École normale supérieure de Cachan

About: École normale supérieure de Cachan is a education organization based out in Cachan, Île-de-France, France. It is known for research contribution in the topics: Decidability & Nonlinear system. The organization has 2717 authors who have published 5585 publications receiving 175925 citations.

On the Representation of de Bruijn Graphs

Abstract: The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers proposed a navigational data structure approach in order to improve memory usage. We prove several theoretical space lower bounds to show the limitations of these types of approaches. We further design and implement a general data structure dbgfm and demonstrate its use on a human whole-genome dataset, achieving space usage of 1.5 GB and a 46% improvement over previous approaches. As part of dbgfm, we develop the notion of frequency-based minimizers and show how it can be used to enumerate all maximal simple paths of the de Bruijn graph using only 43 MB of memory. Finally, we demonstrate that our approach can be integrated into an existing assembler by modifying the ABySS software to use dbgfm.

Distributed Principal Component Analysis for Wireless Sensor Networks

Abstract: The Principal Component Analysis (PCA) is a data dimensionality reduction technique well-suited for processing data from sensor networks. It can be applied to tasks like compression, event detection, and event recognition. This technique is based on a linear transform where the sensor measurements are projected on a set of principal components. When sensor measurements are correlated, a small set of principal components can explain most of the measurements variability. This allows to significantly decrease the amount of radio communication and of energy consumption. In this paper, we show that the power iteration method can be distributed in a sensor network in order to compute an approximation of the principal components. The proposed implementation relies on an aggregation service, which has recently been shown to provide a suitable framework for distributing the computation of a linear transform within a sensor network. We also extend this previous work by providing a detailed analysis of the computational, memory, and communication costs involved. A compression experiment involving real data validates the algorithm and illustrates the tradeoffs between accuracy and communication costs.

Pinning phenomena in the Ginzburg-Landau Model of Superconductivity

Abstract: We study the Ginzburg-Landau energy of superconductors with a term $a_\ep$ modelling the pinning of vortices by impurities in the limit of a large Ginzburg-Landau parameter $\kappa=1/\ep$. The function $a_\ep$ is oscillating between 1/2 and 1 with a scale which may tend to 0 as $\kappa$ tends to infinity. Our aim is to understand that in the large $\kappa$ limit, stable configurations should correspond to vortices pinned at the minimum of $a_\ep$ and to derive the limiting homogenized free-boundary problem which arises for the magnetic field in replacement of the London equation. The method and techniques that we use are inspired from those of Sandier-Serfaty (in which the case $a_\ep \equiv 1$ was treated) and based on energy estimates, convergence of measures and construction of approximate solutions. Because of the term $a_\ep(x)$ in the equations, we also need homogenization theory to describe the fact that the impurities, hence the vortices, form a homogenized medium in the material.

What else is decidable about integer arrays

Abstract: We introduce a new decidable logic for reasoning about infinite arrays of integers. The logic is in the ∃*¬* first-order fragment and allows (1) Presburger constraints on existentially quantified variables, (2) difference constraints as well as periodicity constraints on universally quantified indices, and (3) difference constraints on values. In particular, using our logic, one can express constraints on consecutive elements of arrays (e.g., ¬i ċ 0 ≤ i < n → a[i+1] = a[i]-1) as well as periodic facts (e.g., ¬i ċ i ≡2 0→ a[i] = 0). The decision procedure follows the automata-theoretic approach: we translate formulae into a special class of Buchi counter automata such that any model of a formula corresponds to an accepting run of an automaton, and vice versa. The emptiness problem for this class of counter automata is shown to be decidable as a consequence of earlier results on counter automata with a flat control structure and transitions based on difference constraints.