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- Sheridan K. Houghten, Clement W. H. Lam, Larry H. Thiel, J. A. Parker
- IEEE Trans. Information Theory
- 2003

The largest minimum weight of a self-dual doubly-even binary (n, k, d) code is d = 4bn/24c+ 4. Of such codes with length divisible by 24, the Golay Code is the only (24, 12, 8) code, the Extended Quadratic Residue Code is the only known (48, 24, 12) code, and there is no known (72, 36, 16) code. One may partition the search for a (48, 24, 12) self-dual… (More)

- Daniel A. Ashlock, Sheridan K. Houghten
- 2009 IEEE Symposium on Computational Intelligence…
- 2009

DNA error correcting codes over the edit metric create embeddable markers for sequencing projects that are tolerant of sequencing errors. When a sequence library has multiple sources for its sequences, use of embedded markers permit tracking of sequence origin. Evolutionary algorithms are currently the best known technique for optimizing DNA error… (More)

The maximum possible number of codewords in a q-ary code of length n and minimum distance d is denoted Aq(n,d). It is a fundamental problem in coding theory to determine this value for given parameters q, n and d. Codes that attain the maximum are said to be optimal. Unfortunately, for many different values of these parameters, the maximum number of… (More)

- Farhad Alizadeh Noori, Sheridan K. Houghten
- 2012 IEEE Symposium on Computational Intelligence…
- 2012

Understanding the machinery of gene regulation to control gene expression has been one of the main focuses of bioinformaticians for years. We use a multi-objective genetic algorithm to evolve a specialized version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find and report preliminary… (More)

- Daniel A. Ashlock, Sheridan K. Houghten
- 2005 IEEE Symposium on Computational Intelligence…
- 2005

Error correcting codes over the edit metric have been used as embedded DNA markers in at least one sequencing project. The algorithm used to construct those codes was an evolutionary algorithm with a fitness function with exponential time complexity. Presented here is an substantially faster evolutionary algorithm for locating error correcting codes over… (More)

- Joseph Alexander Brown, Sheridan K. Houghten, Daniel A. Ashlock
- 2010 IEEE Symposium on Computational Intelligence…
- 2010

DNA edit metric codes are used as labels to track the origin of sequence data. This study is the first to treat sophisticated decoders for these error-correcting codes. Side effect machines can provide efficient decoding algorithms for such codes. Two methods for automatically producing decoding algorithms are presented. Side Effect Machines (SEMs),… (More)

- Joseph Alexander Brown, Sheridan K. Houghten, Beatrice M. Ombuki-Berman
- 2009 IEEE Symposium on Computational Intelligence…
- 2009

We provide a preliminary exploration of the use of Genetic Algorithms (GA) upon a Substitution Permutation Network (SPN) cipher. The purpose of the exploration is to determine how to find weak keys. The size of the selected SPN created by Stinson[1] gives a sample for showing the methodology and suitability of an attack using GA. We divide the types of keys… (More)

In this position paper we examine preliminary results of a new type of general error correction decoder for Edit Metric Codes. The Single Classifier Machine Decoder uses the concept of Side Effect Machines(SEMs) created via Genetic Algorithms(GAs) in order to create a mapping from the Edit Metric to the Euclidean Metric to create a decoder. By not having to… (More)

- Joseph Alexander Brown, Daniel A. Ashlock, John Orth, Sheridan K. Houghten
- IEEE Congress on Evolutionary Computation
- 2011

We present a novel method for the creation of photographic mosaic images using fractals generated via evolutionary techniques. A photomosaic is a rendering of an image performed by placing a grid of smaller images that permit the original image to be visible when viewed from a distance. The problem of selecting the smaller images is a computationally… (More)