16,701 research outputs found
Undersampled Phase Retrieval with Outliers
We propose a general framework for reconstructing transform-sparse images
from undersampled (squared)-magnitude data corrupted with outliers. This
framework is implemented using a multi-layered approach, combining multiple
initializations (to address the nonconvexity of the phase retrieval problem),
repeated minimization of a convex majorizer (surrogate for a nonconvex
objective function), and iterative optimization using the alternating
directions method of multipliers. Exploiting the generality of this framework,
we investigate using a Laplace measurement noise model better adapted to
outliers present in the data than the conventional Gaussian noise model. Using
simulations, we explore the sensitivity of the method to both the
regularization and penalty parameters. We include 1D Monte Carlo and 2D image
reconstruction comparisons with alternative phase retrieval algorithms. The
results suggest the proposed method, with the Laplace noise model, both
increases the likelihood of correct support recovery and reduces the mean
squared error from measurements containing outliers. We also describe exciting
extensions made possible by the generality of the proposed framework, including
regularization using analysis-form sparsity priors that are incompatible with
many existing approaches.Comment: 11 pages, 9 figure
Flexible protein folding by ant colony optimization
Protein structure prediction is one of the most challenging topics in bioinformatics.
As the protein structure is found to be closely related to its functions,
predicting the folding structure of a protein to judge its functions is meaningful to
the humanity. This chapter proposes a flexible ant colony (FAC) algorithm for solving
protein folding problems (PFPs) based on the hydrophobic-polar (HP) square lattice
model. Different from the previous ant algorithms for PFPs, the pheromones in the
proposed algorithm are placed on the arcs connecting adjacent squares in the lattice.
Such pheromone placement model is similar to the one used in the traveling salesmen
problems (TSPs), where pheromones are released on the arcs connecting the cities.
Moreover, the collaboration of effective heuristic and pheromone strategies greatly
enhances the performance of the algorithm so that the algorithm can achieve good
results without local search methods. By testing some benchmark two-dimensional
hydrophobic-polar (2D-HP) protein sequences, the performance shows that the proposed
algorithm is quite competitive compared with some other well-known methods
for solving the same protein folding problems
Free energy reconstruction from steered dynamics without post-processing
Various methods achieving importance sampling in ensembles of nonequilibrium
trajectories enable to estimate free energy differences and, by
maximum-likelihood post-processing, to reconstruct free energy landscapes.
Here, based on Bayes theorem, we propose a more direct method in which a
posterior likelihood function is used both to construct the steered dynamics
and to infer the contribution to equilibrium of all the sampled states. The
method is implemented with two steering schedules. First, using non-autonomous
steering, we calculate the migration barrier of the vacancy in Fe-alpha.
Second, using an autonomous scheduling related to metadynamics and equivalent
to temperature-accelerated molecular dynamics, we accurately reconstruct the
two-dimensional free energy landscape of the 38-atom Lennard-Jones cluster as a
function of an orientational bond-order parameter and energy, down to the
solid-solid structural transition temperature of the cluster and without
maximum-likelihood post-processing.Comment: Accepted manuscript in Journal of Computational Physics, 7 figure
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