Zhen Li

Bio: Zhen Li is an academic researcher from Wuhan University. The author has contributed to research in topics: Medicine & Computer science. The author has an hindex of 127, co-authored 1712 publications receiving 71351 citations. Previous affiliations of Zhen Li include Tsinghua University & Hong Kong University of Science and Technology.

PointASNL: Robust Point Clouds Processing using Nonlocal Neural Networks with Adaptive Sampling

Abstract: Raw point clouds data inevitably contains outliers or noise through acquisition from 3D sensors or reconstruction algorithms. In this paper, we present a novel end-to-end network for robust point clouds processing, named PointASNL, which can deal with point clouds with noise effectively. The key component in our approach is the adaptive sampling (AS) module. It first re-weights the neighbors around the initial sampled points from farthest point sampling (FPS), and then adaptively adjusts the sampled points beyond the entire point cloud. Our AS module can not only benefit the feature learning of point clouds, but also ease the biased effect of outliers. To further capture the neighbor and long-range dependencies of the sampled point, we proposed a local-nonlocal (L-NL) module inspired by the nonlocal operation. Such L-NL module enables the learning process insensitive to noise. Extensive experiments verify the robustness and superiority of our approach in point clouds processing tasks regardless of synthesis data, indoor data, and outdoor data with or without noise. Specifically, PointASNL achieves state-of-the-art robust performance for classification and segmentation tasks on all datasets, and significantly outperforms previous methods on real-world outdoor SemanticKITTI dataset with considerate noise. Our code is released through this https URL.

Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model

Abstract: Motivation: Protein contacts contain key information for the understanding of protein structure and function and thus, contact prediction from sequence is an important problem. Recently exciting progress has been made on this problem, but the predicted contacts for proteins without many sequence homologs is still of low quality and not extremely useful for de novo structure prediction. Method: 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 neural networks. The first residual network conducts a series of 1-dimensional convolutional transformation of sequential features; the second residual network conducts a series of 2-dimensional convolutional transformation of pairwise information including output of the first residual network, EC information and pairwise potential. By using very deep residual networks, we can model very complex relationship between sequence and contact map as well as long-range interdependency between contacts and thus, obtain high-quality contact prediction. Results: Our method greatly outperforms existing contact prediction methods and leads to much more accurate contact-assisted protein folding. Tested on the 105 CASP11 targets, 76 CAMEO test proteins and 398 membrane 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 of the 579 test proteins, while that using MetaPSICOV- and CCMpred-predicted contacts can do so for only 79 and 62 of them, respectively. Further, our contact-assisted models also have much better quality than template-based models (especially for membrane proteins). 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 contact prediction. In the recent blind CAMEO benchmark, our method successfully folded one mainly-beta protein of 182 residues with a novel fold.

AIEgen with Fluorescence–Phosphorescence Dual Mechanoluminescence at Room Temperature

Abstract: We report the first example of an AIEgen (DPP-BO) with fluorescence-phosphorescence dual emission under mechanical stimulation. By carefully analyzing the crystal structure of DPP-BO, the efficient intermolecular and intramolecular interactions should account for its unique mechanoluminescence (ML) properties, especially the abnormal phosphorescence, as further confirmed by controlled experiments and theoretical calculations for the presence of ISC transitions. These results provide important information for understanding the complex ML process, possibly opening up a new way to study the inherent mechanism of ML by broadening the application of AIEgens.

I and i

Abstract: There is, I think, something ethereal about i —the square root of minus one. I remember first hearing about it at school. It seemed an odd beast at that time—an intruder hovering on the edge of reality. Usually familiarity dulls this sense of the bizarre, but in the case of i it was the reverse: over the years the sense of its surreal nature intensified. It seemed that it was impossible to write mathematics that described the real world in …

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Highly accurate protein structure prediction with AlphaFold

Abstract: Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort1–4, the structures of around 100,000 unique proteins have been determined5, but this represents a small fraction of the billions of known protein sequences6,7. Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to address this gap and to enable large-scale structural bioinformatics. Predicting the three-dimensional structure that a protein will adopt based solely on its amino acid sequence—the structure prediction component of the ‘protein folding problem’8—has been an important open research problem for more than 50 years9. Despite recent progress10–14, existing methods fall far short of atomic accuracy, especially when no homologous structure is available. Here we provide the first computational method that can regularly predict protein structures with atomic accuracy even in cases in which no similar structure is known. We validated an entirely redesigned version of our neural network-based model, AlphaFold, in the challenging 14th Critical Assessment of protein Structure Prediction (CASP14)15, demonstrating accuracy competitive with experimental structures in a majority of cases and greatly outperforming other methods. Underpinning the latest version of AlphaFold is a novel machine learning approach that incorporates physical and biological knowledge about protein structure, leveraging multi-sequence alignments, into the design of the deep learning algorithm. AlphaFold predicts protein structures with an accuracy competitive with experimental structures in the majority of cases using a novel deep learning architecture.