scientists, in order to garner support for their own stances, exploit similarities between tenets in their own field and accepted statements or positions properly developed within other areas of expertise. We illustrate the scope of application of our proposal with the analysis of a heavily methods-grounded, recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of biogeographical variation through population genetics- and phylogenetics-based computer analyses of diversity in DNA sequences, both within species and between closely related taxa. Toward this end, we briefly summarize the arguments proposed by selected authors representing each side of the controversy: the ‘nested clade analysis’ school versus the ‘statistical phylogeography’ orientation. We claim that whereas both phylogeographic ‘research styles’ borrow epistemic credibility from sources such as formal logic, the familiarity of results from other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning, ‘theory’ plays essentially no role as a foundation of the controversy. Besides underscoring the importance of strictly methodological and other non-theoretical aspects of controversies in current evolutionary biology, our analysis suggests a perspective with potential usefulness for the re-examination of more general philosophy of biology issues, such as the nature of historical inference, rationality, justification, and objectivity

Non-linear regression models for Approximate Bayesian Computation

Approximate Bayesian inference on the basis of summary statistics is well-suited to complex problems for which the likelihood is either mathematically or computationally intractable. However the methods that use rejection suffer from the curse of dimensionality when the number of summary statistics is increased. Here we propose a machine-learning approach to the estimation of the posterior density by introducing two innovations. The new method fits a nonlinear conditional heteroscedastic regression of the parameter on the summary statistics, and then adaptively improves estimation using importance sampling. The new algorithm is compared to the state-of-the-art approximate Bayesian methods, and achieves considerable reduction of the computational burden in two examples of inference in statistical genetics and in a queueing model.Comment: 4 figures; version 3 minor changes; to appear in Statistics and Computin

Computational phylogenetics and the classification of South American languages

In recent years, South Americanist linguists have embraced computational phylogenetic methods to resolve the numerous outstanding questions about the genealogi- cal relationships among the languages of the continent. We provide a critical review of the methods and language classification results that have accumulated thus far, emphasizing the superiority of character-based methods over distance-based ones and the importance of develop- ing adequate comparative datasets for producing well- resolved classifications

Chloroplast microsatellites: measures of genetic diversity and the effect of homoplasy

Chloroplast microsatellites have been widely used in population genetic studies of conifers in recent years. However, their haplotype configurations suggest that they could have high levels of homoplasy, thus limiting the power of these molecular markers. A coalescent-based computer simulation was used to explore the influence of homoplasy on measures of genetic diversity based on chloroplast microsatellites. The conditions of the simulation were defined to fit isolated populations originating from the colonization of one single haplotype into an area left available after a glacial retreat. Simulated data were compared with empirical data available from the literature for a species of Pinus that has expanded north after the Last Glacial Maximum. In the evaluation of genetic diversity, homoplasy was found to have little influence on Nei's unbiased haplotype diversity (H(E)) while Goldstein's genetic distance estimates (D2sh) were much more affected. The effect of the number of chloroplast microsatellite loci for evaluation of genetic diversity is also discussed