Differential evolution with an evolution path: a DEEP evolutionary algorithm

Utilizing cumulative correlation information already existing in an evolutionary process, this paper proposes a predictive approach to the reproduction mechanism of new individuals for differential evolution (DE) algorithms. DE uses a distributed model (DM) to generate new individuals, which is relatively explorative, whilst evolution strategy (ES) uses a centralized model (CM) to generate offspring, which through adaptation retains a convergence momentum. This paper adopts a key feature in the CM of a covariance matrix adaptation ES, the cumulatively learned evolution path (EP), to formulate a new evolutionary algorithm (EA) framework, termed DEEP, standing for DE with an EP. Without mechanistically combining two CM and DM based algorithms together, the DEEP framework offers advantages of both a DM and a CM and hence substantially enhances performance. Under this architecture, a self-adaptation mechanism can be built inherently in a DEEP algorithm, easing the task of predetermining algorithm control parameters. Two DEEP variants are developed and illustrated in the paper. Experiments on the CEC'13 test suites and two practical problems demonstrate that the DEEP algorithms offer promising results, compared with the original DEs and other relevant state-of-the-art EAs

On Fodor on Darwin on Evolution

Jerry Fodor argues that Darwin was wrong about "natural selection" because (1) it is only a tautology rather than a scientific law that can support counterfactuals ("If X had happened, Y would have happened") and because (2) only minds can select. Hence Darwin's analogy with "artificial selection" by animal breeders was misleading and evolutionary explanation is nothing but post-hoc historical narrative. I argue that Darwin was right on all counts. Until Darwin's "tautology," it had been believed that either (a) God had created all organisms as they are, or (b) organisms had always been as they are. Darwin revealed instead that (c) organisms have heritable traits that evolved across time through random variation, with survival and reproduction in (changing) environments determining (mindlessly) which variants were successfully transmitted to the next generation. This not only provided the (true) alternative (c), but also the methodology for investigating which traits had been adaptive, how and why; it also led to the discovery of the genetic mechanism of the encoding, variation and evolution of heritable traits. Fodor also draws erroneous conclusions from the analogy between Darwinian evolution and Skinnerian reinforcement learning. Fodor’s skepticism about both evolution and learning may be motivated by an overgeneralization of Chomsky’s “poverty of the stimulus argument” -- from the origin of Universal Grammar (UG) to the origin of the “concepts” underlying word meaning, which, Fodor thinks, must be “endogenous,” rather than evolved or learned

Fast micro-differential evolution for topological active net optimization

This paper studies the optimization problem of topological active net (TAN), which is often seen in image segmentation and shape modeling. A TAN is a topological structure containing many nodes, whose positions must be optimized while a predefined topology needs to be maintained. TAN optimization is often time-consuming and even constructing a single solution is hard to do. Such a problem is usually approached by a ``best improvement local search'' (BILS) algorithm based on deterministic search (DS), which is inefficient because it spends too much efforts in nonpromising probing. In this paper, we propose the use of micro-differential evolution (DE) to replace DS in BILS for improved directional guidance. The resultant algorithm is termed deBILS. Its micro-population efficiently utilizes historical information for potentially promising search directions and hence improves efficiency in probing. Results show that deBILS can probe promising neighborhoods for each node of a TAN. Experimental tests verify that deBILS offers substantially higher search speed and solution quality not only than ordinary BILS, but also the genetic algorithm and scatter search algorithm

Session 3: Natural Selection as a Causal Theory

Proceedings of the Pittsburgh Workshop in History and Philosophy of Biology, Center for Philosophy of Science, University of Pittsburgh, March 23-24 2001 Session 3: Natural Selection as a Causal Theor

Genomic and proteomic biases inform metabolic engineering strategies for anaerobic fungi.

Anaerobic fungi (Neocallimastigomycota) are emerging non-model hosts for biotechnology due to their wealth of biomass-degrading enzymes, yet tools to engineer these fungi have not yet been established. Here, we show that the anaerobic gut fungi have the most GC depleted genomes among 443 sequenced organisms in the fungal kingdom, which has ramifications for heterologous expression of genes as well as for emerging CRISPR-based genome engineering approaches. Comparative genomic analyses suggest that anaerobic fungi may contain cellular machinery to aid in sexual reproduction, yet a complete mating pathway was not identified. Predicted proteomes of the anaerobic fungi also contain an unusually large fraction of proteins with homopolymeric amino acid runs consisting of five or more identical consecutive amino acids. In particular, threonine runs are especially enriched in anaerobic fungal carbohydrate active enzymes (CAZymes) and this, together with a high abundance of predicted N-glycosylation motifs, suggests that gut fungal CAZymes are heavily glycosylated, which may impact heterologous production of these biotechnologically useful enzymes. Finally, we present a codon optimization strategy to aid in the development of genetic engineering tools tailored to these early-branching anaerobic fungi

On Fodor on Darwin on Evolution

Jerry Fodor argues that Darwin was wrong about "natural selection" because (1) it is only a tautology rather than a scientific law that can support counterfactuals ("If X had happened, Y would have happened") and because (2) only minds can select. Hence Darwin's analogy with "artificial selection" by animal breeders was misleading and evolutionary explanation is nothing but post-hoc historical narrative. I argue that Darwin was right on all counts. Until Darwin's "tautology," it had been believed that either (a) God had created all organisms as they are, or (b) organisms had always been as they are. Darwin revealed instead that (c) organisms have heritable traits that evolved across time through random variation, with survival and reproduction in (changing) environments determining (mindlessly) which variants were successfully transmitted to the next generation. This not only provided the (true) alternative (c), but also the methodology for investigating which traits had been adaptive, how and why; it also led to the discovery of the genetic mechanism of the encoding, variation and evolution of heritable traits. Fodor also draws erroneous conclusions from the analogy between Darwinian evolution and Skinnerian reinforcement learning. Fodor's skepticism about both evolution and learning may be motivated by an overgeneralization of Chomsky's "poverty of the stimulus argument" -- from the origin of Universal Grammar (UG) to the origin of the "concepts" underlying word meaning, which, Fodor thinks, must be "endogenous," rather than evolved or learned

Evolutionary Robotics: a new scientific tool for studying cognition

We survey developments in Artificial Neural Networks, in Behaviour-based Robotics and Evolutionary Algorithms that set the stage for Evolutionary Robotics in the 1990s. We examine the motivations for using ER as a scientific tool for studying minimal models of cognition, with the advantage of being capable of generating integrated sensorimotor systems with minimal (or controllable) prejudices. These systems must act as a whole in close coupling with their environments which is an essential aspect of real cognition that is often either bypassed or modelled poorly in other disciplines. We demonstrate with three example studies: homeostasis under visual inversion; the origins of learning; and the ontogenetic acquisition of entrainment