Skip to main content
Log in

Learning a hidden graph

  • Original Paper
  • Published:
Optimization Letters Aims and scope Submit manuscript

Abstract

We study the problem of learning a hidden graph by edge-detecting queries, each of which tells whether a set of vertices induces an edge of the hidden graph or not. We provide a new information-theoretic lower bound and give a more efficient adaptive algorithm to learn a general graph with \(n\) vertices and \(m\) edges in \(m\log n+10m+3n\) edge-detecting queries.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Aigner, M.: Combinatorial Search. Wiley, New York (1988)

  2. Alon, N., Asodi, V.: Learning a hidden subgraph. SIAM J. Discrete Math. 18, 697–712 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  3. Alon, N., Beigel, R., Kasif, S., Rudich, S., Sudakov, B.: Learning a hidden matching. SIAM J. Comput. 33, 487–501 (2004)

    Article  MATH  MathSciNet  Google Scholar 

  4. Anderson, I.: Combinatorial designs: construction methods. Ellis Horwood, New York (1990)

  5. Angluin, D., Chen, J.: Learning a hidden hypergraph. J. Mach. Learn. Res. 7, 2215–2236 (2006)

    MATH  MathSciNet  Google Scholar 

  6. Angluin, D., Chen, J.: Learning a hidden graph using \(O(\log n)\) queries per edge. J. Comput. Syst. Sci. 74, 546–556 (2008)

    Article  MATH  MathSciNet  Google Scholar 

  7. Beigel, R., Alon, N., Apaydin, M.S., Fortnow, L., Kasif, S.: An optimal procedure for gap closing in whole genome shotgun sequencing. In: Proceedings of 2001 RECOMB, pp. 22–30. ACM Press, New York

  8. Bouvel, M., Grebinski, V., Kucherov, G.: Combinatorial search on graphs motivated by bioinformatics applications: a brief survey. WG, LNCS 3787, pp. 16–27 (2005)

  9. Chang, H., Chen, H.-B., Fu, H.L., Shih, C.H.: Reconstruction of hidden graphs and threshold group testing. J. Comb. Optim. 22, 270–281 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  10. Damaschke, P., Sheikh Muhammad, A.: Competitive group testing and learning hidden vertex covers with minimum adaptivity. Discrete Math. Algebra Appl. 2, 291–311 (2010)

    Article  MATH  MathSciNet  Google Scholar 

  11. Damaschke, P., Sheikh Muhammad, A.: Bounds for nonadaptive group tests to estimate the amount of defectives. Discrete Math. Algebra Appl. 3, 517–536 (2011)

    Article  MATH  MathSciNet  Google Scholar 

  12. Du, D.Z., Hwang, F.K.: Combinatorial Group Testing and its Applications, 2nd edn. World Scientific, Singapore (2000)

    MATH  Google Scholar 

  13. Du, D.Z., Hwang, F.K.: Pooling Designs and Nonadaptive Group Testing: Important Tools for DNA Sequencing. World Scientific, Singapore (2006)

    Google Scholar 

  14. Grebinski, V., Kucherov, G.: Reconstructing a Hamiltonian cycle by querying the graph: application to DNA physical mapping. Discrete Appl. Math. 88, 147–165 (1998)

    Article  MATH  MathSciNet  Google Scholar 

  15. Grebinski, V., Kucherov, G.: Optimal reconstruction of graphs under the additive model. Algorithmica 28, 104–124 (2000)

    Article  MATH  MathSciNet  Google Scholar 

  16. Hwang, F.K., Liu, Y.C.: Error-tolerant pooling designs with inhibitors. J. Comput. Biol. 10, 231–236 (2003)

    Article  Google Scholar 

  17. Nagura, J.: On the interval containing at least one prime number. In: Proceedings of the Japan Academy Series A, vol. 28, pp. 177–181 (1952)

  18. Schlaghoff, J., Triesch, E.: Improved results for competitive group testing. Comb. Prob. Comput. 14, 191–202 (2005)

    Article  MATH  MathSciNet  Google Scholar 

  19. Sorokin, A., Lapidus, A., Capuano, V., Galleron, N., Pujic, P., Ehrlich, S.D.: A new approach using multiplex long accurate PCR and yeast artificial chromosomes for bacterial chromosome mapping and sequencing. Genome Res. 6, 448–453 (1996)

    Article  Google Scholar 

  20. Tettelin, H., Radune, D., Kasif, S., Khouri, H., Salzberg, S.L.: Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project. Genomics 62, 500–507 (1996)

    Article  Google Scholar 

Download references

Acknowledgments

The authors would like to express their gratitude to the referees for their valuable comments and suggestions in improving the presentation of this paper. Partially supported by National Science Council, Taiwan under Grant NSC 99-2811-M-009-056 (H.-L. Fu and C.-H. Shih) and 100-2115-M-390-004-MY2 (H. Chang).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Chih-Huai Shih.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chang, H., Fu, HL. & Shih, CH. Learning a hidden graph. Optim Lett 8, 2341–2348 (2014). https://doi.org/10.1007/s11590-014-0751-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11590-014-0751-9

Keywords

Navigation