Index

_

__call__() (reproduction.GenomeDistanceCache method) __del__() (parallel.ParallelEvaluator method) (threaded.ThreadedEvaluator method) __getitem__() (aggregations.AggregationFunctionSet method) __init__() (ctneat.ctrnn.CTRNN method) (ctneat.ctrnn.CTRNNNodeEval method) (ctneat.discretizer.Discretizer method) (ctneat.iznn.IZNeuron method) (ctneat.iznn.IZNN method)

__lt__() (genes.BaseGene method) __reduce__() (distributed._ExtendedManager method) __repr__() (config.ConfigParameter method) __str__() (genes.BaseGene method) (genome.DefaultGenome method) _determine_mode() (in module distributed) _ExtendedManager (class in distributed) _STATE_FORCED_SHUTDOWN (in module distributed) _STATE_RUNNING (in module distributed) _STATE_SHUTDOWN (in module distributed)

A

activate() (nn.feed_forward.FeedForwardNetwork method) (nn.recurrent.RecurrentNetwork method) activation function, [1], [2], [3], [4], [5] ActivationFunctionSet (class in activations) activations module add() (activations.ActivationFunctionSet method) (aggregations.AggregationFunctionSet method) (reporting.ReporterSet method) add_activation() (genome.DefaultGenomeConfig method) add_aggregation() (genome.DefaultGenomeConfig method) add_connection() (genome.DefaultGenome method) advance() (ctneat.ctrnn.CTRNN method) (ctneat.iznn.IZNeuron method) (ctneat.iznn.IZNN method) (ctrnn.CTRNN method) (iznn.IZNeuron method) (iznn.IZNN method)

advance_event_driven() (ctneat.iznn.IZNN method) advance_rk4() (ctneat.iznn.IZNeuron method) advance_scipy() (ctneat.iznn.IZNeuron method) advance_scipy_events() (ctneat.iznn.IZNeuron method) advance_simple() (ctneat.iznn.IZNN method) aggregation function, [1], [2], [3], [4] AggregationFunctionSet (class in aggregations) aggregations module attributes, [1], [2], [3], [4], [5], [6], [7] module

B

BaseAttribute (class in attributes) BaseGene (class in genes) BaseReporter (class in reporting) best_genome() (statistics.StatisticsReporter method)

best_genomes() (statistics.StatisticsReporter method) best_unique_genomes() (statistics.StatisticsReporter method) bias, [1] BoolAttribute (class in attributes)

C

characterize_attractor_spikes() (in module ctneat.iznn.dynamic_attractors), [1] characterize_attractor_voltage() (in module ctneat.iznn.dynamic_attractors), [1] CHATTERING_PARAMS (in module iznn) check_structural_mutation_surer(), [1] (genome.DefaultGenomeConfig method) checkpoint module Checkpointer (class in checkpoint) chunked() (in module distributed) clamp() (attributes.FloatAttribute method) cluster_attractors() (ctneat.discretizer.Discretizer method) compatibility_disjoint_coefficient, [1], [2] compatibility_threshold, [1] compatibility_weight_coefficient, [1], [2], [3] complete_extinction() (reporting.BaseReporter method) (reporting.ReporterSet method) CompleteExtinctionException compute node, [1] compute_full_connections() (genome.DefaultGenome method) compute_spawn() (reproduction.DefaultReproduction static method) config module Config (class in config) config_item_name() (attributes.BaseAttribute method) ConfigParameter (class in config) configure_crossover() (genome.DefaultGenome method) configure_new() (genome.DefaultGenome method) conn_add_prob, [1], [2] conn_delete_prob, [1], [2] connect_fs_neat_hidden() (genome.DefaultGenome method) connect_fs_neat_nohidden() (genome.DefaultGenome method) connect_full_direct() (genome.DefaultGenome method)

