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Prediction of multiple sequence alignment based on an improved particle swarm optimization

Journal of Bionanoscience 2013年第1期7卷 92-96页

作者： Gao, Yu-Xi Wang, Yan-Min Pei, Zhi-Li Department of Computer Science Jilin Business and Technology College China Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education College of Computer Science and Technology Jilin University China College of Computer Science and Technology Inner Mongolia University for the Nationalities Tongliao 028000 China

In this paper we use an improved Particle Swarm Optimization algorithm to solve Multiple Sequence Alignment (MSA). MSA is a key problem in bioinformatics. The thesis starts with the theory of Particle swarm optimization algorithm and the design an improved algorithm for Multiple Sequence Alignment. The simulated experiments show that the improved algorithm surpasses existing algorithms in performance. Copyright © 2013 American Scientific Publishers.

关键词： Bioinformatics

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Follow up of GW170817 and its electromagnetic counterpart by Australian-led observing programs

arXiv

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arXiv 2017年

作者： Andreoni, I. Ackley, K. Cooke, J. Acharyya, A. Allison, J.R. Anderson, G.E. Ashley, M.C.B. Baade, D. Bailes, M. Bannister, K. Beardsley, A. Bessell, M.S. Bian, F. Bland, P.A. Boer, M. Booler, T. Brandeker, A. Brown, I.S. Buckley, D.A.H. Chang, S.-W. Coward, D.M. Crawford, S. Crisp, H. Crosse, B. Cucchiara, A. Cupák, M. de Gois, J.S. Deller, A. Devillepoix, H.A.R. Dobie, D. Elmer, E. Emrich, D. Farah, W. Farrell, T.J. Franzen, T. Gaensler, B.M. Galloway, D.K. Gendre, B. Giblin, T. Goobar, A. Green, J. Hancock, P.J. Hartig, B.A.D. Howell, E.J. Horsley, L. Hotan, A. Howie, R.M. Hu, L. Hu, Y. James, C.W. Johnston, S. Johnston-Hollitt, M. Kaplan, D.L. Kasliwal, M. Keane, E.F. Kenney, D. Klotz, A. Lau, R. Laugier, R. Lenc, E. Li, X. Liang, E. Lidman, C. Luvaul, L.C. Lynch, C. Ma, B. Macpherson, D. Mao, J. McClelland, D.E. McCully, C. Möller, A. Morales, M.F. Morris, D. Murphy, T. Noysena, K. Onken, C.A. Orange, N.B. Oslowski, S. Pallot, D. Paxman, J. Potter, S.B. Pritchard, T. Raja, W. Ridden-Harper, R. Romero-Colmenero, E. Sadler, E.M. Sansom, E.K. Scalzo, R.A. Schmidt, B.P. Scott, S.M. Seghouani, N. Shang, Z. Shannon, R.M. Shao, L. Shara, M.M. Sharp, R. Sokolowski, M. Sollerman, J. Staff, J. Steele, K. Sun, T. Suntzeff, N.B. Tao, C. Tingay, S. Towner, M.C. Thierry, P. Trott, C. Tucker, B.E. Väisänen, P. Krishnan, V. Venkatraman Walker, M. Wang, L. Wang, X. Wayth, R. Whiting, M. Williams, A. Williams, T. Wolf, C. Wu, C. Wu, X. Yang, J. Yuan, X. Zhang, H. Zhou, J. Zovaro, H. Centre for Astrophysics and Supercomputing Swinburne University of Technology PO Box 218 H29 HawthornVIC3122 Australia Australian Astronomical Observatory 105 Delhi Rd North RydeNSW2113 Australia Monash Centre of Astrophysics Monash University VIC3800 Australia School of Physics & Astronomy Monash University VIC3800 Australia Research School of Astronomy and Astrophysics Australian National University CanberraACT2611 Australia Sydney Institute for Astronomy School of Physics University of Sydney NSW2006 Australia International Centre for Radio Astronomy Research Curtin University BentleyWA6102 Australia School of Physics University of New South Wales NSW2052 Australia Karl-Schwarzschild-Str. 2 Garching bei München85748 Germany ATNF CSIRO Astronomy and Space Science PO Box 76 EppingNSW1710 Australia School of Earth and Space Exploration Arizona State University TempeAZ85287 United States Department of Applied Geology Curtin University GPO Box U1987 PerthWA6845 Australia Artémis/Observatoire de la Cote d’Azur/ CNRS Boulevard de l’Observatoire CS 34229 NICE Cedex 4F 06304 France Department of Astronomy Stockholm University Albanova StockholmSE 10691 Sweden Department of Physics University of Wisconsin–Milwaukee MilwaukeeWI53201 United States South African Astronomical Observatory PO Box 9 Observatory7935 South Africa School of Physics University of Western Australia CrawleyWA6009 Australia University of the Virgin Islands 2 John Brewer’s Bay 00802 St ThomasUS Virgin Islands United States School of Physics and Astronomy University of Nottingham Nottingham United Kingdom ATNF CSIRO Astronomy and Space Science 26 Dick Perry Avenue KensingtonWA6152 Australia Dunlap Institute for Astronomy and Astrophysics University of Toronto ONM5S 3H4 Canada Department of Physics U.S. Air Force Academy 2354 Fairchild Drive CO 80840 United States The Oskar Klein Centre Department of Physics Stockholm University Albanova Stockh

