16148439
Solving the brachytherapy seed localization problem using geometric and linear programming techniques
We propose a technique to solve the Brachytherapy Seed Localization problem in prostate brachytherapy. Our algorithm is based on novel geometric approaches to exploit the special structure of the problem combined with a number of key observations which help us formulate it as an Integer Program. We solve the equivalent linear program and present a variant of randomized rounding to yield an integral solution to our problem. The algorithm is efficient and performs extremely well in practice. We discuss in detail the underlying theory and performance evaluations based on our implementation.
14297439
Geometric permutations of high dimensional spheres
We prove the maximum number of geometric permutations, induced by line transversals to a set of <i>n</i> pairwise disjoint congruent spheres in <i>R<sup>d</sup></i> with <i>d</i> ⪈ 3, is no more than 4 when <i>n</i> is sufficiently large, achieving the best known upper bound for this problem. We also prove the maximum number of geometric permutations of a set of <i>n</i> noncongruent spheres of bounded radius ratio in R<sup>d</sup>, <i>d</i> ⪈ 3, is at most 2<sup>[√2<i>M</i>]+1</sup>, where <i>M</i> is the ratio or the largest radius and the smallest radius. Our result settles a conjecture in combinatorial geometry.
6260724
Finding an optimal path without growing the tree
For problems on computing an optimal path as well as its length in a certain setting, the "standard" approach for finding an actual optimal path is by building (or "growing") a single-source optimal path tree. In this paper, we study a class of optimal path problems with the following phenomenon: The space complexity of the algorithms for reporting the lengths of single-source optimal paths for these problems is asymptotically smaller than the space complexity of the "standard" tree-growing algorithms for finding actual optimal paths. We present a general and efficient algorithmic paradigm for finding an actual optimal path for such problems without having to grow a single-source optimal path tree. Our paradigm is based on the "marriage-before-conquer" strategy, the prune-and-search technique, and a new data structure called clipped trees. The paradigm enables us to compute an actual path for a number of optimal path problems and dynamic programming problems in computational geometry, graph theory, and combinatorial optimization. Our algorithmic solutions improve the space bounds (in certain cases, the time bounds as well) of the previously best known algorithms, and settle some open problems. Our techniques are likely to be applicable to other problems.
21098955
Topological Peeling and Implementation
We present a new approach, called topological peeling, and its implementation for traversing a portion AR of the arrangement formed by n lines within a convex region R on the plane. Topological peeling visits the cells of AR in a fashion of propagating a "wave" of a special shape (called a double-wriggle curve) starting at a single source point. This special traversal fashion enables us to solve several problems (e.g., computing shortest paths) on planar arrangements to which previously best known arrangement traversal techniques such as topological sweep and topological walkm ay not be directly applicable. Our topological peeling algorithm takes O(K + n log(n + r)) time and O(n + r) space, where K is the number of cells in AR and r is the number of boundary vertices of R. Comparing with topological walk, topological peeling uses a simpler and more efficient way to sweep different types of lines, and relies heavily on exploring small local structures, rather than a much larger global structure. Experiments show that, on average, topological peeling outperforms topological walkb y 10 - 15% in execution time.
29728094
Graph Bandwidth of Weighted Caterpillars
Graph bandwidth minimization (GBM) is a classical and challenging problem in graph algorithms and combinatorial optimization. Most of existing researches on this problem have focused on unweighted graphs. In this paper, we study the bandwidth minimization problem of weighted caterpillars, and propose several algorithms for solving various types of caterpillars and general graphs. More specifically, we show that the GBM problem on caterpillars with hair-length at most 2 and the GBM problem on star-shape caterpillars are NP-complete, and give a lower bound of the graph bandwidth for general weighted graphs. For caterpillars with hair-length at most 1, we present an O(n log n log(nwmax))-time algorithm to compute an optimal bandwidth layout, where n is the total number of vertices in the graph and wmax is the maximum wedge weight. For caterpillars with hair-length at most k, we give a k-approximation algorithm. For arbitrary caterpillars and general graphs, we give a heuristic algorithm and some experimental results. Experiments show that the solutions obtained by our heuristic algorithm are roughly within a factor of c log(n) of the lower bound for a small number c, which is consistent with the inapproximability results of this problem (i.e., no constant approximation for the GBM problem unless P = NP). © 2006 Published by Elsevier B.V.
28240465
Motion Tracking and Intensity Surface Recovery in Microscopic Nuclear Images
Current techniques for microscopic imaging do not provide necessary spatial and temporal resolutions for real time visualization of the nucleus. Images can only be acquired in time lapse mode, leading to significant loss of information between image frames. Such data, if available, can be extremely helpful in the study of nuclear organization and function. In this paper, we present a gamut of geometric-technique-based approaches for solving the problem. Our techniques, working together, can effectively recover complicated motion and deformation as well as the change of intensity surfaces from pairs of images in a microscopic image sequence, and has low time complexity, particularly desirable by many biological applications where large amount of DNA need to be processed. These techniques are also readily applicable to other types of images for reconstructing motion and intensity surfaces of deformable objects.
