Bootstrap for neural model selection

Bootstrap techniques (also called resampling computation techniques) have introduced new advances in modeling and model evaluation. Using resampling methods to construct a series of new samples which are based on the original data set, allows to estimate the stability of the parameters. Properties such as convergence and asymptotic normality can be checked for any particular observed data set. In most cases, the statistics computed on the generated data sets give a good idea of the confidence regions of the estimates. In this paper, we debate on the contribution of such methods for model selection, in the case of feedforward neural networks. The method is described and compared with the leave-one-out resampling method. The effectiveness of the bootstrap method, versus the leave-one-out methode, is checked through a number of examples.Comment: A la suite de la conf\'{e}rence ESANN 200

A polynomial delay algorithm for the enumeration of bubbles with length constraints in directed graphs and its application to the detection of alternative splicing in RNA-seq data

We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced by RNA-seq. This is the first polynomial-delay algorithm for this problem and we show that in practice, it is faster than previous approaches. This enables us to deal with larger instances and therefore to discover novel alternative splicing events, especially long ones, that were previously overseen using existing methods.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Phase transition in the R\'enyi-Shannon entropy of Luttinger liquids

The R\'enyi-Shannon entropy associated to critical quantum spins chain with central charge $c=1$ is shown to have a phase transition at some value $n_c$ of the R\'enyi parameter $n$ which depends on the Luttinger parameter (or compactification radius R). Using a new replica-free formulation, the entropy is expressed as a combination of single-sheet partition functions evaluated at $n-$ dependent values of the stiffness. The transition occurs when a vertex operator becomes relevant at the boundary. Our numerical results (exact diagonalizations for the XXZ and $J_1-J_2$ models) are in agreement with the analytical predictions: above $n_c=4/R^2$ the subleading and universal contribution to the entropy is $\ln(L)(R^2-1)/(4n-4)$ for open chains, and $\ln(R)/(1-n)$ for periodic ones (R=1 at the free fermion point). The replica approach used in previous works fails to predict this transition and turns out to be correct only for $n<n_c$. From the point of view of two-dimensional Rokhsar-Kivelson states, the transition reveals a rich structure in the entanglement spectra.Comment: 4 pages, 3 figure

R\'enyi entropy of a line in two-dimensional Ising models

We consider the two-dimensional (2d) Ising model on a infinitely long cylinder and study the probabilities $p_i$ to observe a given spin configuration $i$ along a circular section of the cylinder. These probabilities also occur as eigenvalues of reduced density matrices in some Rokhsar-Kivelson wave-functions. We analyze the subleading constant to the R\'enyi entropy $R_n=1/(1-n) \ln (\sum_i p_i^n)$ and discuss its scaling properties at the critical point. Studying three different microscopic realizations, we provide numerical evidence that it is universal and behaves in a step-like fashion as a function of $n$, with a discontinuity at the Shannon point $n=1$. As a consequence, a field theoretical argument based on the replica trick would fail to give the correct value at this point. We nevertheless compute it numerically with high precision. Two other values of the R\'enyi parameter are of special interest: $n=1/2$ and $n=\infty$ are related in a simple way to the Affleck-Ludwig boundary entropies associated to free and fixed boundary conditions respectively.Comment: 8 pages, 6 figures, 2 tables. To be submitted to Physical Review

R\'enyi entanglement entropies in quantum dimer models : from criticality to topological order

Thanks to Pfaffian techniques, we study the R\'enyi entanglement entropies and the entanglement spectrum of large subsystems for two-dimensional Rokhsar-Kivelson wave functions constructed from a dimer model on the triangular lattice. By including a fugacity $t$ on some suitable bonds, one interpolates between the triangular lattice (t=1) and the square lattice (t=0). The wave function is known to be a massive $\mathbb Z_2$ topological liquid for $t>0$ whereas it is a gapless critical state at t=0. We mainly consider two geometries for the subsystem: that of a semi-infinite cylinder, and the disk-like setup proposed by Kitaev and Preskill [Phys. Rev. Lett. 96, 110404 (2006)]. In the cylinder case, the entropies contain an extensive term -- proportional to the length of the boundary -- and a universal sub-leading constant $s_n(t)$. Fitting these cylinder data (up to a perimeter of L=32 sites) provides $s_n$ with a very high numerical accuracy ($10^{-9}$ at t=1 and $10^{-6}$ at $t=0.5$). In the topological $\mathbb{Z}_2$ liquid phase we find $s_n(t>0)=-\ln 2$, independent of the fugacity $t$ and the R\'enyi parameter $n$. At t=0 we recover a previously known result, $s_n(t=0)=-(1/2)\ln(n)/(n-1)$ for $n1$. In the disk-like geometry -- designed to get rid of the boundary contributions -- we find an entropy $s^{\rm KP}_n(t>0)=-\ln 2$ in the whole massive phase whatever $n>0$, in agreement with the result of Flammia {\it et al.} [Phys. Rev. Lett. 103, 261601 (2009)]. Some results for the gapless limit $R^{\rm KP}_n(t\to 0)$ are discussed.Comment: 33 pages, 17 figures, minor correction

Navigating in a sea of repeats in RNA-seq without drowning

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which transposable elements are one of the main examples. Most transcriptome assemblers are based on de Bruijn graphs and have no clear and explicit model for repeats in RNA-seq data, relying instead on heuristics to deal with them. The results of this work are twofold. First, we introduce a formal model for repre- senting high copy number repeats in RNA-seq data and exploit its properties for inferring a combinatorial characteristic of repeat-associated subgraphs. We show that the problem of identifying in a de Bruijn graph a subgraph with this charac- teristic is NP-complete. In a second step, we show that in the specific case of a local assembly of alternative splicing (AS) events, we can implicitly avoid such subgraphs. In particular, we designed and implemented an algorithm to efficiently identify AS events that are not included in repeated regions. Finally, we validate our results using synthetic data. We also give an indication of the usefulness of our method on real data

Cooperation, the power of a single word. Some experimental evidence on wording and gender effects in a Game of Chicken

Wording has been widely shown to affect decision making. In this paper, we investigate experimentally whether and to what extent, cooperative behaviour in a Game of Chicken may be impated by a very basic change in the labelling of the strategies. Our within-subject experimental design involves two treatments. The only difference between them is that we introduce either a socially-oriented wording (‘I cooperate'/‘I do not cooperate') or colours (red/blue) to designate strategies. The level of cooperation appears to be higher in the socially-oriented context, but only when the uncertainty as regards the type of the partner is manipulated, and especially among females.Social dilemma, Game of Chicken, cooperation, wording effects, gender effects.