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On optimal comparability editing with applications to molecular diagnostics

BMC BIOINFORMATICS 2009年第Sup1期10卷 S61-S61页

作者： Boecker, Sebastian Briesemeister, Sebastian Klau, Gunnar W. CWI NL-1090 GB Amsterdam Netherlands Univ Jena Inst Informat Jena Germany Jena Ctr Bioinformat Jena Germany Univ Tubingen ZBIT WSI Div Simulat Biol Syst D-72074 Tubingen Germany

Background: The COMPARABILITY EDITING problem appears in the context of hierarchical disease classification based on noisy data. We are given a directed graph G representing hierarchical relationships between patient subgroups. The task is to identify the minimum number of edge insertions or deletions to transform G into a transitive graph, that is, if edges (u, v) and (v, w) are present then edge (u, w) must be present, too. Results: We present two new approaches for the problem based on fixed-parameter algorithmics and integer linear programming. In contrast to previously used heuristics, our approaches compute provably optimal solutions. Conclusion: Our computational results demonstrate that our exact algorithms are by far more efficient in practice than a previously used heuristic approach. In addition to the superior running time performance, our algorithms are capable of enumerating all optimal solutions, and naturally solve the weighted version of the problem.

关键词： integer linear program Input Graph Reduction Rule integer linear program Formulation Transitive Graph

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A new graph-based method for pairwise global network alignment

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BMC BIOINFORMATICS 2009年第Sup1期10卷 S59-S59页

作者： Klau, Gunnar W. CWI NL-1090 GB Amsterdam Netherlands

Background: In addition to component-based comparative approaches, network alignments provide the means to study conserved network topology such as common pathways and more complex network motifs. Yet, unlike in classical sequence alignment, the comparison of networks becomes computationally more challenging, as most meaningful assumptions instantly lead to NP-hard problems. Most previous algorithmic work on network alignments is heuristic in nature. Results: We introduce the graph-based maximum structural matching formulation for pairwise global network alignment. We relate the formulation to previous work and prove NP-hardness of the problem. Based on the new formulation we build upon recent results in computational structural biology and present a novel Lagrangian relaxation approach that, in combination with a branch-and-bound method, computes provably optimal network alignments. The Lagrangian algorithm alone is a powerful heuristic method, which produces solutions that are often near-optimal and - unlike those computed by pure heuristics - come with a quality guarantee. Conclusion: Computational experiments on the alignment of protein-protein interaction networks and on the classification of metabolic subnetworks demonstrate that the new method is reasonably fast and has advantages over pure heuristics. Our software tool is freely available as part of the LISA library.

关键词： integer linear program integer linear programming Formulation Structural Match Network Alignment Common Subgraph

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Optimal Post-Routing Redundant Via Insertion 08

Optimal Post-Routing Redundant Via Insertion

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ACM International Symposium on Physical Design

作者： Lee, Kuang-Yao Koh, Cheng-Kok Wang, Ting-Chi Chao, Kai-Yuan Natl Tsing Hua Univ Dept Comp Sci Hsinchu 30043 Taiwan Purdue Univ W Lafayette IN 47907 USA Intel Corp Hillsboro OR 95051 USA

ISBN: (纸本)9781605580487

Redundant via insertion is highly recommended for improving chip yield and reliability. In this paper, we study the problem of double-cut via insertion (DVI) in a post-routing stage, where a single via can have at most one redundant via inserted next to it and the goal is to insert as many redundant vias as possible. The DVI problem can be naturally formulated as a zero-one integer linear program (0-1 ILP). Our main contributions are acceleration methods for reducing the problem size and the number of constraints. Moreover, we extend the 0-1 ILP formulation to handle via density constraints. Experimental results show that our 0-1 ILP is very efficient in computing optimal DVI solution, with tip to 35.3 times speedup over existing heuristic algorithms.

