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Single-cell omics: experimental workflow, data analyses and applications

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Science China(Life Sciences) 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical Laboratory the Affiliated Wuhu Hospital of East China Normal University(The Second People’s Hospital of Wuhu City)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China Shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** exploration of how the genomes orchestrate the formation and maintenance of each cell,and control the cellular phenotypes of various organismsis,is both captivating and *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** technologies have expanded horizontally to include single-cell genome,epigenome,proteome,and metabolome,while vertically,they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

Almost Optimal Time Lower Bound for Approximating Parameterized Clique, CSP, and More, under ETH

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arXiv 2024年

作者： Guruswami, Venkatesan Lin, Bingkai Ren, Xuandi Sun, Yican Wu, Kewen Simons Institute for the Theory of Computing Departments of EECS and Mathematics UC Berkeley United States State Key Laboratory for Novel Software Technology Nanjing University China Department of EECS UC Berkeley United States School of Computer Science Peking University China

The Parameterized Inapproximability Hypothesis (PIH), which is an analog of the PCP theorem in parameterized complexity, asserts that, there is a constant Ε > 0 such that for any computable function f : N → N, no f(k) · nO(1)-time algorithm can, on input a k-variable CSP instance with domain size n, find an assignment satisfying 1 − Ε fraction of the constraints. A recent work by Guruswami, Lin, Ren, Sun, and Wu (STOC’24) established PIH under the Exponential Time Hypothesis (ETH). In this work, we improve the quantitative aspects of PIH and prove (under ETH) that approximating sparse parameterized CSPs within a constant factor requires nk1−o(1) time. This immediately implies that, assuming ETH, finding a (k/2)-clique in an n-vertex graph with a k-clique requires nk1−o(1) time. We also prove almost optimal time lower bounds for approximating k-ExactCover and Max k-Coverage. Our proof follows the blueprint of the previous work to identify a "vector-structured" ETH-hard CSP whose satisfiability can be checked via an appropriate form of "parallel" PCP. Using further ideas in the reduction, we guarantee additional structures for constraints in the CSP. We then leverage this to design a parallel PCP of almost linear size based on Reed-Muller codes and derandomized low degree testing. Copyright © 2024, The Authors. All rights reserved.

关键词： Blueprints

A Novel Load Balancing Scheme for Mobile Edge computing

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arXiv 2021年

作者： Duan, Zhenhua Tian, Cong Zhang, Nan Zhou, Mengchu Yu, Bin Wang, Xiaobing Guo, Jiangen Wu, Ying Institute of Computing Theory and Technology ISN Lab Xidian University Xi’an710071 China Department of Electrical and Computer Engineering New Jersey Institute of Technology NewarkNJ07102 United States

To overcome long propagation delays for data exchange between the remote cloud data center and end devices in Mobile Cloud computing (MCC), Mobile Edge computing (MEC) is emerging to push mobile computing, network control and storage to the network edges. A cloudlet in MEC is a mobility-enhanced small-scale cloud, which contains several MEC servers located in close proximity to mobile devices. The main purpose of a cloudlet is to stably provide services to mobile devices with low latency. When a cloudlet offers hundreds kinds of services to millions of mobile devices, it is critical to balance the loads so as to improve performance. In this paper, we propose a three-layer mobile hybrid hierarchical P2P (MHP2P) model as a cloudlet. MHP2P performs satisfactory service lookup efficiency and system scalability as well as high stability. More importantly, a load balance scheme is provided so that the loads of MHP2P can be well balanced with the increasing of MEC servers and query load. A large number of simulation experiments indicate that the proposed scheme is efficient for enhancing the load balancing performance in MHP2P based MEC systems. Copyright © 2021, The Authors. All rights reserved.

关键词： Mobile edge computing

GNN-Empowered Effective Partial Observation MARL Method for AoI Management in Multi-UAV Network

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arXiv 2024年

作者： Pan, Yuhao Wang, Xiucheng Xu, Zhiyao Cheng, Nan Xu, Wenchao Zhang, Jun-Jie The School of Electronic Engineering Xidian University Xi'An710071 China The State Key Laboratory of ISN School of Telecommunications Engineering Xidian University Xi'An710071 China The School of Artificial Intelligence Xidian University Xi'An710071 China The Department of Computing The Hong Kong Polytechnic University Hong Kong The Northwest Institute of Nuclear Technology Xi'An710024 China

