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On-the-fly analysis of molecular dynamics simulation trajectories of proteins using the Bayesian inference method

JOURNAL OF CHEMICAL PHYSICS 2017年第12期147卷 124108-124108页

作者： Miyashita, Naoyuki Yonezawa, Yasushige Kindai Univ Dept Computat Syst Biol Biol Oriented Sci & Techn 930 Nishimitani Wakayama 6496493 Japan Kindai Univ Inst Adv Technol High Pressure Prot Res Ctr 930 Nishimitani Wakayama 6496493 Japan

Robust and reliable analyses of long trajectories from molecular dynamics simulations are important for investigations of functions and mechanisms of proteins. Structural fitting is necessary for various analyses of protein dynamics, thus removing time-dependent translational and rotational movements. However, the fitting is often difficult for highly flexible molecules. Thus, to address the issues, we proposed a fitting algorithm that uses the Bayesian inference method in combination with rotational fitting-weight improvements, and the well-studied globular protein systems trpcage and lysozyme were used for investigations. The present method clearly identified rigid core regions that fluctuate less than other regions and also separated core regions from highly fluctuating regions with greater accuracy than conventional methods. Our method also provided simultaneous variance-covariance matrix elements composed of atomic coordinates, allowing us to perform principle component analysis and prepare domain cross-correlation map during molecular dynamics simulations in an on-the-fly manner. Published by AIP Publishing.

关键词： PROTEINS MOLECULAR dynamics computer simulation computer algorithms LYSOZYMES GLOBULAR proteins

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A Novel Graph Constructor for Semisupervised Discriminant Analysis: Combined Low-Rank and k-Nearest Neighbor Graph

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COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2017年第20170101期2017卷 9290230-9290230页

作者： Zu, Baokai Xia, Kewen Pan, Yongke Niu, Wenjia Hebei Univ Technol Sch Elect & Informat Engn Tianjin 300401 Peoples R China Key Lab Big Data Computat Hebei Prov Tianjin 300401 Peoples R China Worcester Polytech Inst Dept Comp Sci Worcester MA 01609 USA

Semisupervised Discriminant Analysis (SDA) is a semisupervised dimensionality reduction algorithm, which can easily resolve the out-of-sample problem. Relative works usually focus on the geometric relationships of data points, which are not obvious, to enhance the performance of SDA. Different from these relative works, the regularized graph construction is researched here, which is important in the graph-based semisupervised learning methods. In this paper, we propose a novel graph for Semisupervised Discriminant Analysis, which is called combined low-rank and k-nearest neighbor (LRKNN) graph. In our LRKNN graph, we map the data to the LR feature space and then the kNN is adopted to satisfy the algorithmic requirements of SDA. Since the low-rank representation can capture the global structure and the k-nearest neighbor algorithm can maximally preserve the local geometrical structure of the data, the LRKNN graph can significantly improve the performance of SDA. Extensive experiments on several real-world databases show that the proposed LRKNN graph is an efficient graph constructor, which can largely outperform other commonly used baselines.

关键词： DISCRIMINANT analysis K-nearest neighbor classification LOW-rank matrices SUPERVISED learning (Machine learning) computer algorithms

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Developing a Tile-Based Rendering Method to Improve Rendering Speed of 3D Geospatial Data with HTML5 and WebGL

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JOURNAL OF SENSORS 2017年第10-19期2017卷 9781307-9781307页

作者： Kang, Seokchan Lee, Jiyeong Univ Seoul Dept Geoinformat GSE 163 Seoulsiripdae Ro Seoul South Korea

A dedicated plug-in has been installed to visualize three-dimensional (3D) city modeling spatial data in web-based applications. However, plug-inmethods are gradually becoming obsolete, owing to their limited performance with respect to installation errors, unsupported cross-browsers, and security vulnerability. Particularly, in 2015, the NPAPI service was terminated in most existing web browsers except Internet Explorer. To overcome these problems, the HTML5/WebGL (next-generation web standard, confirmed in October 2014) technology emerged. In particular, WebGL is able to display 3D spatial data without plug-ins in browsers. In this study, we attempted to identify the requirements and limitations of displaying 3D citymodeling spatial data using HTML5/WebGL, and we propose alternative ways based on the bin-packing algorithm that aggregates individual 3D city modeling data including buildings in tile units. The proposed method reduces the operational complexity and the number and volume of transmissions required for rendering processing to improve the speed of 3D data rendering. The proposed method was validated on real data for evaluating its effectiveness in 3D visualization of city modeling data in web-based applications.

