26,639 research outputs found
ABC likelihood-freee methods for model choice in Gibbs random fields
Gibbs random fields (GRF) are polymorphous statistical models that can be
used to analyse different types of dependence, in particular for spatially
correlated data. However, when those models are faced with the challenge of
selecting a dependence structure from many, the use of standard model choice
methods is hampered by the unavailability of the normalising constant in the
Gibbs likelihood. In particular, from a Bayesian perspective, the computation
of the posterior probabilities of the models under competition requires special
likelihood-free simulation techniques like the Approximate Bayesian Computation
(ABC) algorithm that is intensively used in population genetics. We show in
this paper how to implement an ABC algorithm geared towards model choice in the
general setting of Gibbs random fields, demonstrating in particular that there
exists a sufficient statistic across models. The accuracy of the approximation
to the posterior probabilities can be further improved by importance sampling
on the distribution of the models. The practical aspects of the method are
detailed through two applications, the test of an iid Bernoulli model versus a
first-order Markov chain, and the choice of a folding structure for two
proteins.Comment: 19 pages, 5 figures, to appear in Bayesian Analysi
Algorithm engineering for optimal alignment of protein structure distance matrices
Protein structural alignment is an important problem in computational
biology. In this paper, we present first successes on provably optimal pairwise
alignment of protein inter-residue distance matrices, using the popular Dali
scoring function. We introduce the structural alignment problem formally, which
enables us to express a variety of scoring functions used in previous work as
special cases in a unified framework. Further, we propose the first
mathematical model for computing optimal structural alignments based on dense
inter-residue distance matrices. We therefore reformulate the problem as a
special graph problem and give a tight integer linear programming model. We
then present algorithm engineering techniques to handle the huge integer linear
programs of real-life distance matrix alignment problems. Applying these
techniques, we can compute provably optimal Dali alignments for the very first
time
CLP-based protein fragment assembly
The paper investigates a novel approach, based on Constraint Logic
Programming (CLP), to predict the 3D conformation of a protein via fragments
assembly. The fragments are extracted by a preprocessor-also developed for this
work- from a database of known protein structures that clusters and classifies
the fragments according to similarity and frequency. The problem of assembling
fragments into a complete conformation is mapped to a constraint solving
problem and solved using CLP. The constraint-based model uses a medium
discretization degree Ca-side chain centroid protein model that offers
efficiency and a good approximation for space filling. The approach adapts
existing energy models to the protein representation used and applies a large
neighboring search strategy. The results shows the feasibility and efficiency
of the method. The declarative nature of the solution allows to include future
extensions, e.g., different size fragments for better accuracy.Comment: special issue dedicated to ICLP 201
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