Molecular Genetic ProgrammingMolecular Genetic Programming

Soft Computing 5(2):106-113, 2001

P. Wasiewicz, J.J. Mulawka

Summarized by Shin, Soo-Yong

2001.5.18

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

AbstractAbstract

A new implementation of genetic programming by using molecular approach. Based on dataflow techniques Handle graph encoding molecules

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Data flow computerData flow computer

Have fully parallel architectures Data availability rather than a program counter is

used to drive the execution of instructions.

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Representing graphs Representing graphs (logical function graph)(logical function graph) The construction of the graph starts with creating nodes,

which are related to function arguments plus one node – root.

The function’s result is TRUE when at least one leaf of the tree can be reached from the root through the successive nodes.

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Representing graphsRepresenting graphs

V : set of function argument nodes N : number of graph nodes M : number of function arguments E : set of ordered node (arcs)

5’ 3’ 5’ 3’

nodes

5’3’

Restriction site

arc

complement

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Negation operatorNegation operator

xi yizi

xk ykiz

complement

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Negation operatorNegation operator

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

Proposed genetic algorithmProposed genetic algorithm

Initiation Put all strings into test tube

Cutting arc strings by enzyme Concatenation of arc parts. New arcs are created. Evaluation

Ligation & PCR

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

crossovercrossover

before

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crossovercrossover

cut

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

crossovercrossover

After (new)

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

EvaluationEvaluation

Using existing arcs Put TRUE sequences (a, b, c, or d) Making paths by arcs & TRUE sequences Check the length (correct path)

의문점 ? Graph 가 true 가 되었다고 해서 function 이 true 가

될 수 있는가 ?

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

EvaluationEvaluation

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

EvaluationEvaluation

(C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/

ConclusionConclusion

No mutation, only crossover Making edges (by crossover)

Not practical implications