TY - GEN
T1 - The DNA word design problem
T2 - 26th International Joint Conference on Artificial Intelligence, IJCAI 2017
AU - Codish, Michael
AU - Frank, Michael
AU - Lagoon, Vitaly
N1 - Funding Information: ∗Supported by the Israel Science Foundation, grant 182/13.
PY - 2017/1/1
Y1 - 2017/1/1
N2 - A fundamental problem in coding theory concerns the computation of the maximum cardinality of a set S of length n code words over an alphabet of size q, such that every pair of code words has Hamming distance at least d, and the set of additional constraints U on S is satisfied. This problem has application in several areas, one of which is the design of DNA codes where q = 4 and the alphabet is {A, C, G, T}. We describe a new constraint model for this problem and demonstrate that it improves on previous solutions (computes better lower bounds) for various instances of the problem. Our approach is based on a clustering of DNA words into small sets of words. Solutions are then obtained as the union of such clusters. Our approach is SAT based: we specify constraints on clusters of DNA words and solve these using a Boolean satisfiability solver.
AB - A fundamental problem in coding theory concerns the computation of the maximum cardinality of a set S of length n code words over an alphabet of size q, such that every pair of code words has Hamming distance at least d, and the set of additional constraints U on S is satisfied. This problem has application in several areas, one of which is the design of DNA codes where q = 4 and the alphabet is {A, C, G, T}. We describe a new constraint model for this problem and demonstrate that it improves on previous solutions (computes better lower bounds) for various instances of the problem. Our approach is based on a clustering of DNA words into small sets of words. Solutions are then obtained as the union of such clusters. Our approach is SAT based: we specify constraints on clusters of DNA words and solve these using a Boolean satisfiability solver.
UR - http://www.scopus.com/inward/record.url?scp=85031942198&partnerID=8YFLogxK
U2 - https://doi.org/10.24963/ijcai.2017/82
DO - https://doi.org/10.24963/ijcai.2017/82
M3 - Conference contribution
T3 - IJCAI International Joint Conference on Artificial Intelligence
SP - 585
EP - 591
BT - 26th International Joint Conference on Artificial Intelligence, IJCAI 2017
A2 - Sierra, Carles
Y2 - 19 August 2017 through 25 August 2017
ER -