Spatial Evolutionary Generative Adversarial Networks

Generative adversary networks (GANs) suffer from training pathologies such as instability and mode collapse. These pathologies mainly arise from a lack of diversity in their adversarial interactions. Evolutionary generative adversarial networks apply the principles of evolutionary computation to mitigate these problems. We hybridize two of these approaches that promote training diversity. One, E-GAN, at each batch, injects mutation diversity by training the (replicated) generator with three independent objective functions then selecting the resulting best performing generator for the next batch. The other, Lipizzaner, injects population diversity by training a two-dimensional grid of GANs with a distributed evolutionary algorithm that includes neighbor exchanges of additional training adversaries, performance based selection and population-based hyper-parameter tuning. We propose to combine mutation and population approaches to diversity improvement. We contribute a superior evolutionary GANs training method, Mustangs, that eliminates the single loss function used across Lipizzaner's grid. Instead, each training round, a loss function is selected with equal probability, from among the three E-GAN uses. Experimental analyses on standard benchmarks, MNIST and CelebA, demonstrate that Mustangs provides a statistically faster training method resulting in more accurate networks

Evolutionary improvement of programs

Most applications of genetic programming (GP) involve the creation of an entirely new function, program or expression to solve a specific problem. In this paper, we propose a new approach that applies GP to improve existing software by optimizing its non-functional properties such as execution time, memory usage, or power consumption. In general, satisfying non-functional requirements is a difficult task and often achieved in part by optimizing compilers. However, modern compilers are in general not always able to produce semantically equivalent alternatives that optimize non-functional properties, even if such alternatives are known to exist: this is usually due to the limited local nature of such optimizations. In this paper, we discuss how best to combine and extend the existing evolutionary methods of GP, multiobjective optimization, and coevolution in order to improve existing software. Given as input the implementation of a function, we attempt to evolve a semantically equivalent version, in this case optimized to reduce execution time subject to a given probability distribution of inputs. We demonstrate that our framework is able to produce non-obvious optimizations that compilers are not yet able to generate on eight example functions. We employ a coevolved population of test cases to encourage the preservation of the function's semantics. We exploit the original program both through seeding of the population in order to focus the search, and as an oracle for testing purposes. As well as discussing the issues that arise when attempting to improve software, we employ rigorous experimental method to provide interesting and practical insights to suggest how to address these issues

A Coevolutionary Particle Swarm Algorithm for Bi-Level Variational Inequalities: Applications to Competition in Highway Transportation Networks

A climate of increasing deregulation in traditional highway transportation, where the private sector has an expanded role in the provision of traditional transportation services, provides a background for practical policy issues to be investigated. One of the key issues of interest, and the focus of this chapter, would be the equilibrium decision variables offered by participants in this market. By assuming that the private sector participants play a Nash game, the above problem can be described as a Bi-Level Variational Inequality (BLVI). Our problem differs from the classical Cournot-Nash game because each and every player’s actions is constrained by another variational inequality describing the equilibrium route choice of users on the network. In this chapter, we discuss this BLVI and suggest a heuristic coevolutionary particle swarm algorithm for its resolution. Our proposed algorithm is subsequently tested on example problems drawn from the literature. The numerical experiments suggest that the proposed algorithm is a viable solution method for this problem

Simultaneous identification of specifically interacting paralogs and inter-protein contacts by Direct-Coupling Analysis

Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces. Statistical inference methods detecting residue-residue coevolution have recently triggered considerable progress in using sequence data for quaternary protein structure prediction; they require, however, large joint alignments of homologous protein pairs known to interact. The generation of such alignments is a complex computational task on its own; application of coevolutionary modeling has in turn been restricted to proteins without paralogs, or to bacterial systems with the corresponding coding genes being co-localized in operons. Here we show that the Direct-Coupling Analysis of residue coevolution can be extended to connect the different scales, and simultaneously to match interacting paralogs, to identify inter-protein residue-residue contacts and to discriminate interacting from noninteracting families in a multiprotein system. Our results extend the potential applications of coevolutionary analysis far beyond cases treatable so far.Comment: Main Text 19 pages Supp. Inf. 16 page

Three phases in the evolution of the standard genetic code: how translation could get started

A primordial genetic code is proposed, having only four codons assigned, GGC meaning glycine, GAC meaning aspartate/glutamate, GCC meaning alanine-like and GUC meaning valine-like. Pathways of ambiguity reduction enlarged the codon repertoire with CUC meaning leucine, AUC meaning isoleucine, ACC meaning threonine-like and GAG meaning glutamate. Introduction of UNN anticodons, in a next episode of code evolution in which nonsense elimination was the leading theme, introduced a family box structure superposed on the original mirror structure. Finally, growth rate was the leading theme during the remaining repertoire expansion, explaining the ordered phylogenetic pattern of aminoacyl-tRNA synthetases. The special role of natural aptamers in the process is high-lighted, and the error robustness characteristics of the code are shown to have evolved by way of a stepwise, restricted enlargement of the tRNA repertoire, instead of by an exhaustive selection process testing myriads of codes