change str in config (act, agg) from str to callable

algorithm/hyperneat/hyperneat.py

@@ -6,7 +6,7 @@ import numpy as np
 
 from config import Config, HyperNeatConfig
 from core import Algorithm, Substrate, State, Genome, Gene
-from utils import Activation, Aggregation
+from utils import Act, Agg
 from .substrate import analysis_substrate
 from algorithm import NEAT
 
@@ -90,10 +90,7 @@ class HyperNEATGene:
 
     @staticmethod
     def forward(config: HyperNeatConfig, state: State, inputs, transformed):
-        act = Activation.name2func[config.activation]
-        agg = Aggregation.name2func[config.aggregation]
-
-        batch_act, batch_agg = jax.vmap(act), jax.vmap(agg)
+        batch_act, batch_agg = jax.vmap(config.activation), jax.vmap(config.aggregation)
 
         nodes, weights = transformed
 

algorithm/neat/gene/normal.py

@@ -6,7 +6,7 @@ from jax import Array, numpy as jnp
 
 from config import GeneConfig
 from core import Gene, Genome, State
-from utils import Activation, Aggregation, unflatten_conns, topological_sort, I_INT, act, agg
+from utils import Act, Agg, unflatten_conns, topological_sort, I_INT, act, agg
 
 
 @dataclass(frozen=True)
@@ -23,12 +23,12 @@ class NormalGeneConfig(GeneConfig):
     response_mutate_rate: float = 0.7
     response_replace_rate: float = 0.1
 
-    activation_default: str = 'sigmoid'
-    activation_options: Tuple = ('sigmoid',)
+    activation_default: callable = Act.sigmoid
+    activation_options: Tuple = (Act.sigmoid, )
     activation_replace_rate: float = 0.1
 
-    aggregation_default: str = 'sum'
-    aggregation_options: Tuple = ('sum',)
+    aggregation_default: callable = Agg.sum
+    aggregation_options: Tuple = (Agg.sum, )
     aggregation_replace_rate: float = 0.1
 
     weight_init_mean: float = 0.0
@@ -49,18 +49,8 @@ class NormalGeneConfig(GeneConfig):
         assert self.response_replace_rate >= 0.0
 
         assert self.activation_default == self.activation_options[0]
-
-        for name in self.activation_options:
-            assert name in Activation.name2func, f"Activation function: {name} not found"
-
         assert self.aggregation_default == self.aggregation_options[0]
 
-        assert self.aggregation_default in Aggregation.name2func, \
-            f"Aggregation function: {self.aggregation_default} not found"
-
-        for name in self.aggregation_options:
-            assert name in Aggregation.name2func, f"Aggregation function: {name} not found"
-
 
 class NormalGene(Gene):
     node_attrs = ['bias', 'response', 'aggregation', 'activation']
@@ -68,8 +58,6 @@ class NormalGene(Gene):
 
     def __init__(self, config: NormalGeneConfig = NormalGeneConfig()):
         self.config = config
-        self.act_funcs = [Activation.name2func[name] for name in config.activation_options]
-        self.agg_funcs = [Aggregation.name2func[name] for name in config.aggregation_options]
 
     def setup(self, state: State = State()):
         return state.update(
@@ -170,9 +158,9 @@ class NormalGene(Gene):
 
             def hit():
                 ins = values * weights[:, i]
-                z = agg(nodes[i, 4], ins, self.agg_funcs)  # z = agg(ins)
+                z = agg(nodes[i, 4], ins, self.config.aggregation_options)  # z = agg(ins)
                 z = z * nodes[i, 2] + nodes[i, 1]  # z = z * response + bias
-                z = act(nodes[i, 3], z, self.act_funcs)  # z = act(z)
+                z = act(nodes[i, 3], z, self.config.activation_options)  # z = act(z)
 
                 new_values = values.at[i].set(z)
                 return new_values

algorithm/neat/gene/recurrent.py

@@ -48,9 +48,9 @@ class RecurrentGene(NormalGene):
         def body_func(i, values):
             values = values.at[input_idx].set(inputs)
             nodes_ins = values * weights.T
-            values = batch_agg(nodes[:, 4], nodes_ins, self.agg_funcs)  # z = agg(ins)
+            values = batch_agg(nodes[:, 4], nodes_ins, self.config.aggregation_options)  # z = agg(ins)
             values = values * nodes[:, 2] + nodes[:, 1]  # z = z * response + bias
-            values = batch_act(nodes[:, 3], values, self.act_funcs)  # z = act(z)
+            values = batch_act(nodes[:, 3], values, self.config.activation_options)  # z = act(z)
             return values
 
         vals = jax.lax.fori_loop(0, self.config.activate_times, body_func, vals)

