1. Molecular Genetic Programming
Soft Computing 5(2): , 2001
P. Wasiewicz, J.J. Mulawka
Summarized by Shin, Soo-Yong

2. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Abstract
A new implementation of genetic programming by using molecular approach.
Based on dataflow techniques
Handle graph encoding molecules
(C) 2001, SNU Biointelligence Lab, 

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

4. Representing graphs (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, 

5. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Representing 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
complement 3’ 5’
arc
Restriction site
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6. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Negation operator xi zi yi
complement xk yk
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7. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Negation operator
(C) 2001, SNU Biointelligence Lab, 

8. Proposed 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
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9. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
crossover
before
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10. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
crossover
cut
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11. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
crossover
After (new)
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12. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Evaluation
Using existing arcs
Put TRUE sequences (a, b, c, or d)
Making paths by arcs & TRUE sequences
Check the length (correct path)
의문점?
Graph가 true가 되었다고 해서 function이 true가 될 수 있는가?
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13. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Evaluation
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14. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Evaluation
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15. (C) 2001, SNU Biointelligence Lab, http://bi.snu.ac.kr/
Conclusion
No mutation, only crossover
Making edges (by crossover)
Not practical implications
(C) 2001, SNU Biointelligence Lab,