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Prediction of Intrinsically Disordered Proteins with a Low Computational Complexity Method

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Computer Modeling in Engineering & Sciences 2020年第10期125卷 111-123页

作者： Jia Yang Haiyuan Liu hao he Nankai University School of Electronic Information and Optical EngineeringTianjin Key Laboratory of Optoelectronic Sensor and Sensing Network TechnologyTianjin300350China hebei University of Technology Tianjin300400China

The prediction of intrinsically disordered proteins is a hot research area in *** to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingly important to predict those regions through computational *** this paper,we developed a novel scheme by employing sequence complexity to calculate six features for each residue of a protein sequence,which includes the Shannon entropy,the topological entropy,the sample entropy and three amino acid preferences including Remark 465,Deleage/Roux,and Bfactor(2STD).Particularly,we introduced the sample entropy for calculating time series complexity by mapping the amino acid sequence to a time series of *** our knowledge,the sample entropy has not been previously used for predicting IDPs and hence is being used for the first time in our *** addition,the scheme used a properly sized sliding window in every protein sequence which greatly improved the prediction ***,we used seven machine learning algorithms and tested with 10-fold cross-validation to get the results on the dataset R80 collected by Yang et *** of the dataset DIS1556 from the Database of Protein Disorder(DisProt)(https://***)containing experimentally determined intrinsically disordered proteins(IDPs).The results showed that k-Nearest Neighbor was more appropriate and an overall prediction accuracy of 92%.Furthermore,our method just used six features and hence required lower computational complexity.

关键词： Bioinformatics intrinsically disordered proteins machine learning algorithms sequences computational complexity

Effect of Background Ions on the Selection of the Discharge Path

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Chinese Physics Letters 2001年第2期18卷 248-250页

作者： he Zheng-hao LI Jin Impulse Power Research Center of Huazhong University of Science and Technology Wuhan 430074

The effects of the background ions on the selection of the discharge path in an air gap have been studied with two different *** lightning impulse air discharge experiment is conducted using an independent ion generator,while the air discharge experiment uses a lightning impulse superimposed on a dc high voltage used to produce background *** influence of different background ions on the leader development,and thus on the discharge path,is *** results have been obtained with the two *** probability for the discharge path passing through the negative ion space is much higher than that for the passing through the positive ion *** mechanism of the effects of background ions is analysed based on the electron avalanche and the electric field.

关键词： methods lightning passing

SELF-ORGANIZED SEMANTIC FEATURE EVOLUTION FOR AXIOMATIC DESIGN

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Chinese Journal of Mechanical Engineering 2008年第2期21卷 108-113页

作者： hao he FENG Yixiong TAN Jianrong XUE Yang State Key Laboratory of CAD ＆ CG Zhejiang University Hangzhou 310027 China

Aiming at the problem existing in the computer aided design process that how to express the design intents with high-level engineering terminologies, a mechanical product self-organized semantic feature evolution technology for axiomatic design is proposed, so that the constraint relations between mechanical parts could be expressed in a semantic form which is more suitable for designers. By describing the evolution rules for semantic constraint information, the abstract expression of design semantics in mechanical product evolution process is realized and the constraint relations between parts are mapped to the geometric level from the semantic level; With semantic feature relation graph, the abstract semantic description, the semantic relative structure and the semantic constraint information are linked together; And the methods of semantic feature self-organized evolution are classified. Finally, combining a design example of domestic high-speed elevator, how to apply the theory to practical product development is illustrated and this method and its validity is described and verified. According to the study results, the designers are able to represent the design intents at an advanced semantic level in a more intuitional and natural way and the automation, recursion and visualization for mechanical product axiomatic design are also realized.

关键词： Axiomatic design Semantic feature Design intent Self-organized

TRANSFECTION AND CELL FUSION BY FEMTOSECOND LASERS

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Journal of Innovative Optical health Sciences 2011年第2期4卷 113-125页

作者： hao he SIU KAI KONG KAM TAI CHAN Department of Electronic Engineering The Chinese University of Hong Kong ShatinN.T.Hong Kong Department of Biochemistry The Chinese University of Hong Kong ShatinN.T.Hong Kong

Biophotonics is an exciting and fast-expanding frontier which involves the fusion of advanced photonics and *** has not only created many novel methodologies for biomedical research,but also achieved many significant results as an *** to femtosecond(fs)laser technologies,important progresses have been made regarding the manipulation,imaging,and engineering of biological samples ranging from single molecules to tissues in the last 20 *** ultrashort pulses at near-infrared band provide many advantages:high nonlinear efficiency,low absorption by biological samples,high spatial and temporal resolution and confinement,and low *** are noninvasive and easy to *** the mechanism of how fs laser pulses interact with cells remains unclear,experimental results have shown that they could open up the cell membrane and hence made optical transfection and optical cell fusion *** this review,some of the seminal works on transfection and cell fusion by fs lasers are *** ideas behind and the experimental details will be described together with a highlight on their ***,the thermal effect is analyzed based on multiphoton excitation and plasma formation in an aqueous environment to explain the nontoxic characteristic of fs laser ***,some applications of fs laser induced transfection and cellcell fusion with potential major impact in biomedical sciences are proposed.