config/config.py

@@ -1,5 +1,5 @@
 from dataclasses import dataclass
-
+from utils import Act, Agg
 
 @dataclass(frozen=True)
 class BasicConfig:
@@ -68,8 +68,8 @@ class NeatConfig:
 class HyperNeatConfig:
     below_threshold: float = 0.2
     max_weight: float = 3
-    activation: str = "sigmoid"
-    aggregation: str = "sum"
+    activation: callable = Act.sigmoid
+    aggregation: callable = Agg.sum
     activate_times: int = 5
     inputs: int = 2
     outputs: int = 1

examples/func_fit/xor_hyperneat.py

@@ -3,6 +3,7 @@ from pipeline import Pipeline
 from algorithm.neat import NormalGene, NormalGeneConfig
 from algorithm.hyperneat import HyperNEAT, NormalSubstrate, NormalSubstrateConfig
 from problem.func_fit import XOR3d, FuncFitConfig
+from utils import Act
 
 
 if __name__ == '__main__':
@@ -27,8 +28,8 @@ if __name__ == '__main__':
             input_coors=((-1, -1), (-0.5, -1), (0.5, -1), (1, -1)),
         ),
         gene=NormalGeneConfig(
-            activation_default='tanh',
-            activation_options=('tanh', ),
+            activation_default=Act.tanh,
+            activation_options=(Act.tanh, ),
         ),
         problem=FuncFitConfig()
     )

examples/func_fit/xor_recurrent.py

@@ -36,5 +36,6 @@ if __name__ == '__main__':
     algorithm = NEAT(config, RecurrentGene)
     pipeline = Pipeline(config, algorithm, XOR3d)
     state = pipeline.setup()
+    pipeline.pre_compile(state)
     state, best = pipeline.auto_run(state)
     pipeline.show(state, best)

examples/gymnax/cartpole.py

@@ -19,8 +19,8 @@ def example_conf1():
             outputs=1,
         ),
         gene=NormalGeneConfig(
-            activation_default='sigmoid',
-            activation_options=('sigmoid',),
+            activation_default=Act.sigmoid,
+            activation_options=(Act.sigmoid,),
         ),
         problem=GymNaxConfig(
             env_name='CartPole-v1',
@@ -41,8 +41,8 @@ def example_conf2():
             outputs=1,
         ),
         gene=NormalGeneConfig(
-            activation_default='tanh',
-            activation_options=('tanh',),
+            activation_default=Act.tanh,
+            activation_options=(Act.tanh,),
         ),
         problem=GymNaxConfig(
             env_name='CartPole-v1',
@@ -63,8 +63,8 @@ def example_conf3():
             outputs=2,
         ),
         gene=NormalGeneConfig(
-            activation_default='tanh',
-            activation_options=('tanh',),
+            activation_default=Act.tanh,
+            activation_options=(Act.tanh,),
         ),
         problem=GymNaxConfig(
             env_name='CartPole-v1',
@@ -80,5 +80,5 @@ if __name__ == '__main__':
     algorithm = NEAT(conf, NormalGene)
     pipeline = Pipeline(conf, algorithm, GymNaxEnv)
     state = pipeline.setup()
+    pipeline.pre_compile(state)
     state, best = pipeline.auto_run(state)
-    pipeline.show(state, best)

utils/__init__.py

@@ -1,35 +1,4 @@
-from .activation import Activation, act
-from .aggregation import Aggregation, agg
+from .activation import Act, act
+from .aggregation import Agg, agg
 from .tools import *
 from .graph import *
-
-Activation.name2func = {
-    'sigmoid': Activation.sigmoid_act,
-    'tanh': Activation.tanh_act,
-    'sin': Activation.sin_act,
-    'gauss': Activation.gauss_act,
-    'relu': Activation.relu_act,
-    'elu': Activation.elu_act,
-    'lelu': Activation.lelu_act,
-    'selu': Activation.selu_act,
-    'softplus': Activation.softplus_act,
-    'identity': Activation.identity_act,
-    'clamped': Activation.clamped_act,
-    'inv': Activation.inv_act,
-    'log': Activation.log_act,
-    'exp': Activation.exp_act,
-    'abs': Activation.abs_act,
-    'hat': Activation.hat_act,
-    'square': Activation.square_act,
-    'cube': Activation.cube_act,
-}
-
-Aggregation.name2func = {
-    'sum': Aggregation.sum_agg,
-    'product': Aggregation.product_agg,
-    'max': Aggregation.max_agg,
-    'min': Aggregation.min_agg,
-    'maxabs': Aggregation.maxabs_agg,
-    'median': Aggregation.median_agg,
-    'mean': Aggregation.mean_agg,
-}

utils/activation.py

@@ -2,90 +2,89 @@ import jax
 import jax.numpy as jnp
 
 
-class Activation:
-    name2func = {}
+class Act:
 
