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Group Testing with Multiple Mutually-Obscuring Positives

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Information Theory, Combinatorics, and Search Theory

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7777))

Abstract

Group testing is a frequently used tool to identify an unknown set of defective (positive) elements out of a large collection of elements by testing subsets (pools) for the presence of defectives. Various models have been studied in the literature. The most studied case concerns only two types (defective and non-defective) of elements in the given collection. This paper studies a novel and natural generalization of group testing, where more than one type of defectives are allowed with an additional assumption that certain obscuring phenomena occur among different types of defectives. This paper proposes some algorithms for this problem, trying to optimize different measures of performance: the total number of tests required, the number of stages needed to perform all tests and the decoding complexity.

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References

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

    Article  MathSciNet  MATH  Google Scholar 

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

    Article  MathSciNet  MATH  Google Scholar 

  3. Barillot, E., Lacroix, B., Cohen, D.: Theoretical analysis of library screening using an n-dimensional pooling strategy. Nucleic Acids Research, 6241–6247 (1991)

    Google Scholar 

  4. Berger, T., Mehravari, N., Towsley, D., Wolf, J.: Random multipleaccess communication and group testing. IEEE Trans. Commun. 32, 769–779 (1984)

    Article  Google Scholar 

  5. De Bonis, A.: New combinatorial structures with applications to efficient group testing with inhibitors. J. Combin. Optim. 15, 77–94 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  6. De Bonis, A., Gąsieniec, L., Vaccaro, U.: Optimal two-stage algorithms for group testing problems. SIAM J. Comput. 34, 1253–1270 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  7. De Bonis, A., Vaccaro, U.: Optimal algorithms for two group testing problems, and new bounds on generalized superimposed codes. IEEE Trans. Inform. Theory 52, 4673–4680 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  8. Chang, H.L., Chen, H.B., Fu, H.L.: Identification and classification problems on pooling designs for inhibitor models. J. Comput. Biol. 17(7), 927–941 (2010)

    Article  MathSciNet  Google Scholar 

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

    Article  MathSciNet  MATH  Google Scholar 

  10. Chen, H.B., Du, D.Z., Hwang, F.K.: An unexpected meeting of four seemingly unrelated problems: graph testing, DNA complex screening, superimposed codes and secure key distribution. J. Combin. Optim. 14, 121–129 (2007)

    Article  MathSciNet  MATH  Google Scholar 

  11. Chen, H.B., Fu, H.L.: Nonadaptive algorithms for threshold group testing. Discrete Appl. Math. 157(7), 1581–1585 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  12. Chen, H.B., Fu, H.L., Hwang, F.K.: An upper bound of the number of tests in pooling designs for the error-tolerant complex model. Optim. Lett. 2, 425–431 (2008)

    Article  MathSciNet  MATH  Google Scholar 

  13. Cheng, Y.X., Du, D.Z.: Efficient constructions of disjunct matrices with applications to DNA library screening. J. Comput. Biol. 14, 1208–1216 (2007)

    Article  MathSciNet  Google Scholar 

  14. Cheng, Y.X., Du, D.Z.: New constructions of one- and two-stage pooling designs. J. Comput. Biol. 15(2), 195–205 (2008)

    Article  MathSciNet  Google Scholar 

  15. Cheraghchi, M.: Improved Constructions for Non-adaptive Threshold Group Testing. In: Abramsky, S., Gavoille, C., Kirchner, C., Meyer auf der Heide, F., Spirakis, P.G. (eds.) ICALP 2010. LNCS, vol. 6198, pp. 552–564. Springer, Heidelberg (2010)

    Chapter  Google Scholar 

  16. Damaschke, P.: Randomized group testing for mutually obscuring defectives. Inf. Process. Lett. 67, 131–135 (1998)

    Article  MathSciNet  MATH  Google Scholar 

  17. Damaschke, P.: Threshold Group Testing. In: Ahlswede, R., Bäumer, L., Cai, N., Aydinian, H., Blinovsky, V., Deppe, C., Mashurian, H. (eds.) Information Transfer and Combinatorics. LNCS, vol. 4123, pp. 707–718. Springer, Heidelberg (2006)

