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APPROXIMATION BY SOLUTIONS OF THE PLANAR WAVE-EQUATION

SIAM JOURNAL ON NUMERICAL ANALYSIS 1992年第3期29卷 816-830页

作者： VONGOLITSCHEK, M LIGHT, WA UNIV LANCASTER DEPT MATHLANCASTER LA1 4YWENGLAND

Let D subset-of R2 be a compact set, and let f be a continuous real-valued function on D. An algorithm is described that computes the distance (in the uniform norm parallel-to parallel-to on D) between f and the solutions w of the wave equation partial derivative 2w/partial derivative s partial derivative t = 0. If, for some M > 0, W(M) subset-of C(D) is the set of solutions of the wave equation which are in the Lipschitz class Lip(M)1, the algorithm finds in W(M) a function of minimal distance from f.

关键词： BOUNDARY VALUE PROBLEMS WAVE EQUATION GOURSAT PROBLEM shortest path algorithm

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High-Throughput Soft-Output MIMO Detector Based on path-Preserving Trellis-Search algorithm

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IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS 2012年第7期20卷 1235-1247页

作者： Sun, Yang Cavallaro, Joseph R. Rice Univ Dept Elect & Comp Engn Houston TX 77005 USA

In this paper, we propose a novel path-preserving trellis-search (PPTS) algorithm and its high-speed VLSI architecture for soft-output multiple-input-multiple-output (MIMO) detection. We represent the search space of the MIMO signal with an unconstrained trellis, where each node in stage of the trellis maps to a possible complex-valued symbol transmitted by antenna. Based on the trellis model, we convert the soft-output MIMO detection problem into a multiple shortest paths problem subject to the constraint that every trellis node must be covered in this set of paths. The PPTS detector is guaranteed to have soft information for every possible symbol transmitted on every antenna so that the log-likelihood ratio (LLR) for each transmitted data bit can be more accurately formed. Simulation results show that the PPTS algorithm can achieve near-optimal error performance with a low search complexity. The PPTS algorithm is a hardware-friendly data-parallel algorithm because the search operations are evenly distributed among multiple trellis nodes for parallel processing. As a case study, we have designed and synthesized a fully-parallel systolic-array detector and two folded detectors for a 4 x 4 16-QAM system using a 1.08 V TSMC 65-nm CMOS technology. With a 1.18 mm(2) core area, the folded detector can achieve a throughput of 2.1 Gbps. With a 3.19 mm(2) core area, the fully-parallel systolic-array detector can achieve a throughput of 6.4 Gbps.

关键词： Application-specific integrated circuit (ASIC) multiple-input-multiple-output (MIMO) detection shortest path algorithm soft-output MIMO detector VLSI architecture

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Identifying novel protein phenotype annotations by hybridizing protein-protein interactions and protein sequence similarities

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MOLECULAR GENETICS AND GENOMICS 2016年第2期291卷 913-934页

作者： Chen, Lei Zhang, Yu-Hang Huang, Tao Cai, Yu-Dong Shanghai Univ Sch Life Sci Shanghai 200444 Peoples R China Shanghai Maritime Univ Coll Informat Engn Shanghai 201306 Peoples R China Chinese Acad Sci Shanghai Inst Biol Sci Inst Hlth Sci Shanghai 200031 Peoples R China

Studies of protein phenotypes represent a central challenge of modern genetics in the post-genome era because effective and accurate investigation of protein phenotypes is one of the most critical procedures to identify functional biological processes in microscale, which involves the analysis of multifactorial traits and has greatly contributed to the development of modern biology in the post genome era. Therefore, we have developed a novel computational method that identifies novel proteins associated with certain phenotypes in yeast based on the protein-protein interaction network. Unlike some existing network-based computational methods that identify the phenotype of a query protein based on its direct neighbors in the local network, the proposed method identifies novel candidate proteins for a certain phenotype by considering all annotated proteins with this phenotype on the global network using a shortest path (SP) algorithm. The identified proteins are further filtered using both a permutation test and their interactions and sequence similarities to annotated proteins. We compared our method with another widely used method called random walk with restart (RWR). The biological functions of proteins for each phenotype identified by our SP method and the RWR method were analyzed and compared. The results confirmed a large proportion of our novel protein phenotype annotation, and the RWR method showed a higher false positive rate than the SP method. Our method is equally effective for the prediction of proteins involving in all the eleven clustered yeast phenotypes with a quite low false positive rate. Considering the universality and generalizability of our supporting materials and computing strategies, our method can further be applied to study other organisms and the new functions we predicted can provide pertinent instructions for the further experimental verifications.

