Improving SSE parallel code with grow and graft genetic programming

RNAfold predicts the secondary structure of RNA molecules from their base sequence. We apply a mixture of manual and automated genetic improvements to its C source. GI gives a 1.6% improvement to parallel SSE4.1 code. The automatic programming evolutionary system has access to Intel library code and previous revisions. On 4 666 curated structures from RNA STRAND, GGGP gives a combined speed up of 31.9%, with no loss of accuracy (GI code run 1:4 1011 times)

Genetic improvement of GPU software

We survey genetic improvement (GI) of general purpose computing on graphics cards. We summarise several experiments which demonstrate four themes. Experiments with the gzip program show that genetic programming can automatically port sequential C code to parallel code. Experiments with the StereoCamera program show that GI can upgrade legacy parallel code for new hardware and software. Experiments with NiftyReg and BarraCUDA show that GI can make substantial improvements to current parallel CUDA applications. Finally, experiments with the pknotsRG program show that with semi-automated approaches, enormous speed ups can sometimes be had by growing and grafting new code with genetic programming in combination with human input

Evolving better RNAfold structure prediction

Grow and graft genetic programming (GGGP) evolves more than 50000 parameters in a state-of-the-art C program to make functional source code changes which give more accurate predictions of how RNA molecules fold up. Genetic improvement updates 29% of the dynamic programming free energy model parameters. In most cases (50.3%) GI gives better results on 4655 known secondary structures from RNA_STRAND (29.0% are worse and 20.7% are unchanged). Indeed it also does better than parameters recommended by Andronescu, M., et al.: Bioinformatics 23(13) (2007) i19–i28

Genetic Improvement of computational biology software

There is a cultural divide between computer scientists and biologists that needs to be addressed. The two disciplines used to be quite unrelated but many new research areas have arisen from their synergy. We selectively review two multi-disciplinary problems: dealing with contamination in sequencing data repositories and improving software using biology inspired evolutionary computing. Through several examples, we show that ideas from biology may result in optimised code and provide surprising improvements that overcome challenges in speed and quality trade-offs. On the other hand, development of computational methods is essential for maintaining contamination free databases. Computer scientists and biologists must always be sceptical of each others data, just as they would be of their own

Evolving AVX512 Parallel C Code Using GP

Using 512 bit Advanced Vector Extensions, previous development history and Intel documentation, BNF grammar based genetic improvement automatically ports RNAfold to AVX, giving up to a 1.77 fold speed up. The evolved code pull request is an accepted GI software maintenance update to bioinformatics package ViennaRNA

Evaluation of genetic improvement tools for improvement of non-functional properties of software

Genetic improvement (GI) improves both functional properties of software, such as bug repair, and non-functional properties, such as execution time, energy consumption, or source code size. There are studies summarising and comparing GI tools for improving functional properties of software; however there is no such study for improvement of its non-functional properties using GI. Therefore, this research aims to survey and report on the existing GI tools for improvement of non-functional properties of software. We conducted a literature review of available GI tools, and ran multiple experiments on the found open-source tools to examine their usability. We applied a cross-testing strategy to check whether the available tools can work on different programs. Overall, we found 63 GI papers that use a GI tool to improve nonfunctional properties of software, within which 31 are accompanied with open-source code. We were able to successfully run eight GI tools, and found that ultimately only two ---Gin and PyGGI--- can be readily applied to new general software

Genetically improved BarraCUDA.

BACKGROUND: BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised using "Genetic Improvement". RESULTS: The genetically improved (GI) code is up to three times faster on short paired end reads from The 1000 Genomes Project and 60% more accurate on a short BioPlanet.com GCAT alignment benchmark. GPGPU BarraCUDA running on a single K80 Tesla GPU can align short paired end nextGen sequences up to ten times faster than bwa on a 12 core server. CONCLUSIONS: The speed up was such that the GI version was adopted and has been regularly downloaded from SourceForge for more than 12 months

Software is Not Fragile

Trying all simple changes (first order mutations) to executed C, C++ and CUDA source code shows software engineering artefacts are more robust than is often assumed. Of those that compile, up to 89 % run without error. Indeed a few mutants are improvements. Program fitness landscapes are smoother. Analysis of these programs, a parallel nVidia GPGPU kernel, all CUDA samples and the GNU C library shows many lines of code and integer values are repeated and may follow Zipf’s law

Genetic Improvement of Software: a Comprehensive Survey

Genetic improvement (GI) uses automated search to find improved versions of existing software. We present a comprehensive survey of this nascent field of research with a focus on the core papers in the area published between 1995 and 2015. We identified core publications including empirical studies, 96% of which use evolutionary algorithms (genetic programming in particular). Although we can trace the foundations of GI back to the origins of computer science itself, our analysis reveals a significant upsurge in activity since 2012. GI has resulted in dramatic performance improvements for a diverse set of properties such as execution time, energy and memory consumption, as well as results for fixing and extending existing system functionality. Moreover, we present examples of research work that lies on the boundary between GI and other areas, such as program transformation, approximate computing, and software repair, with the intention of encouraging further exchange of ideas between researchers in these fields