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Advances in biomolecular surface meshing and its applications to mathematical modeling

Chinese Science Bulletin 2013年第16期58卷 1843-1849页

作者： CHEN MinXin LU BenZhuo Center for System Biology Department of Mathematics Soochow University State Key Laboratory of Scientific/Engineering Computing Institute of Computational Mathematics Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary Sciences Chinese Academy of Sciences

In the field of molecular modeling and simulation, molecular surface meshes are necessary for many problems, such as molecular structure visualization and analysis, docking problem and implicit solvent modeling and simulation. Recently, with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation, providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure. In this review, we summarize recent works on this issue. First, various definitions of molecular surfaces and corresponding meshing methods are introduced. Second, our recent meshing tool, TMSmesh, and its performances are presented. Finally, we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

关键词：数学建模分子表面应用啮合生物表面网格分子结构分子建模

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EPAS: Efficient privacy-preserving authentication scheme for VANETs-based emergency communication

Journal of Software

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Journal of Software 2013年第8期8卷 1914-1922页

作者： Jia, Xuedan Yuan, Xiaopeng Meng, Lixia Wang, Liangmin School of Computer Science and Telecommunication Engineering Jiangsu University Zhenjiang China School of Electronic Engineering and Optoelectronic Techniques NUST Nanjing China Key Laboratory of Intelligent Computing and Signal Processing MOE Anhui University Hefei China

Vehicular Ad Hoc Networks (VANETs) can provide participants with security services and entertainment information during the driving. To guarantee correct and smooth operations of VANETs, it is necessary to achieve efficient authentication with user privacy preserving. Current solutions either cannot satisfy privacy requirements, or are not efficient in message verification. Moreover, all the existing schemes are RSU-based. We, for the first time, apply VANETs to emergency communication during disaster rescue, and effective authentication scheme is proposed in accordance with the actual environment, where there is no fixed road-side unit (RSU). In this paper, we present an efficient identity based signature scheme EPAS, which satisfies conditional privacy requirements through software solution. In aspect of efficiency, both lightweight signature and batch verification are employed to provide effective authentication. Extensive theoretical and experimental analyses demonstrate the security and efficiency of EPAS in terms of privacy-preserving and low authentication delay. © 2013 ACADEMY PUBLISHER.

关键词： Vehicular ad hoc networks

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Motion deblurring using super-sparsity

Motion deblurring using super-sparsity

引用

20th International Conference on Neural Information Processing, ICONIP 2013

作者： Zhao, Jingxiong Zhao, Haohua Zhang, Keting Zhang, Liqing MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems Department of Computer Science and Engineering Shanghai Jiao Tong University China

ISBN: (纸本)9783642420504

Motion blur is caused by the camera shake during the exposure in which the blur kernel describes the trace of shaking. Based on this generating process of the kernel , we observed that the distribution of the kernel obeys super-sparsity, as the natural images. Recent works mostly exploit various kinds of priors in their models, but focus on the the speed or a close-form formulation for convenience of mathematical calculation ignoring the intrinsic feature of the kernels and images. In this paper we propose a new model with super-sparse prior for the deblurring problem from one single image. Since the close-form formulation of this model doesn't exist, we use a look-up table trick to approximate the solution. Qualitative and quantitative evaluation demonstrate that our model with super-sparse prior can produce stable and high-quality results. © Springer-Verlag 2013.

关键词： Convolution

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Measurement of prompt and nonprompt charmonium suppression in PbPb collisions at 5.02 TeV

