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.

AMOS: A Large-Scale Abdominal Multi-Organ Benchmark for Versatile Medical Image Segmentation

Abstract: Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To mitigate the limitations, we present AMOS, a large-scale, diverse, clinical dataset for abdominal organ segmentation. AMOS provides 500 CT and 100 MRI scans collected from multi-center, multi-vendor, multi-modality, multi-phase, multi-disease patients, each with voxel-level annotations of 15 abdominal organs, providing challenging examples and test-bed for studying robust segmentation algorithms under diverse targets and scenarios. We further benchmark several state-of-the-art medical segmentation models to evaluate the status of the existing methods on this new challenging dataset. We have made our datasets, benchmark servers, and baselines publicly available, and hope to inspire future research. Information can be found at https://amos22.grand-challenge.org.

Prussian blue nanocubes peroxidase mimetic-based colorimetric assay for screening acetylcholinesterase activity and its inhibitor

Abstract: In this paper, a novel, convenient and sensitive colorimetric assay for acetylcholinesterase (AChE) activity and its inhibitor screening is successfully proposed based on the peroxidase-like activity of Prussian blue nanocubes (PB NCs). PB NCs can catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB) by H2O2 to develop a blue color and an absorption peak centered at 652 nm. AChE mediates the hydrolysis of acetylthiocholine (ATCh) to yield a reducing agent thiocholine (TCh) that cause the reduction of oxidized TMB and it can also chelate with Fe3+, both of which result in a blue color fading and a decrease of the absorbance. The generation of TCh is inhibited and the absorbance intensity is recovered after the introduction of AChE inhibitor. Consequently, the assay is also utilized in AChE inhibitor screening. The PB NCs-H2O2-TMB based platform is highly sensitive for AChE activity sensing with a low detection limit of 0.04 mU/mL. In addition, this assay has great potential in discriminatively determining AChE over other enzymes. The proposed method is fairly novel, simple and sensitive, which may pave the way for the detection of other hydrolytic enzyme activities with properly selected substrates.

Synthesis and Characterization of Colloidal Core–Shell Semiconductor Nanowires

Abstract: CdSe colloidal nanowires, generated from solution-liquid-solid approach, have been coated with CdS rods (or ribbons) by using cadmium hexadecyl xanthate (Cd-HDX) as a single source precursor. The use of different solvents and ligands causes pronounced effects on the morphology of the nanowires. The coating process includes nucleation and growth of CdS nanorods onto the core CdSe nanowires, followed by ripening of the CdS nanorods to produce the desired core-shell nanowire structure.

Blockout: Dynamic Model Selection for Hierarchical Deep Networks

Abstract: Most deep architectures for image classification–even those that are trained to classify a large number of diverse categories–learn shared image representations with a single model. Intuitively, however, categories that are more similar should share more information than those that are very different. While hierarchical deep networks address this problem by learning separate features for subsets of related categories, current implementations require simplified models using fixed architectures specified via heuristic clustering methods. Instead, we propose Blockout, a method for regularization and model selection that simultaneously learns both the model architecture and parameters. A generalization of Dropout, our approach gives a novel parametrization of hierarchical architectures that allows for structure learning via back-propagation. To demonstrate its utility, we evaluate Blockout on the CIFAR and Image Net datasets, demonstrating improved classification accuracy, better regularization performance, faster training, and the clear emergence of hierarchical network structures.

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.