关键词： redundant via insertion via density integer linear program

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Traffic Grooming in Optical WDM Mesh Networks

Traffic Grooming in Optical WDM Mesh Networks

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IEEE Region 10 Colloquium/3rd International Conference on Industrial and Information Systems

作者： Ajaykumar, S. Ghosh, S. K. Indian Inst Technol Sch Informat Technol Kharagpur 721302 W Bengal India

ISBN: (纸本)9781424428052

Wavelength Division Multiplexing (WDM) has emerged as the preferred technology for reducing the oplo-electronic bandwidth mismatch by dividing the bandwidth of an optical fiber into multiple non-overlapping wavelength channels, each operating at peak electronic speed of the end users. Traffic grooming is being considered as a key functionality of WDM networks, in which, multiple low-speed traffic requests are groomed onto a single, high-capacity lightpath (wavelength). Mathematical formulation of the traffic grooming problem has been developed for various optimization objectives. The present work focuses on the traffic grooming problem in WDM mesh networks under static traffic scenario, for optimizing network revenue We have verified ILP formulation for the problem using CPLEX 9.1 and have developed three heuristics algorithms for solving the traffic grooming problem while optimizing network revenue. Performance of the three algorithms has been evaluated and a comparative study with the results of solving the ILP model has been carried out. The algorithms have been found to give good performance, especially for larger-sized networks.

关键词： Grooming-node heuristics lightpath integer linear program network revenue traffic grooming wavelength division multiplexing

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Efficient non-unique probes selection algorithms for DNA microarray

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BMC GENOMICS 2008年第Sup1期9卷 S22-S22页

作者： Deng, Ping Thai, My T. Ma, Qingkai Wu, Weili Univ Illinois Springfield Dept Comp Sci Springfield IL 62703 USA Univ Florida Comp & Informat Sci & Engn Dept Gainesville FL 32611 USA SUNY Coll Technol Utica Rome Dept Econ Crime & Justice Studies Utica NY 13502 USA Univ Texas Dallas Dept Comp Sci Richardson TX 75081 USA

Background: Temperature and salt concentration are very helpful experimental conditions for a probe to hybridize uniquely to its intended target. In large families of closely related target sequences, the high degree of similarity makes it impossible to find a unique probe for every target. We studied how to select a minimum set of non-unique probes to identify the presence of at most d targets in a sample where each non-unique probe can hybridize to a set of targets. Results: We proposed efficient algorithms based on integer linear programming to select a minimum number of non-unique probes using d-disjunct matrices. Our non-unique probes selection can also identify up to d targets in a sample with at most k experimental errors. The decoding complexity of our algorithms is as simple as O(n). The experimental results show that the decoding time is much faster than that of the methods using d-separable matrices while running time and solution size are comparable. Conclusions: Since finding unique probes is often not easy, we make use of non-unique probes. Minimizing the number of non-unique probes will result in a smaller DNA microarry design which leads to a smaller chip and considerable reduction of cost. While minimizing the probe set, the decoding ability should not be diminished. Our non-unique probes selection algorithms can identify up to d targets with error tolerance and the decoding complexity is O(n).

关键词： integer linear program Decode Algorithm Greedy Heuristic Unique Probe Probe Candidate

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Mathematical formulation of provisioning of connections with advance reservation in metro WDM ring networks using reconfigurable OADMs (ROADMs) with tuning constraint

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PHOTONIC NETWORK COMMUNICATIONS 2007年第3期14卷 273-285页

作者： Zhu, Hongyue Huang, Anpeng Mukherjee, Biswanath Univ Calif Davis Dept Comp Sci Davis CA 95616 USA

Optical add/drop multiplexers (OADMs) can significantly reduce the cost of metro optical wavelength-division multiplexing (WDM) ring networks by allowing traffic to bypass intermediate nodes without expensive opto-electro-opto (O-E-O) conversion. Some traditional OADMs, called fixed OADMs (FOADMs), can only add/drop traffic on a specific wavelength. Reconfigurable Optical Add/Drop Multiplexers (ROADMs) are emerging, which can add/drop traffic onto/from different wavelengths at different time. ROADMs provide desirable flexibility, enable fast provisioning of dynamic traffic, and save capital expenditure (CapEx) and operational expenditure (OpEx). In order to be cost-effective, some ROADMs employ architectures that tune the ROADM continuously from one wavelength to another, crossing through all the wavelengths in-between, which may cause interference to the connections, if any, on those wavelengths being crossed. In order to prevent existing connections from being interrupted, a constraint needs to be imposed that ROADMs cannot cross working wavelengths when tuning. In this study, the design and the benefits of metro optical WDM network architectures using ROADMs and the impact of this tuning constraint on the performance of the network are investigated. Mathematical formulation of the problem of provisioning of connections with advance reservation, in which the arrival time and departure time of all the connections are known in advance, is presented, and results for a small network are shown.