关键词： Phenotype Protein-protein interaction Protein sequence similarity shortest path algorithm

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Analysis of metabolic networks using a pathway distance metric through linear programming

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METABOLIC ENGINEERING 2003年第3期5卷 211-219页

作者： Simeonidis, E Rison, SCG Thornton, JM Bogle, IDL Papageorgiou, LG UCL Ctr Proc Syst Engn Dept Chem Engn London WC1E 7JE England UCL Dept Biochem & Mol Biol London WC1E 7HX England Univ London Birkbeck Coll Dept Crystallog London WC1E 7HX England

The solution of the shortest path problem in biochemical systems constitutes an important step for studies of their evolution. In this paper, a linear programming (LP) algorithm for calculating minimal pathway distances in metabolic networks is studied. Minimal pathway distances are identified as the smallest number of metabolic steps separating two enzymes in metabolic pathways. The algorithm deals effectively with circularity and reaction directionality. The applicability of the algorithm is illustrated by calculating the minimal pathway distances for Escherichia coli small molecule metabolism enzymes, and then considering their correlations with genome distance (distance separating two genes on a chromosome) and enzyme function (as characterised by enzyme commission number). The results illustrate the effectiveness of the LP model. In addition, the data confirm that propinquity of genes on the genome implies similarity in function (as determined by co-involvement in the same region of the metabolic network), but suggest that no correlation exists between pathway distance and enzyme function. These findings offer insight into the probable mechanism of pathway evolution. (C) 2003 Elsevier Inc. All rights reserved.

关键词： pathway distance shortest path algorithm linear programming metabolic pathways genome distance enzyme function

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Mass estimation of DNA molecules and extraction of ordered restriction maps in optical mapping imagery

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algorithmICA 1999年第2-3期25卷 295-310页

作者： Parida, L Geiger, D NYU Courant Inst Math Sci Dept Comp Sci New York NY 10012 USA

The Human Genome project has been considered "one of the great enterprises of 20th Century Science" [8]. The ultimate goal of many efforts in molecular biology, including the Human Genome Project, is to determine the entire sequence of human DNA and to extract genetic information from it. In this context an important step is to build restriction maps (location of certain identifiable markers) of portions of the DNA [8]. Optimal Mapping [24], [17], [21], a process that fixes elongated DNA molecules onto treated surfaces, is a very promising emerging technology for rapid production of ordered restriction maps. Our modeling and solution of detection, mass estimation, and extraction of ordered restriction maps of DNA molecules attempts to understand/answer questions of significant importance to geneticists, biologists, and chemists. In this paper we first describe the vision process that identifies the DNA molecules along with the restriction sites, and then model the restriction map problem and describe the algorithm that we use to extract the maps from the data. The input to the vision process is an image of the DNA molecules. We propose a simple Markov chain to model the DNA fragments, and use Single Source shortest path (SSSP) algorithms to detect and measure the apparent length of the DNA fragments. This is at the heart of the imaging software in use at the laboratory for over 2 years: the practical implementation continues to undergo various fine-tuning processes. In the second part we model the ordered restriction map as a combinatorial problem which we call the Binary Flip Cut (BFC) problem. We prove hardness results for this and several of its variants and offer a practical solution using techniques from mean field annealing/EM algorithm and demonstrate its effectiveness in practice.

关键词： flip cut optical mapping shortest path algorithm

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Automatic vertebra segmentation on dynamic magnetic resonance imaging

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JOURNAL OF MEDICAL IMAGING 2017年第1期4卷 014504页

作者： Onal, Sinan Chen, Xin Lai-Yuen, Susana Hart, Stuart Southern Illinois Univ Edwardsville Dept Mech & Ind Engn Edwardsville IL 62025 USA Univ S Florida Dept Ind & Management Syst Engn Tampa FL USA Univ S Florida Coll Med Obstet & Gynecol Tampa FL USA

The automatic extraction of the vertebra's shape from dynamic magnetic resonance imaging (MRI) could improve understanding of clinical conditions and their diagnosis. It is hypothesized that the shape of the sacral curve is related to the development of some gynecological conditions such as pelvic organ prolapse (POP). POP is a critical health condition for women and consists of pelvic organs dropping from their normal position. Dynamic MRI is used for assessing POP and to complement clinical examination. Studies have shown some evidence on the association between the shape of the sacral curve and the development of POP. However, the sacral curve is currently extracted manually limiting studies to small datasets and inconclusive evidence. A method composed of an adaptive shortest path algorithm that enhances edge detection and linking, and an improved curve fitting procedure is proposed to automate the identification and segmentation of the sacral curve on MRI. The proposed method uses predetermined pixels surrounding the sacral curve that are found through edge detection to decrease computation time compared to other model-based segmentation algorithms. Moreover, the proposed method is fully automatic and does not require user input or training. Experimental results show that the proposed method can accurately identify sacral curves for nearly 91% of dynamic MRI cases tested in this study. The proposed model is robust and can be used to effectively identify bone structures on MRI. (C) 2017 Society of Photo-Optical Instrumentation Engineers (SPIE)

关键词： edge detection magnetic resonance imaging pelvic organ prolapsed sacral bone shortest path algorithm

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VLSI Architecture for Layered Decoding of QC-LDPC Codes With High Circulant Weight

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IEEE TRANSACTIONS ON VERY LARGE SCALE INTEGRATION (VLSI) SYSTEMS 2013年第10期21卷 1960-1964页

