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ERNe: Evolving Reaction Networks

ERNe (Evolving Reaction Networks) is an efficient derivative of the NEAT algorithm directed at the evolution of biochemical systems or molecular programs.

ERNe's original paper was published in IEEE Transactions on Evolutionary Computation.

System requirements

Java 8 (JRE, JDK)

Quick start

Build with Gradle

./gradlew dist

Run the example

cd build/dist
./start.sh use.math.square.RunSquare

Result files will be generated inside result/ directory. To display result of a run

./start.sh erne.ResultReader <path_to_result>

Run on a cluster

  • Modify Hazelcast configuration to specify the computational nodes' IP addresses
vi config/hazelcast.xml
  • Copy dist directory to each node.

  • Start the computational service at each node (excluding the main node):

cd dist/
./start.sh
  • Run the example at the main node:
./start.sh use.math.square.RunSquare

Development

Create Eclipse project

./gradlew eclipse

Create IntelliJ project

./gradlew idea

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Efficient derivative of the NEAT algorithm

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