Research

Under funding of the ANR GAMMA action, I pursue my studies of constrained versions of the Random Generation of combinatorial objects, mainly motivated by bioinformatics applications. In collaboration with M. Soria, A. Darrasse and C. Pivoteau, we study a transposition of Boltzmann samplers, exhaustively studied by my collaborators, to the so-called weighted random generation. This non-uniform scheme, obtained by adding weights to atomic objects, was shown to be more suitable for real-life applications. Although the generation of random objects according to a generalized Boltzmann distribution can be obtained through a simple modification of the usual Boltzmann scheme, but an analysis of the rejection still remains to be carried in such a context.

Moreover the computation of suitable weights, for which I proposed a heuristic resolution tool in my PhD thesis, could be greatly helped by recent advances obtained by C. Pivoteau, B. Salvy and M. Soria. Based on a combinatorial reinterpretation of the Newton iteration, they were able to show the convergence of such a procedure for approximating the value of a generating function, for computing its coefficients ... without solving the associated algebraic system !!! In addition to making the Boltzmann scheme fully automated, it also allows to foresee a better approach for the computation of suitable weights in the weighted scheme.

Publications

Software

    GenRGenS

    A software dedicated to the random generation of sequences. Supports different classes of models, including weighted context-free grammars, Markov models, ProSITE patterns, etc ...
    [Web site] [Reference]

    DIAL

    A web server which performs three-dimensional alignment and motif search for experimentally-determined 3D structures of RNA. Takes into account sequential, secondary structure (Determined using RNAView), and 3D backbone (Dihedral angles) similarities.
    [Webserver] [Reference]

    GenRWalks

    A Java applet coded as a proof of concept of researches (In collaboration with Mireille Bousquet-Mélou, see submitted article) led on properties of uni-dimensional walks under various constraints.
    Performs random generation and display of walks that are either unconstrained, positive or culminating on the positive quarter plane, using various algorithmic approaches (Recursive, rejection, Boltzmann sampling ...). Plus, it looks good ! ;)
    [Applet page] [Reference]

    VARNA

    A lightweight Java Applet dedicated to the quick drawing of an RNA secondary structure. VARNA is open-source and distributed under the terms of the GNU GPL license. Automatically scales up and down to take the most out of a limited space. Can draw multiple structures simultaneously. Accepts a wide range of documented and illustrated options, and offers basic user interaction.
    [Web site]