arXiv

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arXiv 2017年

作者： Sirunyan, A.M. Tumasyan, A. Adam, W. Bergauer, T. Dragicevic, M. Erö, J. Escalante Del Valle, A. Frühwirth, R. Jeitler, M. Krammer, N. Lechner, L. Liko, D. Madlener, T. Mikulec, I. Pitters, F.M. Rad, N. Schieck, J. Schöfbeck, R. Spanring, M. Templ, S. Waltenberger, W. Wulz, C.-E. Zarucki, M. Chekhovsky, V. Litomin, A. Makarenko, V. Suarez Gonzalez, J. Darwish, M.R. de Wolf, E.A. Di Croce, D. Janssen, X. Kello, T. Lelek, A. Pieters, M. Rejeb Sfar, H. van Haevermaet, H. van Mechelen, P. van Putte, S. van Remortel, N. Blekman, F. Bols, E.S. Chhibra, S.S. D’Hondt, J. de Clercq, J. Lontkovskyi, D. Lowette, S. Marchesini, I. Moortgat, S. Morton, A. Python, Q. Tavernier, S. van Doninck, W. van Mulders, P. Beghin, D. Bilin, B. Clerbaux, B. de Lentdecker, G. Dorney, B. Favart, L. Grebenyuk, A. Kalsi, A.K. Makarenko, I. Moureaux, L. Pétré, L. Popov, A. Postiau, N. Starling, E. Thomas, L. Vander Velde, C. Vanlaer, P. Vannerom, D. Wezenbeek, L. Cornelis, T. Dobur, D. Gruchala, M. Khvastunov, I. Niedziela, M. Roskas, C. Skovpen, K. Tytgat, M. Verbeke, W. Vermassen, B. Vit, M. Bruno, G. Bury, F. Caputo, C. David, P. Delaere, C. Delcourt, M. Donertas, I.S. Giammanco, A. Lemaitre, V. Mondal, K. Prisciandaro, J. Taliercio, A. Teklishyn, M. Vischia, P. Wertz, S. Wuyckens, S. Alves, G.A. Hensel, C. Moraes, A. Aldá Júnior, W.L. Belchior Batista Das Chagas, E. Brandao Malbouisson, H. Carvalho, W. Chinellato, J. Coelho, E. da Costa, E.M. da Silveira, G.G. de Jesus Damiao, D. Fonseca De Souza, S. Martins, J. Matos Figueiredo, D. Medina Jaime, M. Mora Herrera, C. Mundim, L. Nogima, H. Rebello Teles, P. Sanchez Rosas, L.J. Santoro, A. Silva Do Amaral, S.M. Sznajder, A. Thiel, M. Torres Da Silva De Araujo, F. Vilela Pereira, A. Bernardes, C.A. Calligaris, L. Fernandez Perez Tomei, T.R. Gregores, E.M. Lemos, D.S. Mercadante, P.G. Novaes, S.F. Padula, Sandra S. Aleksandrov, A. Antchev, G. Atanasov, I. Hadjiiska, R. Iaydjiev, P. Misheva, M. Rodozov, M. Shopova, M. Sultanov, G. Bonchev, M. Dimitrov, A. Ivanov, T. Litov, L. Pavlov, B. Yerevan Physics Institute Yerevan Armenia Institut für Hochenergiephysik Wien Austria Institute for Nuclear Problems Minsk Belarus Universiteit Antwerpen Antwerpen Belgium Vrije Universiteit Brussel Brussel Belgium L'Université libre de Bruxelles Bruxelles Belgium Ghent University Ghent Belgium Université Catholique de Louvain Louvain-la-Neuve Belgium Centro Brasileiro de Pesquisas Fisicas Rio de Janeiro Brazil Universidade do Estado do Rio de Janeiro Rio de Janeiro Brazil Universidade Estadual Paulista São Paulo Brazil Universidade Federal do ABC São Paulo Brazil Institute for Nuclear Research and Nuclear Energy Bulgarian Academy of Sciences Sofia Bulgaria University of Sofia Sofia Bulgaria Beihang University Beijing China Department of Physics Tsinghua University Beijing China Institute of High Energy Physics Beijing China State Key Laboratory of Nuclear Physics and Technology Peking University Beijing China Sun Yat-Sen University Guangzhou China Institute of Modern Physics and Key Laboratory of Nuclear Physics and Ion-beam Application MOE Fudan University Shanghai China Zhejiang University Hangzhou China Universidad de Los Andes Bogota Colombia Universidad de Antioquia Medellin Colombia University of Split Faculty of Electrical Engineering Mechanical Engineering and Naval Architecture Split Croatia University of Split Faculty of Science Split Croatia Institute Rudjer Boskovic Zagreb Croatia University of Cyprus Nicosia Cyprus Charles University Prague Czech Republic Escuela Politecnica Nacional Quito Ecuador Universidad San Francisco de Quito Quito Ecuador Academy of Scientific Research and Technology of the Arab Republic of Egypt Egyptian Network of High Energy Physics Cairo Egypt Center for High Energy Physics CHEP-FU Fayoum University El-Fayoum Egypt National Institute of Chemical Physics and Biophysics Tallinn Estonia Department of Physics University of Helsinki Helsinki Finland Helsinki Institute of Physics Helsinki Finland

