GV

GeezerVison

The World Wide Web, restored to 800 pixels of glory.

Home|About|Gaming cabinet|Archives|How it works|Starter sites

On this site

  • Sign in
  • ActionsCI/CD and automation
  • CodespacesCloud development environments
  • All Features
  • Documentation
  • Training
  • Certifications
  • Build with Copilot
  • Customize Copilot
  • Integrations
  • Trending repos
  • GitHub Sponsors
  • Developer articles
  • Enterprises

This view

  • Original page
  • New address

GeezerVison is showing github.com — Add cascade-NEAT mutation. · CBenoit/NEToolKit@3a557ef

This repository was archived by the owner on Jul 1, 2021. It is now read-only.

File tree

Expand file treeCollapse file tree
Open diff view settings
Filter options
  • NEToolKitExamples/src
    • genome_mutations_crossovers.cpp
  • NEToolKit
    • include/netkit/neat
      • gene.h
      • genome.h
      • neat_primitive_types.h
      • parameters.h
    • src/neat
      • dynamic_population.cpp
      • gene.cpp
      • genome.cpp
      • species.cpp
Expand file treeCollapse file tree
Open diff view settings
Collapse file

‎NEToolKit/include/netkit/neat/gene.h‎

Copy file name to clipboardExpand all lines: NEToolKit/include/netkit/neat/gene.h
+1-1Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,7 +18,7 @@ struct gene {
1818
neuron_id_t to;
1919
neuron_value_t weight;
2020
bool enabled;
21-
// TODO: ability to be frozen?
21+
bool frozen;
2222

2323
friend std::ostream& operator<<(std::ostream& os, const gene& g);
2424
friend serializer& operator<<(serializer& ser, const gene& g);
Collapse file

‎NEToolKit/include/netkit/neat/genome.h‎

Copy file name to clipboardExpand all lines: NEToolKit/include/netkit/neat/genome.h
+6Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -44,6 +44,9 @@ class genome {
4444
bool random_mutate();
4545
bool mutate_add_link();
4646
bool mutate_add_neuron(); // pick a random enabled link and split it
47+
bool mutate_add_cascade(); // add a hidden neuron that has inputs from all input nodes
48+
// and hidden nodes and is connected to all outputs.
49+
// In addition, all existing connection are frozen.
4750
bool mutate_remove_neuron();
4851
bool mutate_reenable_gene(); // reenable a random disabled gene
4952
bool mutate_toggle_enable();
@@ -59,6 +62,9 @@ class genome {
5962

6063
network generate_network() const;
6164

65+
private:
66+
std::vector<size_t> helper_generate_candidate_idx();
67+
6268
public:
6369
static const neuron_id_t BIAS_ID; // the first neuron is always the bias (see definition).
6470

Collapse file

‎NEToolKit/include/netkit/neat/neat_primitive_types.h‎

Copy file name to clipboardExpand all lines: NEToolKit/include/netkit/neat/neat_primitive_types.h
+2-1Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,8 @@ using tick_t = unsigned long;
1313
enum mutation_t {
1414
ADD_LINK = 0,
1515
ADD_NEURON = 1,
16-
REMOVE_NEURON = 2, // these three are treated a bit differently (see genome.cpp random_mutate method)
16+
REMOVE_NEURON = 2,
17+
ADD_CASCADE = 3, // these four are treated a bit differently (see genome.cpp random_mutate method)
1718
REMOVE_GENE,
1819
REENABLE_GENE,
1920
TOGGLE_ENABLE,
Collapse file

‎NEToolKit/include/netkit/neat/parameters.h‎

Copy file name to clipboardExpand all lines: NEToolKit/include/netkit/neat/parameters.h
+1Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -8,6 +8,7 @@ struct parameters {
88
mutation_probs[ADD_LINK] = 0.06;
99
mutation_probs[ADD_NEURON] = 0.03;
1010
mutation_probs[REMOVE_NEURON] = 0.03;
11+
mutation_probs[ADD_CASCADE] = 0.00; // see Cascade-NEAT. You might want to disable ADD_NEURON and ADD_LINK.
1112
mutation_probs[REMOVE_GENE] = 0.03;
1213
mutation_probs[REENABLE_GENE] = 0.03;
1314
mutation_probs[TOGGLE_ENABLE] = 0.03;
Collapse file

‎NEToolKit/src/neat/dynamic_population.cpp‎

Copy file name to clipboardExpand all lines: NEToolKit/src/neat/dynamic_population.cpp
+1-1Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33

