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change project structure and using .ini as config file

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wls2002
2023-06-15 11:05:26 +08:00
parent 47fb0151f4
commit acedd67617
30 changed files with 97 additions and 301 deletions
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neat/genome/mutate.py Normal file
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from typing import Tuple
from functools import partial
import jax
import numpy as np
from jax import numpy as jnp
from jax import jit, vmap, Array
from .utils import fetch_random, fetch_first, I_INT, unflatten_connections
from .genome import add_node, delete_node_by_idx, delete_connection_by_idx, add_connection
from .graph import check_cycles
# TODO: Temporally delete single_structural_mutation, for i need to run it as soon as possible.
@jit
def mutate(rand_key: Array,
nodes: Array,
connections: Array,
new_node_key: int,
input_idx: Array,
output_idx: Array,
bias_mean: float = 0,
bias_std: float = 1,
bias_mutate_strength: float = 0.5,
bias_mutate_rate: float = 0.7,
bias_replace_rate: float = 0.1,
response_mean: float = 1.,
response_std: float = 0.,
response_mutate_strength: float = 0.,
response_mutate_rate: float = 0.,
response_replace_rate: float = 0.,
weight_mean: float = 0.,
weight_std: float = 1.,
weight_mutate_strength: float = 0.5,
weight_mutate_rate: float = 0.7,
weight_replace_rate: float = 0.1,
act_default: int = 0,
act_list: Array = None,
act_replace_rate: float = 0.1,
agg_default: int = 0,
agg_list: Array = None,
agg_replace_rate: float = 0.1,
enabled_reverse_rate: float = 0.1,
add_node_rate: float = 0.2,
delete_node_rate: float = 0.2,
add_connection_rate: float = 0.4,
delete_connection_rate: float = 0.4,
):
"""
:param output_idx:
:param input_idx:
:param agg_default:
:param act_default:
:param rand_key:
:param nodes: (N, 5)
:param connections: (2, N, N)
:param new_node_key:
:param bias_mean:
:param bias_std:
:param bias_mutate_strength:
:param bias_mutate_rate:
:param bias_replace_rate:
:param response_mean:
:param response_std:
:param response_mutate_strength:
:param response_mutate_rate:
:param response_replace_rate:
:param weight_mean:
:param weight_std:
:param weight_mutate_strength:
:param weight_mutate_rate:
:param weight_replace_rate:
:param act_list:
:param act_replace_rate:
:param agg_list:
:param agg_replace_rate:
:param enabled_reverse_rate:
:param add_node_rate:
:param delete_node_rate:
:param add_connection_rate:
:param delete_connection_rate:
:return:
"""
def m_add_node(rk, n, c):
return mutate_add_node(rk, n, c, new_node_key, bias_mean, response_mean, act_default, agg_default)
def m_add_connection(rk, n, c):
return mutate_add_connection(rk, n, c, input_idx, output_idx)
def m_delete_node(rk, n, c):
return mutate_delete_node(rk, n, c, input_idx, output_idx)
def m_delete_connection(rk, n, c):
return mutate_delete_connection(rk, n, c)
r1, r2, r3, r4, rand_key = jax.random.split(rand_key, 5)
# mutate add node
aux_nodes, aux_connections = m_add_node(r1, nodes, connections)
nodes = jnp.where(rand(r1) < add_node_rate, aux_nodes, nodes)
connections = jnp.where(rand(r1) < add_node_rate, aux_connections, connections)
# mutate add connection
aux_nodes, aux_connections = m_add_connection(r3, nodes, connections)
nodes = jnp.where(rand(r3) < add_connection_rate, aux_nodes, nodes)
connections = jnp.where(rand(r3) < add_connection_rate, aux_connections, connections)
# mutate delete node
aux_nodes, aux_connections = m_delete_node(r2, nodes, connections)
nodes = jnp.where(rand(r2) < delete_node_rate, aux_nodes, nodes)
connections = jnp.where(rand(r2) < delete_node_rate, aux_connections, connections)
# mutate delete connection
aux_nodes, aux_connections = m_delete_connection(r4, nodes, connections)
nodes = jnp.where(rand(r4) < delete_connection_rate, aux_nodes, nodes)
