The structural variations of multidomain proteins with flexible parts mediate many biological processes, and a structure ensemble can be determined by selecting a weighted combination of representative structures from a simulated structure pool, producing the best fit to experimental constraints such as interatomic distance. In this study, a hybrid structure-based and physics-based atomistic force field with an efficient sampling strategy is adopted to simulate a model di-domain protein against experimental paramagnetic relaxation enhancement (PRE) data that correspond to distance constraints. The molecular dynamics simulations produce a wide range of conformations depicted on a protein energy landscape. Subsequently, a conformational ensemble recovered with low-energy structures and the minimum-size restraint is identified in good agreement with experimental PRE rates, and the result is also supported by chemical shift perturbations and small-angle X-ray scattering data. It is illustrated that the regularizations of energy and ensemble-size prevent an arbitrary interpretation of protein conformations. Moreover, energy is found to serve as a critical control to refine the structure pool and prevent data overfitting, because the absence of energy regularization exposes ensemble construction to the noise from high-energy structures and causes a more ambiguous representation of protein conformations. Finally, we perform structure-ensemble optimizations with a topology-based structure pool, to enhance the understanding on the ensemble results from different sources of pool candidates.

Remarkable achievements have been obtained by deep neural networks in the last several years. However, the breakthrough in neural networks accuracy is always accompanied by explosive growth of computation and parameters, which leads to a severe limitation of model deployment. In this paper, we propose a novel knowledge distillation technique named self-distillation to address this problem. Self-distillation attaches several attention modules and shallow classifiers at different depths of neural networks and distills knowledge from the deepest classifier to the shallower classifiers. Different from the conventional knowledge distillation methods where the knowledge of the teacher model is transferred to another student model, self-distillation can be considered as knowledge transfer in the same model - from the deeper layers to the shallow layers. Moreover, the additional classifiers in self-distillation allow the neural network to work in a dynamic manner, which leads to a much higher acceleration. Experiments demonstrate that self-distillation has consistent and significant effectiveness on various neural networks and datasets. On average, 3.49% and 2.32% accuracy boost are observed on CIFAR100 and ImageNet. Besides, experiments show that self-distillation can be combined with other model compression methods, including knowledge distillation, pruning and lightweight model design.

The Chan-Vese (CV) model is a classic region-based method in image segmentation. However, its piecewise constant assumption does not always hold for practical applications. Many improvements have been proposed but the issue is still far from well solved. In this work, we propose an unsupervised image segmentation approach that integrates the CV model with deep neural networks, which significantly improves the original CV model's segmentation accuracy. Our basic idea is to apply a deep neural network that maps the image into a latent space to alleviate the violation of the piecewise constant assumption in image space. We formulate this idea under the classic Bayesian framework by approximating the likelihood with an evidence lower bound (ELBO) term while keeping the prior term in the CV model. Thus, our model only needs the input image itself and does not require pre-training from external datasets. Moreover, we extend the idea to multi-phase case and dataset based unsupervised image segmentation. Extensive experiments validate the effectiveness of our model and show that the proposed method is noticeably better than other unsupervised segmentation approaches.

In its simplest form, convolution neural networks (CNNs) consist of a fully connected layer g composed with a sequence of convolution layers T . Although g is known to have the universal approximation property, it is not known if CNNs, which has the form g ◦ T inherits this property, especially when the kernel size in T is small. In this paper, we show that under suitable conditions, CNNs does inherit the universal approximation property and its sample complexity can be characterized. In addition, we discuss concretely how the nonlinearity of T can improve the approximation power. Finally, we show that when the target function class has a certain compositional form, convolutional networks are far more advantageous compared with fully connected networks, in terms of number of parameters needed to achieve a desired accuracy.

Collecting paired training data is difficult in practice, but the unpaired samples broadly exist. Current approaches aim at generating synthesized training data from the unpaired samples by exploring the relationship between the corrupted and clean data. This work proposes LUD-VAE, a deep generative method to learn the joint probability density function from data sampled from marginal distributions. Our approach is based on a carefully designed probabilistic graphical model in which the clean and corrupted data domains are conditionally independent. Using variational inference, we maximize the evidence lower bound (ELBO) to estimate the joint probability density function. Furthermore, we show that the ELBO is computable without paired samples under the inference invariant assumption. This property provides the mathematical rationale of our approach in the unpaired setting. Finally, we apply our method to real-world image denoising and super-resolution tasks and train the models using the synthetic data generated by the LUD-VAE. Experimental results validate the advantages of our method over other learnable approaches.