connect_full_nodirect() (genome.DefaultGenome method) connect_partial_direct() (genome.DefaultGenome method) connect_partial_nodirect() (genome.DefaultGenome method) connection, [1], [2], [3], [4], [5], [6], [7], [8], [9] continuous-time, [1], [2], [3] copy() (genes.BaseGene method) create() (ctneat.ctrnn.CTRNN static method) (ctneat.iznn.IZNN static method) (ctrnn.CTRNN static method) (iznn.IZNN static method) (nn.feed_forward.FeedForwardNetwork static method) (nn.recurrent.RecurrentNetwork static method) create_connection() (genome.DefaultGenome static method) create_new() (reproduction.DefaultReproduction method) create_node() (genome.DefaultGenome static method) creates_cycle() (in module graphs) crossover, [1], [2], [3] crossover() (genes.BaseGene method) ctneat.ctrnn module ctneat.ctrnn.ctrnn_visualize module ctneat.discretizer module ctneat.iznn module ctneat.iznn.dynamic_attractors module, [1] ctrnn, [1] module CTRNN (class in ctneat.ctrnn) (class in ctrnn) CTRNNNodeEval (class in ctneat.ctrnn) (class in ctrnn)

D

default see X_default DefaultClassConfig (class in config) DefaultConnectionGene (class in genes) DefaultGenome, [1], [2] (class in genome) DefaultGenomeConfig (class in genome) DefaultNodeGene (class in genes) DefaultReproduction, [1] (class in reproduction) DefaultSpeciesSet (class in reproduction) DefaultStagnation (class in stagnation) discrete-time discretization

discretize() (ctneat.discretizer.Discretizer method) Discretizer (class in ctneat.discretizer) disjoint, [1], [2] disretizer distance() (ctneat.iznn.IZNodeGene method) (genes.DefaultConnectionGene method) (genes.DefaultNodeGene method) (genome.DefaultGenome method) (iznn.IZNodeGene method) distributed module DistributedEvaluator (class in distributed) draw_ctrnn_dynamics() (in module ctneat.ctrnn.ctrnn_visualize) draw_ctrnn_net() (in module ctneat.ctrnn.ctrnn_visualize) draw_ctrnn_trajectory() (in module ctneat.ctrnn.ctrnn_visualize) dynamic_attractors_pipeline() (in module ctneat.iznn.dynamic_attractors), [1]

E

elitism, [1], [2] enabled, [1] enabled_default, [1] end_generation() (reporting.BaseReporter method) (reporting.ReporterSet method)

evaluate() (distributed.DistributedEvaluator method) (parallel.ParallelEvaluator method) (threaded.ThreadedEvaluator method) excess, [1]

F

FAST_SPIKING_PARAMS (in module iznn) feed-forward see feedforward feed_forward, [1], [2], [3] feed_forward_layers() (in module graphs) feedforward, [1], [2] FeedForwardNetwork (class in nn.feed_forward) fingerprint_attractors() (in module ctneat.iznn.dynamic_attractors), [1] fired (ctneat.iznn.IZNN property)

fitness, [1], [2], [3], [4], [5], [6] fitness criterion fitness function, [1], [2], [3], [4], [5], [6], [7], [8], [9] fitness_criterion, [1], [2], [3] fitness_threshold, [1], [2], [3], [4], [5] FloatAttribute (class in attributes) format() (config.ConfigParameter method) found_solution(), [1], [2], [3] (reporting.BaseReporter method) (reporting.ReporterSet method)

G

gene, [1], [2] generation, [1], [2], [3], [4], [5] genes module genetic distance, [1], [2], [3] genome, [1], [2], [3], [4], [5] module GenomeDistanceCache (class in reproduction) genomic distance, [1], [2], [3], [4], [5], [6], [7], [8], [9] get() (activations.ActivationFunctionSet method) (aggregations.AggregationFunctionSet method) get_config_params() (attributes.BaseAttribute method) (genes.BaseGene class method) get_fitness_mean() (statistics.StatisticsReporter method) get_fitness_median() (statistics.StatisticsReporter method)

get_fitness_stat() (statistics.StatisticsReporter method) get_fitness_stdev() (statistics.StatisticsReporter method) get_fitnesses() (reproduction.Species method) get_inqueue() (distributed._ExtendedManager method) get_max_time_step() (ctneat.ctrnn.CTRNN method) get_namespace() (distributed._ExtendedManager method) get_new_node_key() (genome.DefaultGenomeConfig method) get_outqueue() (distributed._ExtendedManager method) get_species() (reproduction.DefaultSpeciesSet method) get_species_fitness() (statistics.StatisticsReporter method) get_species_id() (reproduction.DefaultSpeciesSet method) get_species_sizes() (statistics.StatisticsReporter method) get_time_step_msec() (ctneat.iznn.IZNN method) (iznn.IZNN method) graphs module