关键词： Cities & towns -- computer network resources Three-dimensional modeling (computer graphics) computer algorithms HTML (Document markup language) Web-based user interfaces

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A Highly Parallel and Scalable Motion Estimation Algorithm with GPU for HEVC

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SCIENTIFIC PROGRAMMING 2017年第Pt.2期2017卷 1-15页

作者： Xue, Yun-gang Su, Hua-You Ren, Ju Wen, Mei Zhang, Chun-yuan Xiao, Li-quan Natl Univ Def Technol Sch Comp Changsha 410073 Hunan Peoples R China

We propose a highly parallel and scalable motion estimation algorithm, named multilevel resolution motion estimation (MLRME for short), by combining the advantages of local full search and downsampling. By subsampling a video frame, a large amount of computation is saved. While using the local full-search method, it can exploit massive parallelism and make full use of the powerful modern many-core accelerators, such as GPU and Intel Xeon Phi. We implanted the proposed MLRME into HM12.0, and the experimental results showed that the encoding quality of the MLRME method is close to that of the fast motion estimation in HEVC, which declines by less than 1.5%. We also implemented the MLRME with CUDA, which obtained 30-60x speed-up compared to the serial algorithm on single CPU. Specifically, the parallel implementation of MLRME on a GTX 460 GPU can meet the real-time coding requirement with about 25 fps for the 2560 x 1600 video format, while, for 832 x 480, the performance is more than 100 fps.

关键词： GRAPHICS processing units (computers) MOTION estimation (Signal processing) computer algorithms CUDA (computer architecture) ENCODING

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A Distributed Tactile Sensor for Intuitive Human-Robot Interfacing

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JOURNAL OF SENSORS 2017年第4-27期2017卷 1357061-1357061页

作者： Cirillo, Andrea Cirillo, Pasquale De Maria, Giuseppe Natale, Ciro Pirozzi, Salvatore Univ Campania Luigi Vanvitelli Dipartimento Ingn Ind & Informaz Via Roma 29 I-81031 Aversa Italy

Safety of human-robot physical interaction is enabled not only by suitable robot control strategies but also by suitable sensing technologies. For example, if distributed tactile sensors were available on the robot, they could be used not only to detect unintentional collisions, but also as human-machine interface by enabling a new mode of social interaction with the machine. Starting from their previous works, the authors developed a conformable distributed tactile sensor that can be easily conformed to the different parts of the robot body. Its ability to estimate contact force components and to provide a tactile map with an accurate spatial resolution enables the robot to handle both unintentional collisions in safe human-robot collaboration tasks and intentional touches where the sensor is used as human-machine interface. In this paper, the authors present the characterization of the proposed tactile sensor and they show how it can be also exploited to recognize haptic tactile gestures, by tailoring recognition algorithms, well known in the image processing field, to the case of tactile images. In particular, a set of haptic gestures has been defined to test three recognition algorithms on a group of 20 users. The paper demonstrates how the same sensor originally designed to manage unintentional collisions can be successfully used also as human-machine interface.

关键词： Tactile sensors Human-robot interaction Robot control systems computer algorithms Human-machine relationship

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Dynamic Shift Coordinated Control Based on Motor Active Speed Synchronization with the New Hybrid System

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SHOCK AND VIBRATION 2017年第Pt.4期2017卷 1-1页

作者： Yan, Ting Yang, Lin Yan, Bin Zhou, Wei Chen, Liang Zhou, Wei Shanghai Jiao Tong Univ Inst Automot Elect Technol Sch Mech Engn Shanghai 200240 Peoples R China Shanghai 01 Power Technol Co Ltd Shanghai 200240 Peoples R China

Considering the inherent disadvantages that severely affect driving comfortability during the shift process in HEVs, a dynamic shift coordinated control based on motor active speed synchronization is proposed to improve shift quality by reduction of shift vibration. The whole control scheme is comprised of three phases, preparatory phase, speed regulation phase, and synchronization phase, which are implemented consecutively in order. The key to inhibiting impact and jerk depends on the speed regulation phase, where motor active speed synchronization is utilized to reach the minimum speed difference between the two ends of synchronizer. A new hybrid system with superior performances is applied to present the validity of the adopted control algorithm during upshift or downshift, which can represent planetary gear system and conventional AMT shift procedure, respectively. Bench test, simulation, and road test results show that, compared with other methods, the proposed dynamic coordinated control can achieve shifting control in real time to effectively improve gear-shift comfort and shorten power interruption transients, with robustness in both conventional AMT and planetary gear train.

