s: Jan. 1992 -- Dec. 1994 ffl CTI: Current Technology Index Jan./Feb. 1993 -- Jan./Feb. 1994 ffl DAI: Dissertation Abstracts International: Vol. 53 No. 1 -- Vol. 55 No. 4 (1994) ffl EEA: Electrical & Electronics Abstracts: Jan. 1991 -- Dec. 1994 ffl P: Index to Scientific & Technical Proceedings: Jan. 1986 -- Feb. 1995 (except Nov. 1994) ffl EI A: The Engineering Index Annual: 1987 -- 1992 ffl EI M: The Engineering Index Monthly: Jan. 1993 -- Dec. 1994 The following GA researchers have already kindly supplied their complete autobibliographies and/or proofread references to their papers: Dan Adler, Patrick Argos, Jarmo T. Alander, James E. Baker, Wolfgang Banzhaf, Ralf Bruns, I. L. Bukatova, Thomas Back, Yuval Davidor, Dipankar Dasgupta, Marco Dorigo, Bogdan Filipic, Terence C. Fogarty, David B. Fogel, Toshio Fukuda, Hugo de Garis, Robert C. Glen, David E. Goldberg, Martina Gorges-Schleuter, Jeffrey Horn, Aristides T. Hatjimihail, Mark J. Jakiela, Richard S. Judson, Akihiko Konaga...

Many metabolomics, and other high-content or high-throughput, experiments are set up such that the primary aim is the discovery of biomarker metabolites that can discriminate, with a certain level of certainty, between nominally matched ‘case ’ and ‘control ’ samples. However, it is unfortunately very easy to find markers that are apparently persuasive but that are in fact entirely spurious, and there are well-known examples in the proteomics literature. The main types of danger are not entirely independent of each other, but include bias, inadequate sample size (especially relative to the number of metabolite variables and to the required statistical power to prove that a biomarker is discriminant), excessive false discovery rate due to multiple hypothesis testing, inappropriate choice of particular numerical methods, and overfitting (generally caused by the failure to perform adequate validation and cross-validation). Many studies fail to take these into account, and thereby fail to discover anything of true significance (despite their claims). We summarise these problems, and provide pointers to a substantial existing literature that should assist in the improved design and evaluation of metabolomics experiments, thereby allowing robust scientific conclusions to be drawn from the available data. We provide a list of some of the simpler checks that might improve one’s confidence that a candidate biomarker is not simply a statistical artefact, and suggest a series of preferred tests and visualisation tools that can assist readers and authors in assessing papers. These tools can be applied to individual metabolites by using multiple univariate tests performed in parallel across all metabolite peaks. They may also be applied to the validation of multivariate models. We stress in

Abstract. Mackey-Glass chaotic time series prediction and nuclear protein classification show the feasibility of evaluating genetic programming populations directly on parallel consumer gaming graphics processing units. Using a Linux KDE computer equipped with an nVidia GeForce 8800 GTX graphics processing unit card the C++ SPMD interpretter evolves programs at Giga GP operations per second (895 million GPops). We use the RapidMind general processing on GPU (GPGPU) framework to evaluate an entire population of a quarter of a million individual programs on a non-trivial problem in 4 seconds. An efficient reverse polish notation (RPN) tree based GP is given. 1

We automatically generate an nVidia parallel CUDA graphics card kernel with identical functionality to existing highly optimised ancient sequential C code. Essentially generic GPGPU C++ code supplied by the hardware manufacturer is converted into a BNF grammar. Strongly typed genetic programming uses the BNF to generate compilable and runnable graphics card kernels, which terminate. Their fitness is given by running the population on a GPU against a test suite used to test the original sequential code. I will briefly introduce genetic programming (GP) but try to assume most of the audience are familiar with the essential idea of using Darwin’s idea of species evolution by randomly selecting better individuals from a population of individuals (in our case programs). Each new population is created by randomly breeding from the better individuals in the previous generation. In genetic programming [Poli et al., 2008] we need to start by creating the initial population of random programs. We usually also need an automated way of selecting better programs. This is usually done by testing. There are a number of ways of mutating better programs and a number of ways to combine two better parent programs to create children programs. Many mutants are very poor. Some children are like

