Mutation #13
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Mutation #13
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younik
suggested changes
Jan 25, 2024
chromax/simulator.py
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| if mutation is None: | ||
| self.mutation = 0.0 | ||
| elif mutation > 0 and mutation < 1: | ||
| self.mutation = mutation | ||
| else: | ||
| raise ValueError( | ||
| f"mutation must be between 0 and 1, but got {mutation}" | ||
| ) |
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To simplify this, you can use as default 0 in init definition mutation: float = 0f
Then here, something like this:
if mutation < 0 or mutation > 0:
raise ValueError(
f"mutation must be between 0 and 1, but got {mutation}"
)
self.mutation = mutation
chromax/simulator.py
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| print(f'shape is {self.random_key.shape} {self.random_key[0]}') | ||
| return |
chromax/functional.py
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| rec_sites = samples < recombination_vec | ||
| crossover_mask = jax.lax.associative_scan(jnp.logical_xor, rec_sites) | ||
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| crossover_mask = crossover_mask.astype(jnp.int8) | ||
| haploid = jnp.take_along_axis(individual, crossover_mask[:, None], axis=-1) | ||
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| mutation_samples = jax.random.uniform(mutate_random_key, shape=haploid.shape) | ||
| mutation_sites = mutation_samples > mutate_probability |
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should be mutation_samples < mutate_probability, isn't it?
If mutate_probability = 0, mutation_sites should always be False
chromax/functional.py
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| random_keys = jax.random.split(random_key, num=len(parents) * 2 * parents.shape[3]) | ||
| random_keys = random_keys.reshape(len(parents), 2, parents.shape[3], 2) | ||
| offsprings = _cross(parents, recombination_vec, random_keys) | ||
| cross_random_key = jax.random.split(cross_random_key, num=len(parents) * 2 * parents.shape[3]) | ||
| cross_random_key = cross_random_key.reshape(len(parents), 2, parents.shape[3], 2) | ||
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| mutate_split_key = jax.random.split(mutate_split_key, num=len(parents) * 2 * parents.shape[3]) | ||
| mutate_split_key = mutate_split_key.reshape(len(parents), 2, parents.shape[3], 2) | ||
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| offsprings = _cross(parents, recombination_vec, cross_random_key, mutate_split_key, mutate_probability) |
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I would avoid adding the other keys as argument, but I would generate them internally here.
So you can do:
random_keys = jax.random.split(random_key, num=2 * len(parents) * 2 * parents.shape[3])
random_keys = random_keys.reshape(3, len(parents), 2, parents.shape[3], 2)
cross_random_key, mutate_random_key = random_keysAlso, use default value of 0 for mutate_probability, so previous code will continue working
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random_keys = random_keys.reshape(3, len(parents), 2, parents.shape[3], 2)
you mean
random_keys = random_keys.reshape(2, len(parents), 2, parents.shape[3], 2)?
chromax/functional.py
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| cross_random_key: jax.random.PRNGKeyArray, | ||
| mutate_random_key: jax.random.PRNGKeyArray, | ||
| mutate_probability: float, |
|
have a look new change |
|
Merged, thank you! @oddoking |
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add mutation random key and mutate prob