Search For:

Displaying 1-15 out of 15 total
Protein Chain Pair Simplification under the Discrete Fréchet Distance
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Tim Wylie,Binhai Zhu
Issue Date:November 2013
pp. 1372-1383
For protein structure alignment and comparison, a lot of work has been done using RMSD as the distance measure, which has drawbacks under certain circumstances. Thus, the discrete Fréchet distance was recently applied to the problem of protein (backbone) s...
 
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Nan Liu, Haitao Jiang, Daming Zhu, Binhai Zhu
Issue Date:July 2013
pp. 905-913
Scaffold filling is a new combinatorial optimization problem in genome sequencing. The one-sided scaffold filling problem can be described as given an incomplete genome I and a complete (reference) genome G, fill the missing genes into I such that the numb...
 
Scaffold Filling under the Breakpoint and Related Distances
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Haitao Jiang, Chunfang Zheng,D. Sankoff, Binhai Zhu
Issue Date:July 2012
pp. 1220-1229
Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, a problem on filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G was studied. The objective is to minimiz...
 
Moving Network Voronoi Diagram
Found in: International Symposium on Voronoi Diagrams in Science and Engineering
By Chenglin Fan, Jianbiao He, Jun Luo, Binhai Zhu
Issue Date:June 2010
pp. 142-150
We study the problem of moving network Voronoi diagram: given a network with $n$ nodes and $E$ edges. Suppose there are $m$ sites (cars, postmen, \emph{etc}) moving along the network edges, we design the algorithms to compute the dynamic network Voronoi di...
 
Automatically Approximating 3D Points with Co-Axisal Objects
Found in: Computational Science and its Applications, International Conference
By Russell Tempero, Sergey Bereg, Xiangxu Meng, Changhe Tu, Chenglei Yang, Binhai Zhu
Issue Date:July 2008
pp. 373-381
In this paper, we investigate the problem of approximating a set S of 3D points with co-axisal objects typically from CAD/CAM (namely, cylindrical segments, cones and conical frustums). The objective is to minimize the sume of volumes of these objects (as ...
 
Voronoi Diagram and Delaunay Triangulation: Applications and Challenges in Bioinformatics
Found in: International Symposium on Voronoi Diagrams in Science and Engineering
By Binhai Zhu
Issue Date:July 2006
pp. 2-3
In this talk, I first cover the applications of Voronoi Diagram and Delaunay Triangulation based on my personal experience. On the successful part, I will cover the history and development of the Jump-and-Walk algorithm, which is known as the first subline...
   
WebSail: From On-line Learning to Web Search
Found in: Web Information Systems Engineering, International Conference on
By Zhixiang Chen, Xiannong Meng, Richard H. Fowler, Binhai Zhu
Issue Date:June 2000
pp. 0206
In this paper, we investigate the applicability of on-line learning algorithms to the real-world problem of web search. Consider that web documents are indexed using n Boolean features. We first present a practically efficient on-line learning algorithm TW...
 
A randomized algorithm for Voronoi diagram of line segments on coarse grained multiprocessors
Found in: Parallel Processing Symposium, International
By Xiaotie Deng, Binhai Zhu
Issue Date:April 1996
pp. 192
We present a randomized parallel algorithm for the Voronoi diagram of line segments on coarse grained parallel machines, which, for any input of n line segments on P processors (n= Ω (P3 + ε ), for any ε > 0) requires (with high probability) O([n log n/...
 
An Improved Approximation Algorithm for Scaffold Filling to Maximize the Common Adjacencies
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Binhai Zhu, Daming Zhu, Haitao Jiang, Nan Liu
Issue Date:July 2013
pp. 905-913
Scaffold filling is a new combinatorial optimization problem in genome sequencing. The one-sided scaffold filling problem can be described as given an incomplete genome $(I)$ and a complete (reference) genome $(G)$, fill the missing genes into $(I)$ such t...
     
Protein Chain Pair Simplification under the Discrete Fréchet Distance
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Binhai Zhu, Tim Wylie
Issue Date:November 2013
pp. 1372-1383
For protein structure alignment and comparison, a lot of work has been done using RMSD as the distance measure, which has drawbacks under certain circumstances. Thus, the discrete Fréchet distance was recently applied to the problem of protein (backbo...
     
Scaffold Filling under the Breakpoint and Related Distances
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Binhai Zhu, Chunfang Zheng, David Sankoff, Haitao Jiang
Issue Date:July 2012
pp. 1220-1229
Motivated by the trend of genome sequencing without completing the sequence of the whole genomes, a problem on filling an incomplete multichromosomal genome (or scaffold) I with respect to a complete target genome G was studied. The objective is to minimiz...
     
Guarding a terrain by two watchtowers
Found in: Proceedings of the twenty-first annual symposium on Computational geometry (SCG '05)
By Binhai Zhu, Haim Kaplan, Ovidiu Daescu, Pankaj K. Agarwal, Sergey Bereg, Simeon Ntafos
Issue Date:June 2005
pp. 346-355
Given a polyhedral terrain T with n vertices, the two-watchtower problem for T calls for finding two vertical segments, called watchtowers, of smallest common height, whose bottom endpoints (bases) lie on T, and whose top endpoints guard T, in the sense th...
     
A polynomial time solution for labeling a rectilinear map
Found in: Proceedings of the thirteenth annual symposium on Computational geometry (SCG '97)
By Binhai Zhu, Chung Keung Poon, Franis Chin
Issue Date:June 1997
pp. 451-453
An interactive visualization of weighted three-dimensional α-hulls is presented for static and dynamic spheres. The α-hull is analytically computed and represented by a triangulated mesh. The entire surface is computed and displayed in real-time ...
     
On the sectional area of convex polytopes
Found in: Proceedings of the twelfth annual symposium on Computational geometry (SCG '96)
By Binhai Zhu, David Avis, Godfried Toussaint, Jack Snoeyink, Prosenjit Bose, Thomas C. Shermer
Issue Date:May 1996
pp. 411-412
An interactive visualization of weighted three-dimensional α-hulls is presented for static and dynamic spheres. The α-hull is analytically computed and represented by a triangulated mesh. The entire surface is computed and displayed in real-time ...
     
Fast randomized point location without preprocessing in two- and three-dimensional Delaunay triangulations
Found in: Proceedings of the twelfth annual symposium on Computational geometry (SCG '96)
By Binhai Zhu, Ernst P. Mucke, Isaac Saias
Issue Date:May 1996
pp. 274-283
An interactive visualization of weighted three-dimensional α-hulls is presented for static and dynamic spheres. The α-hull is analytically computed and represented by a triangulated mesh. The entire surface is computed and displayed in real-time ...
     
 1