International Journal of Hybrid Intelligent Systems

International Journal of Hybrid Intelligent Systems

Volume 2, No. 1(2005), pp. 01-12

DNA Computing Approach to Semantic Knowledge Representation
Yusei Tsuboi, Zuwairie Ibrahim and Osamu Ono

Abstract: DNA computing has a lot of potential, in terms of ability to implement a relational database with circular molecules.
In this work, a new DNA-based semantic model is proposed and described theoretically for implementing DNA based memories.
This model, referred to as ‘semantic model based on molecular computing’ (SMC), has the structure of a graph formed by
the set of all attribute-value pairs contained in the set of represented objects, plus a tag node for each object. Each path in
the network, from an initial object-representing tag node to a terminal node represents the object named on the tag. Input
of a set of input strands will result in the formation of object-representing dsDNAs via parallel self-assembly, from encoded
ssDNAs representing (value, attribute)-pairs (nodes), as directed by ssDNA splinting strands representing relations (edges) in
the network. The computational complexity of the implementation is estimated via simple simulation, which indicates the
advantage of the approach over a sequential model. We believe that the semantic models are rather suitable for DNA-based
memory, and that this proposal is the first such approach in the semantic networks area..

Keywords: DNA Computing, semantic model