Transcript JavaGenes: Evolving Graphs Al Globus, Veridian MRJ Technology Solutions, Inc. [email protected] http://www.nas.nasa.gov/~globus/home.html John Lawton, UCSC Todd Wipke, UCSC Sean Atsatt, Sierra Imaging,Inc.

JavaGenes: Evolving
Graphs
Al Globus, Veridian MRJ Technology Solutions, Inc.
[email protected]
http://www.nas.nasa.gov/~globus/home.html
John Lawton, UCSC
Todd Wipke, UCSC
Sean Atsatt, Sierra Imaging,Inc.
Crossover
Strings
abcd wxyz
abcd wxyz
abyz wxcd
Trees
Graphs
Graph Crossover
Rip Two Parents Apart
Combine into a Child
Molecule Fitness Function
All-pairs-shortest-path (APSP) distance
• Assign extended types to each atom =
(element, |single bonds|, |double bonds|,
|triple bonds|)
• Find shortest bond path between each pair of
atoms
• Create bag with one item per pair of atoms
– item = (type1, type2, path length)
– bag = set with repeated items
• Tanimoto distance = |intersection| / |union|
Evolving Molecules
size median shortest failures(%)
benzene
purine
100
100
3
51
0
6
0
0
N
N
N
N
cubane
100
30
4
0
O
N
diazepam
200
NA
453
71
N
Cl
cholesterol
200
NA
1414
74
O
O
O
morphine
200
NA
9769
97
O
N
Circuits
Directed graphs
 More node types (and, nand, or, nor, xor, nxor, plus
initial 0 or 1 for each type)
 Exactly one input and one output node per graph
 Crossover generates unconnected circuits on very
rare occasion
 Fitness function: number of right answers on 100
randomly generated inputs
• Serial logic (one bit input and output at each step)
• Logic simulator assumes all devices require unit time

Circuits
name
size
median
shortest
delay
600
18
6
13
parity
600
21
0
6
NA
NA
100
add
200
failures(%)
Conclusions
Evolving graphs using genetic operators is possible
 Molecules and circuits have been evolved
 Molecular evolution is reasonably successful
 Non-trivial circuits have yet to be evolved
 This is a new technique that will require substantial
refinement
• open source in the near future
 Where self-assembly problems can be cast as graphs
JavaGenes may be of some utility
