Non stationary operator selection with island models

The purpose of adaptive operator selection is to choose dynamically the most suitable variation operator of an evolutionary algorithm at each iteration of the search process. These variation operators are applied on individuals of a population which evolves, according to an evolutionary process, in order to find an optimal solution. Of course the efficiency of an operator may change during the search and therefore its application should be precisely controlled. In this paper, we use dynamic island models as operator selection mechanisms. A sub-population is associated to each operators and individuals are allowed to migrate from one sub-population to another one. In order to evaluate the performance of this adaptive selection mechanism, we propose an abstract operator representation using fitness improvement distributions that allow us to define non stationary operators with mutual interactions. Our purpose is to show that the adaptive selection is able to identify not only good operators but also suitable sequences of operators

Computing and visually analyzing mutual information in molecular co-evolution

<p>Abstract</p> <p>Background</p> <p>Selective pressure in molecular evolution leads to uneven distributions of amino acids and nucleotides. In fact one observes correlations among such constituents due to a large number of biophysical mechanisms (folding properties, electrostatics, ...). To quantify these correlations the mutual information -after proper normalization - has proven most effective. The challenge is to navigate the large amount of data, which in a study for a typical protein cannot simply be plotted.</p> <p>Results</p> <p>To visually analyze mutual information we developed a matrix visualization tool that allows different views on the mutual information matrix: filtering, sorting, and weighting are among them. The user can interactively navigate a huge matrix in real-time and search e.g., for patterns and unusual high or low values. A computation of the mutual information matrix for a sequence alignment in FASTA-format is possible. The respective stand-alone program computes in addition proper normalizations for a null model of neutral evolution and maps the mutual information to <it>Z</it>-scores with respect to the null model.</p> <p>Conclusions</p> <p>The new tool allows to compute and visually analyze sequence data for possible co-evolutionary signals. The tool has already been successfully employed in evolutionary studies on HIV1 protease and acetylcholinesterase. The functionality of the tool was defined by users using the tool in real-world research. The software can also be used for visual analysis of other matrix-like data, such as information obtained by DNA microarray experiments. The package is platform-independently implemented in <monospace>Java</monospace> and free for academic use under a GPL license.</p

Mutual Attraction Guided Search: a novel solution method to the Traveling Salesman Problem with vehicle dynamics

Traveling Salesman Problem (TSP) solution techniques are often used for route planning for automated vehicles. Most TSP solution methods focus on path length as the fitness reference, however in many cases, traversal time is of more practical importance. Mutual Attraction Guided Search (MAGS) is a novel solution method that uses an iterative process to simultaneously optimize both angle of travel through each target as well as the ordering of the targets in order to optimize path traversal time. MAGS deterministically locates a locally optimum solution quickly and can optimize for the acceleration limits of a specific vehicle rather than requiring a constant vehicle speed. Since the basic form of MAGS finds a solution deterministically, it has no mechanism for escaping local minima, therefore an evolutionary form is also developed that alternates between local search with MAGS and global search using evolutionary operators to combine and mutate solutions. This hybridization provides the necessary balance between local and global search that is required to locate a globally optimal solution. A fitness based on approximate travel time based on the maximum velocity achievable at each point on the path is calculated using the curvature of the path and the dynamic constraints of the vehicle. The performance of both the basic and evolutionary forms of MAGS are compared against path length based Euclidean and curvature constrained TSP methods --Abstract, page iii

Economy of LIfe: Charismatic Dynamics and the Spirit of Gift

The dominant mode of globalization has mostly reinforced the disembedding of states and markets from the social practices and civic virtues of civil society writ large. In this process, abstract economic values linked to instrumental reason and procedural fairness have supplanted civic virtues of courage, reasonableness and substantive justice. As such, the global ‘market-state’ reflects the centralization of power and the concentration of wealth that is undermining democratic politics and genuinely competitive economies. However, the growing economic interdependence around the world also offers new opportunities for reciprocity, mutuality and fraternity among communities and nations. To promote an ethos of responsible and virtuous action, what is required is the full breadth of political and economic reason. Christian social teaching offers conceptual and practical resources that are indispensable to the search for broader notions of rationality. Among these resources are non-instrumental conceptions of justice and the common good in the social doctrine of the Catholic Church and cognate traditions in Anglicanism and Eastern Orthodoxy. Closely connected to this is the idea of ‘civil economy’. As Pope Benedict XVI has suggested in his encyclical Caritas in veritate, ‘civil economy’ embeds state-guaranteed rights and market contracts in the social bonds and civic virtues that bind together the intermediary institutions of civil society. In this manner, it binds the ‘logic of contract’ to the ‘logic of gratuitous gift exchange’. The spirit of gift exchange translates into concrete practices of reciprocal trust and mutual assistance that underpin virtues such as reciprocal fraternity and the pursuit of the universal common good in which all can share. As such, ‘civil economy’ reconnects activities that are primarily for state-administrative or economic-commercial purposes to practices that pursue social purposes

Holographic entropy relations

We develop a framework for the derivation of new information theoretic quantities which are natural from a holographic perspective. We demonstrate the utility of our techniques by deriving the tripartite information (the quantity associated to monogamy of mutual information) using a set of abstract arguments involving bulk extremal surfaces. Our arguments rely on formal manipulations of surfaces and not on local surgery or explicit computation of entropies through the holographic entanglement entropy prescriptions. As an application, we show how to derive a family of similar information quantities for an arbitrary number of parties. The present work establishes the foundation of a broader program that aims at the understanding of the entanglement structures of geometric states for an arbitrary number of parties. We stress that our method is completely democratic with respect to bulk geometries and is equally valid in static and dynamical situations. While rooted in holography, we expect that our construction will provide a useful characterization of multipartite correlations in quantum field theories.Comment: v1: 58 pages, 1 pdf figur

Self-adaptive exploration in evolutionary search

We address a primary question of computational as well as biological research on evolution: How can an exploration strategy adapt in such a way as to exploit the information gained about the problem at hand? We first introduce an integrated formalism of evolutionary search which provides a unified view on different specific approaches. On this basis we discuss the implications of indirect modeling (via a ``genotype-phenotype mapping'') on the exploration strategy. Notions such as modularity, pleiotropy and functional phenotypic complex are discussed as implications. Then, rigorously reflecting the notion of self-adaptability, we introduce a new definition that captures self-adaptability of exploration: different genotypes that map to the same phenotype may represent (also topologically) different exploration strategies; self-adaptability requires a variation of exploration strategies along such a ``neutral space''. By this definition, the concept of neutrality becomes a central concern of this paper. Finally, we present examples of these concepts: For a specific grammar-type encoding, we observe a large variability of exploration strategies for a fixed phenotype, and a self-adaptive drift towards short representations with highly structured exploration strategy that matches the ``problem's structure''.Comment: 24 pages, 5 figure