update HyperNEAT;

All example can currently run!

tensorneat/examples/brax/ant.py

@@ -11,8 +11,8 @@ if __name__ == "__main__":
                 genome=DefaultGenome(
                     num_inputs=27,
                     num_outputs=8,
-                    max_nodes=50,
-                    max_conns=100,
+                    max_nodes=100,
+                    max_conns=200,
                     node_gene=DefaultNodeGene(
                         activation_options=(Act.tanh,),
                         activation_default=Act.tanh,
@@ -21,6 +21,8 @@ if __name__ == "__main__":
                 ),
                 pop_size=1000,
                 species_size=10,
+                compatibility_threshold=3.5,
+                survival_threshold=0.01,
             ),
         ),
         problem=BraxEnv(

tensorneat/examples/brax/half_cheetah.py

@@ -17,6 +17,7 @@ if __name__ == "__main__":
                         activation_options=(Act.tanh,),
                         activation_default=Act.tanh,
                     ),
+                    output_transform=Act.tanh
                 ),
                 pop_size=1000,
                 species_size=10,

tensorneat/examples/brax/reacher.py

@@ -17,6 +17,7 @@ if __name__ == "__main__":
                         activation_options=(Act.tanh,),
                         activation_default=Act.tanh,
                     ),
+                    output_transform=Act.tanh,
                 ),
                 pop_size=100,
                 species_size=10,

tensorneat/examples/brax/walker.py

@@ -17,6 +17,7 @@ if __name__ == "__main__":
                         activation_options=(Act.tanh,),
                         activation_default=Act.tanh,
                     ),
+                    output_transform=Act.tanh
                 ),
                 pop_size=10000,
                 species_size=10,

tensorneat/examples/func_fit/xor3d_hyperneat.py

@@ -9,11 +9,9 @@ if __name__ == "__main__":
     pipeline = Pipeline(
         algorithm=HyperNEAT(
             substrate=FullSubstrate(
-                input_coors=[(-1, -1), (0.333, -1), (-0.333, -1), (1, -1)],
+                input_coors=[(-1, -1), (0.333, -1), (-0.333, -1), (1, -1)],  # 3(XOR3d inputs) + 1(bias)
                 hidden_coors=[
-                    (-1, -0.5),
-                    (0.333, -0.5),
-                    (-0.333, -0.5),
+                    (-1, -0.5), (0.333, -0.5), (-0.333, -0.5),
                     (1, -0.5),
                     (-1, 0),
                     (0.333, 0),
@@ -25,14 +23,14 @@ if __name__ == "__main__":
                     (1, 0.5),
                 ],
                 output_coors=[
-                    (0, 1),
+                    (0, 1),  # one output
                 ],
             ),
             neat=NEAT(
                 species=DefaultSpecies(
                     genome=DefaultGenome(
-                        num_inputs=4,  # [-1, -1, -1, 0]
-                        num_outputs=1,
+                        num_inputs=4,  # [*coor1, *coor2]
+                        num_outputs=1,  # the weight of connection between two coor1 and coor2
                         max_nodes=50,
                         max_conns=100,
                         node_gene=DefaultNodeGene(

tensorneat/examples/gymnax/cartpole_hyperneat.py

@@ -1,53 +1,74 @@
-import jax.numpy as jnp
+import jax
 
-from config import *
 from pipeline import Pipeline
-from algorithm import NEAT
-from algorithm.neat.gene import NormalGene, NormalGeneConfig
-from algorithm.hyperneat import HyperNEAT, NormalSubstrateConfig, NormalSubstrate
-from problem.rl_env import GymNaxConfig, GymNaxEnv
-
-
-def example_conf():
-    return Config(
-        basic=BasicConfig(seed=42, fitness_target=500, pop_size=10000),
-        neat=NeatConfig(
-            inputs=4,
-            outputs=1,
-        ),
-        gene=NormalGeneConfig(
-            activation_default=Act.tanh,
-            activation_options=(Act.tanh,),
-        ),
-        hyperneat=HyperNeatConfig(activation=Act.sigmoid, inputs=4, outputs=2),
-        substrate=NormalSubstrateConfig(
-            input_coors=((-1, -1), (-0.5, -1), (0, -1), (0.5, -1), (1, -1)),
-            hidden_coors=(
-                # (-1, -0.5), (-0.5, -0.5), (0, -0.5), (0.5, -0.5),
-                (1, 0),
-                (-1, 0),
-                (-0.5, 0),
-                (0, 0),
-                (0.5, 0),
-                (1, 0),
-                # (1, 0.5), (-1, 0.5), (-0.5, 0.5), (0, 0.5), (0.5, 0.5), (1, 0.5),
-            ),
-            output_coors=((-1, 1), (1, 1)),
-        ),
-        problem=GymNaxConfig(
-            env_name="CartPole-v1",
-            output_transform=lambda out: jnp.argmax(
-                out
-            ),  # the action of cartpole is {0, 1}
-        ),
-    )
+from algorithm.neat import *
+from algorithm.hyperneat import *
+from utils import Act
 