Unmanned Aerial Vehicles (UAVs), due to their low cost and high flexibility, have been widely used in various scenarios to enhance network performance. However, the optimization of UAV trajectories in unknown areas or areas without sufficient prior information, still faces challenges related to poor planning performance and low distributed execution. These challenges arise when UAVs rely solely on their own observation information and the information from other UAVs within their communicable range, without access to global information. To address these challenges, this paper proposes the Qedgix framework, which combines graph neural networks (GNNs) and the QMIX algorithm to achieve distributed optimization of the Age of Information (AoI) for users in unknown scenarios. The framework utilizes GNNs to extract information from UAVs, users within the observable range, and other UAVs within the communicable range, thereby enabling effective UAV trajectory planning. Due to the discretization and temporal features of AoI indicators, the Qedgix framework employs QMIX to optimize distributed partially observable Markov decision processes (Dec-POMDP) based on centralized training and distributed execution (CTDE) with respect to mean AoI values of users. By modeling the UAV network optimization problem in terms of AoI and applying the Kolmogorov-Arnold representation theorem, the Qedgix framework achieves efficient neural network training through parameter sharing based on permutation invariance. Simulation results demonstrate that the proposed algorithm significantly improves convergence speed while reducing the mean AoI values of users. The code is available at https://***/UNIC-Lab/Qedgix. Copyright © 2024, The Authors. All rights reserved.

关键词： Markov processes

Experimental Demonstration of Inequivalent Mutually Unbiased Bases

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Physical Review Letters 2024年第8期132卷 080202-080202页

作者： Wen-Zhe Yan Yunting Li Zhibo Hou Huangjun Zhu Guo-Yong Xiang Chuan-Feng Li Guang-Can Guo CAS Key Laboratory of Quantum Information University of Science and Technology of China Hefei 230026 People’s Republic of China CAS Center For Excellence in Quantum Information and Quantum Physics University of Science and Technology of China Hefei 230026 People’s Republic of China State Key Laboratory of Surface Physics and Department of Physics Fudan University Shanghai 200433 China Institute for Nanoelectronic Devices and Quantum Computing Fudan University Shanghai 200433 China Center for Field Theory and Particle Physics Fudan University Shanghai 200433 China Hefei National Laboratory University of Science and Technology of China Hefei 230088 People’s Republic of China

Quantum measurements based on mutually unbiased bases (MUBs) play crucial roles in foundational studies and quantum information processing. It is known that there exist inequivalent MUBs, but little is known about their operational distinctions, not to say experimental demonstration. In this Letter, by virtue of a simple estimation problem, we experimentally demonstrate the operational distinctions between inequivalent triples of MUBs in dimension 4 based on high-precision photonic systems. The experimental estimation fidelities coincide well with the theoretical predictions with only 0.16% average deviation, which is 25 times less than the difference (4.1%) between the maximum estimation fidelity and the minimum estimation fidelity. Our experiments clearly demonstrate that inequivalent MUBs have different information extraction capabilities and different merits for quantum information processing.

关键词： Quantum foundations Quantum information processing Quantum measurements Quantum optics

Efficient generation of arbitrary photon-number-squeezed light via shortcuts to adiabaticity

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Optics Express 2025年第12期33卷 26356-26372页

作者： Jia-Wen Yu Ke-Xiong Yan Yuan Qiu Jie Song Ye-Hong Chen Yan Xia Fujian Key Laboratory of Quantum Information and Quantum Optics (Fuzhou University) Fuzhou 350116 China Department of Physics Fuzhou University Fuzhou 350116 China School of Physics Harbin Institute of Technology Harbin 150001 China Quantum Information Physics Theory Research Team RIKEN Center for Quantum computing (RQC) Wako-shi Saitama 351-0198 Japan yehong.chen@*** xia-208@***

The implementation of shortcuts to adiabaticity (STA) enables a substantial reduction in the evolution time relative to traditional adiabatic methods, concurrently mitigating detrimental environmental interference. In this manuscript, we present a protocol using STA for the one-step generation of squeezed-light states of arbitrary photons. By starting from different initial Fock states, high-fidelity (>0.99) squeezed-light states can be generated with the same control Hamiltonian. We investigate the protocol’s robustness under conditions of systematic errors and environmental noises through numerical simulations, which confirm the feasibility of the proposed scheme. The protocol may facilitate the investigation of quantum state control process, with the potential for significant impact in the near future.

