Skip to content

A public python implementation of the DeepHyperNEAT system for evolving neural networks. Developed by Felix Sosa and Kenneth Stanley. See paper here:


Notifications You must be signed in to change notification settings


Folders and files

Last commit message
Last commit date

Latest commit



98 Commits

Repository files navigation

Deep HyperNEAT: Extending HyperNEAT to Evolve the Architecture and Depth of Deep Networks

Maintenance made-with-python

NOTE: This implementation is under development. Updates will be pushed over time, bringing in new functionality, tests, and various other elements. The purpose of this repo is to allow others to have a codebase to understand, use, or improve upon DeepHyperNEAT.

Using DeepHyperNEAT

To run DHN in its current form, you need to create a task file. For reference, see

This task file must contain:

  • Necessary imports:
     from genome import Genome # Genome class
     from population import Population # Population class
     from phenomes import FeedForwardCPPN # CPPN class
     from decode import decode # Decoder for CPPN -> Substrate
     from visualize import draw_net # optional, for visualizing networks
  • Substrate parameters
    • Input dimensions
    • Output dimensions
    • Sheet dimensions (optional)
     sub_in_dims = [1,2] # Is of type list
     sub_sh_dims = [1,3] # Is of type list
     sub_o_dims = 1 # Is of type integer
  • Evolutionary parameters
    • Population size
    • Population elitism
    • Max number of generations
     pop_key = 0 # Key for population
     pop_size = 150
     pop_elitism = 2 # Number of members of pop to keep each generation
  • The task (defined as a function in python)
    • Task parameters:
      • Task inputs
      • Expected outputs (optional)
     def task(genomes):
     	task_inputs = [1,2,3]
     	expected_outputs = [2,4,6]
     	for key, genome in genomes:
     		cppn = CPPN.create(genome) # Create cppn from genome
     		substrate = decode(cppn,sub_in_dims,sub_o_dims,sub_sh_dims) # Decode cppn into substrate
     		error = 0.0 # Initialize error for current genome
     		for inputs, expected in zip(xor_inputs, expected_outputs):
     			inputs = inputs + (1.0,) # Append inputs with bias value
     			actual_output = substrate.activate(inputs)[0] # Query substrate
     			error += error_func(actual_output,expected) # Evaluate error = 1.0 - error # Assign fitness
  • A call to DHN to attempt to solve the task
     pop = Population(pop_key, pop_size, pop_elitism)
     solution =,num_generations) # Returns the solution to the task

Primary Modules

These modules are associated with the primary function of the DeepHyperNEAT (DHN) algorihtm.

Contains all functionality of the genome, a Compositional Pattern Producing Network (CPPN) and its mutation operators.

Contains multiple representations for feed-forward and recurrent neural networks for the CPPN and the Substrate.

Contains all functionality and information of the populations used in DHN.

A library of activation functions that can be used for the CPPN and Substrate.

Contains all functionality needed for the reproductive behavior in DHN.

Contains all functionality needed for speciation in DHN.

Contains all functionality needed for stagnation schemes used in speciation.

Contains all functionality needed to decode a given CPPN into a Substrate.

Secondary Modules

These modules are intended for secondary functionality such as reporting evolutionary statistics, visualizing the CPPN and Substrate, and various utility functions used throughout the primary modules.

Contains various functions for reporting evolutionary statistics during and after an evolutionary run.

Contains functions for visualizing a CPPN or Substrate.

Contains common functions and iterators used throughout DHN.