Understanding Evolutionary Potential in Virtual CPU Instruction Set Architectures

We investigate fundamental decisions in the design of instruction set architectures for linear genetic programs that are used as both model systems in evolutionary biology and underlying solution representations in evolutionary computation. We subjected digital organisms with each tested architecture to seven different computational environments designed to present a range of evolutionary challenges. Our goal was to engineer a general purpose architecture that would be effective under a broad range of evolutionary conditions. We evaluated six different types of architectural features for the virtual CPUs: (1) genetic flexibility: we allowed digital organisms to more precisely modify the function of genetic instructions, (2) memory: we provided an increased number of registers in the virtual CPUs, (3) decoupled sensors and actuators: we separated input and output operations to enable greater control over data flow. We also tested a variety of methods to regulate expression: (4) explicit labels that allow programs to dynamically refer to specific genome positions, (5) position-relative search instructions, and (6) multiple new flow control instructions, including conditionals and jumps. Each of these features also adds complication to the instruction set and risks slowing evolution due to epistatic interactions. Two features (multiple argument specification and separated I/O) demonstrated substantial improvements int the majority of test environments. Some of the remaining tested modifications were detrimental, thought most exhibit no systematic effects on evolutionary potential, highlighting the robustness of digital evolution. Combined, these observations enhance our understanding of how instruction architecture impacts evolutionary potential, enabling the creation of architectures that support more rapid evolution of complex solutions to a broad range of challenges

C to O-O Translation: Beyond the Easy Stuff

Can we reuse some of the huge code-base developed in C to take advantage of modern programming language features such as type safety, object-orientation, and contracts? This paper presents a source-to-source translation of C code into Eiffel, a modern object-oriented programming language, and the supporting tool C2Eif. The translation is completely automatic and supports the entire C language (ANSI, as well as many GNU C Compiler extensions, through CIL) as used in practice, including its usage of native system libraries and inlined assembly code. Our experiments show that C2Eif can handle C applications and libraries of significant size (such as vim and libgsl), as well as challenging benchmarks such as the GCC torture tests. The produced Eiffel code is functionally equivalent to the original C code, and takes advantage of some of Eiffel's object-oriented features to produce safe and easy-to-debug translations

A universal ultraviolet-optical colour-colour-magnitude relation of galaxies

Although the optical colour-magnitude diagram of galaxies allows one to select red sequence objects, neither can it be used for galaxy classification without additional observational data such as spectra or high-resolution images, nor to identify blue galaxies at unknown redshifts. We show that adding the near ultraviolet colour to the optical CMD reveals a tight relation in the three-dimensional colour-colour-magnitude space smoothly continuing from the "blue cloud" to the "red sequence". We found that 98 per cent of 225,000 low-redshift (Z<0.27) galaxies follow a smooth surface g-r=F(M,NUV-r) with a standard deviation of 0.03-0.07 mag making it the tightest known galaxy photometric relation. There is a strong correlation between morphological types and integrated NUV-r colours. Rare galaxy classes such as E+A or tidally stripped systems become outliers that occupy distinct regions in the 3D parameter space. Using stellar population models for galaxies with different SFHs, we show that (a) the (NUV-r, g-r) distribution is formed by objects having constant and exponentially declining SFR with different characteristic timescales; (b) colour evolution for exponentially declining models goes along the relation suggesting its weak evolution up-to a redshift of 0.9; (c) galaxies with truncated SFHs have very short transition phase offset from the relation thus explaining the rareness of E+A galaxies. This relation can be used as a powerful galaxy classification tool when morphology remains unresolved. Its mathematical consequence is the photometric redshift estimates from 3 broad-band photometric points. This approach works better than most existing photometric redshift techniques applied to multi-colour datasets. Therefore, the relation can be used as an efficient selection technique for galaxies at intermediate redshifts (0.3<Z<0.8) using optical imaging surveys.Comment: 15 pages, 10 figures, accepted to MNRAS. This is an updated version that addresses referee's remarks. All relations have been recomputed using Petrosian magnitudes. The best-fitting relations in the electronic form are available at the project web-page: http://specphot.sai.msu.ru/galaxies

