151 research outputs found
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins
Membrane proteins constitute a large portion of the human proteome and
perform a variety of important functions as membrane receptors, transport
proteins, enzymes, signaling proteins, and more. The computational studies of
membrane proteins are usually much more complicated than those of globular
proteins. Here we propose a new continuum model for Poisson-Boltzmann
calculations of membrane channel proteins. Major improvements over the existing
continuum slab model are as follows: 1) The location and thickness of the slab
model are fine-tuned based on explicit-solvent MD simulations. 2) The highly
different accessibility in the membrane and water regions are addressed with a
two-step, two-probe grid labeling procedure, and 3) The water pores/channels
are automatically identified. The new continuum membrane model is optimized (by
adjusting the membrane probe, as well as the slab thickness and center) to best
reproduce the distributions of buried water molecules in the membrane region as
sampled in explicit water simulations. Our optimization also shows that the
widely adopted water probe of 1.4 {\AA} for globular proteins is a very
reasonable default value for membrane protein simulations. It gives an overall
minimum number of inconsistencies between the continuum and explicit
representations of water distributions in membrane channel proteins, at least
in the water accessible pore/channel regions that we focus on. Finally, we
validate the new membrane model by carrying out binding affinity calculations
for a potassium channel, and we observe a good agreement with experiment
results.Comment: 40 pages, 6 figures, 5 table
LSUN: Construction of a Large-scale Image Dataset using Deep Learning with Humans in the Loop
While there has been remarkable progress in the performance of visual
recognition algorithms, the state-of-the-art models tend to be exceptionally
data-hungry. Large labeled training datasets, expensive and tedious to produce,
are required to optimize millions of parameters in deep network models. Lagging
behind the growth in model capacity, the available datasets are quickly
becoming outdated in terms of size and density. To circumvent this bottleneck,
we propose to amplify human effort through a partially automated labeling
scheme, leveraging deep learning with humans in the loop. Starting from a large
set of candidate images for each category, we iteratively sample a subset, ask
people to label them, classify the others with a trained model, split the set
into positives, negatives, and unlabeled based on the classification
confidence, and then iterate with the unlabeled set. To assess the
effectiveness of this cascading procedure and enable further progress in visual
recognition research, we construct a new image dataset, LSUN. It contains
around one million labeled images for each of 10 scene categories and 20 object
categories. We experiment with training popular convolutional networks and find
that they achieve substantial performance gains when trained on this dataset
SUN3D: A Database of Big Spaces Reconstructed Using SfM and Object Labels
Existing scene understanding datasets contain only a limited set of views of a place, and they lack representations of complete 3D spaces. In this paper, we introduce SUN3D, a large-scale RGB-D video database with camera pose and object labels, capturing the full 3D extent of many places. The tasks that go into constructing such a dataset are difficult in isolation -- hand-labeling videos is painstaking, and structure from motion (SfM) is unreliable for large spaces. But if we combine them together, we make the dataset construction task much easier. First, we introduce an intuitive labeling tool that uses a partial reconstruction to propagate labels from one frame to another. Then we use the object labels to fix errors in the reconstruction. For this, we introduce a generalization of bundle adjustment that incorporates object-to-object correspondences. This algorithm works by constraining points for the same object from different frames to lie inside a fixed-size bounding box, parameterized by its rotation and translation. The SUN3D database, the source code for the generalized bundle adjustment, and the web-based 3D annotation tool are all available at http://sun3d.cs.princeton.edu.American Society for Engineering Education. National Defense Science and Engineering Graduate FellowshipUnited States. Office of Naval Research. Multidisciplinary University Research Initiative (N000141010933
3D ShapeNets: A Deep Representation for Volumetric Shapes
3D shape is a crucial but heavily underutilized cue in today's computer
vision systems, mostly due to the lack of a good generic shape representation.
With the recent availability of inexpensive 2.5D depth sensors (e.g. Microsoft
Kinect), it is becoming increasingly important to have a powerful 3D shape
representation in the loop. Apart from category recognition, recovering full 3D
shapes from view-based 2.5D depth maps is also a critical part of visual
understanding. To this end, we propose to represent a geometric 3D shape as a
probability distribution of binary variables on a 3D voxel grid, using a
Convolutional Deep Belief Network. Our model, 3D ShapeNets, learns the
distribution of complex 3D shapes across different object categories and
arbitrary poses from raw CAD data, and discovers hierarchical compositional
part representations automatically. It naturally supports joint object
recognition and shape completion from 2.5D depth maps, and it enables active
object recognition through view planning. To train our 3D deep learning model,
we construct ModelNet -- a large-scale 3D CAD model dataset. Extensive
experiments show that our 3D deep representation enables significant
performance improvement over the-state-of-the-arts in a variety of tasks.Comment: to be appeared in CVPR 201
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