Condensed Matter Theory

Abstract:

We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.

Abstract:

© 7th International Conference on Learning Representations, ICLR 2019. All Rights Reserved. Deep neural networks (DNNs) generalize remarkably well without explicit regularization even in the strongly over-parametrized regime where classical learning theory would instead predict that they would severely overfit. While many proposals for some kind of implicit regularization have been made to rationalise this success, there is no consensus for the fundamental reason why DNNs do not strongly overfit. In this paper, we provide a new explanation. By applying a very general probability-complexity bound recently derived from algorithmic information theory (AIT), we argue that the parameter-function map of many DNNs should be exponentially biased towards simple functions. We then provide clear evidence for this strong bias in a model DNN for Boolean functions, as well as in much larger fully conected and convolutional networks trained on CIFAR10 and MNIST. As the target functions in many real problems are expected to be highly structured, this intrinsic simplicity bias helps explain why deep networks generalize well on real world problems. This picture also facilitates a novel PAC-Bayes approach where the prior is taken over the DNN input-output function space, rather than the more conventional prior over parameter space. If we assume that the training algorithm samples parameters close to uniformly within the zero-error region then the PAC-Bayes theorem can be used to guarantee good expected generalization for target functions producing high-likelihood training sets. By exploiting recently discovered connections between DNNs and Gaussian processes to estimate the marginal likelihood, we produce relatively tight generalization PAC-Bayes error bounds which correlate well with the true error on realistic datasets such as MNIST and CIFAR10and for architectures including convolutional and fully connected networks.