add method 'create_crossover_function' and 'create_distance_function'

algorithms/neat/genome/__init__.py

@@ -1,5 +1,5 @@
 from .genome import create_initialize_function, expand, expand_single, pop_analysis
-from .distance import distance
+from .distance import create_distance_function
 from .mutate import create_mutate_function
 from .forward import create_forward_function
-from .crossover import batch_crossover
+from .crossover import create_crossover_function

algorithms/neat/genome/crossover.py

@@ -8,6 +8,13 @@ from jax import numpy as jnp
 from .utils import flatten_connections, unflatten_connections
 
 
+def create_crossover_function(batch: bool):
+    if batch:
+        return batch_crossover
+    else:
+        return crossover
+
+
 @vmap
 def batch_crossover(randkeys: Array, batch_nodes1: Array, batch_connections1: Array, batch_nodes2: Array,
                     batch_connections2: Array) -> Tuple[Array, Array]:

algorithms/neat/genome/distance.py

@@ -4,21 +4,41 @@ from jax import numpy as jnp
 from .utils import flatten_connections, EMPTY_NODE, EMPTY_CON
 
 
+def create_distance_function(config, type: str):
+    """
+    :param config:
+    :param type: {'o2o', 'o2m'}, for one-to-one or one-to-many distance calculation
+    :return:
+    """
+    disjoint_coe = config.neat.genome.compatibility_disjoint_coefficient
+    compatibility_coe = config.neat.genome.compatibility_weight_coefficient
+    if type == 'o2o':
+        return lambda nodes1, connections1, nodes2, connections2: \
+            distance(nodes1, connections1, nodes2, connections2, disjoint_coe, compatibility_coe)
+    elif type == 'o2m':
+        func = vmap(distance, in_axes=(None, None, 0, 0, None, None))
+        return lambda nodes1, connections1, batch_nodes2, batch_connections2: \
+            func(nodes1, connections1, batch_nodes2, batch_connections2, disjoint_coe, compatibility_coe)
+    else:
+        raise ValueError(f'unknown distance type: {type}, should be one of ["o2o", "o2m"]')
+
+
 @jit
-def distance(nodes1: Array, connections1: Array, nodes2: Array, connections2: Array) -> Array:
+def distance(nodes1: Array, connections1: Array, nodes2: Array, connections2: Array, disjoint_coe: float = 1.,
+             compatibility_coe: float = 0.5) -> Array:
     """
     Calculate the distance between two genomes.
     nodes are a 2-d array with shape (N, 5), its columns are [key, bias, response, act, agg]
     connections are a 3-d array with shape (2, N, N), axis 0 means [weights, enable]
     """
 
-    nd = node_distance(nodes1, nodes2)  # node distance
+    nd = node_distance(nodes1, nodes2, disjoint_coe, compatibility_coe)  # node distance
 
     # refactor connections
     keys1, keys2 = nodes1[:, 0], nodes2[:, 0]
     cons1 = flatten_connections(keys1, connections1)
     cons2 = flatten_connections(keys2, connections2)
-    cd = connection_distance(cons1, cons2)  # connection distance
+    cd = connection_distance(cons1, cons2, disjoint_coe, compatibility_coe)  # connection distance
     return nd + cd
 
 

algorithms/neat/pipeline.py

@@ -6,7 +6,7 @@ import numpy as np
 
 from .species import SpeciesController
 from .genome import create_initialize_function, create_mutate_function, create_forward_function
-from .genome import batch_crossover
+from .genome import create_crossover_function
 from .genome import expand, expand_single
 
 
@@ -27,6 +27,7 @@ class Pipeline:
         self.initialize_func = create_initialize_function(config)
         self.pop_nodes, self.pop_connections, self.input_idx, self.output_idx = self.initialize_func()
         self.mutate_func = create_mutate_function(config, self.input_idx, self.output_idx, batch=True)
+        self.crossover_func = create_crossover_function(batch=True)
 
         self.generation = 0
 
@@ -102,7 +103,7 @@ class Pipeline:
         wpc = self.pop_connections[crossover_pair[:, 0]]  # winner pop connections
         lpn = self.pop_nodes[crossover_pair[:, 1]]  # loser pop nodes
         lpc = self.pop_connections[crossover_pair[:, 1]]  # loser pop connections
-        npn, npc = batch_crossover(crossover_rand_keys, wpn, wpc, lpn, lpc)  # new pop nodes, new pop connections
+        npn, npc = self.crossover_func(crossover_rand_keys, wpn, wpc, lpn, lpc)  # new pop nodes, new pop connections
 
         # mutate
         mutate_rand_keys = jax.random.split(k2, self.pop_size)

algorithms/neat/species.py

@@ -5,7 +5,7 @@ import jax
 import numpy as np
 from numpy.typing import NDArray
 
-from .genome import distance
+from .genome import create_distance_function
 
 
 class Species(object):
@@ -47,8 +47,8 @@ class SpeciesController:
         self.species_idxer = count(0)
         self.species: Dict[int, Species] = {}  # species_id -> species
 
-        self.distance = distance
-        self.o2m_distance = jax.vmap(distance, in_axes=(None, None, 0, 0))
+        self.o2o_distance = create_distance_function(self.config, type='o2o')
+        self.o2m_distance = create_distance_function(self.config, type='o2m')
 
     def speciate(self, pop_nodes: NDArray, pop_connections: NDArray, generation: int) -> None:
         """
@@ -106,7 +106,7 @@ class SpeciesController:
                 # the representatives of new species
                 sid, rid = list(zip(*[(k, v) for k, v in new_representatives.items()]))
                 distances = [
-                    self.distance(pop_nodes[i], pop_connections[i], pop_nodes[r], pop_connections[r])
+                    self.o2o_distance(pop_nodes[i], pop_connections[i], pop_nodes[r], pop_connections[r])
                     for r in rid
                 ]
                 distances = np.array(distances)

examples/xor.py

@@ -1,6 +1,7 @@
 from typing import Callable, List
 from functools import partial
 
+import jax
 import numpy as np
 
 from utils import Configer
@@ -17,12 +18,13 @@ def evaluate(forward_func: Callable) -> List[float]:
     :return:
     """
     outs = forward_func(xor_inputs)
+    outs = jax.device_get(outs)
     fitnesses = 4 - np.sum((outs - xor_outputs) ** 2, axis=(1, 2))
     return fitnesses.tolist()  # returns a list
 
 
-# @using_cprofile
-@partial(using_cprofile, root_abs_path='/mnt/e/neat-jax/', replace_pattern="/mnt/e/neat-jax/")
+@using_cprofile
+# @partial(using_cprofile, root_abs_path='/mnt/e/neat-jax/', replace_pattern="/mnt/e/neat-jax/")
 def main():
     config = Configer.load_config()
     pipeline = Pipeline(config, seed=11323)

utils/default_config.json

@@ -9,7 +9,7 @@
         "population": {
             "fitness_criterion": "max",
             "fitness_threshold": 76,
-            "generation_limit": 1000,
+            "generation_limit": 100,
             "pop_size": 100,
             "reset_on_extinction": "False"
         },