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The weight-constrained maximum-density subtree problem and related problems in trees

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Abstract

Given a tree T=(V,E) of n nodes such that each node v is associated with a value-weight pair (val v ,w v ), where value val v is a real number and weight w v is a non-negative integer, the density of T is defined as \(\frac{\sum_{v\in V}{\mathit{val}}_{v}}{\sum_{v\in V}w_{v}}\). A subtree of T is a connected subgraph (V′,E′) of T, where V′⊆V and E′⊆E. Given two integers w min  and w max , the weight-constrained maximum-density subtree problem on T is to find a maximum-density subtree T′=(V′,E′) satisfying w min ≤∑vV w v w max . In this paper, we first present an O(w max  n)-time algorithm to find a weight-constrained maximum-density path in a tree T, and then present an O(w 2max  n)-time algorithm to find a weight-constrained maximum-density subtree in T. Finally, given a node subset SV, we also present an O(w 2max  n)-time algorithm to find a weight-constrained maximum-density subtree in T which covers all the nodes in S.

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References

  1. Arslan A, Eğecioğlu Ö, Pevzner P (2001) A new approach to sequence comparison: normalized sequence alignment. Bioinformatics 17:327–337

    Article  Google Scholar 

  2. Chao KM (1998) On computing all suboptimal alignments. Inf Sci 105:189–207

    Article  MATH  Google Scholar 

  3. Chao KM, Hardison RC, Miller W (1994) Recent developments in linear-space alignment methods: a survey. J Comput Biol 1:271–291

    Article  Google Scholar 

  4. Chung KM, Lu HI (2004) An optimal algorithm for the maximum-density segment problem. SIAM J Comput 34(2):373–387

    Article  MathSciNet  MATH  Google Scholar 

  5. Goldwasser MH, Kao MY, Lu HI (2002) Fast algorithms for finding maximum-density segments of a sequence with applications to bioinformatics. In: Proceedings of the second international workshop of algorithms in bioinformatics. Lecture notes in computer science, vol 2452, Rome, Italy. Springer, Berlin, pp 157–171

    Chapter  Google Scholar 

  6. Guo L, Jiang S, Xiao L, Zhang X (2005) Fast and low-cost search schemes by exploiting localities in P2P networks. J Parallel Distrib Comput 65(6):729–742

    Article  Google Scholar 

  7. Huang X (1994) An algorithm for identifying regions of a DNA sequence that satisfy a content requirement. Comput Appl Biosci 10(3):219–225

    Google Scholar 

  8. Inman RB (1966) A denaturation map of the 1 phage DNA molecule determined by electron microscopy. J Mol Biol 18:464–476

    Article  Google Scholar 

  9. Jiang S, Guo L, Zhang X, Wang H (2008) LightFlood: minimizing redundant messages and maximizing the scope of peer-to-peer search. IEEE Trans Parallel Distrib Syst 19(5):601–614

    Article  Google Scholar 

  10. Kim SK (2003) Linear-time algorithm for finding a maximum-density segment of a sequence. Inf Process Lett 86(6):339–342

    Article  MATH  Google Scholar 

  11. Lau HC, Ngo TH, Nguyen BN (2006) Finding a length-constrained maximum-sum or maximum-density subtree and its application to logistics. Discrete Optim 3(4):385–391

    Article  MathSciNet  MATH  Google Scholar 

  12. Lin YL, Jiang T, Chao KM (2002) Algorithms for locating the length-constrained heaviest segments, with applications to biomolecular sequences analysis. J Comput Syst Sci 65(3):570–586

    Article  MathSciNet  MATH  Google Scholar 

  13. Lin YL, Huang X, Jiang T, Chao KM (2003) MAVG: locating non-overlapping maximum average segments in a given sequence. Bioinformatics 19(1):151–152

    Article  Google Scholar 

  14. Lin RR, Kuo WH, Chao KM (2005) Finding a length-constrained maximum-density path in a tree. J Comb Optim 9(2):147–156

    Article  MathSciNet  MATH  Google Scholar 

  15. Liu X, Liu Y, Xiao L (2006) Improving query response delivery quality in peer-to-peer systems. IEEE Trans Parallel Distrib Syst 17(11):1335–1347

    Article  Google Scholar 

  16. Liu Y, Xiao L, Liu X, Ni LM, Zhang X (2005) Location awareness in unstructured peer-to-peer systems. IEEE Trans Parallel Distrib Syst 16(2):163–174

    Article  Google Scholar 

  17. Macaya G, Thiery JP, Bernardi G (1976) An approach to the organization of eukaryotic genomes at a macromolecular level. J Mol Biol 108:237–254

    Article  Google Scholar 

  18. Nekrutenko A, Li WH (2000) Assessment of compositional heterogeneity within and between eukaryotic genomes. Genome Res 10:1986–1995

    Article  Google Scholar 

  19. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European molecular biology open software suite. Trends Genet 16(6):276–277

    Article  Google Scholar 

  20. Sipser M (1997) Introduction to the theory of computation. PWS Publishing Company, Boston

    MATH  Google Scholar 

  21. Stojanovic N, Florea L, Riemer C, Gumucio D, Slightom J, Goodman M, Miller W, Hardison R (1999) Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucl Acids Res 27:3899–3910

    Article  Google Scholar 

  22. Su HH, Lu CL, Tang CY (2008) An improved algorithm for finding a length-constrained maximum-density subtree in a tree. Inf Process Lett 109:161–164

    Article  MathSciNet  Google Scholar 

  23. Wang C, Xiao L (2007) An effective P2P search scheme to exploit file sharing heterogeneity. IEEE Trans Parallel Distrib Syst 18(2):1–13

    Article  MATH  Google Scholar 

  24. West DB (2001) Introduction to graph theory, 2nd edn. Prentice Hall, Upper Saddle River

    Google Scholar 

  25. Wu BY, Chao KM, Tang CY (1999) An efficient algorithm for the length-constrained heaviest path problem on a tree. Inf Process Lett 69:63–67

    Article  MathSciNet  Google Scholar 

  26. Xiao L, Liu Y, Ni LM (2005) Improving unstructured peer-to-peer systems by adaptive connection establishment. IEEE Trans Parallel Distrib Syst 54(9):1091–1102

    Google Scholar 

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Correspondence to Sun-Yuan Hsieh.

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An extended abstract of this paper appeared in Proceedings of the 16th Annual International Symposium on Algorithms and Computation (ISAAC 2005), Lecture Notes in Computer Science, vol. 3827, pp. 944–953, 2005.

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Hsieh, SY., Chou, TY. The weight-constrained maximum-density subtree problem and related problems in trees. J Supercomput 54, 366–380 (2010). https://doi.org/10.1007/s11227-009-0328-z

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  • DOI: https://doi.org/10.1007/s11227-009-0328-z

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