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update recurrent genome

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root
2024-07-10 16:27:49 +08:00
parent 1d606eb1c3
commit 649d4b0552
8 changed files with 490 additions and 46 deletions
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15
examples/tmp.py
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import jax, jax.numpy as jnp
from tensorneat.algorithm import NEAT
from tensorneat.algorithm.neat import DefaultGenome
from tensorneat.algorithm.neat import DefaultGenome, RecurrentGenome
key = jax.random.key(0)
genome = DefaultGenome(num_inputs=5, num_outputs=3, max_nodes=100, max_conns=500, init_hidden_layers=())
genome = DefaultGenome(num_inputs=5, num_outputs=3, max_nodes=100, max_conns=500, init_hidden_layers=(1, 2 ,3))
state = genome.setup()
nodes, conns = genome.initialize(state, key)
print(genome.repr(state, nodes, conns))
inputs = jnp.array([1, 2, 3, 4, 5])
transformed = genome.transform(state, nodes, conns)
outputs = genome.forward(state, transformed, inputs)
print(outputs)
network = genome.network_dict(state, nodes, conns)
print(network)
genome.visualize(network)

16
examples/tmp2.py Normal file
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import jax, jax.numpy as jnp
arr = jnp.ones((10, 10))
a = jnp.array([
[1, 2, 3],
[4, 5, 6]
])
def attach_with_inf(arr, idx):
target_dim = arr.ndim + idx.ndim - 1
expand_idx = jnp.expand_dims(idx, axis=tuple(range(idx.ndim, target_dim)))
return jnp.where(expand_idx == 1, jnp.nan, arr[idx])
b = attach_with_inf(arr, a)
print(b)

415
network.svg Normal file
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Side by Side

After

Width:  |  Height:  |  Size: 18 KiB

3
tensorneat/algorithm/neat/gene/base.py
View File

@@ -34,9 +34,6 @@ class BaseGene(StatefulBaseClass):
def forward(self, state, attrs, inputs):
raise NotImplementedError
def update_by_batch(self, state, attrs, batch_inputs):
raise NotImplementedError
@property
def length(self):
return len(self.fixed_attrs) + len(self.custom_attrs)

2
tensorneat/algorithm/neat/genome/base.py
View File

@@ -64,7 +64,7 @@ class BaseGenome(StatefulBaseClass):
all_init_conns_in_idx.append(in_idx)
all_init_conns_out_idx.append(out_idx)
all_init_nodes.extend(in_layer)
all_init_nodes.extend(layer_indices[-1])
all_init_nodes.extend(layer_indices[-1]) # output layer
if max_nodes < len(all_init_nodes):
raise ValueError(

15
tensorneat/algorithm/neat/genome/default.py
View File

@@ -78,31 +78,34 @@ class DefaultGenome(BaseGenome):
def cond_fun(carry):
values, idx = carry
return (idx < self.max_nodes) & (cal_seqs[idx] != I_INF)
return (idx < self.max_nodes) & (
cal_seqs[idx] != I_INF
) # not out of bounds and next node exists
def body_func(carry):
values, idx = carry
i = cal_seqs[idx]
def input_node():
z = self.node_gene.input_transform(state, nodes_attrs[i], values[i])
new_values = values.at[i].set(z)
return new_values
return values
def otherwise():
# calculate connections
conn_indices = u_conns[:, i]
hit_attrs = attach_with_inf(conns_attrs, conn_indices)
hit_attrs = attach_with_inf(conns_attrs, conn_indices) # fetch conn attrs
ins = vmap(self.conn_gene.forward, in_axes=(None, 0, 0))(
state, hit_attrs, values
)
# calculate nodes
z = self.node_gene.forward(
state,
nodes_attrs[i],
ins,
is_output_node=jnp.isin(i, self.output_idx),
is_output_node=jnp.isin(nodes[0], self.output_idx), # nodes[0] -> the key of nodes
)
# set new value
new_values = values.at[i].set(z)
return new_values

