17,574 research outputs found
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 is shown to have a phase transition at some value of
the R\'enyi parameter 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
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 models) are in agreement with the
analytical predictions: above the subleading and universal
contribution to the entropy is for open chains, and
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 . 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 to observe a given spin
configuration 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
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 , with a discontinuity at the Shannon point . 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: and 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 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 topological liquid for
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 . Fitting these cylinder data (up to a perimeter of L=32
sites) provides with a very high numerical accuracy ( at t=1 and
at ). In the topological liquid phase we find
, independent of the fugacity and the R\'enyi parameter
. At t=0 we recover a previously known result,
for . In the disk-like geometry --
designed to get rid of the boundary contributions -- we find an entropy in the whole massive phase whatever , in agreement with
the result of Flammia {\it et al.} [Phys. Rev. Lett. 103, 261601 (2009)]. Some
results for the gapless limit 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 (âI cooperate'/âI 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.
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