8292124
Effective retrieval with distributed collections
Abstract : This paper evaluates the retrieval effectiveness of distributed information retrieval systems in realistic environments. We find that when a large number of collections are available, the retrieval effectiveness is significantly worse than that of centralized systems, mainly because typical queries are not adequate for the purpose of choosing the right collections. We propose two techniques to address the problem. One is to use phrase information in the collection selection index and the other is query expansion. Both techniques enhance the discriminatory power of typical queries for choosing the right collections and hence significantly improve retrieval results. Query expansion, in particular, brings the effectiveness of searching a large set of distributed collections close to that of searching a centralized collection.
19232033
Protein Threading by Linear Programming: Theoretical Analysis and Computational Results
In a previous paper (Xu, Li, Kim, and Xu, Journal of Bioinformatics and Computational Biology, vol. 1, no. 1, pp. 95–117, 2003), we have used an integer programming approach to implement a protein threading program RAPTOR for protein 3D structure prediction, based on the threading model treating pairwise contacts rigorously and allowing variable gaps. We have solved the integer program by the canonical branch-and-bound method. In this paper we present a branch-and-cut method, a careful theoretical analysis of our formulation and why our approach is so effective. The result of cutting plane analysis is that two types of well-known cuts for this problem are already implied in the constraint set, which provides us some intuition that our formulation would be very effective. Experimental results show that for about 99 percent of real threading instances, the linear relaxations of their integer programs solve to integral optimal solutions directly. For the rest one percent of real instances, the integral solutions can be obtained with only several branch nodes. Experimental results also show that no special template or sequence features result in more possibilities of fractional solutions. This indicates that extra effort to seek for cutting planes to strengthen the existing formulation is unnecessary.
17686330
Protein Threading by Linear Programming
Protein three-dimensional structure prediction through threading approach has been extensively studied and various models and algorithms have been proposed. In order to further explore ways to improve accuracy and efficiency of the threading process, this paper investigates the effectiveness of a new method: protein threading via linear programming. Based on the contact map model of protein 3D structure, we formulate the protein threading problem as a large scale integer programming problem, then relax to a linear programming problem, and finally solve the integer program by a branch-and-bound method. The final solution is optimal with respect to energy functions incorporating pairwise interaction and allowing variable gaps. The algorithm has been implemented as software package RAPTOR--RApid Protein Threading predictOR. Experimental results for fold recognition show that RAPTOR significantly outperforms other programs at the fold similarity level. The RAPTOR webserver is at http://www.cs.uwaterloo.ca/-j3xu/RAPTOR_form.htm.
14580037
An architectural framework for providing reliability and security support
This paper explores hardware-implemented error-detection and security mechanisms embedded as modules in a hardware-level framework called the reliability and security engine (RSE), which is implemented as an integral part of a modern microprocessor. The RSE interacts with the processor through an input/output interface. The CHECK instruction, a special extension of the instruction set architecture of the processor, is the interface of the application with the RSE. The detection mechanisms described here in detail are: (I) the memory layout randomization (MLR) module, which randomizes the memory layout of a process in order to foil attackers who assume a fixed system layout, (2) the data dependency tracking (DDT) module, which tracks the dependencies among threads of a process and maintains checkpoints of shared memory pages in order to rollback the threads when an offending (potentially malicious) thread is terminated, and (3) the instruction checker module (ICM), which checks an instruction for its validity or the control-flow of the program just as the instruction enters the pipeline for execution. Performance simulations for the studied modules indicate low overhead of the proposed solutions.
9688726
Motion Editing in 3D Video Database
As the next generation of media, 3D video is attracting increased attention. 3D video is a sequence of three dimensional mesh models, captured and generated for a real dynamic object. In this paper, we present a simple framework of motion editing in 3D video database to re-use 3D video data. Our system is composed of two modules. In the first module, a motion database is automatically set up from original 3D video sequences off-line by analyzing the feature vectors of each frame. It is observed that our original 3D video sequences have a two-level temporal structure. A fine-to-coarse method is proposed to extract such a structure. 3D video is segmented into the fine-level structure by a three reference frame strategy and then is clustered into the coarse-level structure. In the second module, users can synthesize the motions to edit a new 3D video sequence online. A cost function is optimized to transit between two motions with the users' requirements. All the algorithms in the system are based on the analysis in feature vector space and the edited 3D video sequence is played using OpenGL.