7,760 research outputs found
A^2-Net: Molecular Structure Estimation from Cryo-EM Density Volumes
Constructing of molecular structural models from Cryo-Electron Microscopy
(Cryo-EM) density volumes is the critical last step of structure determination
by Cryo-EM technologies. Methods have evolved from manual construction by
structural biologists to perform 6D translation-rotation searching, which is
extremely compute-intensive. In this paper, we propose a learning-based method
and formulate this problem as a vision-inspired 3D detection and pose
estimation task. We develop a deep learning framework for amino acid
determination in a 3D Cryo-EM density volume. We also design a sequence-guided
Monte Carlo Tree Search (MCTS) to thread over the candidate amino acids to form
the molecular structure. This framework achieves 91% coverage on our newly
proposed dataset and takes only a few minutes for a typical structure with a
thousand amino acids. Our method is hundreds of times faster and several times
more accurate than existing automated solutions without any human intervention.Comment: 8 pages, 5 figures, 4 table
Extremal Optimization for Graph Partitioning
Extremal optimization is a new general-purpose method for approximating
solutions to hard optimization problems. We study the method in detail by way
of the NP-hard graph partitioning problem. We discuss the scaling behavior of
extremal optimization, focusing on the convergence of the average run as a
function of runtime and system size. The method has a single free parameter,
which we determine numerically and justify using a simple argument. Our
numerical results demonstrate that on random graphs, extremal optimization
maintains consistent accuracy for increasing system sizes, with an
approximation error decreasing over runtime roughly as a power law t^(-0.4). On
geometrically structured graphs, the scaling of results from the average run
suggests that these are far from optimal, with large fluctuations between
individual trials. But when only the best runs are considered, results
consistent with theoretical arguments are recovered.Comment: 34 pages, RevTex4, 1 table and 20 ps-figures included, related papers
available at http://www.physics.emory.edu/faculty/boettcher
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Computing robust viewpoints with multi-constraints using tree annealing
In order to compute camera viewpoints during sensor planning, Tarabanis et al. (1991) present a group of feature detectability constraints which include six nonlinear inequalities in an eight-dimensional real space. It is difficult to compute robust viewpoints which satisfy all feature detectability constraints. In this paper, the viewpoint setting is formulated as an unconstrained optimization problem. Then a tree annealing algorithm, which is a general-purpose technique for finding minima of functions of continuously-valued variables, is applied to solve this nonlinear multiconstraint optimization problem. Our results show that the technique is quite effective to get robust viewpoints even in the presence of considerable amounts of noise
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