关键词： SHIFT PROCESSES coordinated control Shift quality Planetary gear trains geared system reduction downshift AMT gene hybrid systems Shift Road tests computer algorithms

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Acceleration of Image Segmentation Algorithm for (Breast) Mammogram Images Using High-Performance Reconfigurable Dataflow computers

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COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017年第20170101期2017卷 7909282-7909282页

作者： Milankovic, Ivan L. Mijailovic, Nikola V. Filipovic, Nenad D. Peulic, Aleksandar S. Univ Kragujevac Fac Engn Sestre Janjic 6 Kragujevac Serbia BioIRC Res & Dev Ctr Bioengn Prvoslava Stojanov 6-1 Kragujevac Serbia

Image segmentation is one of the most common procedures in medical imaging applications. It is also a very important task in breast cancer detection. Breast cancer detection procedure based on mammography can be divided into several stages. The first stage is the extraction of the region of interest from a breast image, followed by the identification of suspicious mass regions, their classification, and comparison with the existing image database. It is often the case that already existing image databases have large sets of data whose processing requires a lot of time, and thus the acceleration of each of the processing stages in breast cancer detection is a very important issue. In this paper, the implementation of the already existing algorithm for region-of-interest based image segmentation for mammogram images on High-Performance Reconfigurable Dataflow computers (HPRDCs) is proposed. As a dataflow engine (DFE) of such HPRDC, Maxeler's acceleration card is used. The experiments for examining the acceleration of that algorithm on the Reconfigurable Dataflow computers (RDCs) are performed with two types of mammogram images with different resolutions. There were, also, several DFE configurations and each of them gave a different acceleration value of algorithm execution. Those acceleration values are presented and experimental results showed good acceleration.

关键词： SEGMENTATION (Image processing) MAMMOGRAMS computer algorithms DATA flow computing DIAGNOSTIC imaging

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Performance Analysis of Two-Dimensional Maximum Likelihood Direction-of-Arrival Estimation Algorithm Using the UCA

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INTERNATIONAL JOURNAL OF ANTENNAS AND PROPAGATION 2017年第2-9期2017卷 28-28页

作者： Cho, Yun-Seong Seo, Jeong-Min Lee, Joon-Ho Sejong Univ Dept Informat & Commun Engn Kwangjin Ku 98 Kunja Dong Seoul 143747 South Korea

We address the performance analysis of the maximum likelihood (ML) direction-of-arrival (DOA) estimation algorithm in the case of azimuth/elevation estimation of two incident signals using the uniform circular array (UCA). Based on the Taylor series expansion and approximation, we get explicit expressions of the root mean square errors (RMSEs) of the azimuths and elevations. The validity of the derived expressions is shown by comparing the analytic results with the simulation results. The derivation in this paper is further verified by illustrating the consistency of the analytic results with the Cramer-Rao lower bound (CRLB).

关键词： computer algorithms Taylor’s series Uniform circular motion Standard deviations Simulation methods & models

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Perspective: Dissipative particle dynamics

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JOURNAL OF CHEMICAL PHYSICS 2017年第15期146卷 150901-150901页

作者： Espanol, Pep Warren, Patrick B. Univ Nacl Educ Distancia Dept Fis Fundamental Aptdo 60141 E-28080 Madrid Spain Unilever R&D Port Sunlight Quarry Rd East Wirral CH63 3JW Merseyside England

Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent coarse-grained portions of the system under study and allow, therefore, reaching time and length scales that would be otherwise unreachable from microscopic simulations. The method has been conceptually refined since its introduction almost twenty five years ago. This perspective surveys the major conceptual improvements in the original DPD model, along with its microscopic foundation, and discusses outstanding challenges in the field. We summarize some recent advances and suggest avenues for future developments. Published by AIP Publishing.

关键词： PARTICLE dynamics analysis ENERGY dissipation computer algorithms COMPLEX fluids MICROSCOPY

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Image Enhancement via Subimage Histogram Equalization Based on Mean and Variance

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COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2017年第1期2017卷 1-12页

作者： Zhuang, Liyun Guan, Yepeng Shanghai Univ Sch Commun & Informat Engn Shanghai Peoples R China Huaiyin Inst Technol Fac Elect & Informat Engn Huaian Peoples R China Minist Educ Key Lab Adv Displays & Syst Applicat Shanghai Peoples R China

This paper puts forward a novel image enhancement method via Mean and Variance based Subimage Histogram Equalization (MVSIHE), which effectively increases the contrast of the input image with brightness and details well preserved compared with some other methods based on histogram equalization (HE). Firstly, the histogram of input image is divided into four segments based on the mean and variance of luminance component, and the histogram bins of each segment are modified and equalized, respectively. Secondly, the result is obtained via the concatenation of the processed subhistograms. Lastly, the normalizationmethod is deployed on intensity levels, and the integration of the processed image with the input image is performed. 100 benchmark images from a public image database named CVG-UGR-Database are used for comparison with other state-of-the-art methods. Theexperiment results showthat the algorithmcan not only enhance image information effectively but alsowell preserve brightness and details of the original image.

关键词： IMAGE enhancement (Imaging systems) HISTOGRAMS ANALYSIS of variance IMAGE processing computer algorithms

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