H

hidden node, [1], [2]

homologous, [1], [2] host_is_local() (in module distributed)

I

id info(), [1] (reporting.BaseReporter method) (reporting.ReporterSet method) init_attributes() (genes.BaseGene method) init_mean, [1], [2], [3] init_stdev, [1], [2], [3] init_type, [1], [2], [3] init_value() (attributes.BoolAttribute method) (attributes.FloatAttribute method) (attributes.StringAttribute method) initial_connection, [1], [2], [3], [4] input node, [1], [2] interpret() (config.ConfigParameter method) INTRINSICALLY_BURSTING_PARAMS (in module iznn)

InvalidActivationFunction InvalidAggregationFunction is_master() (distributed.DistributedEvaluator method) is_primary() (distributed.DistributedEvaluator method) is_valid() (activations.ActivationFunctionSet method) (aggregations.AggregationFunctionSet method) IZGenome (class in ctneat.iznn) (class in iznn) IZNeuron (class in ctneat.iznn) (class in iznn) iznn module IZNN (class in ctneat.iznn) (class in iznn) IZNodeGene (class in ctneat.iznn) (class in iznn)

K

key, [1], [2], [3], [4], [5], [6]

L

LOW_THRESHOLD_SPIKING_PARAMS (in module iznn)

M

map_clusters_to_outputs() (ctneat.discretizer.Discretizer method) math_util module max_aggregation() (in module aggregations) max_stagnation, [1] max_value, [1], [2], [3] maxabs_aggregation() (in module aggregations) mean() (in module math_util) mean_aggregation() (in module aggregations) median() (in module math_util) median2() (in module math_util) median_aggregation() (in module aggregations) min_aggregation() (in module aggregations) min_species_size, [1], [2] min_value, [1], [2], [3] MODE_AUTO (in module distributed) MODE_PRIMARY (in module distributed) MODE_SECONDARY (in module distributed) ModeError module activations aggregations attributes checkpoint config ctneat.ctrnn ctneat.ctrnn.ctrnn_visualize ctneat.discretizer ctneat.iznn ctneat.iznn.dynamic_attractors, [1] ctrnn distributed genes genome graphs iznn math_util nn.feed_forward nn.recurrent parallel population reporting reproduction stagnation statistics threaded

mutate see mutation mutate() (genes.BaseGene method) (genome.DefaultGenome method) mutate_add_connection() (genome.DefaultGenome method) mutate_add_node() (genome.DefaultGenome method) mutate_delete_connection() (genome.DefaultGenome method) mutate_delete_node() (genome.DefaultGenome method) mutate_power, [1], [2], [3] mutate_rate, [1], [2], [3], [4], [5], [6], [7], [8] mutate_value() (attributes.BoolAttribute method) (attributes.FloatAttribute method) (attributes.StringAttribute method) mutation, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12], [13], [14]

N

nn.feed_forward module nn.recurrent module no_fitness_termination, [1], [2], [3], [4]

node, [1], [2], [3], [4], [5], [6], [7], [8], [9], [10] node_add_prob, [1], [2] node_delete_prob, [1], [2] num_hidden, [1] num_inputs, [1] num_outputs, [1]

O

options see X_options

output node, [1], [2]