关键词： optical network WDM ring network metropolitan area network (MAN) reconfigurability optical add/drop multiplexer tuning constraint ROADM advance reservation mathematical formulation integer linear program

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Direct maximum parsimony phylogeny reconstruction from genotype data

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BMC BIOINFORMATICS 2007年第1期8卷 472-472页

作者： Sridhar, Srinath Lam, Fumei Blelloch, Guy E. Ravi, R. Schwartz, Russell Carnegie Mellon Univ Dept Biol Sci Pittsburgh PA 15213 USA Carnegie Mellon Univ Dept Comp Sci Pittsburgh PA 15213 USA Brown Univ Dept Comp Sci Providence RI 02912 USA Carnegie Mellon Univ Tepper Sch Business Pittsburgh PA 15213 USA

Background: Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis, and the search for genetic predictors of disease. Efficient methods are available for reconstruction of maximum parsimony trees from haplotype data, but such data are difficult to determine directly for autosomal DNA. Data more commonly is available in the form of genotypes, which consist of conflated combinations of pairs of haplotypes from homologous chromosomes. Currently, there are no general algorithms for the direct reconstruction of maximum parsimony phylogenies from genotype data. Hence phylogenetic applications for autosomal data must therefore rely on other methods for first computationally inferring haplotypes from genotypes. Results: In this work, we develop the first practical method for computing maximum parsimony phylogenies directly from genotype data. We show that the standard practice of first inferring haplotypes from genotypes and then reconstructing a phylogeny on the haplotypes often substantially overestimates phylogeny size. As an immediate application, our method can be used to determine the minimum number of mutations required to explain a given set of observed genotypes. Conclusion: Phylogeny reconstruction directly from unphased data is computationally feasible for moderate-sized problem instances and can lead to substantially more accurate tree size inferences than the standard practice of treating phasing and phylogeny construction as two separate analysis stages. The difference between the approaches is particularly important for downstream applications that require a lower-bound on the number of mutations that the genetic region has undergone.

关键词： Maximum Parsimony integer linear program Steiner Tree integer linear program Formulation Ancestral Recombination Graph

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Robust routing algorithms based on Valiant load balancing for wavelength-division-multiplexing mesh networks

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OPTICAL ENGINEERING 2006年第8期45卷 085003-1-085003页

作者： Zhang, Xiaoning Li, Lemin Univ Elect Sci & Technol China Key Lab Broadband Opt Fiber Transmiss & Commun Ne Chengdu 610054 Peoples R China

In wavelength-division-multiplexing (WDM) mesh networks, previous routing algorithms are commonly used under the specific future traffic demand;however, it is difficult to predict the future traffic demand accurately in a practical sense. We propose a novel robust routing scheme based on Valiant load balancing in WDM mesh networks for the model of polyhedral uncertainty (i.e., hose model) and apply the scheme to low-speed connections with a traffic grooming approach. Our objective is to minimize total network cost. A mathematic formulation of the Valiant load-balancing robust routing scheme is presented and two fast heuristics are also proposed. When implementing the robust routing scheme to WDM mesh networks, a new traffic grooming algorithm called MHF (minimizing hop first) is proposed. We evaluate the MHF with the Valiant load-balancing robust routing scheme compared with traditional traffic-grooming algorithms. (c) 2006 Society of Photo-Optical Instrumentation Engineers.

关键词： integer linear program wavelength-division multiplexing robust routing hose model Valiant load balancing demand uncertainty

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Complementary optimal approaches for survivable WDM mesh network design: Transceiver deployment and traffic engineering

Complementary optimal approaches for survivable WDM mesh net...

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International Conference on Photonics in Switching

作者： Resendo, Leandro C. Ribeiro, Moises R. N. Univ Fed Espirito Santo Dept Elect Engn PO 0190-11 BR-29060970 Vitoria Brazil

ISBN: (纸本)9780780397897

An integer linear program model is presented for performing the most economical deployment of transceivers to enable network survivability. However, there is always room left for improvements in the traffic engineering protection scheme yielded. A complementary formulation then finds out how to also use protection resources elsewhere;substantially increasing the global network availability as a result. A study case shows that optimal traffic engineering can extend full link protection to 8 (out of 10) links over networks designed for 2 single failures.

关键词： protection reconfiguration traffic grooming integer linear program traffic engineering

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Consecutive Ones Decomposition of integer Matrices and Applications

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Electronic Notes in Discrete Mathematics 2006年 27卷 47-48页

作者： Hamacher, Horst W. Fachbereich Mathematik Technische Universitaet Kaiserslautern Kaiserslautern Germany

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