| Name | Description | Type | Package | Framework |
| FactorHyperNEATGenome | Create a Genome for use with HyperNEAT. | Class | org.encog.neural.hyperneat | HeatonReasearch |
| HyperNEATCODEC | Class | org.encog.neural.hyperneat | HeatonReasearch | |
| HyperNEATGenome | Class | org.encog.neural.hyperneat | HeatonReasearch | |
| Substrate | The substrate defines the structure of the produced HyperNEAT network. | Class | org.encog.neural.hyperneat.substrate | HeatonReasearch |
| SubstrateFactory | Produce substrates for various topologies. | Class | org.encog.neural.hyperneat.substrate | HeatonReasearch |
| SubstrateLink | ----------------------------------------------------------------------------- http://www. | Class | org.encog.neural.hyperneat.substrate | HeatonReasearch |
| SubstrateNode | A substrate node. | Class | org.encog.neural.hyperneat.substrate | HeatonReasearch |