Convergence rates for the distribution of program outputs

Fitness distributions (landscapes) of programs tend to a limit as they get bigger. Markov chain convergence theorems give general upper bounds on the linear program sizes needed for convergence. Tight bounds (exponential in N, N log N and smaller) are given for five computer models (any, average, cyclic, bit flip and Boolean). Mutation randomizes a genetic algorithm population in 1 4 (l + 1)(log(l) + 4) generations. Results for a genetic programming (GP) like model are confirmed by experiment.

The distribution of amorphous computer outputs

Fitness distributions (landscapes) of programs tend to a limit as they get bigger. Markov minorization gives upper bounds ((15.3 + 2.30m) / log I) on the length of program run on random or average computing devices. I is the size of the instruction set and m size of output register. Almost all programs are constants. Convergence is exponential with 90 % of programs of length 1.6 n2 N yielding constants (n = size input register and size of memory = N). This is supported by experiment. 1 The Amorphous or Average Computer In Computer Science we are used to the notion that computers are highly designed, precision engineered artifacts. Nevertheless we can theoretically analyse more amorphous computing devices. Indeed nanotechnology may be a route to their practical construction and use. Consider an abstract machine whose instruction set, rather than being designed, is chosen at random. We can consider random linear computer programs as Markov processes which move the computer from one state to another [1]. 1.1 Convergence of Outputs We start by considering what happens when a single instruction is executed. Then consider two consecutive instructions, then a program of a instructions and so on

Automated DNA Motif Discovery

Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal. The evolved motif suggests the presence of Thymine followed by one or more Adenines etc. early in transcripts indicate a non-protein coding gene. Keywords: pseudogene, short and microRNAs, non-coding transcripts, systems biology, machine learning, Bioinformatics, motif, regular expression, strongly typed genetic programming, context-free grammar.Comment: 12 pages, 2 figure

Improving 3D medical image registration CUDA software with genetic programming

Genetic Improvement (GI) is shown to optimise, in some cases by more than 35%, a critical component of health-care industry software across a diverse range of six nVidia graphics processing units (GPUs). GP and other search based software engineering techniques can automatically op-timise the current rate limiting CUDA parallel function in the Nifty Reg open source C++ project used to align or reg-ister high resolution nuclear magnetic resonance NMRI and other diagnostic NIfTI images. Future Neurosurgery tech-niques will require hardware acceleration, such as GPGPU, to enable real time comparison of three dimensional in the-atre images with earlier patient images and reference data. With millimetre resolution brain scan measurements com-prising more than ten million voxels the modified kernel can process in excess of 3 billion active voxels per second

Kinetic Enhancement of Raman Backscatter, and Electron Acoustic Thomson Scatter

1-D Eulerian Vlasov-Maxwell simulations are presented which show kinetic enhancement of stimulated Raman backscatter (SRBS) due to electron trapping in regimes of heavy linear Landau damping. The conventional Raman Langmuir wave is transformed into a set of beam acoustic modes [L. Yin et al., Phys. Rev. E 73, 025401 (2006)]. For the first time, a low phase velocity electron acoustic wave (EAW) is seen developing from the self-consistent Raman physics. Backscatter of the pump laser off the EAW fluctuations is reported and referred to as electron acoustic Thomson scatter. This light is similar in wavelength to, although much lower in amplitude than, the reflected light between the pump and SRBS wavelengths observed in single hot spot experiments, and previously interpreted as stimulated electron acoustic scatter [D. S. Montgomery et al., Phys. Rev. Lett. 87, 155001 (2001)]. The EAW is strongest well below the phase-matched frequency for electron acoustic scatter, and therefore the EAW is not produced by it. The beating of different beam acoustic modes is proposed as the EAW excitation mechanism, and is called beam acoustic decay. Supporting evidence for this process, including bispectral analysis, is presented. The linear electrostatic modes, found by projecting the numerical distribution function onto a Gauss-Hermite basis, include beam acoustic modes (some of which are unstable even without parametric coupling to light waves) and a strongly-damped EAW similar to the observed one. This linear EAW results from non-Maxwellian features in the electron distribution, rather than nonlinearity due to electron trapping.Comment: 15 pages, 16 figures, accepted in Physics of Plasmas (2006

Rootstock influences postharvest anthracnose development in 'Hass' avocado

Rootstock studies conducted on ‘Hass’ avocado found that rootstock had a significant impact on postharvest anthracnose susceptibility. This is the first record of such an effect for avocado. The severity and incidence of anthracnose was significantly lower on ‘Hass’ grafted to ‘Velvick’ Guatemalan seedling rootstock compared with the ‘Duke 6’ Mexican seedling rootstock. Differences in anthracnose susceptibility were related to significant differences in concentrations of antifungal dienes in the leaves and mineral nutrients in the leaves and fruits from trees grafted to different rootstocks. Leaf diene concentrations were up to 1.5 times higher in ‘Hass’ trees on the ‘Velvick’ than the ‘Duke 6’ rootstock. In ungrafted nursery stock trees, diene concentrations were around 3 times higher in ‘Velvick’ than ‘Duke 6’ leaves. The ‘Velvick’/‘Hass’ combination also had a significantly lower leaf N concentration, a significantly higher fruit flesh Mn concentration, and significantly lower and higher leaf N/Ca and Ca+Mg/K ratios, respectively. A significant correlation (r = 0.82) between anthracnose severity and skin N/Ca ratio was also evident