Evaluating strategies of phylogenetic analyses by the coherence of their results

I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more it reflects the historical signal common to the analysed data. Under this hypothesis, the capacity of an analytical strategy to extract historical signal should correlate positively with the coherence of the obtained results. I apply this approach to a series of analyses on empirical data, basing the coherence measure on the Robinson-Foulds distances between the obtained trees. At first approximation, the analytical strategies most suitable for the data produce the most coherent results. However, risks of false positives and false negatives are identified, which are difficult to rule out.Comment: 6 pages, 3 figures, accepted for publication in Comptes Rendus Palevol, based on a work presented at the "Journ\'ees d'automne 2012 de la Soci\'et\'e Fran\c{c}aise de Syst\'ematique" (http://www.normalesup.org/~bli/Papers/SFS_2012_BL.pdf

Resolving tricky nodes in the tree of life through amino acid recoding

Genomic data allowed a detailed resolution of the Tree of Life, but ''tricky nodes'' such as the root of the animals remain unresolved. Genome-scale datasets are heterogeneous as genes and species are exposed to different pressures, and this can negatively impacts phylogenetic accuracy. We use simulated genomic- scale datasets and show that recoding amino acid data improves accuracy when the model does not account for the compositional heterogeneity of the amino acid alignment. We apply our findings to three datasets addressing the root of the animal tree, where the debate centers on whether sponges (Porifera) or comb jellies (Ctenophora) represent the sister of all other animals. We show that results from empirical data follow predictions from simulations and suggest that, at the least in phylogenies inferred from amino acid sequences, a placement of the ctenophores as sister to all the other animals is best explained as a tree reconstruction artifact

Models and algorithms for the microdata protection problem

This article focuses on the mathematical modeling and an algorithmic approach to microdata protection based on a strategy of local suppression and global recoding. Protecting sensitive individual information using such an approach must be balanced against the usefulness of the resulting edited datafile. We discuss the two subproblems of suppression and recoding of microdata in light of the information loss that occurs. We combine them into an overall disclosure problem formulated as a combinatorial optimization problem. We describe how to decompose the problem into smaller more tractable parts and how to use local search methods to find good approximations of the optimal solution.Keywords:Mathematical modeling; optimization algorithms. <br/

On Using Expansions to the Base of -2

This short note investigates the effects of using expansions to the base of -2. The main applications we have in mind are cryptographic protocols, where the crucial operation is computation of scalar multiples. For the recently proposed groups arising from Picard curves this leads to a saving of at least 7% for the computation of an m-fold. For more general non-hyperelliptic genus 3 curves we expect a larger speed-up.Comment: 5 page

Pastiche

The term "pastiche" originally means a "pasty" or "pie" dish containing several different ingredients. It has come to be used synonymously with a variety of terms whose meanings are rarely fixed with clarity: parody, montage, quotation, allusion, irony, burlesque, travesty, and plagiarism. Al;though some definitions of pastiche strive to remain neutral, others have taken on a pejorative sense. Still others are more positive, especially within the realms of twentieth-century postmodern art and architecture

Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology

This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).&#xd;&#xa

A new Low-Power recoding algorithm for multiplierless single/multiple constant multiplication.

International audienceOptimizing the number of additions in constant coefficient multiplication is conjectured to be a NP-hard problem. In this paper, we report a new heuristic requiring an average of 29.10 % and 10.61 % less additions than the standard canonical signed digit representation (CSD) and the double base number system (DBNS), respectively, for 64-bit coefficients. The maximum number of additions per coefficient is bounded by (N/4)+2, and the time-complexity of the recoding is linearly proportional to N, where N is the bit-size of the constant. These performances are achieved using a new redundant version of radix-28 recoding