P

parallel module ParallelEvaluator (class in parallel) parse() (config.ConfigParameter method) parse_config() (ctneat.iznn.IZGenome class method) (genes.BaseGene class method) (genome.DefaultGenome class method) (reproduction.DefaultReproduction class method) (reproduction.DefaultSpeciesSet class method) (stagnation.DefaultStagnation class method) perform_rqa_analysis() (in module ctneat.iznn.dynamic_attractors), [1] pin, [1] pop_size, [1], [2], [3], [4]

population module Population (class in population) post_evaluate() (reporting.BaseReporter method) (reporting.ReporterSet method) (statistics.StatisticsReporter method) post_reproduction() (reporting.BaseReporter method) (reporting.ReporterSet method) primary compute node see primary node primary node, [1] product_aggregation() (in module aggregations)

R

rate_to_false_add, [1] rate_to_true_add, [1] recovery (ctneat.iznn.IZNN property) recurrent, [1], [2], [3], [4] RecurrentNetwork (class in nn.recurrent) REGULAR_SPIKING_PARAMS (in module iznn) remove() (reporting.ReporterSet method) replace_rate, [1], [2], [3] ReporterSet (class in reporting) reporting module reproduce() (reproduction.DefaultReproduction method) reproduction, [1] module

required_for_output() (in module graphs) resample_data() (in module ctneat.iznn.dynamic_attractors), [1] reset() (ctneat.ctrnn.CTRNN method) (ctneat.iznn.IZNeuron method) (ctneat.iznn.IZNN method) (ctrnn.CTRNN method) (iznn.IZNeuron method) (iznn.IZNN method) (nn.recurrent.RecurrentNetwork method) reset_on_extinction, [1], [2], [3], [4], [5] RESONATOR_PARAMS (in module iznn) response, [1] restore_checkpoint() (checkpoint.Checkpointer static method) run() (population.Population method) run_network() (ctneat.discretizer.Discretizer method)

S

save() (config.Config method) (genome.DefaultGenomeConfig method) (statistics.StatisticsReporter method) save_checkpoint() (checkpoint.Checkpointer method) save_genome_fitness() (statistics.StatisticsReporter method) save_species_count() (statistics.StatisticsReporter method) save_species_fitness() (statistics.StatisticsReporter method) secondary compute node see secondary node secondary node, [1] secondary_state (distributed._ExtendedManager attribute) set_inputs() (ctneat.iznn.IZNN method) (iznn.IZNN method) set_node_value() (ctneat.ctrnn.CTRNN method) set_secondary_state() (distributed._ExtendedManager method) single_structural_mutation, [1], [2], [3] size() (genome.DefaultGenome method) softmax() (in module math_util) solve_for_interval() (ctneat.iznn.IZNeuron method) speciate() (reproduction.DefaultSpeciesSet method) species, [1], [2] Species (class in reproduction) species_elitism, [1], [2] species_fitness_func, [1], [2]

species_stagnant() (reporting.BaseReporter method) (reporting.ReporterSet method) stagnation, [1], [2], [3] module start() (distributed._ExtendedManager method) (distributed.DistributedEvaluator method) (threaded.ThreadedEvaluator method) start_generation() (reporting.BaseReporter method) (reporting.ReporterSet method) stat_functions (in module math_util) state (ctneat.iznn.IZNN property) statistics module StatisticsReporter (class in statistics) stdev() (in module math_util) StdOutReporter (class in reporting) stop() (distributed._ExtendedManager method) (distributed.DistributedEvaluator method) (threaded.ThreadedEvaluator method) StringAttribute (class in attributes) structural_mutation_surer, [1], [2], [3], [4] sum_aggregation() (in module aggregations) survival_threshold, [1], [2]

T

THALAMO_CORTICAL_PARAMS (in module iznn) threaded module

ThreadedEvaluator (class in threaded)

U

UnknownConfigItemError

update() (reproduction.Species method) (stagnation.DefaultStagnation method)

V

validate_activation() (in module activations) validate_aggregation() (in module aggregations)

variance() (in module math_util) voltages (ctneat.iznn.IZNN property)

W

weight, [1] write_config() (config.DefaultClassConfig class method) (genome.DefaultGenome class method)

write_pretty_params() (in module config)

X

X_default, [1], [2], [3], [4]

X_options, [1], [2], [3]