The discovery of the first electromagnetic counterpart to a gravitational wave signal has generated follow-up observations by over 50 facilities world-wide, ushering in the new era of multi-messenger astronomy. In this paper, we present follow-up observations of the gravitational wave event GW170817 and its electromagnetic counterpart SSS17a/DLT17ck (IAU label AT2017gfo) by 14 Australian telescopes and partner observatories as part of Australian-based and Australian-led research programs. We report early- to late-time multi-wavelength observations, including optical imaging and spectroscopy, mid-infrared imaging, radio imaging, and searches for fast radio bursts. Our optical spectra reveal that the transient source afterglow cooled from approximately 6400K to 2100K over a 7-day period and produced no significant optical emission lines. The spectral profiles, cooling rate, and photometric light curves are consistent with the expected outburst and subsequent processes of a binary neutron star merger. Star formation in the host galaxy probably ceased at least a Gyr ago, although there is evidence for a galaxy merger. Binary pulsars with short (100 Myr) decay times are therefore unlikely progenitors, but pulsars like PSR B1534+12 with its 2.7 Gyr coalescence time could produce such a merger. The displacement (∼2.2 kpc) of the binary star system from the centre of the main galaxy is not unusual for stars in the host galaxy or stars originating in the merging galaxy, and therefore any constraints on the kick velocity imparted to the progenitor are poor. Copyright © 2017, The Authors. All rights reserved.

关键词： Gravity waves

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Image resizing by color energy updating

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Guangxue Jingmi Gongcheng/Optics and Precision engineering 2013年第SUPPL期21卷 264-270页

作者： Zhao, Hong-Wei Wang, Zhen Liu, Ping-Ping Li, Qing-Liang School of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education Changchun 130012 China

A new image resizing algorithm was proposed based on a color space and an energy updating mechanism. First, the concept of color space was introduced into image resizing algorithm and the pixel's energy function was re-built based on the gradient of gray space and color space. Three kinds of color energy functions were tested and the energy function in HSI space was finally chosen because of its excellent performance. Additionally, since image resizing might badly corrupt the contours of main areas in an original image and might further affect the understanding of the image, an energy updating mechanism was proposed. The energy updating mechanism could increase the neighborhood energy values where a pixel had been deleted. By doing so, it could decrease the probability that seams cross this area again, thus the contour of this area could be protected well. In experiments, the degree of Scale Invariant Feature Transform (SIFT) matching between original image and resized image with different λ values was calculated. The best performance shows that the proportion between the color and gray energy functions was 7:3. By comparing the proposed method with other two state of arts algorithms, it indicates that the shape of main area will be better preserved with the proposed algorithm without introducing any more complexity.

关键词： Color

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Solving the optimal power flow problem via a non-interior path following algorithm

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Journal of Computational Information Systems 2013年第3期9卷 1191-1198页

作者： Su, Menglong Liu, Le Wang, Jian Cai, Hua Mathematics and Information Science College Luoyang Normal University Luoyang 471022 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China College of Mathematics and Information Science Ocean University of China Qingdao 266000 China College of Mathematics Jilin University Changchun 130012 China

In this paper, we propose a non-interior path following algorithm for solving the optimal power flow problem. By using the new approach, we can choose initial guesses arbitrarily in the whole space of n dimensional Euclidean space. This can improve the computational efficiency of the algorithm greatly than before. Some numerical examples are presented to illustrate the results of this paper. Copyright © 2013 Binary Information Press.

关键词： Computational efficiency

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Some new signature schemes and secret sharing schemes based on the Gröbner basis cryptosystems

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Journal of Computational Information Systems 2013年第13期9卷 5133-5140页

作者： Li, Hengyan Chang, Shuizhen Xu, Zhonghai Mathematics and Information Science College North China University of Water Resources and Electric Power Zhengzhou 450011 China Mathematics and Information Science College Luoyang Normal University Luoyang 471022 China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun 130012 China National Key Laboratory of Science and Technology on Advanced Composites in Special Environments Harbin Institute of Technology Harbin 150080 China

In this paper, we introduce some new signature schemes and secret sharing schemes from the known Gröbner basis cryptosystems. Then, we discuss the issues related to the security of these schemes. Finally, we draw... 详细信息

关键词： Cryptography

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Effective and stable feature selection method based on filter for gene signature identification in paired microarray data

