clear out js files

1 files changed, 0 insertions, 218 deletions

diff --git a/src/genome/genome.js b/src/genome/genome.js
deleted file mode 100644
index 20974fc..0000000
--- a/src/genome/genome.js
+++ /dev/null
@@ -1,218 +0,0 @@
-'use strict';

-

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

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

-

-

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

-export function validate_genome(genome) {

-  const { n_input, n_internal, n_output } = genome;

-  console.log(n_input + n_internal);

-  return genome.genes.reduce(

-    (acc, [source, sink, weight]) => acc && (

-      (source < n_input+n_internal) &&

-      (sink >= n_input)

-    ),

-    true

-  );

-}

-

-// parse a genome into a useable neural net

-export function parse_genome(genome) {

-  const { n_input, n_internal, n_output } = genome;

-

-  const n = genome.genes.reduce(

-    (acc, [source, sink, weight]) => acc.connect(source, sink, weight),

-    network(n_input, n_internal, n_output)

-  );

-

-  return n;

-}

-

-

-// --===== mutations =====--

-

-function clamp(value, min, max) {

-  if (value > max) { return max; }

-  if (value < min) { return min; }

-  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;

-

-  const new_source = r < 0.5 ? source-1 : source+1;

-

-  return [

-    clamp(new_source, 0, n_input+n_internal-1), 

-    sink, 

-    weight,

-  ];

-}

-

-

-// 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;

-

-  const new_sink = r < 0.5 ? sink-1 : sink+1;

-

-  return [

-    source, 

-    clamp(new_sink,  n_input+n_internal, n_input+n_internal+n_output-1), 

-    weight,

-  ];

-}

-

-

-// 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;

-  

-  const rr = (2*r)-1;

-  const move = weight_max * rr;

-  const new_weight = (2*weight + move)/3;

-

-  return [

-    source,

-    sink,

-    clamp(new_weight, -weight_max, weight_max),

-  ];

-}

-

-

-

-// 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(genome, r) {

-  const expand_index = Math.floor(genome.n_internal * r) + genome.n_input;

-  const new_genes = genome.genes.map(([source, sink, weight]) => [

-    source >= expand_index ? source+1 : source,

-    sink >= expand_index ? sink+1 : sink,

-    weight,

-  ]);

-

-  return {

-    ...genome, 

-    n_internal: genome.n_internal+1, 

-    genes: new_genes,

-  };

-}

-

-

-// 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(genome, r) {

-  const { n_input, n_internal, n_output } = genome;

-  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_genes = genome.genes.map(([source, sink, weight]) => [

-    new_source(source), 

-    new_sink(sink), 

-    weight,

-  ]);

-

-  return {

-    ...genome,

-    n_internal: n_internal-1,

-    genes: new_genes,

-  };

-}

-

-

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

-export function mut_genome_insert(genome, weight_max, r1=Math.random(), r2=Math.random(), r3=Math.random()) {

-  const { n_input, n_internal, n_output } = genome;

-  const source = Math.floor((n_input + n_internal) * r1);

-  const sink   = Math.floor((n_internal + n_output) * r2) + n_input;

-  const weight = weight_max * ((2*r3)-1);

-

-  return {

-    ...genome,

-    genes: [...genome.genes, [source, sink, weight]],

-  };

-}

-

-

-// delete a gene from the genome

-export function mut_genome_delete(genome, r) {

-  const del_idx = Math.floor(r * genome.genes.length);

-  const genes = genome.genes.filter((_, idx) => idx != del_idx);

-  return { ...genome, genes };

-}

-

-

-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}`);

-  }

-}