211,334 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
DeepCoder: Semi-parametric Variational Autoencoders for Automatic Facial Action Coding
Human face exhibits an inherent hierarchy in its representations (i.e.,
holistic facial expressions can be encoded via a set of facial action units
(AUs) and their intensity). Variational (deep) auto-encoders (VAE) have shown
great results in unsupervised extraction of hierarchical latent representations
from large amounts of image data, while being robust to noise and other
undesired artifacts. Potentially, this makes VAEs a suitable approach for
learning facial features for AU intensity estimation. Yet, most existing
VAE-based methods apply classifiers learned separately from the encoded
features. By contrast, the non-parametric (probabilistic) approaches, such as
Gaussian Processes (GPs), typically outperform their parametric counterparts,
but cannot deal easily with large amounts of data. To this end, we propose a
novel VAE semi-parametric modeling framework, named DeepCoder, which combines
the modeling power of parametric (convolutional) and nonparametric (ordinal
GPs) VAEs, for joint learning of (1) latent representations at multiple levels
in a task hierarchy1, and (2) classification of multiple ordinal outputs. We
show on benchmark datasets for AU intensity estimation that the proposed
DeepCoder outperforms the state-of-the-art approaches, and related VAEs and
deep learning models.Comment: ICCV 2017 - accepte
On-the-fly adaptivity for nonlinear twoscale simulations using artificial neural networks and reduced order modeling
A multi-fidelity surrogate model for highly nonlinear multiscale problems is
proposed. It is based on the introduction of two different surrogate models and
an adaptive on-the-fly switching. The two concurrent surrogates are built
incrementally starting from a moderate set of evaluations of the full order
model. Therefore, a reduced order model (ROM) is generated. Using a hybrid
ROM-preconditioned FE solver, additional effective stress-strain data is
simulated while the number of samples is kept to a moderate level by using a
dedicated and physics-guided sampling technique. Machine learning (ML) is
subsequently used to build the second surrogate by means of artificial neural
networks (ANN). Different ANN architectures are explored and the features used
as inputs of the ANN are fine tuned in order to improve the overall quality of
the ML model. Additional ANN surrogates for the stress errors are generated.
Therefore, conservative design guidelines for error surrogates are presented by
adapting the loss functions of the ANN training in pure regression or pure
classification settings. The error surrogates can be used as quality indicators
in order to adaptively select the appropriate -- i.e. efficient yet accurate --
surrogate. Two strategies for the on-the-fly switching are investigated and a
practicable and robust algorithm is proposed that eliminates relevant technical
difficulties attributed to model switching. The provided algorithms and ANN
design guidelines can easily be adopted for different problem settings and,
thereby, they enable generalization of the used machine learning techniques for
a wide range of applications. The resulting hybrid surrogate is employed in
challenging multilevel FE simulations for a three-phase composite with
pseudo-plastic micro-constituents. Numerical examples highlight the performance
of the proposed approach
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