Effective and stable feature selection method based on filte...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Zhongbo Cao Yan Wang Ying Sun Wei Du Yanchun Liang College of Computer Science and Technology Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Changchun China

A huge amount of microarray datasets are produced with big number of genes and small samples. Feature selection methods have become a very sharp tool to select the gene signatures from the whole gene set. In recent years, researchers are concerned much about the datasets containing samples of cancer as well as corresponding control tissues. However, few feature selection methods consider the effect of paired samples. In this article, we propose a new feature selection method for paired microarray datasets based on the original paired t-test approach. We apply on the paired datasets across six common cancer types. Through comparison with some widely used methods on the performance of prediction power, stability of gene lists and functional stability, our method shows excellent performance. The proposed method has good effectiveness, stability and consistency, which enables the method to be applicative to feature selection for paired microarray expression data analysis.

关键词： Stability analysis Cancer Accuracy Signal to noise ratio Gene expression Redundancy Liver

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A New Mobile Visual Search System Based on the Human Visual System

A New Mobile Visual Search System Based on the Human Visual ...

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第四届国际仿生工程学术会议

作者： Bo Zhao Hongwei Zhao Pingping Liu Guihe Qin School of Computer Science and Technology Jilin University Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education

We describe a novel mobile visual search system based on the saliency mechanism and sparse coding principle of the human visual system (HVS). In the feature extraction step, we first divide an image into different regions using the saliency extraction algorithm. Then scale-invariant feature transform (SIFT) descriptors in all regions are extracted while regional identities are preserved based on their various saliency levels. According to the sparse coding principle in the HVS, we adopt a local neighbor preserving Hash function to establish the binary sparse expression of the SIFT features. In the searching step,

关键词： mobile vision search, human vision system, saliency, sparse coding, Hash, SIFT descriptor.

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A novel image retrieval method based on mutual information descriptors

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9th International Conference on Intelligent Computing, ICIC 2013

作者： Hou, Gang Zhang, Ke Zhang, Xiaoxue Kong, Jun Zhang, Ming College of Communication Engineering Jilin University Changchun China College of Humanities and Sciences Northeast Normal University Changchun China School of Computer Science and Information Technology Northeast Normal University Changchun China Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education Jilin University Changchun China

ISBN: (纸本)9783642394812

In this paper, we propose a novel image retrieval method based on mutual information descriptors (MIDs). Under the physiological property of human eyes and human visual perception theory, MIDs are extracted to encode the internal correlation relationship among multiple image feature spaces, characterizing image contents with mutual information features based on the low-level image features, such as color, shape etc., then, the mutual information features fusion strategy is used to imitate the information transfer process in nervous system. When using the MIDs proposed to image retrieval, we can get many advantages such as low dimensionality, a certain robustness of geometric distortions and noise, and describing the human visual retrieval mechanism effectively. Experimental results show that MIDs have high indexing and retrieving performance compared with existing methods for content-based image retrieval (CBIR). © 2013 Springer-Verlag.

关键词： Vision

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Optical flow computation based on spline functionals

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Jilin Daxue Xuebao (Gongxueban)/Journal of Jilin University (engineering and Technology Edition) 2013年第SUPPL.1期43卷 165-168页

作者： Guo, Xiao-Xin Yang, Guang Xu, Zhi-Wen College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University Changchun 130012 China

A mathematical model using the spline functional as smooth constraints was presented. The second-and fourth-order partial differential equations constraints were two special cases in the model. The necessary condition for optical flow minimization problem solution was also presented. This model provided a basis for formal representation and numerical computation of optical flow from a methodological point of view. The significance of this mathematical model lay in the simplification of the equations for optical flow computation into linear algebraic equations. The simplification can contribute to discrete representation of the optical flow equation, and also verify that the use of smoothness constraints can ensure the existence and uniqueness of the solution from the view of the algebraic equations.

关键词： Optical flows

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Intensity preserving technology in image restoration

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Jilin Daxue Xuebao (Gongxueban)/Journal of Jilin University (engineering and Technology Edition) 2013年第SUPPL.1期43卷 106-109页

作者： Guo, Xiao-Xin Xu, Zhi-Wen Che, Xiang-Jiu College of Computer Science and Technology Jilin University Changchun 130012 China Key Laboratory of Symbol Computation and Knowledge Engineering of the Ministry of Education Jilin University Changchun 130012 China

A new approach of image restoration for the sequence of fluorescein angiography was proposed. First, the intensity constraint was incorporated into Miller regularization equation to obtain the ability to preserve the high intensity of pixels. Thus, the restored image would be influenced not only by the smoothness constraints, but also by the intensity constraints. Secondly, in the process of the restoration, we use an intensity template obtained from the pre-filtering procedure was used to achieve the intensity constraints. The template represented an image composed by the desired intensity value. The experiments show that the proposed scheme gains a better result in both high intensity preservation and image restoration.

关键词： Image reconstruction

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