44
netkit::dynamic_population::dynamic_population(base_neat* neat_instance)
55
: base_population(neat_instance)
6-
, m_marked_for_removal()
6+
, m_marked_for_removal()
77
, m_lookup_genome_id(0) {}
88

99
netkit::dynamic_population::dynamic_population(dynamic_population&& other) noexcept
Collapse file

‎NEToolKit/src/neat/gene.cpp‎

Copy file name to clipboardExpand all lines: NEToolKit/src/neat/gene.cpp
+5-2Lines changed: 5 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,12 @@ netkit::gene::gene(innov_num_t innov_num_, neuron_id_t from_id_, neuron_id_t to_
55
, from(from_id_)
66
, to(to_id_)
77
, weight(weight_)
8-
, enabled(true) {}
8+
, enabled(true)
9+
, frozen(false) {}
910

1011
std::ostream& netkit::operator<<(std::ostream& os, const gene& g) {
1112
os << "<gene: from = " << g.from << " to = " << g.to << " weight = " << g.weight
12-
<< " innovation = " << g.innov_num << " enabled = " << g.enabled << ">";
13+
<< " innovation = " << g.innov_num << " enabled = " << g.enabled << " frozen = " << g.frozen << ">";
1314
return os;
1415
}
1516

@@ -19,6 +20,7 @@ netkit::serializer& netkit::operator<<(serializer& ser, const gene& g) {
1920
ser.append(g.to);
2021
ser.append(g.weight);
2122
ser.append(g.enabled);
23+
ser.append(g.frozen);
2224
ser.new_line();
2325

2426
return ser;
@@ -30,6 +32,7 @@ netkit::deserializer& netkit::operator>>(netkit::deserializer& des, gene& g) {
3032
des.get_next(g.to);
3133
des.get_next(g.weight);
3234
des.get_next(g.enabled);
35+
des.get_next(g.frozen);
3336

3437
return des;
3538
}
Collapse file

‎NEToolKit/src/neat/genome.cpp‎

Copy file name to clipboardExpand all lines: NEToolKit/src/neat/genome.cpp
+71-15Lines changed: 71 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -168,6 +168,7 @@ bool netkit::genome::random_mutate() {
168168
std::bernoulli_distribution add_neuron_true(m_neat->params.mutation_probs[ADD_NEURON]);
169169
std::bernoulli_distribution remove_neuron_true(m_neat->params.mutation_probs[REMOVE_NEURON]);
170170
std::bernoulli_distribution add_link_true(m_neat->params.mutation_probs[ADD_LINK]);
171+
std::bernoulli_distribution add_cascade_true(m_neat->params.mutation_probs[ADD_CASCADE]);
171172
if (add_neuron_true(m_neat->rand_engine)) {
172173
// let's add a new neuron!
173174
return mutate_add_neuron();
@@ -177,10 +178,12 @@ bool netkit::genome::random_mutate() {
177178
} else if (add_link_true(m_neat->rand_engine)) {
178179
// We do not add a new neuron AND a new link at the same time.
179180
return mutate_add_link();
181+
} else if (add_cascade_true(m_neat->rand_engine)) {
182+
return mutate_add_cascade();
180183
} else { // We can do any other mutation if there was no structural mutation.
181184
// The two first values are the add neuron and add link mutations.
182185
std::vector<mutation_t> mutations_to_perform;
183-
mutations_to_perform.reserve(NUMBER_OF_MUTATIONS - 3);
186+
mutations_to_perform.reserve(NUMBER_OF_MUTATIONS - 4);
184187
for (size_t mut_id = 2; mut_id < NUMBER_OF_MUTATIONS; ++mut_id) {
185188
std::bernoulli_distribution select_mutation(m_neat->params.mutation_probs[mut_id]);
186189
if (select_mutation(m_neat->rand_engine)) {
@@ -263,7 +266,7 @@ bool netkit::genome::mutate_add_neuron() {
263266

264267
int sel_idx = -1; // selected gene index
265268
for (int idx : candidates_idx) {
266-
if (m_genes[idx].enabled) {
269+
if (m_genes[idx].enabled && !m_genes[idx].frozen) {
267270
sel_idx = idx;
268271
break;
269272
}
@@ -316,6 +319,43 @@ bool netkit::genome::mutate_add_neuron() {
316319
return true;
317320
}
318321