    Chapter  Google Scholar 

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

    Google Scholar 

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

    Google Scholar 

  20. D’yachkov, A.G.: Superimposed designs and codes for nonadaptive search of mutually obscuring defectives. In: Proc. 2003 IEEE Int. Symp. Inf. Theory, p. 134 (2003)

    Google Scholar 

  21. D’yachkov, A.G., Rykov, V.V.: Bounds on the length of disjunct codes. Problemy Peredachi Inform. 18(3), 7–13 (1982)

    MathSciNet  MATH  Google Scholar 

  22. D’yachkov, A.G., Rykov, V.V.: A survey of superimposed code theory. Problems Control Inform. Theory 12, 229–242 (1983)

    MathSciNet  MATH  Google Scholar 

  23. D’yachkov, A.G.: Lectures on designing screening experiments, Lecture Note Series 10, pages (monograph, pp. 112), Combinatorial and Computational Mathematics Center, Pohang University of Science and Technology (POSTECH), Korea Republic (2004)

    Google Scholar 

  24. D’yachkov, A.G., Rykov, V.V.: On superimposed codes. In: Fourth International Workshop Algebraic and Combinatorial Coding Theory, Novgorod, Russia, pp. 83–85 (1994)

    Google Scholar 

  25. D’yachkov, A.G., Rykov, V.V., Antonov, M.G.: New bounds on rate of the superimposed codes. In: The 10th All-Union Symposium for the Redundancy Problem in Information Systems, Papers, Part 1, St-Petersburg (1989)

    Google Scholar 

  26. Farach, M., Kannan, S., Knill, E., Muthukrishnan, S.: Group testing problem with sequences in experimental molecular biology. In: Proc. Compression and Complexity of Sequences, pp. 357–367 (1997)

    Google Scholar 

  27. Hong, E.H., Ladner, R.E.: Group testing for image compression. IEEE Trans. Image Process. 11, 901–911 (2002)

    Article  Google Scholar 

  28. Hong, Y.W., Scaglione, A.: On multiple access for distributed dependent sensors: a content-based group testing approach. In: IEEE Information Theory Workshop, pp. 298–303 (2004)

    Google Scholar 

  29. Hwang, F.K., Sós, V.T.: Nonadaptive hypergeometric group testing. Studia Scient. Math. Hungarica 22 (1987)

    Google Scholar 

  30. Kautz, W.H., Singleton, R.R.: Nonrandom binary superimposed codes. IEEE Trans. Inform. Theory 10, 363–377 (1964)

    Article  MATH  Google Scholar 

  31. Pevzner, P.A., Lipshutz, R.: Towards DNA Sequencing Chips. In: Privara, I., Ružička, P., Rovan, B. (eds.) MFCS 1994. LNCS, vol. 841, pp. 143–158. Springer, Heidelberg (1994)

    Chapter  Google Scholar 

  32. Porat, E., Rothschild, A.: Explicit non-adaptive combinatorial group testing schemes. In: Proceedings of the 35th International Colloquium on Automata, Languages and Programming (ICALP), pp. 748–759 (2008)

    Google Scholar 

  33. Stinson, D.R., Wei, R.: Generalized cover-free families. Discrete Math., 463–477 (2004)

    Google Scholar 

  34. Stinson, D.R., Wei, R., Zhu, L.: Some new bounds for cover-free families. J. Combin. Theory Ser. A, 224–234 (2000)

    Google Scholar 

  35. Torney, D.C.: Sets pooling designs. Ann. Combin., 95–101 (1999)

    Google Scholar 

  36. Vermeirssen, V., Deplancke, B., Barrasa, M.I., Reece-Hoyes, J.S., et al.: Matrix and steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping. Nature Methods 4, 659–664 (2007)

    Article  Google Scholar 

  37. Yu, H., Braun, P., Yildirim, M.A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al.: High-quality binary protein interaction map of the yeast interactome network. Science 322, 104–110 (2008)

    Article  Google Scholar 

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Chen, HB., Fu, HL. (2013). Group Testing with Multiple Mutually-Obscuring Positives. In: Aydinian, H., Cicalese, F., Deppe, C. (eds) Information Theory, Combinatorics, and Search Theory. Lecture Notes in Computer Science, vol 7777. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36899-8_28

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  • DOI: https://doi.org/10.1007/978-3-642-36899-8_28

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-36898-1

  • Online ISBN: 978-3-642-36899-8

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