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Dear-DIA^(XMBD): Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

Research 2024年第1期6卷 707-720页

作者： Qingzu He Chuan-Qi Zhong Xiang Li Huan Guo Yiming Li Mingxuan Gao Rongshan Yu Xianming Liu Fangfei Zhang Donghui Guo Fangfu Ye Tiannan Guo Jianwei Shuai Jiahuai Han Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials ResearchXiamen UniversityXiamen 361005China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)and Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325001China School of Life Sciences Xiamen UniversityXiamen 361102China State Key Laboratory of Cellular Stress Biology Innovation Center for Cell Signaling NetworkXiamen 361102China Department of Computer Science Xiamen UniversityXiamen 361005China National Institute for Data Science in Health and Medicine School of MedicineXiamen UniversityXiamen 361102China Bruker(Beijing)Scientific Technology Co.Ltd. BeijingChina Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhou 310024China Westlake Omics Ltd. Yunmeng Road 1HangzhouChina Department of Electronic Engineering Xiamen UniversityXiamen 361005China

Data-Independent acquisition(DIA)technology for protein identification from mass spectrometry and related algorithms is developing rapidly.The spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising direction.In this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA data.Dear-DIA^(XMBD) first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms,then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes,and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and peptides.We show that Dear-DIA^(XMBD) performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms.

关键词： Deep Auto Independent

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Cosmology-Independent Photon Mass Limits from Localized Fast Radio Bursts by Using Artificial Neural Networks

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Chinese Physics Letters 2024年第5期41卷 177-183页

作者：冉景遇王宝魏俊杰 Purple Mountain Observatory Chinese Academy of SciencesNanjing 210023China School of Astronomy and Space Sciences University of Science and Technology of ChinaHefei 230026China

A hypothetical photon mass m_(γ) can produce a frequency-dependent vacuum dispersion of light, which leads to an additional time delay between photons with different frequencies when they propagate through a fixed distance. The dispersion measure and redshift measurements of fast radio bursts(FRBs) have been widely used to constrain the rest mass of the photon. However, all current studies analyzed the effect of the frequency-dependent dispersion for massive photons in the standard ΛCDM cosmological context. In order to alleviate the circularity problem induced by the presumption of a specific cosmological model based on the fundamental postulate of the masslessness of photons, here we employ a new model-Independent smoothing technique, artificial neural network(ANN), to reconstruct the Hubble parameter H(z) function from 34 cosmic-chronometer measurements.By combining observations of 32 well-localized FRBs and the H(z) function reconstructed by ANN, we obtain an upper limit of m_(γ) ≤ 3.5 × 10^(-51)kg, or equivalently m_(γ) ≤ 2.0 × 10^(-15)eV/c^(2)(m_(γ) ≤ 6.5 × 10^(-51)kg, or equivalently m_(γ) ≤ 3.6 × 10^(-15)eV/c_(2)) at the 1σ(2σ) confidence level. This is the first cosmology-Independent photon mass limit derived from extragalactic sources.

关键词： dispersion limit Independent

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Five Independent Cases of Human Infection with Avian Influenza H5N6—Sichuan Province,China,2021

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China CDC weekly 2021年第36期3卷 751-756,I0001页

作者： Chongkun Xiao Jianan Xu Yu Lan Zhongping Huang Lijun Zhou Yaxin Guo Xiyan Li Lei Yang George F.Gao Dayan Wang William J.Liu Xingyu Zhou Huiping Yang Sichuan Center for Disease Control and Prevention ChengduSichuanChina NHC Key Laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina.

Summary What is known about this topic?The emerging H5Ny lineages of the avian influenza virus(AIV)with genomic reassortments have posed a continuous threat to animals and human beings.Since the first case of avian influenza A(H5N6)virus infection in 2014,the World Health Organization has reported a total of 38 cases by August 6,2021.

