Improved Constructions for Non-adaptive Threshold Group Testing

The basic goal in combinatorial group testing is to identify a set of up to d defective items within a large population of size n ≫ d using a pooling strategy. Namely, the items can be grouped together in pools, and a single measurement would reveal whether there are one or more defectives in the pool. The threshold model is a generalization of this idea where a measurement returns positive if the number of defectives in the pool passes a fixed threshold u, negative if this number is below a fixed lower threshold l ≤ u, and may behave arbitrarily otherwise. We study non-adaptive threshold group testing (in a possibly noisy setting) and show that, for this problem, O(dg+2(log d) log(n/d)) measurements (where g := u - l) suffice to identify the defectives, and also present almost matching lower bounds. This significantly improves the previously known (non-constructive) upper bound O(du+1log(n/d)). Moreover, we obtain a framework for explicit construction of measurement schemes using lossless condensers. The number of measurements resulting from this scheme is ideally bounded by O(dg+3(log d) log n). Using state-of-the-art constructions of lossless condensers, however, we come up with explicit testing schemes with O(dg+3(log d)quasipoly(log n)) and O(dg+3+βpoly(log n)) measurements, for arbitrary constant β < 0.

[1]  D. Du,et al.  Combinatorial Group Testing and Its Applications , 1993 .

[2]  A. Macula Probabilistic nonadaptive group testing in the presence of errors and DNA library screening , 1999 .

[3]  Weili Wu,et al.  Construction of d(H)-disjunct matrix for group testing in hypergraphs , 2006, J. Comb. Optim..

[4]  Ding-Zhu Du,et al.  Molecular Biology and Pooling Design , 2007 .

[5]  Graham Cormode,et al.  What's hot and what's not: tracking most frequent items dynamically , 2003, TODS.

[6]  F. MacWilliams,et al.  The Theory of Error-Correcting Codes , 1977 .

[7]  Alexander Schliep,et al.  Group testing with DNA chips: generating designs and decoding experiments , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[8]  Miklós Ruszinkó,et al.  On the upper bound of the size of the r -cover-free families , 1994 .

[9]  Jack K. Wolf,et al.  Born again group testing: Multiaccess communications , 1985, IEEE Trans. Inf. Theory.

[10]  Hung-Lin Fu,et al.  Reconstruction of hidden graphs and threshold group testing , 2011, J. Comb. Optim..

[11]  Sampath Kannan,et al.  Group testing problems with sequences in experimental molecular biology , 1997, Proceedings. Compression and Complexity of SEQUENCES 1997 (Cat. No.97TB100171).

[12]  Jaikumar Radhakrishnan,et al.  Tight bounds for depth-two superconcentrators , 1997, Proceedings 38th Annual Symposium on Foundations of Computer Science.

[13]  Peter Damaschke Threshold Group Testing , 2006, GTIT-C.

[14]  Hung-Lin Fu,et al.  Nonadaptive algorithms for threshold group testing , 2009, Discret. Appl. Math..

[15]  Vladimir S. Lebedev,et al.  On optimal superimposed codes , 2004 .

[16]  Ding-Zhu Du,et al.  A survey on combinatorial group testing algorithms with applications to DNA Library Screening , 1999, Discrete Mathematical Problems with Medical Applications.

[17]  D. Balding,et al.  Efficient pooling designs for library screening. , 1994, Genomics.

[18]  Arkadii G. D'yachkov,et al.  New constructions of superimposed codes , 2000, IEEE Trans. Inf. Theory.

[19]  H. Stichtenoth,et al.  A tower of Artin-Schreier extensions of function fields attaining the Drinfeld-Vladut bound , 1995 .

[20]  Ely Porat,et al.  Search Methodologies , 2022 .

[21]  Venkatesan Guruswami,et al.  Unbalanced expanders and randomness extractors from Parvaresh--Vardy codes , 2007, JACM.

[22]  Avi Wigderson,et al.  Randomness conductors and constant-degree lossless expanders , 2002, STOC '02.

[23]  Richard E. Ladner,et al.  Group testing for image compression , 2000, Proceedings DCC 2000. Data Compression Conference.

[24]  Hung-Lin Fu,et al.  An upper bound of the number of tests in pooling designs for the error-tolerant complex model , 2008, Optim. Lett..

[25]  R. Dorfman The Detection of Defective Members of Large Populations , 1943 .

[26]  Lie Zhu,et al.  Some New Bounds for Cover-Free Families , 2000, J. Comb. Theory, Ser. A.

[27]  Graham Cormode,et al.  Combinatorial Algorithms for Compressed Sensing , 2006 .

[28]  Ding-Zhu Du,et al.  New Constructions of One- and Two-Stage Pooling Designs , 2008, J. Comput. Biol..

[29]  Mahdi Cheraghchi,et al.  Noise-resilient group testing: Limitations and constructions , 2008, Discret. Appl. Math..

[30]  Arkadii G. D'yachkov,et al.  New Applications and Results of Superimposed Code Theory Arising from the Potentialities of Molecular Biology , 2000 .

[31]  Mahdi Cheraghchi,et al.  Applications of Derandomization Theory in Coding , 2011, ArXiv.

[32]  Douglas R. Stinson,et al.  Generalized cover-free families , 2004, Discret. Math..

[33]  Arkadii G. D'yachkov,et al.  Families of Finite Sets in which No Intersection of Sets Is Covered by the Union of s Others , 2002, J. Comb. Theory, Ser. A.

[34]  M. Tsfasman,et al.  Modular curves, Shimura curves, and Goppa codes, better than Varshamov‐Gilbert bound , 1982 .

[35]  Weili Wu,et al.  On error-tolerant DNA screening , 2006, Discret. Appl. Math..

[36]  Ely Porat,et al.  k -Mismatch with Don't Cares , 2007, ESA.

[37]  Ding-Zhu Du,et al.  An unexpected meeting of four seemingly unrelated problems: graph testing, DNA complex screening, superimposed codes and secure key distribution , 2007, J. Comb. Optim..

[38]  Amnon Ta-Shma,et al.  Constructing Small-Bias Sets from Algebraic-Geometric Codes , 2009, FOCS.

[39]  Ron M. Roth,et al.  Introduction to Coding Theory , 2019, Discrete Mathematics.

[40]  D. Du,et al.  Pooling Designs And Nonadaptive Group Testing: Important Tools For Dna Sequencing , 2006 .

[41]  Richard C. Singleton,et al.  Nonrandom binary superimposed codes , 1964, IEEE Trans. Inf. Theory.