Hong Zhang

YuPeng Huang, Hong Zhang, Siyuan Jiang et al.

Virtual screening, including molecular docking, plays an essential role in drug discovery. Many traditional and machine-learning based methods are available to fulfil the docking task. The traditional docking methods are normally extensively time-consuming, and their performance in blind docking remains to be improved. Although the runtime of docking based on machine learning is significantly decreased, their accuracy is still limited. In this study, we take the advantage of both traditional and machine-learning based methods, and present a method Deep Site and Docking Pose (DSDP) to improve the performance of blind docking. For the traditional blind docking, the entire protein is covered by a cube, and the initial positions of ligands are randomly generated in the cube. In contract, DSDP can predict the binding site of proteins and provide an accurate searching space and initial positions for the further conformational sampling. The docking task of DSDP makes use of the score function and a similar but modified searching strategy of AutoDock Vina, accelerated by implementation in GPUs. We systematically compare its performance with the state-of-the-art methods, including Autodock Vina, GNINA, QuickVina, SMINA, and DiffDock. DSDP reaches a 29.8% top-1 success rate (RMSD < 2 Å) on an unbiased and challenging test dataset with 1.2 s wall-clock computational time per system. Its performances on DUD-E dataset and the time-split PDBBind dataset used in EquiBind, TankBind, and DiffDock are also effective, presenting a 57.2% and 41.8% top-1 success rate with 0.8 s and 1.0 s per system, respectively.

Yulin Wang, Xuran Pan, Shiji Song et al.

In this paper, we propose a novel implicit semantic data augmentation (ISDA) approach to complement traditional augmentation techniques like flipping, translation or rotation. Our work is motivated by the intriguing property that deep networks are surprisingly good at linearizing features, such that certain directions in the deep feature space correspond to meaningful semantic transformations, e.g., adding sunglasses or changing backgrounds. As a consequence, translating training samples along many semantic directions in the feature space can effectively augment the dataset to improve generalization. To implement this idea effectively and efficiently, we first perform an online estimate of the covariance matrix of deep features for each class, which captures the intra-class semantic variations. Then random vectors are drawn from a zero-mean normal distribution with the estimated covariance to augment the training data in that class. Importantly, instead of augmenting the samples explicitly, we can directly minimize an upper bound of the expected cross-entropy (CE) loss on the augmented training set, leading to a highly efficient algorithm. In fact, we show that the proposed ISDA amounts to minimizing a novel robust CE loss, which adds negligible extra computational cost to a normal training procedure. Although being simple, ISDA consistently improves the generalization performance of popular deep models (ResNets and DenseNets) on a variety of datasets, e.g., CIFAR-10, CIFAR-100 and ImageNet. Code for reproducing our results is available at https://github.com/blackfeather-wang/ISDA-for-Deep-Networks.

Moein Shakeri, Hong Zhang

Extracting moving objects from a video sequence and estimating the background of each individual image are fundamental issues in many practical applications such as visual surveillance, intelligent vehicle navigation, and traffic monitoring. Recently, some methods have been proposed to detect moving objects in a video via low-rank approximation and sparse outliers where the background is modeled with the computed low-rank component of the video and the foreground objects are detected as the sparse outliers in the low-rank approximation. All of these existing methods work in a batch manner, preventing them from being applied in real time and long duration tasks. In this paper, we present an online sequential framework, namely contiguous outliers representation via online low-rank approximation (COROLA), to detect moving objects and learn the background model at the same time. We also show that our model can detect moving objects with a moving camera. Our experimental evaluation uses simulated data and real public datasets and demonstrates the superior performance of COROLA in terms of both accuracy and execution time.