关键词： H5N6 Independent Human

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Independent Component Analysis and Graph Theoretical Analysis in Patients with Narcolepsy

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Neuroscience Bulletin 2019年第4期35卷 743-755页

作者： Fulong Xiao Chao Lu Dianjiang Zhao Qihong Zou Liyue Xu Jing Li Jun Zhang Fang Han Sleep Medicine Center Department of Respiratory and Critical Care Medicine Peking University People's Hospital Beijing 100044 China Department of Radiology Peking University International Hospital Beijing 102206 China Center for MRI Research Academy for Advanced Interdisciplinary Studies Peking University Beijing 100871 China PKU-UPenn Sleep Center Peking University International Hospital Beijing 102206 China Department of Neurology Peking University People's Hospital Beijing 100044 China

The present study was aimed to evaluate restingstate functional connectivity and topological properties of brain networks in narcolepsy patients compared with healthy controls.Resting-state fMRI was performed in 26 adult narcolepsy patients and 30 matched healthy controls.MRI data were first analyzed by group Independent component analysis,then a graph theoretical method was applied to evaluate the topological properties in the whole brain.Small-world network parameters and nodal topological properties were measured.Altered topological properties in brain areas between groups were selected as regionof-interest seeds,then the functional connectivity among these seeds was compared between groups.Partial correlation analysis was performed to evaluate the relationship between the severity of sleepiness and functional connectivity or topological properties in the narcolepsy patients.Twenty-one Independent components out of 48 were obtained.Compared with healthy controls,the narcolepsy patients exhibited significantly decreased functional connectivity within the executive and salience networks,along with increased functional connectivity in the bilateral frontal lobes within the executive network.There were no differences in small-world network properties between patients and controls.The altered brain areas in nodal topological properties between groups were mainly in the inferior frontal cortex,basal ganglia,anterior cingulate,sensory cortex,supplementary motor cortex,and visual cortex.In the partial correlation analysis,nodal topological properties in the putamen,anterior cingulate,and sensory cortex as well as functional connectivity between these regions were correlated with the severity of sleepiness(sleep latency,REM sleep latency,and Epworth sleepiness score)among narcolepsy patients.Altered connectivity within the executive and salience networks was found in narcolepsy patients.Functional connection changes between the left frontal cortex and left caudate nucleus may be one of the parameters describing the sev

关键词： Narcolepsy Functional connectivity Independent component analysis Graph theory

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Continuous-Variable Measurement-Device-Independent Quantum Key Distribution with One-Time Shot-Noise Unit Calibration

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Chinese Physics Letters 2021年第4期38卷 1-6页

作者：黄露雨张一辰喻松 State Key Laboratory of Information Photonics and Optical Communications Beijing University of Posts and TelecommunicationsBeijing 100876China

Imperfections in practical detectors,including limited detection efficiency,and inherent electronic noise,can seriously decrease the transmission distance of continuous-variable measurement-device-Independent quantum key distribution systems.Owing to the difficulties inherent in realizing a high-efficiency fiber homodyne detector,challenges still exist in continuous-variable measurement-device-Independent quantum key distribution system implementation.We offer an alternative approach in an attempt to solve these difficulties and improve the potential for system implementation.Here,a novel practical detector modeling method is utilized,which is combined with a one-time shot-noise-unit calibration method for the purpose of system realization.The new modeling method benefits greatly from taking advantage of one-time shot-noise-unit calibration methods,such as measuring electronic noise and shot noise directly to a novel shot-noise unit,so as to eliminate the statistical fluctuations found in previous methods;this makes the implementation of such systems simpler,and the calibration progress more accurate.We provide a simulation of the secret key rate versus distance with different parameters.In addition,the minimal detection efficiency required at each distance,as well as the contrast between the two methods,are also shown,so as to provide a reference in terms of system realization.