Assessment of Source Code Obfuscation Techniques

Obfuscation techniques are a general category of software protections widely adopted to prevent malicious tampering of the code by making applications more difficult to understand and thus harder to modify. Obfuscation techniques are divided in code and data obfuscation, depending on the protected asset. While preliminary empirical studies have been conducted to determine the impact of code obfuscation, our work aims at assessing the effectiveness and efficiency in preventing attacks of a specific data obfuscation technique - VarMerge. We conducted an experiment with student participants performing two attack tasks on clear and obfuscated versions of two applications written in C. The experiment showed a significant effect of data obfuscation on both the time required to complete and the successful attack efficiency. An application with VarMerge reduces by six times the number of successful attacks per unit of time. This outcome provides a practical clue that can be used when applying software protections based on data obfuscation.Comment: Post-print, SCAM 201

The GalMer database: Galaxy Mergers in the Virtual Observatory

We present the GalMer database, a library of galaxy merger simulations, made available to users through tools compatible with the Virtual Observatory (VO) standards adapted specially for this theoretical database. To investigate the physics of galaxy formation through hierarchical merging, it is necessary to simulate galaxy interactions varying a large number of parameters: morphological types, mass ratios, orbital configurations, etc. On one side, these simulations have to be run in a cosmological context, able to provide a large number of galaxy pairs, with boundary conditions given by the large-scale simulations, on the other side the resolution has to be high enough at galaxy scales, to provide realistic physics. The GalMer database is a library of thousands simulations of galaxy mergers at moderate spatial resolution and it is a compromise between the diversity of initial conditions and the details of underlying physics. We provide all coordinates and data of simulated particles in FITS binary tables. The main advantages of the database are VO access interfaces and value-added services which allow users to compare the results of the simulations directly to observations: stellar population modelling, dust extinction, spectra, images, visualisation using dedicated VO tools. The GalMer value-added services can be used as virtual telescope producing broadband images, 1D spectra, 3D spectral datacubes, thus making our database oriented towards the usage by observers. We present several examples of the GalMer database scientific usage obtained from the analysis of simulations and modelling their stellar population properties, including: (1) studies of the star formation efficiency in interactions; (2) creation of old counter-rotating components; (3) reshaping metallicity profiles in elliptical galaxies; (4) orbital to internal angular momentum transfer; (5) reproducing observed colour bimodality of galaxies.Comment: 15 pages, 11 figures, 10 tables accepted to A&A. Visualisation of GalMer simulations, access to snapshot files and value-added tools described in the paper are available at http://galmer.obspm.fr

FMA: A Dataset For Music Analysis

We introduce the Free Music Archive (FMA), an open and easily accessible dataset suitable for evaluating several tasks in MIR, a field concerned with browsing, searching, and organizing large music collections. The community's growing interest in feature and end-to-end learning is however restrained by the limited availability of large audio datasets. The FMA aims to overcome this hurdle by providing 917 GiB and 343 days of Creative Commons-licensed audio from 106,574 tracks from 16,341 artists and 14,854 albums, arranged in a hierarchical taxonomy of 161 genres. It provides full-length and high-quality audio, pre-computed features, together with track- and user-level metadata, tags, and free-form text such as biographies. We here describe the dataset and how it was created, propose a train/validation/test split and three subsets, discuss some suitable MIR tasks, and evaluate some baselines for genre recognition. Code, data, and usage examples are available at https://github.com/mdeff/fmaComment: ISMIR 2017 camera-read

Adaptive evolution is substantially impeded by Hill–Robertson interference in Drosophila

Hill–Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald–Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect

Spacelab software development and integration concepts study report, volume 1

The proposed software guidelines to be followed by the European Space Research Organization in the development of software for the Spacelab being developed for use as a payload for the space shuttle are documented. Concepts, techniques, and tools needed to assure the success of a programming project are defined as they relate to operation of the data management subsystem, support of experiments and space applications, use with ground support equipment, and for integration testing