9436128
Computing Optimal Beams in Two and Three Dimensions
The problem of computing an optimal beam among weighted regions (called the optimal beam problem) arises in several applied areas such as radiation therapy, stereotactic brain surgery, medical surgery, geological exploration, manufacturing, and environmental engineering. In this paper, we present computational geometry techniques that enable us to develop efficient algorithms for solving various optimal beam problems among weighted regions in two and three dimensional spaces. In particular, we consider two types of problems: the covering problems (seeking an optimal beam to contain a specified target region), and the piercing problems (seeking an optimal beam of a fixed shape to pierce the target region). We investigate several versions of these problems, with a variety of beam shapes and target region shapes in 2-D and 3-D. Our algorithms are based on interesting combinations of computational geometry techniques and optimization methods, and transform the optimal beam problems to solving a collection of instances of certain special non-linear optimization problems. Our approach makes use of interesting geometric observations, such as utilizing some new features of Minkowski sums.
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.
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.
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.
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.
240982
Data streaming algorithms for estimating entropy of network traffic
Using entropy of traffic distributions has been shown to aid a wide variety of network monitoring applications such as anomaly detection, clustering to reveal interesting patterns, and traffic classification. However, realizing this potential benefit in practice requires accurate algorithms that can operate on high-speed links, with low CPU and memory requirements. In this paper, we investigate the problem of estimating the entropy in a streaming computation model. We give lower bounds for this problem, showing that neither approximation nor randomization alone will let us compute the entropy efficiently. We present two algorithms for randomly approximating the entropy in a time and space efficient manner, applicable for use on very high speed (greater than OC-48) links. The first algorithm for entropy estimation is inspired by the structural similarity with the seminal work of Alon et al. for estimating frequency moments, and we provide strong theoretical guarantees on the error and resource usage. Our second algorithm utilizes the observation that the performance of the streaming algorithm can be enhanced by separating the high-frequency items (or elephants) from the low-frequency items (or mice). We evaluate our algorithms on traffic traces from different deployment scenarios.
47532017
On fundamental tradeoffs between delay bounds and computational complexity in packet scheduling algorithms
We clarify, extend, and solve a long-standing open problem concerning the computational complexity for packet scheduling algorithms to achieve tight end-to-end delay bounds. We first focus on the difference between the time a packet finishes service in a scheduling algorithm and its virtual finish time under a GPS (General Processor Sharing) scheduler, called GPS-relative delay. We prove that, under a slightly restrictive but reasonable computational model, the lower bound computational complexity of any scheduling algorithm that guarantees O(1) GPS-relative delay bound is /spl Omega/(logn). We also discover that, surprisingly, the complexity lower bound remains the same even if the delay bound is relaxed to O(n/sup a/) for 0<a<1. This implies that the delay-complexity tradeoff curve is flat in the "interval" [O(1),O(n)). We later conditionally extend both complexity results (for O(1) or O(n/sup a/) delay) to a much stronger computational model, the linear decision tree. Finally, we show that the same complexity lower bounds are conditionally applicable to guaranteeing tight end-to-end delay bounds, if the delay bounds are provided through the Latency Rate (LR) framework.
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.
42254231
A novel cache architecture to support layer-four packet classification at memory access speeds
Existing and emerging layer-4 switching technologies require packet classification to be performed on more than one header field, known as layer-4 lookup. Currently, the fastest general layer-8 lookup scheme delivers a throughput of 1 million lookups per second (MLPS), far off from 25/75 MLPS needed to support 50/150 Gbps layer-4 router. We propose the use of route caching to speed up layer-4 lookup, and design and implement a cache architecture for this purpose. We investigated the locality behavior of the Interent traffic (at layer-4) and propose a near-LRU algorithm that can best harness this behavior. In implementation, to best approximate fully-associative near-LRU using relatively inexpensive set-associative hardware, we invented a dynamic set-associative scheme that exploits the nice properties of N-universal hash functions. The cache architecture achieves a high and stable hit ratio above 90 percent and a fast throughput up to 75 MLPS at a reasonable cost.
8946964
Extending Network Lifetime for Precision-Constrained Data Aggregation in Wireless Sensor Networks
This paper exploits the tradeoff between data quality and energy consumption to extend the lifetime of wireless sensor networks. We consider the applications that require some aggregate form of sensed data with precision guarantees. Our key idea is to differentiate the precisions of data collected from different sensor nodes to balance their energy consumption. This is achieved by partitioning the precision constraint of data aggregation and allocating error bounds to individual sensor nodes in a coordinated fashion. Three factors affecting the lifetime of sensor nodes are identified: (1) the changing pattern of sensor readings; (2) the residual energy of sensor nodes; and (3) the communication cost between the sensor nodes and the base station. We analyze the optimal precision allocation in terms of network lifetime and propose an adaptive precision allocation scheme that dynamically adjusts the error bounds of sensor nodes. Experimental results using real data traces show that the proposed scheme significantly improves network lifetime compared to existing methods.