关键词： realization Independent eliminate

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Quantum Algorithm for Approximating Maximum Independent Sets

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Chinese Physics Letters 2021年第3期38卷 17-21页

作者：余泓烨 Frank Wilczek 吴飙 Department of Physics and Astronomy Stony Brook UniversityStony BrookNY 11794USA Center for Theoretical Physics Massachusetts Institute of TechnologyCambridgeMassachusetts 02139USA D.Lee Institute Shanghai Jiao Tong UniversityShanghai 200240China Wilczek Quantum Center School of Physics and AstronomyShanghai Jiao Tong UniversityShanghai 200240China Department of Physics Stockholm UniversityStockholm SE-10691Sweden Department of Physics and Origins Project Arizona State UniversityTempe AZ 25287USA International Center for Quantum Materials School of PhysicsPeking UniversityBeijing 100871China Collaborative Innovation Center of Quantum Matter Beijing 100871China

We present a quantum algorithm for approximating maximum Independent sets of a graph based on quantum non-Abelian adiabatic mixing in the sub-Hilbert space of degenerate ground states,which generates quantum annealing in a secondary Hamiltonian.For both sparse and dense random graphs G,numerical simulation suggests that our algorithm on average finds an Independent set of size close to the maximum size α(G) in low polynomial time.The best classical algorithms,by contrast,produce Independent sets of size about half of α(G)in polynomial time.

关键词： quantum polynomial Independent

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Batch process monitoring based on WGNPE–GSVDD related and Independent variables

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Chinese Journal of Chemical Engineering 2018年第12期26卷 2549-2561页

作者： Yongyong Hui Xiaoqiang Zhao College of Electrical and Information Engineering Lanzhou University of Technology Lanzhou 730050China Key Laboratory of Gansu Advanced Control for Industrial Processes Lanzhou University of TechnologyLanzhou 730050China National Experimental Teaching Center of Electrical and Control Engineering Lanzhou University of TechnologyLanzhou 730050China

In many batch processes, there are related or independence relationships among process variables. The traditional monitoring method usually carries out a single statistical model according to the related or Independent method, and in the feature extraction there is not fully taken into account the characterization of fault information, it will make the process monitoring ineffective, so a fault monitoring method based on WGNPE(weighted global neighborhood preserving embedding)–GSVDD(greedy support vector data description) related and Independent variables is proposed. First, mutual information method is used to separate the related variables and Independent variables. Secondly, WGNPE method is used to extract the local and global structures of the related variables in batch process and highlight the fault information, GSVDD method is used to extract the process information of the Independent variables quickly and effectively. Finally, the statistical monitoring model is established to achieve process monitoring based on WGNPE and GSVDD. The effectiveness of the proposed method was verified by the penicillin fermentation process.

关键词： Batch process Monitoring Related and Independent variables Global-local Support vector data description

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广义Independent Biclique攻击框架及其应用

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计算机学报 2018年第2期41卷 349-367页

作者：崔竞一郭建胜刘翼鹏信息工程大学郑州450001 信息保障技术重点实验室北京100072

该文对Biclique攻击框架及其实现方法进行了研究.Biclique攻击是一种结合Biclique初始结构与中间相遇攻击的一种攻击方法,有平衡Biclique攻击、非平衡Biclique攻击、Star攻击等多种攻击形式.该文提出了广义Biclique结构的概念,对Bicliqu... 详细信息