关键词： Biophotonics transfection cell fusion femtosecond laser

Homonyms Discovery in Folksonomy Based on User Community Analysis

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Journal of Electronic Science and Technology 2016年第3期14卷 275-280页

作者： Shi-Min Shan Yi Cui Ying-hao he School of Software Dalian University of TechnologyDalian 116024China the school of management dalian university of technologyDalian 116024China

to the capability of reflecting social perception on semantic of resources, folksonomy has been proposed to improve the social learning for education and scholar researching. However, its actual impact is significantly influenced by the semantic ambiguity problem of tags. So, in this paper, we proposed a novel way of detecting homonyms, one of the main sources of tag＇s semantic ambiguity problem, in noisy folksonomies. The study is based on two hypotheses： 1） Users having different interests tend to have different understanding of the same tag. 2） Users having similar interest tend to have common understanding of the same tag. Therefore, we firstly discover user communities according to users＇ interests. Then, tag contexts are discovered in subsets of folksonomy on the basis of user communities. The experimental results show that our method is effective and outperform the method finding tag contexts using all tags in folksonomy with overlapping clustering algorithm especially when various users having different interests are contained by the folksonomyo

关键词： Community detection Folksonomy semantic ambiguity homonym.

Anderson Acceleration of Gradient Methods with Energy for Optimization Problems

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Communications on Applied Mathematics and Computation 2024年第2期6卷 1299-1318页

作者： Hailiang Liu Jia-hao he Xuping Tian Department of Mathematics Iowa State UniversityAmesIAUSA Department of Agricultural and Biosystems Engineering Iowa State UniversityAmesIAUSA

Anderson acceleration(AA)is an extrapolation technique designed to speed up fixed-point *** optimization problems,we propose a novel algorithm by combining the AA with the energy adaptive gradient method(AEGD)[arXiv:2010.05109].The feasibility of our algorithm is ensured in light of the convergence theory for AEGD,though it is not a fixed-point *** provide rigorous convergence rates of AA for gradient descent(GD)by an acceleration factor of the gain at each implementation of *** experimental results show that the proposed AA-AEGD algorithm requires little tuning of hyperparameters and exhibits superior fast convergence.

关键词： Anderson acceleration(AA) Gradient descent(GD) Energy stability

Review of fiber superluminescent pulse amplifications

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High Power Laser Science and Engineering 2016年第3期4卷 106-112页

作者： Haitao Zhang Xinglai Shen he hao Qinghua Li Mali Gong Center for Photonics and Electronics State Key Laboratory of Precision Measurement and Instruments Department of Precision Instruments Tsinghua University

High coherence of the laser is indispensable light sources in modern long or short-distance imaging systems, because the high coherence leads to coherent artifacts such as speckle that corrupt image formation. To deliver low coherence pulses in fiber amplifiers, we utilize the superluminescent pulsed light with broad bandwidth, nonlongitudinal mode structure and chaotic mode phase as the seed source of the cascaded fiber amplifiers. The influence of fiber superluminescent pulse amplification(SPA) on the limitations of the performance is analyzed. A review of our research results for SPA in the fibers are present, including the nonlinear theories of this low coherent light sources, i.e., self-focusing(SF), stimulated Raman scattering(SRS) and self-phase modulation(SPM) effects, and the experiment results of the nanosecond pulses with peak power as high as 4.8 MW and pulse energy as much as 55 mJ. To improve the brightness of SPA light in the future work, we introduce our novel evaluation term and a more reasonable criterion, which is denoted by a new parameter of brightness factor for active large mode area fiber designs. A core-doped active large pitch fiber with a core diameter of 190 μm and a mode-field diameter of 180 μm is designed by this method. The designed fiber allows near diffracted limited beam quality operation, and it can achieve 100 mJ pulse energy and 540 W average power by analyzing the mode coupling effects induced by heat.

关键词： superluminescent pulse amplification fiber amplification incoherent nonlinear effects very large mode field

PARAMETERS OPTIMIZATION OF CONTINUOUS WAVELET TRANSFORM AND ITS APPLICATION IN ACOUSTIC EMISSION SIGNAL ANALYSIS OF ROLLING BEARING

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Chinese Journal of Mechanical Engineering 2007年第2期20卷 104-108页

作者： ZHANG Xinming he Yongyong hao Rujiang CHU Fulei State Key Laboratory of Tribology Tsinghua University Beijng 100084 China

Morlet wavelet is suitable to extract the impulse components of mechanical fault signals. And thus its continuous wavelet transform （CWT） has been successfully used in the field of fault diagnosis. The principle of scale selection in CWT is discussed. Based on genetic algorithm, an optimization strategy for the waveform parameters of the mother wavelet is proposed with wavelet entropy as the optimization target. Based on the optimized waveform parameters, the wavelet scalogram is used to analyze the simulated acoustic emission （AE） signal and real AE signal of rolling bearing. The results indicate that the proposed method is useful and efficient to improve the quality of CWT.

关键词： Rolling bearing Fault diagnosis Acoustic emission (AE) Continuous wavelet transform (CWT) Genetic algorithm

Growth and Characterization of Perovskite K1-yLiyTa1-xNbxO3∶Ce

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Journal of Rare Earths 2006年第Z1期24卷 261-263页

作者： Tian hao he Chongjun Shen Yanqing Xin Jiangbo Zhou Zhongxiang Department of Physics Harbin Institute of Technology Harbin 150001 China Department of Physics Harbin Institute of Technology Harbin 150001 China Department of Physics Harbin Institute of Technology Harbin 150001 China Department of Physics Harbin Institute of Technology Harbin 150001 China Department of Physics Harbin Institute of Technology Harbin 150001 China

The grown Ce doped potassium lithium tantalite niobate (KLTN) crystals and characterize their physical properties were reported. The top seeded solution growth method was described. The specifics of a particular KLTN∶Ce growth were presented. X-ray diffraction spectra of paraelectric and ferroelectric KLTN crystals were illustrated. Dielectric and absorption studies on KLTN∶Ce were carried out compared with pure KLTN.

关键词： top seeded solution growth KLTN X-ray diffraction dielectric materials