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Combinatorial Pattern Matching

18th Annual Symposium, CPM 2007, London, Canada, July 9-11, 2007, Proceedings

  • Conference proceedings
  • © 2007

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Editors:
  1. Bin Ma
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  2. Kaizhong Zhang
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Part of the book series: Lecture Notes in Computer Science (LNCS, volume 4580)

Part of the book sub series: Theoretical Computer Science and General Issues (LNTCS)

Included in the following conference series:

Conference proceedings info: CPM 2007.

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About this book

The papers contained in this volume were presented at the 18th Annual S- posium on Combinatorial Pattern Matching (CPM 2007) held at the University of Western Ontario, in London, Ontario, Canada from July 9 to 11, 2007. All the papers presented at the conference are original research contri- tions on computational pattern matching and analysis, data compression and compressed text processing, su?x arrays and trees, and computational biology. They were selected from 64 submissions. Each submission was reviewed by at least three reviewers. The committee decided to accept 32 papers. The p- gramme also included three invited talks by Tao Jiang from the University of California, Riverside, USA, S. Muthukrishnan from Rutgers University, USA, and Frances Yao from City University of Hong Kong, Hong Kong. Combinatorial Pattern Matching addresses issues of searching and matching stringsandmorecomplicatedpatternssuchastrees,regularexpressions,graphs, point sets, and arrays.The goal is to derive non-trivial combinatorial properties of such structures and to exploit these properties in order to either achieve superior performance for the corresponding computational problems or pinpoint conditions under which searches cannot be performed e?ciently.

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Table of contents (35 papers)

  1. Front Matter

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  3. Session 1: Alogirthmic Techniques I

    1. Speeding Up HMM Decoding and Training by Exploiting Sequence Repetitions

      • Shay Mozes, Oren Weimann, Michal Ziv-Ukelson
      Pages 4-15

    2. On Demand String Sorting over Unbounded Alphabets

      • Carmel Kent, Moshe Lewenstein, Dafna Sheinwald
      Pages 16-27

  4. Session 2: Approximate Pattern Matching

    1. Finding Witnesses by Peeling

      • Yonatan Aumann, Moshe Lewenstein, Noa Lewenstein, Dekel Tsur
      Pages 28-39

    2. Cache-Oblivious Index for Approximate String Matching

      • Wing-Kai Hon, Tak-Wah Lam, Rahul Shah, Siu-Lung Tam, Jeffrey Scott Vitter
      Pages 40-51

    3. Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts

      • Philip Bille, Rolf Fagerberg, Inge Li Gørtz
      Pages 52-62

    4. Self-normalised Distance with Don’t Cares

      • Peter Clifford, Raphaël Clifford
      Pages 63-70

  5. Session 3: Data Compression I

    1. Move-to-Front, Distance Coding, and Inversion Frequencies Revisited

      • Travis Gagie, Giovanni Manzini
      Pages 71-82

    2. A Lempel-Ziv Text Index on Secondary Storage

      • Diego Arroyuelo, Gonzalo Navarro
      Pages 83-94

    3. Dynamic Rank-Select Structures with Applications to Run-Length Encoded Texts

      • Sunho Lee, Kunsoo Park
      Pages 95-106

    4. Most Burrows-Wheeler Based Compressors Are Not Optimal

      • Haim Kaplan, Elad Verbin
      Pages 107-118

  6. Session 4: Computational Biology I

    1. Non-breaking Similarity of Genomes with Gene Repetitions

      • Zhixiang Chen, Bin Fu, Jinhui Xu, Boting Yang, Zhiyu Zhao, Binhai Zhu
      Pages 119-130

    2. A New and Faster Method of Sorting by Transpositions

      • Maxime Benoît-Gagné, Sylvie Hamel
      Pages 131-141

    3. Finding Compact Structural Motifs

      • Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu
      Pages 142-149

  7. Session 5: Computational Biology II

    1. Improved Algorithms for Inferring the Minimum Mosaic of a Set of Recombinants

      • Yufeng Wu, Dan Gusfield
      Pages 150-161

    2. Computing Exact p-Value for Structured Motif

      • Jing Zhang, Xi Chen, Ming Li
      Pages 162-172

  8. Session 6: Algorithmic Techniques II

    1. Improved Sketching of Hamming Distance with Error Correcting

      • Ely Porat, Ohad Lipsky
      Pages 173-182
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