该文对Biclique攻击框架及其实现方法进行了研究.Biclique攻击是一种结合Biclique初始结构与中间相遇攻击的一种攻击方法,有平衡Biclique攻击、非平衡Biclique攻击、Star攻击等多种攻击形式.该文提出了广义Biclique结构的概念,对Biclique结构重新进行了定义,涵盖了现有Biclique结构.同时提出了一种广义Biclique结构分类方式,按照维数分为高维Biclique结构与低维Biclique结构.通过进一步研究发现,高维Biclique结构可由低维Biclique结构直接构造得到,从而提出了一种高维Biclique结构构造方法,降低了结构构造过程的复杂度,同时利用该方法所得到的Biclique结构,结合计算与预计算技术,可以给出时间复杂度更优的Biclique攻击结果.在此基础上,设计并提出了一个广义Independent Biclique攻击框架,借助自动化实现技术能够面向比特构造出算法包括平衡Biclique结构、Star结构、非平衡Biclique结构在内的多种结构,同时能够给出算法在广义Biclique攻击下的安全性分析结果.最后,以LBlock算法为例,利用框架综合分析了其在Biclique攻击下的安全性,同时改进了AES-128算法基于Star结构的相关分析结果.获得分析结果如下:(1)针对LBlock算法,分别给出了两个低维Biclique攻击结果与两个高维Biclique攻击结果.构造了明文方向6轮4维的平衡Biclique结构,给出了数据复杂度更优的平衡Biclique攻击结果,其时间复杂度为2^(78.425)次全轮LBlock算法加密,数据复杂度为2^(40)选择明文;构造了明文方向6轮4维Star结构,给出了首个最低数据复杂度下全轮LBlock算法攻击结果,时间复杂度为2^(78.66)次全轮LBlock算法加密,数据复杂度为2个已知明文;构造了明文方向6轮8维平衡Biclique结构,给出了目前最优的全轮LBlock算法分析结果,其时间复杂度为2^(78.14)次全轮LBlock算法加密,数据复杂度为2^(60)个选择明文;构造了明文方向6轮规模2~4×2~8的非平衡Biclique结构,在2^(40)个选择明文条件下,给出了时间复杂度为2^(78.24)的全轮LBlock算法分析结果;(2)针对AES-128算法,改进了算法在Star攻击下的安全性.通过构造密文方向2.5轮Star结构代替明文方向的2轮Star结构,改进了最低数据复杂度下全轮AES-128的分析结果,其时间复杂度为2^(126.66)次全轮AES加密,数据复杂度为2个已知明文.

关键词： Biclique攻击 Independent Biclique结构广义Biclique结构攻击框架 AES算法 LBlock算法

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Surface potential-based analytical model for InGaZnO thin-film transistors with Independent dual-gates

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Chinese Physics B 2020年第4期29卷 415-419页

作者：何伊妮邓联文覃婷廖聪维罗衡黄生祥 School of Physics and Electronics Central South UniversityChangsha 410083China

An analytical drain current model on the basis of the surface potential is proposed for indium-gallium zinc oxide(InGaZnO)thin-film transistors(TFTs)with an Independent dual-gate(IDG)structure.For a unified expression of carriers’distribution for the sub-threshold region and the conduction region,the concept of equivalent flat-band voltage and the Lambert W function are introduced to solve the Poisson equation,and to derive the potential distribution of the active layer.In addition,the regional integration approach is used to develop a compact analytical current-voltage model.Although only two fitting parameters are required,a good agreement is obtained between the calculated results by the proposed model and the simulation results by TCAD.The proposed current-voltage model is then implemented by using Verilog-A for SPICE simulations of a dual-gate InGaZnO TFT integrated inverter circuit.

关键词： analytical model Independent dual-gate indium-gallium zinc oxide(InGaZnO) surface potential

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Control performance and energy saving of multi-level pressure switching control system based on Independent metering control

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High Technology Letters 2020年第2期26卷 224-234页

作者：曹晓明 Yao Jing Sha Tong Wang Pei College of Mechanical Engineering Yanshan UniversityQinhuangdao 066004P.R.China School of Mechanical Engineering Nanjing Institute of TechnologyNanjing 210000P.R.China

Aiming at the problem of large energy consumption in hydraulic control system with large load and variable working conditions,based on the multi-level pressure switching control system(MPSCS),a multi-level pressure switching control system based on Independent metering control is proposed combined with the Independent metering control technology.The configuration principle of the system is given,the mathematical model of this system is established,and the control strategy of the system under 4 different working quadrants is put forward.Finally,the control performance and energy saving characteristics of the system are tested.The test results show that the switching of high and low pressure power supply has a certain effect on the response of step position and ramp position under impedance working condition.The displacement curves show slow climbing or abrupt change of ramp position,and the position accuracy is less than 1 mm.The multi-level pressure switching control system based on Independent metering control can recover and store energy under the transcendence working conditions.The control accuracy is about 1 mm,and the energy recovery rate is about 70%~80%.

关键词： multi-level pressure Independent metering control displacement control energy saving hydraulic switching system

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