4,156 research outputs found
iPose: Instance-Aware 6D Pose Estimation of Partly Occluded Objects
We address the task of 6D pose estimation of known rigid objects from single
input images in scenarios where the objects are partly occluded. Recent
RGB-D-based methods are robust to moderate degrees of occlusion. For RGB
inputs, no previous method works well for partly occluded objects. Our main
contribution is to present the first deep learning-based system that estimates
accurate poses for partly occluded objects from RGB-D and RGB input. We achieve
this with a new instance-aware pipeline that decomposes 6D object pose
estimation into a sequence of simpler steps, where each step removes specific
aspects of the problem. The first step localizes all known objects in the image
using an instance segmentation network, and hence eliminates surrounding
clutter and occluders. The second step densely maps pixels to 3D object surface
positions, so called object coordinates, using an encoder-decoder network, and
hence eliminates object appearance. The third, and final, step predicts the 6D
pose using geometric optimization. We demonstrate that we significantly
outperform the state-of-the-art for pose estimation of partly occluded objects
for both RGB and RGB-D input
Free energy landscape of mechanically unfolded model proteins: extended Jarzinsky versus inherent structure reconstruction
The equilibrium free energy landscape of off-lattice model heteropolymers as
a function of an internal coordinate, namely the end-to-end distance, is
reconstructed from out-of-equilibrium steered molecular dynamics data. This
task is accomplished via two independent methods: by employing an extended
version of the Jarzynski equality (EJE) and the inherent structure (IS)
formalism. A comparison of the free energies estimated with these two schemes
with equilibrium results obtained via the umbrella sampling technique reveals a
good quantitative agreement among all the approaches in a range of temperatures
around the ``folding transition'' for the two examined sequences. In
particular, for the sequence with good foldability properties, the mechanically
induced structural transitions can be related to thermodynamical aspects of
folding. Moreover, for the same sequence the knowledge of the landscape profile
allows for a good estimation of the life times of the native configuration for
temperatures ranging from the folding to the collapse temperature. For the
random sequence, mechanical and thermal unfolding appear to follow different
paths along the landscape.Comment: Latex manuscript, 20 pages, 23 figures, submitted to Physical Review
Distances and classification of amino acids for different protein secondary structures
Window profiles of amino acids in protein sequences are taken as a
description of the amino acid environment. The relative entropy or
Kullback-Leibler distance derived from profiles is used as a measure of
dissimilarity for comparison of amino acids and secondary structure
conformations. Distance matrices of amino acid pairs at different conformations
are obtained, which display a non-negligible dependence of amino acid
similarity on conformations. Based on the conformation specific distances
clustering analysis for amino acids is conducted.Comment: 15 pages, 8 figure
Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
We present the results of a self-consistent, unified molecular dynamics study
of simple model heteropolymers in the continuum with emphasis on folding,
sequence design and the determination of the interaction parameters of the
effective potential between the amino acids from the knowledge of the native
states of the designed sequences.Comment: 8 pages, 3 Postscript figures, uses RevTeX. Submitted to Physical
Review Letter
A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells
In previous works [physics/0204035, physics/0404052, physics/0509126] a
procedure was described for dividing the -dimensional
conformational space of a molecular system into a number of discrete cells,
this partition allowed the building of a combinatorial structure from data
sampled in molecular dynamics trajectories: the graph of cells, that encodes
the set of cells in conformational space that are visited by the system in its
thermal wandering. Here we outline a set of procedures for extracting useful
information from this structure: 1st) interesting regions in the volume
occupied by the system in conformational space can be bounded by a polyhedral
cone whose faces are determined empirically from a set of relations between the
coordinates of the molecule, 2nd) it is also shown that this cone can be
decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a
cone can be encoded by a simple combinatorial sequence.Comment: added an intrduction and reference
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