322+
bool netkit::genome::mutate_add_cascade() {
323+
for (gene& g : m_genes) { // freeze all existing genes.
324+
g.frozen = true;
325+
}
326+
327+
neuron_id_t new_neuron_id = m_neat->innov_pool.next_hidden_neuron_id();
328+
329+
std::uniform_real_distribution<netkit::neuron_value_t> perturbator(-m_neat->params.initial_weight_perturbation,
330+
m_neat->params.initial_weight_perturbation);
331+
332+
// connect all hidden neurons to this neuron.
333+
for (size_t i = m_number_of_outputs + m_number_of_inputs + 1; i < m_known_neuron_ids.size(); ++i) {
334+
gene new_gene(m_neat->innov_pool.next_innovation(),
335+
m_known_neuron_ids[i], new_neuron_id, perturbator(m_neat->rand_engine));
336+
m_neat->innov_pool.register_gene(new_gene);
337+
add_gene(new_gene);
338+
}
339+
340+
// connect all inputs (and the bias) to the new neuron.
341+
for (size_t i = 0; i < m_number_of_inputs + 1; ++i) {
342+
gene new_gene(m_neat->innov_pool.next_innovation(),
343+
m_known_neuron_ids[i], new_neuron_id, perturbator(m_neat->rand_engine));
344+
m_neat->innov_pool.register_gene(new_gene);
345+
add_gene(new_gene);
346+
}
347+
348+
// connect the new neuron to all outputs.
349+
for (size_t i = m_number_of_inputs + 1; i < m_number_of_outputs + m_number_of_inputs + 1; ++i) {
350+
gene new_gene(m_neat->innov_pool.next_innovation(),
351+
new_neuron_id, m_known_neuron_ids[i], perturbator(m_neat->rand_engine));
352+
m_neat->innov_pool.register_gene(new_gene);
353+
add_gene(new_gene);
354+
}
355+
356+
return true;
357+
}
358+
319359
bool netkit::genome::mutate_remove_neuron() {
320360
if (m_known_neuron_ids.size() == m_number_of_inputs + m_number_of_outputs + 1) {
321361
return false;
@@ -336,7 +376,7 @@ bool netkit::genome::mutate_remove_neuron() {
336376
bool netkit::genome::mutate_reenable_gene() {
337377
std::vector<gene*> candidates;
338378
for (gene& g : m_genes) {
339-
if (!g.enabled) {
379+
if (!g.enabled && !g.frozen) {
340380
candidates.push_back(&g);
341381
}
342382
}
@@ -351,33 +391,34 @@ bool netkit::genome::mutate_reenable_gene() {
351391
}
352392

353393
bool netkit::genome::mutate_toggle_enable() {
354-
if (m_genes.empty()) {
394+
std::vector<size_t> candidates_idx = helper_generate_candidate_idx();
395+
if (candidates_idx.empty()) {
355396
return false;
356397
}
357398

358-
std::uniform_int_distribution<size_t> gene_selector(0, m_genes.size() - 1);
399+
std::uniform_int_distribution<size_t> gene_selector(0, candidates_idx.size() - 1);
359400
size_t rnd_val = gene_selector(m_neat->rand_engine);
360-
m_genes[rnd_val].enabled = !m_genes[rnd_val].enabled;
401+
m_genes[candidates_idx[rnd_val]].enabled = !m_genes[candidates_idx[rnd_val]].enabled;
361402

362403
return true;
363404
}
364405

365406
bool netkit::genome::mutate_weights() {
366-
if (m_genes.empty()) {
407+
std::vector<size_t> candidates_idx = helper_generate_candidate_idx();
408+
if (candidates_idx.empty()) {
367409
return false;
368410
}
369411

370412
std::uniform_real_distribution<netkit::neuron_value_t> perturbator(-m_neat->params.weight_mutation_power,
371413
m_neat->params.weight_mutation_power);
372-
std::vector<size_t> candidates_idx(m_genes.size());
373-
std::iota(candidates_idx.begin(), candidates_idx.end(), 0);
374414
std::shuffle(candidates_idx.begin(), candidates_idx.end(), m_neat->rand_engine);
375415

376416
size_t nb_genes = 1;
377-
if (m_genes.size() > 1) {
378-
std::uniform_int_distribution<size_t> nb_genes_selector(0, m_genes.size() - 1);
417+
if (candidates_idx.size() > 1) {
418+
std::uniform_int_distribution<size_t> nb_genes_selector(0, candidates_idx.size() - 1);
379419
nb_genes = nb_genes_selector(m_neat->rand_engine);
380420
}
421+
381422
for (size_t i = 0; i < nb_genes; ++i) {
382423
m_genes[candidates_idx[i]].weight += perturbator(m_neat->rand_engine);
383424
}
@@ -389,19 +430,22 @@ bool netkit::genome::mutate_reset_weights() {
389430
std::uniform_real_distribution<netkit::neuron_value_t> perturbator(-m_neat->params.initial_weight_perturbation,
390431
m_neat->params.initial_weight_perturbation);
391432
for (gene& g : m_genes) {
392-
g.weight = perturbator(m_neat->rand_engine);
433+
if (!g.frozen) {
434+
g.weight = perturbator(m_neat->rand_engine);
435+
}
393436
}
394437

