add genome creation & mutation trial

4 files changed, 130 insertions, 2 deletions

diff --git a/src/genome/genome.js b/src/genome/genome.js
index d2650b5..bc569ff 100644
--- a/src/genome/genome.js
+++ b/src/genome/genome.js
@@ -1,6 +1,7 @@
 'use strict';

 

-import { network } from '../mind/topology';

+import { random_choice } from '../util.js';

+import { network } from '../mind/topology.js';

 

 

 // check if a given genome is valid and compute its size

@@ -25,6 +26,7 @@ export function get_size(num_input, num_output, genome) {
 }

 

 

+// parse a genome into a useable neural net

 export function parse_genome(num_input, num_output, genome) {

   const size = get_size(num_input, num_output, genome);

   if (size < 0) {

@@ -49,6 +51,7 @@ function clamp(value, min, max) {
   return value;

 }

 

+// adjust the source input of a gene

 export function mut_gene_source(n_input, n_internal, n_output, gene, r) {

   const [source, sink, weight] = gene;

 

@@ -62,6 +65,7 @@ export function mut_gene_source(n_input, n_internal, n_output, gene, r) {
 }

 

 

+// adjust the sink target of a gene

 export function mut_gene_sink(n_input, n_internal, n_output, gene, r) {

   const [source, sink, weight] = gene;

 

@@ -75,6 +79,9 @@ export function mut_gene_sink(n_input, n_internal, n_output, gene, r) {
 }

 

 

+// modify a gene's weight

+// only adjusts the weight by performing a weighted average, so as to

+// more gently modify the generated net

 export function mut_gene_weight(weight_max, gene, r) {

   const [source, sink, weight] = gene;

   

@@ -90,6 +97,9 @@ export function mut_gene_weight(weight_max, gene, r) {
 }

 

 

+

+// expand the size of the neural net encoded by the genome

+// relabels internal indices so that there is one extra internal neuron

 export function mut_genome_expand(

   [n_input, n_internal, n_output, genome], r

 ) {

@@ -106,11 +116,16 @@ export function mut_genome_expand(
 }

 

 

+// contract the size of the neural net encoded by the genome

+// relabels internal indices so that there is one less internal neuron

 export function mut_genome_contract(

   [n_input, n_internal, n_output, genome], r

 ) {

   const contract_idx = Math.floor(n_internal * r) + n_input;

+

+  // decrement sources on the contract index too, to prevent invalid genomes

   const new_source = (source) => source >= contract_idx ? source-1 : source;

+  // decrement sinks only after the contract index

   const new_sink   = (sink)   => sink > contract_idx ? sink-1 : sink;

 

   const new_genome = genome.map(([source, sink, weight]) => [

@@ -125,6 +140,7 @@ export function mut_genome_contract(
 }

 

 

+// append a newly generated gene to the end of the genome

 export function mut_genome_insert(

   [n_input, n_internal, n_output, genome], 

   weight_max, 

@@ -141,6 +157,7 @@ export function mut_genome_insert(
 }

 

 

+// delete a gene from the genome

 export function mut_genome_delete(

   [n_input, n_internal, n_output, genome], r

 ) {

@@ -148,3 +165,71 @@ export function mut_genome_delete(
   const new_genome = genome.filter((_, idx) => idx != del_idx);

   return [n_input, n_internal, n_output, new_genome];

 }

+

+

+function mut_gene(

+  [n_input, n_internal, n_output, genome], 

+  weight_max, r1, r2, r3

+) {

+  const gene_idx = Math.floor(genome.length * r1);

+  const mod = random_choice(['source', 'sink', 'weight'], r2);

+  let new_gene;

+  if (mod == 'source') {

+    new_gene = mut_gene_source(

+      n_input, n_internal, n_output, 

+      genome[gene_idx],

+      r3

+    );

+  } else if (mod == 'sink') {

+    new_gene = mut_gene_sink(

+      n_input, n_internal, n_output, 

+      genome[gene_idx],

+      r3

+    );

+  } else {

+    new_gene = mut_gene_weight(

+      weight_max, genome[gene_idx], r3

+    );

+  }

+

+  const new_genome = genome.map((gene, idx) => {

+    if (idx == gene_idx) { return new_gene; }

+    return gene;

+  });

+

+  return [

+    n_input, n_internal, n_output, new_genome

+  ];

+}

+

+

+export function mutate_genome(obj, weight_max) {

+  const mut = random_choice([

+    'gene', 'gene', 'gene',

+    'gene', 'gene', 'gene',

+    'gene', 'gene', 'gene',

+    'insert', 'delete',

+    'insert', 'delete',

+    'expand', 'contract',

+  ], Math.random());

+

+  if (mut == 'gene') {

+    return mut_gene(

+      obj, weight_max, 

+      Math.random(), Math.random(), Math.random()

+    );

+  } else if (mut == 'insert') {

+    return mut_genome_insert(

+      obj, weight_max, 

+      Math.random(), Math.random(), Math.random()

+    );

+  } else if (mut == 'delete') {

+    return mut_genome_delete(obj, Math.random());

+  } else if (mut == 'expand') {

+    return mut_genome_expand(obj, Math.random());

+  } else if (mut == 'contract') {

+    return mut_genome_contract(obj, Math.random());

+  } else {

+    throw new Error(`bad mut value: ${mut}`);

+  }

+}

diff --git a/src/genome/trial.js b/src/genome/trial.js
new file mode 100644
index 0000000..2ce23bf
--- /dev/null
+++ b/src/genome/trial.js
@@ -0,0 +1,37 @@
+import { 
+  get_size,
+  mut_genome_insert, mutate_genome,
+} from './genome.js';
+
+const recurse = (f, x0, n) => {
+  if (n == 0) { 
+    return x0; 
+  } else {
+    return f(recurse(f, x0, n-1));
+  }
+};
+
+
+const n_input = 5;
+const n_output = 5;
+
+
+const [_1, _2, _3, genome] = recurse(
+  s => mut_genome_insert(
+    s, 4, 
+    Math.random(), Math.random(), Math.random()
+  ), 
+  [n_input, 10, n_output, []], 
+  20);
+
+
+const n_internal = get_size(n_input, n_output, genome) - n_input - n_output;
+console.log([n_input, n_internal, n_output, genome]);
+
+const mutation = recurse(
+  s => mutate_genome(s, 4),
+  [n_input, n_internal, n_output, genome],
+  40
+);
+
+console.log(mutation);
diff --git a/src/mind/topology.js b/src/mind/topology.js
index 576ee83..127351e 100644
--- a/src/mind/topology.js
+++ b/src/mind/topology.js
@@ -1,6 +1,6 @@
 'use strict';
 
-import { create } from '../util';
+import { create } from '../util.js';
 
 
 const DEFAULT_WEIGHT_MAX = 4;
diff --git a/src/util.js b/src/util.js
index 9f52551..4e23d9d 100644
--- a/src/util.js
+++ b/src/util.js
@@ -8,3 +8,9 @@ export function create(obj, proto=Object.prototype) {
 

   return Object.create(proto, props);

 };

+

+

+export function random_choice(collection, r) {

+  const idx = Math.floor(collection.length * r);

+  return collection[idx];

+}