The nuclear modification factors of J/ψ and ψ(2S) mesons are measured in PbPb collisions at a centre-of-mass energy per nucleon pair of √sNN = 5.02 TeV. The analysis is based on PbPb and pp data samples collected by CMS at the LHC in 2015, corresponding to integrated luminosities of 464 µb−1 and 28 pb−1, respectively. The measurements are performed in the dimuon rapidity range of |y| T) from pT = 3 GeV/c in the most forward region and up to 50 GeV/c. Both prompt and nonprompt (coming from b hadron decays) J/ψ mesons are observed to be increasingly suppressed with centrality, with a magnitude similar to the one observed at √sNN = 2.76 TeV for the two J/ψ meson components. No dependence on rapidity is observed for either prompt or nonprompt J/ψ mesons. An indication of a lower prompt J/ψ meson suppression at pT > 25 GeV/c is seen with respect to that observed at intermediate pT. The prompt ψ(2S) meson yield is found to be more suppressed than that of the prompt J/ψ mesons in the entire pT range. © 2017, CC BY.

关键词： Binary alloys

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A frequency boosting method for motor imagery EEG classification in BCI-FES rehabilitation training system

A frequency boosting method for motor imagery EEG classifica...

引用

10th International Symposium on Neural Networks, ISNN 2013

作者： Liang, Jianyi Zhang, Hao Liu, Ye Wang, Hang Li, Junhua Zhang, Liqing MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China

ISBN: (纸本)9783642390678

Common Spatial Pattern (CSP) and Support Vector Machine (SVM) are usually adopted for feature extraction and classification of two-class motor imagery. However, in a motor imagery based BCI-FES rehabilitation system, stroke patients usually are not able to conduct correct motor imagery like healthy people due to the injury of motor cortex. Therefore, motor imagery EEG of stroke patients lacks of specific discriminant features as appearances of healthy people, which significantly blocks CSP to seek the optimal projection subspace. In this paper, a method, which filters EEG into a variety of bands and improves performance through boosting principle based on a set of weak CSP-SVM classifiers, was proposed to solve the problem mentioned above and was evaluated on the EEG datasets of three stroke subjects. The proposed method outperformed the traditional CSP-SVM method in terms of classification accuracy. From data analysis, we observed that optimal spectral band for classification had been changing along with rehabilitation training, which may reveal mechanisms that dominant frequency band may be changed along with rehabilitation training and spectral power distribution may be changed in different stages of rehabilitation. In addition, this work also demonstrated the feasibility of our SJTU-BCMI BCI-FES rehabilitation training system. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Support vector machines

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Causal neurofeedback based BCI-FES rehabilitation for post-stroke patients

Causal neurofeedback based BCI-FES rehabilitation for post-s...

引用

20th International Conference on Neural Information Processing, ICONIP 2013

作者： Wang, Hang Liu, Ye Zhang, Hao Li, Junhua Zhang, Liqing MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China

ISBN: (纸本)9783642420535

BCI-FES therapy has been proved to be an effective way to help post-stroke patients restore motor function of paralyzed limbs. In the existing BCI-FES system, patients can only asynchronously receive feedback in the form of FES or robot-assisted arm movements, and such a system does not provide a positive feedback corresponding to patient's motor imagery. In this work, we propose a causal related BCI-FES rehabilitation training platform, consisting top-down and bottom-up causal chains to achieve a better rehabilitation performance. We compare our system with a popular BCI-FES system on EEG data recorded from ten patients divided in two groups. The results show that almost all patients have achieved improvements in the motor function recovery after our training. © Springer-Verlag 2013.

关键词： Patient treatment

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Optimal calculation of tensor learning approaches

Optimal calculation of tensor learning approaches

引用

10th International Symposium on Neural Networks, ISNN 2013

作者： Huang, Kai Zhang, Liqing MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China

ISBN: (纸本)9783642390647

Most algorithms have been extended to the tensor space to create algorithm versions with direct tensor inputs. However, very unfortunately basically all objective functions of algorithms in the tensor space are non-convex. However, sub-problems constructed by fixing all the modes but one are often convex and very easy to solve. However, this method may lead to difficulty converging;iterative algorithms sometimes get stuck in a local minimum and have difficulty converging to the global solution. Here, we propose a computational framework for constrained and unconstrained tensor methods. Using our methods, the algorithm convergence situation can be improved to some extent and better solutions obtained. We applied our technique to Uncorrelated Multilinear Principal Component Analysis (UMPCA), Tensor Rank one Discriminant Analysis (TR1DA) and Support Tensor Machines (STM);Experiment results show the effectiveness of our method. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Tensors

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Hidden Markov model for action recognition using joint angle acceleration

Hidden Markov model for action recognition using joint angle...