作者： Sun, Yang Cavallaro, Joseph R. Rice Univ Dept Elect & Comp Engn Houston TX 77005 USA

In this brief, we propose a high-throughput layered decoder architecture to support a broader family of quasicyclic low-density parity-check (QC-LDPC) codes, whose parity-check matrices are constructed from arrays of circulant submatrices. Each nonzero circulant submatrix is a superposition of K cyclic-shifted identity matrices, where the circulant weight K >= 1. We propose a novel layered decoder architecture to support QC-LDPC codes with any circulant weight. We present a block-serial decoding architecture which processes a layer of a parity check matrix block by block, where each block is a Z x Z circulant matrix with a circulant weight of K. In the case study, we demonstrate an LDPC decoder design for the China Mobile Multimedia Broadcasting (CMMB) standard, which was synthesized for a TSMC 65-nm CMOS technology. With a core area of 3.9 mm(2), the CMMB LDPC decoder achieves a maximum throughput of 1.1 Gb/s with 15 iterations.

关键词： ASIC MIMO detection shortest path algorithm soft-output MIMO detector VLSI architecture

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Estimation of time-dependent, stochastic route travel times using artificial neural networks

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TRANSPORTATION PLANNING AND TECHNOLOGY 2000年第1期24卷 25-48页

作者： Fu, LP Rilett, LR Univ Waterloo Dept Civil Engn Waterloo ON N2L 3G1 Canada Texas A&M Univ Syst Dept Civil Engn College Stn TX 77843 USA Texas A&M Univ Syst Texas Transportat Inst College Stn TX 77843 USA

This paper presents an artificial neural network (ANN) based method for estimating route travel times between individual locations in an urban traffic network. Fast and accurate estimation of route travel times is required by the vehicle routing and scheduling process involved in many fleet vehicle operation systems such as dial-a-ride paratransit, school bus, and private delivery services. The methodology developed in this paper assumes that route travel times are time-dependent and stochastic and their means and standard deviations need to be estimated. Three feed-forward neural networks are developed to model the travel time behaviour during different time periods of the day the AM peak, the PM peak, and the off-peak. These models are subsequently trained and tested using data simulated on the road network for the City of Edmonton, Alberta. A comparison of the ANN model with a traditional distance-based model and a shortest path algorithm is then presented. The practical implication of the ANN method is subsequently demonstrated within a dial-a-ride paratransit vehicle routing and scheduling problem. The computational results show that the ANN-based route travel time estimation model is appropriate, with respect to accuracy and speed, for use in real applications.

关键词： artificial neural network travel time shortest path algorithm travel distance function vehicle routing scheduling dial-a-ride paratransit

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A novel approach for smart cities in convergence to wireless sensor networks

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SUSTAINABLE CITIES AND SOCIETY 2017年 35卷 440-448页

作者： Jain, Bindiya Brar, Gursewak Malhotra, Jyoteesh Rani, Shalli IKG Punjab Tech Univ Jalndhar Pb India BBSBEC Fatehgarh Sahib India Guru Nanak Dev Univ Jalandhar India SSD Womens Inst Technol Dept Comp Sci Bathinda Pb India

Internet of things (IoT) for Smart cities has been gradually bringing a sea of technological changes in our day to day life, which in turn helps to make our life more comfortable. Sensing and timely disseminating the information to the base station is the main feature in Internet of Things enabled applications. This function is carried out by the base layer of IoT paradigm and it is consisted of wireless sensor networks (WSNs). In this paper, we propose a WSN-IoT paradigm for real-time applications. The main focus is to find the means of providing information as early as possible to receiver which is prerequisite in smart cities. In this paper, routing is based on the shortest path which is selected using TOPSIS optimization and achieves balance between performance and energy consumption with regard to four criteria's: 1) Least distance of selected nodes from the base station, 2) Residual Energy, 3) minimum Euclidean distance between mth selected node and 4) next optimum nth node in the transmission range and number of neighboring nodes. Finally, Simulations are conducted in MATLAB in order to demonstrate how the proposed method would work to locate the best node in each cycle and confirm its effectiveness.

关键词： Internet of things Wireless sensor networks Routing TOPSIS shortest path algorithm Smart city

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Three-dimensional object metamorphosis through energy minimization

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COMPUTERS & GRAPHICS 1998年第2-3期22卷 195-202页

作者： Korfiatis, I Paker, Y Univ London Queen Mary & Westfield Coll Dept Comp Sci London E1 4NS England

This paper presents a technique for smoothly blending some categories of three-dimensional polygonal objects. Polygon blending is usually considered a two-part process: generating vertex correspondences and interpolating between corresponding vertices to create the intermediate polygons. This paper considers the problem of automatic vertex correspondence determination. The proposed algorithm is based on the work of Sederberg and Greenwood [Computer, Graphics 26(2), 25-34, 1992]. The resulting solution tends to associate regions of the two objects which look alike. (C) 1998 Elsevier Science Ltd. All rights reserved.

关键词： metamorphosis energy minimization shortest path algorithm surface reconstruction from planar contours 3D animation

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