connections = jnp.where(rand(r4) < delete_connection_rate, aux_connections, connections)
nodes, connections = mutate_values(rand_key, nodes, connections, bias_mean, bias_std, bias_mutate_strength,
bias_mutate_rate, bias_replace_rate, response_mean, response_std,
response_mutate_strength, response_mutate_rate, response_replace_rate,
weight_mean, weight_std, weight_mutate_strength,
weight_mutate_rate, weight_replace_rate, act_list, act_replace_rate, agg_list,
agg_replace_rate, enabled_reverse_rate)
return nodes, connections
@jit
def mutate_values(rand_key: Array,
nodes: Array,
cons: Array,
bias_mean: float = 0,
bias_std: float = 1,
bias_mutate_strength: float = 0.5,
bias_mutate_rate: float = 0.7,
bias_replace_rate: float = 0.1,
response_mean: float = 1.,
response_std: float = 0.,
response_mutate_strength: float = 0.,
response_mutate_rate: float = 0.,
response_replace_rate: float = 0.,
weight_mean: float = 0.,
weight_std: float = 1.,
weight_mutate_strength: float = 0.5,
weight_mutate_rate: float = 0.7,
weight_replace_rate: float = 0.1,
act_list: Array = None,
act_replace_rate: float = 0.1,
agg_list: Array = None,
agg_replace_rate: float = 0.1,
enabled_reverse_rate: float = 0.1) -> Tuple[Array, Array]:
"""
Mutate values of nodes and connections.
Args:
rand_key: A random key for generating random values.
nodes: A 2D array representing nodes.
cons: A 3D array representing connections.
bias_mean: Mean of the bias values.
bias_std: Standard deviation of the bias values.
bias_mutate_strength: Strength of the bias mutation.
bias_mutate_rate: Rate of the bias mutation.
bias_replace_rate: Rate of the bias replacement.
response_mean: Mean of the response values.
response_std: Standard deviation of the response values.
response_mutate_strength: Strength of the response mutation.
response_mutate_rate: Rate of the response mutation.
response_replace_rate: Rate of the response replacement.
weight_mean: Mean of the weight values.
weight_std: Standard deviation of the weight values.
weight_mutate_strength: Strength of the weight mutation.
weight_mutate_rate: Rate of the weight mutation.
weight_replace_rate: Rate of the weight replacement.
act_list: List of the activation function values.
act_replace_rate: Rate of the activation function replacement.
agg_list: List of the aggregation function values.
agg_replace_rate: Rate of the aggregation function replacement.
enabled_reverse_rate: Rate of reversing enabled state of connections.
Returns:
A tuple containing mutated nodes and connections.
"""
k1, k2, k3, k4, k5, rand_key = jax.random.split(rand_key, num=6)
bias_new = mutate_float_values(k1, nodes[:, 1], bias_mean, bias_std,
bias_mutate_strength, bias_mutate_rate, bias_replace_rate)
response_new = mutate_float_values(k2, nodes[:, 2], response_mean, response_std,
response_mutate_strength, response_mutate_rate, response_replace_rate)
weight_new = mutate_float_values(k3, cons[:, 2], weight_mean, weight_std,
weight_mutate_strength, weight_mutate_rate, weight_replace_rate)
act_new = mutate_int_values(k4, nodes[:, 3], act_list, act_replace_rate)
agg_new = mutate_int_values(k5, nodes[:, 4], agg_list, agg_replace_rate)
# mutate enabled
r = jax.random.uniform(rand_key, cons[:, 3].shape)
enabled_new = jnp.where(r < enabled_reverse_rate, 1 - cons[:, 3], cons[:, 3])
enabled_new = jnp.where(~jnp.isnan(cons[:, 3]), enabled_new, jnp.nan)
nodes = nodes.at[:, 1].set(bias_new)
nodes = nodes.at[:, 2].set(response_new)
nodes = nodes.at[:, 3].set(act_new)
nodes = nodes.at[:, 4].set(agg_new)
cons = cons.at[:, 2].set(weight_new)
cons = cons.at[:, 3].set(enabled_new)
return nodes, cons
@jit
def mutate_float_values(rand_key: Array, old_vals: Array, mean: float, std: float,
mutate_strength: float, mutate_rate: float, replace_rate: float) -> Array:
"""
Mutate float values of a given array.