     @staticmethod
-    def sigmoid_act(z):
+    def sigmoid(z):
         z = jnp.clip(z * 5, -60, 60)
         return 1 / (1 + jnp.exp(-z))
 
     @staticmethod
-    def tanh_act(z):
+    def tanh(z):
         z = jnp.clip(z * 2.5, -60, 60)
         return jnp.tanh(z)
 
     @staticmethod
-    def sin_act(z):
+    def sin(z):
         z = jnp.clip(z * 5, -60, 60)
         return jnp.sin(z)
 
     @staticmethod
-    def gauss_act(z):
+    def gauss(z):
         z = jnp.clip(z * 5, -3.4, 3.4)
         return jnp.exp(-z ** 2)
 
     @staticmethod
-    def relu_act(z):
+    def relu(z):
         return jnp.maximum(z, 0)
 
     @staticmethod
-    def elu_act(z):
+    def elu(z):
         return jnp.where(z > 0, z, jnp.exp(z) - 1)
 
     @staticmethod
-    def lelu_act(z):
+    def lelu(z):
         leaky = 0.005
         return jnp.where(z > 0, z, leaky * z)
 
     @staticmethod
-    def selu_act(z):
+    def selu(z):
         lam = 1.0507009873554804934193349852946
         alpha = 1.6732632423543772848170429916717
         return jnp.where(z > 0, lam * z, lam * alpha * (jnp.exp(z) - 1))
 
     @staticmethod
-    def softplus_act(z):
+    def softplus(z):
         z = jnp.clip(z * 5, -60, 60)
         return 0.2 * jnp.log(1 + jnp.exp(z))
 
     @staticmethod
-    def identity_act(z):
+    def identity(z):
         return z
 
     @staticmethod
-    def clamped_act(z):
+    def clamped(z):
         return jnp.clip(z, -1, 1)
 
     @staticmethod
-    def inv_act(z):
+    def inv(z):
         z = jnp.maximum(z, 1e-7)
         return 1 / z
 
     @staticmethod
-    def log_act(z):
+    def log(z):
         z = jnp.maximum(z, 1e-7)
         return jnp.log(z)
 
     @staticmethod
-    def exp_act(z):
+    def exp(z):
         z = jnp.clip(z, -60, 60)
         return jnp.exp(z)
 
     @staticmethod
-    def abs_act(z):
+    def abs(z):
         return jnp.abs(z)
 
     @staticmethod
-    def hat_act(z):
+    def hat(z):
         return jnp.maximum(0, 1 - jnp.abs(z))
 
     @staticmethod
-    def square_act(z):
+    def square(z):
         return z ** 2
 
     @staticmethod
-    def cube_act(z):
+    def cube(z):
         return z ** 3
 
 

utils/aggregation.py

@@ -2,38 +2,37 @@ import jax
 import jax.numpy as jnp
 
 
-class Aggregation:
-    name2func = {}
+class Agg:
 
     @staticmethod
-    def sum_agg(z):
+    def sum(z):
         z = jnp.where(jnp.isnan(z), 0, z)
         return jnp.sum(z, axis=0)
 
     @staticmethod
-    def product_agg(z):
+    def product(z):
         z = jnp.where(jnp.isnan(z), 1, z)
         return jnp.prod(z, axis=0)
 
     @staticmethod
-    def max_agg(z):
+    def max(z):
         z = jnp.where(jnp.isnan(z), -jnp.inf, z)
         return jnp.max(z, axis=0)
 
     @staticmethod
-    def min_agg(z):
+    def min(z):
         z = jnp.where(jnp.isnan(z), jnp.inf, z)
         return jnp.min(z, axis=0)
 
     @staticmethod
-    def maxabs_agg(z):
+    def maxabs(z):
         z = jnp.where(jnp.isnan(z), 0, z)
         abs_z = jnp.abs(z)
         max_abs_index = jnp.argmax(abs_z)
         return z[max_abs_index]
 
     @staticmethod
-    def median_agg(z):
+    def median(z):
         n = jnp.sum(~jnp.isnan(z), axis=0)
 
         z = jnp.sort(z)  # sort
@@ -44,7 +43,7 @@ class Aggregation:
         return median
 
     @staticmethod
-    def mean_agg(z):
+    def mean(z):
         aux = jnp.where(jnp.isnan(z), 0, z)
         valid_values_sum = jnp.sum(aux, axis=0)
         valid_values_count = jnp.sum(~jnp.isnan(z), axis=0)