Efficient Two-Stage Group Testing Algorithms for Genetic Screening

Efficient two-stage group testing algorithms that are particularly suited for rapid and less-expensive DNA library screening and other large scale biological group testing efforts are investigated in this paper. The main focus is on novel combinatorial constructions in order to minimize the number of individual tests at the second stage of a two-stage disjunctive testing procedure. Building on recent work by Levenshtein (2003) and Tonchev (2008), several new infinite classes of such combinatorial designs are presented.Comment: 14 pages; to appear in "Algorithmica". Part of this work has been presented at the ICALP 2011 Group Testing Workshop; arXiv:1106.368

Coding Theory and Algebraic Combinatorics

This chapter introduces and elaborates on the fruitful interplay of coding theory and algebraic combinatorics, with most of the focus on the interaction of codes with combinatorial designs, finite geometries, simple groups, sphere packings, kissing numbers, lattices, and association schemes. In particular, special interest is devoted to the relationship between codes and combinatorial designs. We describe and recapitulate important results in the development of the state of the art. In addition, we give illustrative examples and constructions, and highlight recent advances. Finally, we provide a collection of significant open problems and challenges concerning future research.Comment: 33 pages; handbook chapter, to appear in: "Selected Topics in Information and Coding Theory", ed. by I. Woungang et al., World Scientific, Singapore, 201

New Combinatorial Construction Techniques for Low-Density Parity-Check Codes and Systematic Repeat-Accumulate Codes

This paper presents several new construction techniques for low-density parity-check (LDPC) and systematic repeat-accumulate (RA) codes. Based on specific classes of combinatorial designs, the improved code design focuses on high-rate structured codes with constant column weights 3 and higher. The proposed codes are efficiently encodable and exhibit good structural properties. Experimental results on decoding performance with the sum-product algorithm show that the novel codes offer substantial practical application potential, for instance, in high-speed applications in magnetic recording and optical communications channels.Comment: 10 pages; to appear in "IEEE Transactions on Communications

Classification of Cyclic Steiner Quadruple Systems

The problem of classifying cyclic Steiner quadruple systems (CSQSs) is considered. A computational approach shows that the number of isomorphism classes of such designs with orders 26 and 28 is 52,170 and 1,028,387, respectively. It is further shown that CSQSs of order 2p, where p is a prime, are isomorphic iff they are multiplier equivalent. Moreover, no CSQSs of order less than or equal to 38 are isomorphic but not multiplier equivalent

Frequency permutation arrays

Motivated by recent interest in permutation arrays, we introduce and investigate the more general concept of frequency permutation arrays (FPAs). An FPA of length n=m lambda and distance d is a set T of multipermutations on a multiset of m symbols, each repeated with frequency lambda, such that the Hamming distance between any distinct x,y in T is at least d. Such arrays have potential applications in powerline communication. In this paper, we establish basic properties of FPAs, and provide direct constructions for FPAs using a range of combinatorial objects, including polynomials over finite fields, combinatorial designs, and codes. We also provide recursive constructions, and give bounds for the maximum size of such arrays.Comment: To appear in Journal of Combinatorial Design

Resolving sets for Johnson and Kneser graphs

A set of vertices $S$ in a graph $G$ is a {\em resolving set} for $G$ if, for any two vertices $u,v$, there exists $x\in S$ such that the distances $d(u,x) \neq d(v,x)$. In this paper, we consider the Johnson graphs $J(n,k)$ and Kneser graphs $K(n,k)$, and obtain various constructions of resolving sets for these graphs. As well as general constructions, we show that various interesting combinatorial objects can be used to obtain resolving sets in these graphs, including (for Johnson graphs) projective planes and symmetric designs, as well as (for Kneser graphs) partial geometries, Hadamard matrices, Steiner systems and toroidal grids.Comment: 23 pages, 2 figures, 1 tabl