395438
return true;
396439
}
397440

398441
bool netkit::genome::mutate_remove_gene() {
399-
if (m_genes.empty()) {
442+
std::vector<size_t> candidates_idx = helper_generate_candidate_idx();
443+
if (candidates_idx.empty()) {
400444
return false;
401445
}
402446

403-
std::uniform_int_distribution<size_t> gene_selector(0, m_genes.size() - 1);
404-
m_genes.erase(m_genes.begin() + gene_selector(m_neat->rand_engine));
447+
std::uniform_int_distribution<size_t> gene_selector(0, candidates_idx.size() - 1);
448+
m_genes.erase(m_genes.begin() + candidates_idx[gene_selector(m_neat->rand_engine)]);
405449
// TODO: check if a neuron goes unknown afterward. /!\ do not remove bias, input and output neurons.
406450

407451
return true;
@@ -491,6 +535,18 @@ netkit::network netkit::genome::generate_network() const {
491535
return std::move(net);
492536
}
493537

538+
std::vector<size_t> netkit::genome::helper_generate_candidate_idx() {
539+
std::vector<size_t> candidates_idx;
540+
candidates_idx.reserve(m_genes.size());
541+
for (size_t i = 0; i < m_genes.size(); ++i) {
542+
if (!m_genes[i].frozen) {
543+
candidates_idx.emplace_back(i);
544+
}
545+
}
546+
547+
return candidates_idx;
548+
}
549+
494550
bool netkit::genome::reenable_gene_ok() const {
495551
std::bernoulli_distribution distrib(0.25); // TODO: externalize in parameters
496552
return distrib(m_neat->rand_engine);
Collapse file

‎NEToolKit/src/neat/species.cpp‎

Copy file name to clipboardExpand all lines: NEToolKit/src/neat/species.cpp
+2-1Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,8 @@
55
#include "netkit/neat/base_neat.h"
66
#include "netkit/neat/base_population.h"
77

8-
netkit::species::species(base_neat* neat_instance, base_population* population, species_id_t id, const genome& representant)
8+
netkit::species::species(base_neat* neat_instance, base_population* population, species_id_t id,
9+
const genome& representant)
910
: m_members()
1011
, m_avg_fitness(0)
1112
, m_avg_adjusted_fitness(0)
Collapse file

‎NEToolKitExamples/src/genome_mutations_crossovers.cpp‎

Copy file name to clipboardExpand all lines: NEToolKitExamples/src/genome_mutations_crossovers.cpp
+9-1Lines changed: 9 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@ void run_genome_mutations_crossovers() {
1010
params.number_of_inputs = 2;
1111
params.number_of_outputs = 2;
1212
params.compatibility_threshold = 2;
13-
netkit::neat neat(std::move(params));
13+
netkit::neat neat(params);
1414

1515
netkit::genome geno(&neat);
1616
std::cout << "\nInitial genome: " << geno << std::endl;
@@ -21,6 +21,9 @@ void run_genome_mutations_crossovers() {
2121
geno.mutate_add_link();
2222
std::cout << "\nMutate add link:" << std::endl << geno << std::endl;
2323

24+
geno.mutate_add_cascade();
25+
std::cout << "\nMutate add cascade:" << std::endl << geno << std::endl;
26+
2427
geno.mutate_toggle_enable();
2528
std::cout << "\nMutate toggle enable:" << std::endl << geno << std::endl;
2629

@@ -42,6 +45,11 @@ void run_genome_mutations_crossovers() {
4245
geno.mutate_remove_neuron();
4346
std::cout << "\nMutate remove neuron:" << std::endl << geno << std::endl;
4447

48+
for (int j = 0; j < 20; ++j) {
49+
geno.mutate_weights();
50+
}
51+
std::cout << "\nMutate weights:" << std::endl << geno << std::endl;
52+
4553
for (size_t i = 0; i < 20; i++) {
4654
geno2.random_mutate();
4755
}

0 commit comments

Comments
0 (0)
You are visitor 01402520 — GeezerVison does not store the pages you look up.
Best viewed with Netscape Navigator 4.7 or Internet Explorer 6 at 800×600. No cookies required.