+from problem.rl_env import GymNaxEnv
 
 if __name__ == "__main__":
-    conf = example_conf()
+    pipeline = Pipeline(
+        algorithm=HyperNEAT(
+            substrate=FullSubstrate(
+                input_coors=[
+                    (-1, -1),
+                    (-0.5, -1),
+                    (0, -1),
+                    (0.5, -1),
+                    (1, -1),
+                ],  # 4(problem inputs) + 1(bias)
+                hidden_coors=[
+                    (-1, -0.5),
+                    (0.333, -0.5),
+                    (-0.333, -0.5),
+                    (1, -0.5),
+                    (-1, 0),
+                    (0.333, 0),
+                    (-0.333, 0),
+                    (1, 0),
+                    (-1, 0.5),
+                    (0.333, 0.5),
+                    (-0.333, 0.5),
+                    (1, 0.5),
+                ],
+                output_coors=[
+                    (-1, 1),
+                    (1, 1),  # one output
+                ],
+            ),
+            neat=NEAT(
+                species=DefaultSpecies(
+                    genome=DefaultGenome(
+                        num_inputs=4,  # [*coor1, *coor2]
+                        num_outputs=1,  # the weight of connection between two coor1 and coor2
+                        max_nodes=50,
+                        max_conns=100,
+                        node_gene=DefaultNodeGene(
+                            activation_default=Act.tanh,
+                            activation_options=(Act.tanh,),
+                        ),
+                        output_transform=Act.tanh,  # the activation function for output node in NEAT
+                    ),
+                    pop_size=10000,
+                    species_size=10,
+                    compatibility_threshold=3.5,
+                    survival_threshold=0.03,
+                ),
+            ),
+            activation=Act.tanh,  # the activation function for output node in HyperNEAT
+            activate_time=10,
+            output_transform=jax.numpy.argmax,  # action of cartpole is in {0, 1}
+        ),
+        problem=GymNaxEnv(
+            env_name="CartPole-v1",
+        ),
+        generation_limit=300,
+        fitness_target=500,
+    )
 
-    algorithm = HyperNEAT(conf, NormalGene, NormalSubstrate)
-    pipeline = Pipeline(conf, algorithm, GymNaxEnv)
+    # initialize state
     state = pipeline.setup()
-    pipeline.pre_compile(state)
+    # print(state)
+    # run until terminate
     state, best = pipeline.auto_run(state)

tensorneat/examples/gymnax/mountain_car.py

@@ -26,7 +26,7 @@ if __name__ == "__main__":
             env_name="MountainCar-v0",
         ),
         generation_limit=10000,
-        fitness_target=0,
+        fitness_target=-86,
     )
 
     # initialize state

tensorneat/examples/gymnax/mountain_car_continuous.py

@@ -17,6 +17,7 @@ if __name__ == "__main__":
                         activation_options=(Act.tanh,),
                         activation_default=Act.tanh,
                     ),
+                    output_transform=Act.tanh
                 ),
                 pop_size=10000,
                 species_size=10,
@@ -26,7 +27,7 @@ if __name__ == "__main__":
             env_name="MountainCarContinuous-v0",
         ),
         generation_limit=10000,
-        fitness_target=500,
+        fitness_target=99,
     )
 
     # initialize state

tensorneat/examples/gymnax/pendulum.py

@@ -17,7 +17,7 @@ if __name__ == "__main__":
                         activation_options=(Act.tanh,),
                         activation_default=Act.tanh,
                     ),
-                    output_transform=lambda out: out
+                    output_transform=lambda out: Act.tanh(out)
                     * 2,  # the action of pendulum is [-2, 2]
                 ),
                 pop_size=10000,
@@ -28,7 +28,7 @@ if __name__ == "__main__":
             env_name="Pendulum-v1",
         ),
         generation_limit=10000,
-        fitness_target=0,
+        fitness_target=-10,
     )
 
     # initialize state

tensorneat/examples/gymnax/reacher.py

@@ -23,7 +23,7 @@ if __name__ == "__main__":
             env_name="Reacher-misc",
         ),
         generation_limit=10000,
-        fitness_target=500,
+        fitness_target=90,
     )
 
     # initialize state