Improved Lower Bounds for Constant GC-Content DNA Codes

The design of large libraries of oligonucleotides having constant GC-content and satisfying Hamming distance constraints between oligonucleotides and their Watson-Crick complements is important in reducing hybridization errors in DNA computing, DNA microarray technologies, and molecular bar coding. Various techniques have been studied for the construction of such oligonucleotide libraries, ranging from algorithmic constructions via stochastic local search to theoretical constructions via coding theory. We introduce a new stochastic local search method which yields improvements up to more than one third of the benchmark lower bounds of Gaborit and King (2005) for n-mer oligonucleotide libraries when n <= 14. We also found several optimal libraries by computing maximum cliques on certain graphs.Comment: 4 page

Improved Constructions of Frameproof Codes

Frameproof codes are used to preserve the security in the context of coalition when fingerprinting digital data. Let $M_{c,l}(q)$ be the largest cardinality of a $q$-ary $c$-frameproof code of length $l$ and $R_{c,l}=\lim_{q\rightarrow \infty}M_{c,l}(q)/q^{\lceil l/c\rceil}$. It has been determined by Blackburn that $R_{c,l}=1$ when $l\equiv 1\ (\bmod\ c)$, $R_{c,l}=2$ when $c=2$ and $l$ is even, and $R_{3,5}=5/3$. In this paper, we give a recursive construction for $c$-frameproof codes of length $l$ with respect to the alphabet size $q$. As applications of this construction, we establish the existence results for $q$-ary $c$-frameproof codes of length $c+2$ and size $\frac{c+2}{c}(q-1)^2+1$ for all odd $q$ when $c=2$ and for all $q\equiv 4\pmod{6}$ when $c=3$. Furthermore, we show that $R_{c,c+2}=(c+2)/c$ meeting the upper bound given by Blackburn, for all integers $c$ such that $c+1$ is a prime power.Comment: 6 pages, to appear in Information Theory, IEEE Transactions o

Graphical t-designs with block sizes three and four

AbstractAll graphical t-designs with 2⩽t<k⩽4 are determined

On graphical quintuple systems

In this paper, we prove with the aid of symbolic computational tools, that there does not exist a non-trivial graphical 4-(λ, 5, ν) design for any λ and ν

Polynomial Time Algorithm for Min-Ranks of Graphs with Simple Tree Structures

The min-rank of a graph was introduced by Haemers (1978) to bound the Shannon capacity of a graph. This parameter of a graph has recently gained much more attention from the research community after the work of Bar-Yossef et al. (2006). In their paper, it was shown that the min-rank of a graph G characterizes the optimal scalar linear solution of an instance of the Index Coding with Side Information (ICSI) problem described by the graph G. It was shown by Peeters (1996) that computing the min-rank of a general graph is an NP-hard problem. There are very few known families of graphs whose min-ranks can be found in polynomial time. In this work, we introduce a new family of graphs with efficiently computed min-ranks. Specifically, we establish a polynomial time dynamic programming algorithm to compute the min-ranks of graphs having simple tree structures. Intuitively, such graphs are obtained by gluing together, in a tree-like structure, any set of graphs for which the min-ranks can be determined in polynomial time. A polynomial time algorithm to recognize such graphs is also proposed.Comment: Accepted by Algorithmica, 30 page

Strongly Regular Graphs Constructed from pp-ary Bent Functions

In this paper, we generalize the construction of strongly regular graphs in [Y. Tan et al., Strongly regular graphs associated with ternary bent functions, J. Combin.Theory Ser. A (2010), 117, 668-682] from ternary bent functions to $p$-ary bent functions, where $p$ is an odd prime. We obtain strongly regular graphs with three types of parameters. Using certain non-quadratic $p$-ary bent functions, our constructions can give rise to new strongly regular graphs for small parameters.Comment: to appear in Journal of Algebraic Combinatoric