15,958 research outputs found
Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model
Recently exciting progress has been made on protein contact prediction, but
the predicted contacts for proteins without many sequence homologs is still of
low quality and not very useful for de novo structure prediction. This paper
presents a new deep learning method that predicts contacts by integrating both
evolutionary coupling (EC) and sequence conservation information through an
ultra-deep neural network formed by two deep residual networks. This deep
neural network allows us to model very complex sequence-contact relationship as
well as long-range inter-contact correlation. Our method greatly outperforms
existing contact prediction methods and leads to much more accurate
contact-assisted protein folding. Tested on three datasets of 579 proteins, the
average top L long-range prediction accuracy obtained our method, the
representative EC method CCMpred and the CASP11 winner MetaPSICOV is 0.47, 0.21
and 0.30, respectively; the average top L/10 long-range accuracy of our method,
CCMpred and MetaPSICOV is 0.77, 0.47 and 0.59, respectively. Ab initio folding
using our predicted contacts as restraints can yield correct folds (i.e.,
TMscore>0.6) for 203 test proteins, while that using MetaPSICOV- and
CCMpred-predicted contacts can do so for only 79 and 62 proteins, respectively.
Further, our contact-assisted models have much better quality than
template-based models. Using our predicted contacts as restraints, we can (ab
initio) fold 208 of the 398 membrane proteins with TMscore>0.5. By contrast,
when the training proteins of our method are used as templates, homology
modeling can only do so for 10 of them. One interesting finding is that even if
we do not train our prediction models with any membrane proteins, our method
works very well on membrane protein prediction. Finally, in recent blind CAMEO
benchmark our method successfully folded 5 test proteins with a novel fold
The Cityscapes Dataset for Semantic Urban Scene Understanding
Visual understanding of complex urban street scenes is an enabling factor for
a wide range of applications. Object detection has benefited enormously from
large-scale datasets, especially in the context of deep learning. For semantic
urban scene understanding, however, no current dataset adequately captures the
complexity of real-world urban scenes.
To address this, we introduce Cityscapes, a benchmark suite and large-scale
dataset to train and test approaches for pixel-level and instance-level
semantic labeling. Cityscapes is comprised of a large, diverse set of stereo
video sequences recorded in streets from 50 different cities. 5000 of these
images have high quality pixel-level annotations; 20000 additional images have
coarse annotations to enable methods that leverage large volumes of
weakly-labeled data. Crucially, our effort exceeds previous attempts in terms
of dataset size, annotation richness, scene variability, and complexity. Our
accompanying empirical study provides an in-depth analysis of the dataset
characteristics, as well as a performance evaluation of several
state-of-the-art approaches based on our benchmark.Comment: Includes supplemental materia
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