57
tensorneat/algorithm/neat/genome/recurrent.py
View File

@@ -1,12 +1,13 @@
from typing import Callable
import jax, jax.numpy as jnp
import jax
from jax import vmap, numpy as jnp
from .utils import unflatten_conns
from . import BaseGenome
from .base import BaseGenome
from .operations import DefaultMutation, DefaultCrossover, DefaultDistance
from .utils import unflatten_conns, extract_node_attrs, extract_conn_attrs
from ..gene import DefaultNodeGene, DefaultConnGene
from .operations import DefaultMutation, DefaultCrossover
from tensorneat.common import attach_with_inf
class RecurrentGenome(BaseGenome):
"""Default genome class, with the same behavior as the NEAT-Python"""
@@ -17,14 +18,17 @@ class RecurrentGenome(BaseGenome):
self,
num_inputs: int,
num_outputs: int,
max_nodes = 50,
max_conns = 100,
max_nodes=50,
max_conns=100,
node_gene=DefaultNodeGene(),
conn_gene=DefaultConnGene(),
mutation=DefaultMutation(),
crossover=DefaultCrossover(),
distance=DefaultDistance(),
output_transform=None,
input_transform=None,
init_hidden_layers=(),
activate_time=10,
output_transform: Callable = None,
):
super().__init__(
num_inputs,
@@ -35,29 +39,25 @@ class RecurrentGenome(BaseGenome):
conn_gene,
mutation,
crossover,
distance,
output_transform,
input_transform,
init_hidden_layers,
)
self.activate_time = activate_time
if output_transform is not None:
try:
_ = output_transform(jnp.zeros(num_outputs))
except Exception as e:
raise ValueError(f"Output transform function failed: {e}")
self.output_transform = output_transform
def transform(self, state, nodes, conns):
u_conns = unflatten_conns(nodes, conns)
return nodes, conns, u_conns
def restore(self, state, transformed):
def forward(self, state, transformed, inputs):
nodes, conns, u_conns = transformed
return nodes, conns
def forward(self, state, inputs, transformed):
nodes, conns = transformed
vals = jnp.full((self.max_nodes,), jnp.nan)
nodes_attrs = nodes[:, 1:] # remove index
nodes_attrs = vmap(extract_node_attrs)(nodes)
conns_attrs = vmap(extract_conn_attrs)(conns)
expand_conns_attrs = attach_with_inf(conns_attrs, u_conns)
def body_func(_, values):
@@ -65,14 +65,14 @@ class RecurrentGenome(BaseGenome):
values = values.at[self.input_idx].set(inputs)
# calculate connections
node_ins = jax.vmap(
jax.vmap(self.conn_gene.forward, in_axes=(None, 1, None)),
in_axes=(None, 1, 0),
)(state, conns, values)
node_ins = vmap(
vmap(self.conn_gene.forward, in_axes=(None, 0, None)),
in_axes=(None, 0, 0),
)(state, expand_conns_attrs, values)
# calculate nodes
is_output_nodes = jnp.isin(jnp.arange(self.max_nodes), self.output_idx)
values = jax.vmap(self.node_gene.forward, in_axes=(None, 0, 0, 0))(
is_output_nodes = jnp.isin(nodes[:, 0], self.output_idx)
values = vmap(self.node_gene.forward, in_axes=(None, 0, 0, 0))(
state, nodes_attrs, node_ins.T, is_output_nodes
)
@@ -87,3 +87,6 @@ class RecurrentGenome(BaseGenome):
def sympy_func(self, state, network, precision=3):
raise ValueError("Sympy function is not supported for Recurrent Network!")
def visualize(self, network):
raise ValueError("Visualize function is not supported for Recurrent Network!")

9
tensorneat/common/tools.py
View File

@@ -6,12 +6,11 @@ from jax import numpy as jnp, Array, jit, vmap
I_INF = np.iinfo(jnp.int32).max # infinite int
# TODO: strange implementation
def attach_with_inf(arr, idx):
expand_size = arr.ndim - idx.ndim
expand_idx = jnp.expand_dims(
idx, axis=tuple(range(idx.ndim, expand_size + idx.ndim))
)
target_dim = arr.ndim + idx.ndim - 1
expand_idx = jnp.expand_dims(idx, axis=tuple(range(idx.ndim, target_dim)))
return jnp.where(expand_idx == I_INF, jnp.nan, arr[idx])