Args:
rand_key: A random key for generating random values.
old_vals: A 1D array of float values to be mutated.
mean: Mean of the values.
std: Standard deviation of the values.
mutate_strength: Strength of the mutation.
mutate_rate: Rate of the mutation.
replace_rate: Rate of the replacement.
Returns:
A mutated 1D array of float values.
"""
k1, k2, k3, rand_key = jax.random.split(rand_key, num=4)
noise = jax.random.normal(k1, old_vals.shape) * mutate_strength
replace = jax.random.normal(k2, old_vals.shape) * std + mean
r = jax.random.uniform(k3, old_vals.shape)
new_vals = old_vals
new_vals = jnp.where(r < mutate_rate, new_vals + noise, new_vals)
new_vals = jnp.where(
jnp.logical_and(mutate_rate < r, r < mutate_rate + replace_rate),
replace,
new_vals
)
new_vals = jnp.where(~jnp.isnan(old_vals), new_vals, jnp.nan)
return new_vals
@jit
def mutate_int_values(rand_key: Array, old_vals: Array, val_list: Array, replace_rate: float) -> Array:
"""
Mutate integer values (act, agg) of a given array.
Args:
rand_key: A random key for generating random values.
old_vals: A 1D array of integer values to be mutated.
val_list: List of the integer values.
replace_rate: Rate of the replacement.
Returns:
A mutated 1D array of integer values.
"""
k1, k2, rand_key = jax.random.split(rand_key, num=3)
replace_val = jax.random.choice(k1, val_list, old_vals.shape)
r = jax.random.uniform(k2, old_vals.shape)
new_vals = old_vals
new_vals = jnp.where(r < replace_rate, replace_val, new_vals)
new_vals = jnp.where(~jnp.isnan(old_vals), new_vals, jnp.nan)
return new_vals
@jit
def mutate_add_node(rand_key: Array, nodes: Array, cons: Array, new_node_key: int,
default_bias: float = 0, default_response: float = 1,
default_act: int = 0, default_agg: int = 0) -> Tuple[Array, Array]:
"""
Randomly add a new node from splitting a connection.
:param rand_key:
:param new_node_key:
:param nodes:
:param cons:
:param default_bias:
:param default_response:
:param default_act:
:param default_agg:
:return:
"""
# randomly choose a connection
i_key, o_key, idx = choice_connection_key(rand_key, nodes, cons)
def nothing(): # there is no connection to split
return nodes, cons
def successful_add_node():
# disable the connection
new_nodes, new_cons = nodes, cons
new_cons = new_cons.at[idx, 3].set(False)
# add a new node
new_nodes, new_cons = \
add_node(new_nodes, new_cons, new_node_key,
bias=default_bias, response=default_response, act=default_act, agg=default_agg)
# add two new connections
w = new_cons[idx, 2]
new_nodes, new_cons = add_connection(new_nodes, new_cons, i_key, new_node_key, weight=1, enabled=True)
new_nodes, new_cons = add_connection(new_nodes, new_cons, new_node_key, o_key, weight=w, enabled=True)
return new_nodes, new_cons
# if from_idx == I_INT, that means no connection exist, do nothing
nodes, cons = jax.lax.cond(idx == I_INT, nothing, successful_add_node)
return nodes, cons
# TODO: Need we really need to delete a node?
@jit
def mutate_delete_node(rand_key: Array, nodes: Array, cons: Array,
input_keys: Array, output_keys: Array) -> Tuple[Array, Array]:
"""
Randomly delete a node. Input and output nodes are not allowed to be deleted.