引用

20th International Conference on Neural Information Processing, ICONIP 2013

作者： Huang, Sha Zhang, Liqing MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China

ISBN: (纸本)9783642420504

This paper proposes a recognition method of human actions in video by adding new features, the joint angle acceleration to the feature space. In this method, human body is described as three-dimensional skeletons. The features consist of vectors of several important joint angles on the human body and the joint angle accelerations are also considered as a part of features. Hidden Markov Model (HMM) is used as classification scheme. The HMM models are trained by sequences extracted from the CMU graphics lab motion capture database 1. This method is invariant to scale, coordinate system and transition. A system is implemented to recognize 4 different types of actions (walk, run, jump and jumping jack) both on the dataset of CMU and Weizmann[7]. Each video clip contains a single action type. The experimental results show excellent performance of the proposed approach. A maximum 10.3% accuracy gain can be achieved by our method compared with the method without considering acceleration. © Springer-Verlag 2013.

关键词： Hidden Markov models

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UMPCA based feature extraction for ECG

UMPCA based feature extraction for ECG

引用

10th International Symposium on Neural Networks, ISNN 2013

作者： Li, Dong Huang, Kai Zhang, Hanlin Zhang, Liqing MOE-Microsoft Key Laboratory for Intelligent Computing and Intelligent Systems Department of Computer Science and Engineering Shanghai Jiao Tong University Shanghai 200240 China

ISBN: (纸本)9783642390647

In this paper, we propose an algorithm for 12-leads ECG signals feature extraction by Uncorrelated Multilinear Principal Component Analysis(UMPCA). However, traditional algorithms usually base on 2-leads ECG signals and do not efficiently work out for 12-leads signals. Our algorithm aims at the natural 12-leads ECG signals. We firstly do the Short Time Fourier Transformation(STFT) on the raw ECG data and obtain 3rd-order tensors in the spatial-spectral- temporal domain, then take UMPCA to find a Tensor-to-Vector Projection(TVP) for feature extraction. Finally the Support Vector Machine(SVM) classifier is applied to achieve a high accuracy with these features. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Tensors

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Scaling and correlation of human movements in cyberspace and physical space

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Physical Review E 2014年第5期90卷 050802(R)-050802(R)页

作者： Zhi-Dan Zhao Zi-Gang Huang Liang Huang Huan Liu Ying-Cheng Lai Web Sciences Center University of Electronic Science and Technology of China Chengdu 610054 China School of Electrical Computer and Energy Engineering Arizona State University Tempe Arizona 85287 USA Institute of Computational Physics and Complex Systems and Key Laboratory for Magnetism and Magnetic Materials of MOE Lanzhou University Lanzhou Gansu 730000 China School of Computing Informatics and Decision Systems Engineering Arizona State University Tempe Arizona 85287 USA Department of Physics Arizona State University Tempe Arizona 85287 USA

Understanding the dynamics of human movements is key to issues of significant current interest such as behavioral prediction, recommendation, and control of epidemic spreading. We collect and analyze big data sets of human movements in both cyberspace (through browsing of websites) and physical space (through mobile towers) and find a superlinear scaling relation between the mean frequency of visit 〈f〉 and its fluctuation σ:σ∼〈f〉β with β≈1.2. The probability distribution of the visiting frequency is found to be a stretched exponential function. We develop a model incorporating two essential ingredients, preferential return and exploration, and show that these are necessary for generating the scaling relation extracted from real data. A striking finding is that human movements in cyberspace and physical space are strongly correlated, indicating a distinctive behavioral identifying characteristic and implying that the behaviors in one space can be used to predict those in the other.

关键词： CYBERSPACE CORRELATION (Statistics) HUMAN mechanics BEHAVIORAL research PREDICTION models EPIDEMIOLOGY -- Mathematical models

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