75 lines
2.6 KiB
Python
75 lines
2.6 KiB
Python
import jax, jax.numpy as jnp
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from .base import BaseCrossover
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class DefaultCrossover(BaseCrossover):
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def __call__(self, state, randkey, genome, nodes1, conns1, nodes2, conns2):
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"""
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use genome1 and genome2 to generate a new genome
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notice that genome1 should have higher fitness than genome2 (genome1 is winner!)
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"""
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randkey1, randkey2 = jax.random.split(randkey, 2)
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# crossover nodes
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keys1, keys2 = nodes1[:, 0], nodes2[:, 0]
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# make homologous genes align in nodes2 align with nodes1
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nodes2 = self.align_array(keys1, keys2, nodes2, is_conn=False)
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# For not homologous genes, use the value of nodes1(winner)
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# For homologous genes, use the crossover result between nodes1 and nodes2
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new_nodes = jnp.where(
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jnp.isnan(nodes1) | jnp.isnan(nodes2),
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nodes1,
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self.crossover_gene(randkey1, nodes1, nodes2, is_conn=False),
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)
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# crossover connections
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con_keys1, con_keys2 = conns1[:, :2], conns2[:, :2]
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conns2 = self.align_array(con_keys1, con_keys2, conns2, is_conn=True)
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new_conns = jnp.where(
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jnp.isnan(conns1) | jnp.isnan(conns2),
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conns1,
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self.crossover_gene(randkey2, conns1, conns2, is_conn=True),
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)
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return new_nodes, new_conns
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def align_array(self, seq1, seq2, ar2, is_conn: bool):
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"""
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After I review this code, I found that it is the most difficult part of the code.
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Please consider carefully before change it!
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make ar2 align with ar1.
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:param seq1:
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:param seq2:
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:param ar2:
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:param is_conn:
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:return:
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align means to intersect part of ar2 will be at the same position as ar1,
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non-intersect part of ar2 will be set to Nan
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"""
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seq1, seq2 = seq1[:, jnp.newaxis], seq2[jnp.newaxis, :]
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mask = (seq1 == seq2) & (~jnp.isnan(seq1))
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if is_conn:
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mask = jnp.all(mask, axis=2)
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intersect_mask = mask.any(axis=1)
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idx = jnp.arange(0, len(seq1))
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idx_fixed = jnp.dot(mask, idx)
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refactor_ar2 = jnp.where(
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intersect_mask[:, jnp.newaxis], ar2[idx_fixed], jnp.nan
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)
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return refactor_ar2
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def crossover_gene(self, randkey, g1, g2, is_conn):
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r = jax.random.uniform(randkey, shape=g1.shape)
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new_gene = jnp.where(r > 0.5, g1, g2)
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if is_conn: # fix enabled
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enabled = jnp.where(g1[:, 2] + g2[:, 2] > 0, 1, 0) # any of them is enabled
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new_gene = new_gene.at[:, 2].set(enabled)
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return new_gene
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