:param rand_key:
:param nodes:
:param cons:
:param input_keys:
:param output_keys:
:return:
"""
# randomly choose a node
node_key, node_idx = choice_node_key(rand_key, nodes, input_keys, output_keys,
allow_input_keys=False, allow_output_keys=False)
def nothing():
return nodes, cons
def successful_delete_node():
# delete the node
aux_nodes, aux_cons = delete_node_by_idx(nodes, cons, node_idx)
# delete all connections
aux_cons = jnp.where(((aux_cons[:, 0] == node_key) | (aux_cons[:, 1] == node_key))[:, jnp.newaxis],
jnp.nan, aux_cons)
return aux_nodes, aux_cons
nodes, cons = jax.lax.cond(node_idx == I_INT, nothing, successful_delete_node)
return nodes, cons
@jit
def mutate_add_connection(rand_key: Array, nodes: Array, cons: Array,
input_keys: Array, output_keys: Array) -> Tuple[Array, Array]:
"""
Randomly add a new connection. The output node is not allowed to be an input node. If in feedforward networks,
cycles are not allowed.
:param rand_key:
:param nodes:
:param cons:
:param input_keys:
:param output_keys:
:return:
"""
# randomly choose two nodes
k1, k2 = jax.random.split(rand_key, num=2)
i_key, from_idx = choice_node_key(k1, nodes, input_keys, output_keys,
allow_input_keys=True, allow_output_keys=True)
o_key, to_idx = choice_node_key(k2, nodes, input_keys, output_keys,
allow_input_keys=False, allow_output_keys=True)
con_idx = fetch_first((cons[:, 0] == i_key) & (cons[:, 1] == o_key))
def successful():
new_nodes, new_cons = add_connection(nodes, cons, i_key, o_key, weight=1, enabled=True)
return new_nodes, new_cons
def already_exist():
new_cons = cons.at[con_idx, 3].set(True)
return nodes, new_cons
def cycle():
return nodes, cons
is_already_exist = con_idx != I_INT
unflattened = unflatten_connections(nodes, cons)
is_cycle = check_cycles(nodes, unflattened, from_idx, to_idx)
choice = jnp.where(is_already_exist, 0, jnp.where(is_cycle, 1, 2))
nodes, cons = jax.lax.switch(choice, [already_exist, cycle, successful])
return nodes, cons
@jit
def mutate_delete_connection(rand_key: Array, nodes: Array, cons: Array):
"""
Randomly delete a connection.
:param rand_key:
:param nodes:
:param cons:
:return:
"""
# randomly choose a connection
i_key, o_key, idx = choice_connection_key(rand_key, nodes, cons)
def nothing():
return nodes, cons
def successfully_delete_connection():
return delete_connection_by_idx(nodes, cons, idx)
nodes, cons = jax.lax.cond(idx == I_INT, nothing, successfully_delete_connection)
return nodes, cons
@partial(jit, static_argnames=('allow_input_keys', 'allow_output_keys'))
def choice_node_key(rand_key: Array, nodes: Array,
input_keys: Array, output_keys: Array,
allow_input_keys: bool = False, allow_output_keys: bool = False) -> Tuple[Array, Array]:
"""
Randomly choose a node key from the given nodes. It guarantees that the chosen node not be the input or output node.
:param rand_key:
:param nodes:
:param input_keys:
:param output_keys:
:param allow_input_keys:
:param allow_output_keys:
:return: return its key and position(idx)
"""
node_keys = nodes[:, 0]
mask = ~jnp.isnan(node_keys)
if not allow_input_keys:
mask = jnp.logical_and(mask, ~jnp.isin(node_keys, input_keys))
if not allow_output_keys:
mask = jnp.logical_and(mask, ~jnp.isin(node_keys, output_keys))
idx = fetch_random(rand_key, mask)
key = jnp.where(idx != I_INT, nodes[idx, 0], jnp.nan)
return key, idx
@jit
def choice_connection_key(rand_key: Array, nodes: Array, cons: Array) -> Tuple[Array, Array, Array]:
"""
Randomly choose a connection key from the given connections.
:param rand_key:
:param nodes:
:param cons:
:return: i_key, o_key, idx
"""
idx = fetch_random(rand_key, ~jnp.isnan(cons[:, 0]))
i_key = jnp.where(idx != I_INT, cons[idx, 0], jnp.nan)
o_key = jnp.where(idx != I_INT, cons[idx, 1], jnp.nan)
return i_key, o_key, idx
@jit
def rand(rand_key):
return jax.random.uniform(rand_key, ())