We use evolutionary computation (EC) to automatically find problems which demonstrate the strength and weaknesses of modern search heuristics. In particular, we analyze particle swarm optimization (PSO), differential evolution (DE), and covariance matrix adaptation-evolution strategy (CMA-ES). Each evolutionary algorithm is contrasted with the others and with a robust nonstochastic gradient follower (i.e., a hill climber) based on Newton–Raphson. The evolved benchmark problems yield insights into the operation of PSOs, illustrate benefits and drawbacks of different population sizes, velocity limits, and constriction (friction) coefficients. The fitness landscapes made by genetic programming reveal new swarm phenomena, such as deception, thereby explaining how they work and allowing us to devise better extended particle swarm systems. The method could be applied to any type of optimizer.

Grammatical Evolution (GE) is a grammar based GA to generate computer programs which has been shown to be comparable with GP when applied to a diverse array of problems. GE has the distinction that its input is a BNF, which permits it to generate programs in any language, of arbitrary complexity, including loops, multiple line functions etc. Part of the power of GE is that it is closer to natural DNA than GP, and thus can benefit from natural phenomena such as a separation of search and solution spaces through a genotype to phenotype mapping, and a genetic code degeneracy which can give rise to silent mutations (Mutations that have no effect on the phenotype). We have previously shown how runs of GE are competitive with GP, and in this paper we analyse characteristics such as genotypic diversity, and individual genotypic length, in an attempt to shed light on the power of the system. Results indicate that GE can use certain features of the system to its benefit ...

Abstract. Genetic programming, in conjunction with advanced analytical instruments, is a novel tool for the investigation of complex biological systems at the whole-tissue level. In this study, samples from tomato fruit grown hydroponically under both high- and low-salt conditions were analysed using .Fourier-transform infrared spectroscopy FTIR, with the aim of identifying spectral and biochemical features linked to salinity in the growth environment. FTIR spectra of whole tissue extracts are not amenable to direct visual analysis, so numerical modelling methods were used to generate models .capable of classifying the samples based on their spectral characteristics. Genetic programming GP provided models with a better prediction accuracy to the conventional data modelling methods used, whilst being much easier to interpret in terms of the variables used. Examination of the GP-derived models showed that there were a small number of spectral regions that were consistently being used. In particular, the spectral region containing absorbances potentially due to a cyanidernitrile functional group was identified as discriminatory. The explanatory power of the GP models enabled a chemical interpretation of the biochemical differences to be proposed. The combination of FTIR and GP is therefore a powerful and novel analytical tool that, in this study, improves our understanding of the biochemistry of salt tolerance in tomato plants. .Keywords: metabolome, tomato fruit, salinity, Fourier transform infra-red spectroscopy FTIR, chemometrics

Grammatical Evolution (GE) is a grammar-based GA which generates computer programs. GE has the distinction that its input is a BNF, which permits it to generate programs in any language, of arbitrary complexity. Part of the power of GE is that it is closer to natural DNA than other Evolutionary Algorithms, and thus can benefit from natural phenomena such as a separation of search and solution spaces through a genotype to phenotype mapping, and a genetic code degeneracy which can give rise to silent mutations that have no effect on the phenotype. It has previously been shown how runs of GE are competitive with GP, and in this paper we analyse the feature of genetic code degeneracy, and its implications for genotypic diversity. Results show that genetic diversity is improved as a result of degeneracy in the genetic code for the problem domains addressed here.

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Abstract. Genetic programming (GP) offers a generic method of automatically fusing together classifiers using their receiver operating characteristics (ROC) to yield superior ensembles. We combine decision trees (C4.5) and artificial neural networks (ANN) on a difficult pharmaceutical data mining (KDD) drug discovery application. Specifically predicting inhibition of a P450 enzyme. Training data came from high throughput screening (HTS) runs. The evolved model may be used to predict behaviour of virtual (i.e. yet to be manufactured) chemicals. Measures to reduce over fitting are also described. 1