关键词： Four wave mixing Numerical simulation Optical parametric oscillators Quantum electrodynamics Quantum technology Squeezed states

Parameterized Inapproximability Hypothesis under ETH

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arXiv 2023年

The Parameterized Inapproximability Hypothesis (PIH) asserts that no fixed parameter tractable (FPT) algorithm can distinguish a satisfiable CSP instance, parameterized by the number of variables, from one where every assignment fails to satisfy an ϵ fraction of constraints for some absolute constant ϵ > 0. PIH plays the role of the PCP theorem in parameterized complexity. However, PIH has only been established under Gap-ETH, a very strong assumption with an inherent gap. In this work, we prove PIH under the Exponential Time Hypothesis (ETH). This is the first proof of PIH from a gap-free assumption. Our proof is self-contained and elementary. We identify an ETH-hard CSP whose variables take vector values, and constraints are either linear or of a special parallel structure. Both kinds of constraints can be checked with constant soundness via a "parallel PCP of proximity" based on the Walsh-Hadamard code. © 2023, CC BY.

关键词： Parameterization

Feasibility Analysis of the Sanchez-Pomraning Method to Treat the Particle Size Distribution in Particle-Dispersed Fuel

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SSRN

SSRN 2024年

作者： Qin, Shuai Zhang, Qian Feng, Xing Liang, Yuechao Laboratory for Advanced Nuclear Energy Theory and Applications Zhejiang Institute of Modern Physics Department of Physics Zhejiang University Zhejiang Hangzhou310027 China Huaneng Shandong Shidao Bay Nuclear Power Co. LTD. Shandong Rongcheng264300 China Laboratory of Digitizing Software for Frontier Equipment National University of Defense Technology Hunan Changsha410073 China National Key Laboratory of Parallel and Distributed Computing National University of Defense Technology Hunan Changsha410073 China

The non-uniform size of particles appears in the particle-dispersed fuel generally, but this phenomenon is usually neglected. This study aims to evaluate the feasibility of the Sanchez-Pomraning method to solve the particle size distribution problem in particle-dispersed fuel. The Pu-rich agglomerate phenomenon in the MOX fuel and manufacturing tolerance in the Fully Ceramic Microencapsulated (FCM) fuel are calculated by ALPHA-DH code, which implements the Sanchez-Pomraning method based on the MOC transport calculation and improved subgroup resonance calculation. Numerical results show that the Sanchez-Pomraning method has the capability to treat the particle size distribution effect accurately, where the differences bwtween the Sanchez-Pomraning method and the Monte Carlo method are generally lower than 160 pcm. For the Pu-rich agglomerate phenomenon, the results show that ignoring the Pu-rich agglomerate effect introduces the reactivity difference of around 600 pcm, and ignoring the size distribution of the Pu agglomerate will cause the reactivity of up to 200 pcm in the extra-high or extra-low Pu enrichment. The more discrete size distribution and the smaller Pu-spots, the more significant influence will occur in the MOX fuel. For the FCM fuel, the influence brought by the TRISO particle size distribution can be ignored when only TRISO particles are filled. However, ignoring the size distribution when TRISO particles and poison particles are both added into the FCM fuel introduces the differences reaching 600-1000 pcm. These results demonstrate the importance of considering the particle size distribution for analyzing the MOX fuel and FCM fuel in practice. And the Sanchez-Pomraning method is reliable to analyze the effect of particle size distribution. © 2024, The Authors. All rights reserved.

关键词： Particle size analysis

Deconfined classical criticality in the anisotropic quantum spin-12 XY model on the square lattice

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arXiv 2024年

作者： Mudry, Christopher Aksoy, Ömer M. Chamon, Claudio Furusaki, Akira Condensed Matter Theory Group PSI Center for Scientific Computing Theory and Data Villigen PSI5232 Switzerland Institut de Physique EPF Lausanne LausanneCH-1015 Switzerland Department of Physics Massachusetts Institute of Technology CambridgeMA02139 United States Department of Physics Boston University BostonMA02215 United States RIKEN Center for Emergent Matter Science Saitama Wako351-0198 Japan Condensed Matter Theory Laboratory RIKEN Saitama Wako351-0198 Japan

The anisotropic quantum spin-12 XY model on a linear chain was solved by Lieb, Schultz, and Mattis in 1961 [Ann. Phys. 16, 407 (1961)] and shown to display a continuous quantum phase transition at the O(2) symmetric point separating two gapped phases with competing Ising long-range order. For the square lattice, the following is known. The two competing Ising ordered phases extend to finite temperatures, up to a boundary where a transition to the paramagnetic phase occurs, and meet at the O(2) symmetric critical line along the temperature axis that ends at a tricritical point at the Berezinskii-Kosterlitz-Thouless transition temperature where the two competing phases meet the paramagnetic phase. We show that the first-order zero-temperature (quantum) phase transition that separates the competing phases as a function of the anisotropy parameter is smoothed by thermal fluctuations into deconfined classical criticality. © 2024, CC BY.

关键词： Paramagnetism