create function "distance_numpy", serve as o2o distance function

algorithms/neat/genome/distance.py

@@ -1,5 +1,7 @@
 from jax import jit, vmap, Array
 from jax import numpy as jnp
+import numpy as np
+from numpy.typing import NDArray
 
 from .utils import flatten_connections, EMPTY_NODE, EMPTY_CON
 
@@ -14,7 +16,11 @@ def create_distance_function(config, type: str):
     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)
+            distance_numpy(nodes1, connections1, nodes2, connections2, disjoint_coe, compatibility_coe)
+
+        # 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: \
@@ -23,6 +29,89 @@ def create_distance_function(config, type: str):
         raise ValueError(f'unknown distance type: {type}, should be one of ["o2o", "o2m"]')
 
 
+def distance_numpy(nodes1: NDArray, connection1: NDArray, nodes2: NDArray,
+                   connection2: NDArray, disjoint_coe: float = 1., compatibility_coe: float = 0.5):
+    """
+    use in o2o distance.
+    o2o can't use vmap, numpy should be faster than jax function
+    :param nodes1:
+    :param connection1:
+    :param nodes2:
+    :param connection2:
+    :param disjoint_coe:
+    :param compatibility_coe:
+    :return:
+    """
+    def analysis(nodes, connections):
+        nodes_dict = {}
+        idx2key = {}
+        for i, node in enumerate(nodes):
+            if np.isnan(node[0]):
+                continue
+            key = int(node[0])
+            nodes_dict[key] = (node[1], node[2], node[3], node[4])
+            idx2key[i] = key
+
+        connections_dict = {}
+        for i in range(connections.shape[1]):
+            for j in range(connections.shape[2]):
+                if np.isnan(connections[0, i, j]) and np.isnan(connections[1, i, j]):
+                    continue
+                key = (idx2key[i], idx2key[j])
+
+                weight = connections[0, i, j] if not np.isnan(connections[0, i, j]) else None
+                enabled = (connections[1, i, j] == 1) if not np.isnan(connections[1, i, j]) else None
+                connections_dict[key] = (weight, enabled)
+
+        return nodes_dict, connections_dict
+
+    nodes1, connections1 = analysis(nodes1, connection1)
+    nodes2, connections2 = analysis(nodes2, connection2)
+
+    nd = 0.0
+    if nodes1 or nodes2:  # otherwise, both are empty
+        disjoint_nodes = 0
+        for k2 in nodes2:
+            if k2 not in nodes1:
+                disjoint_nodes += 1
+
+        for k1, n1 in nodes1.items():
+            n2 = nodes2.get(k1)
+            if n2 is None:
+                disjoint_nodes += 1
+            else:
+                if np.isnan(n1[0]):  # n1[1] is nan means input nodes
+                    continue
+                d = abs(n1[0] - n2[0]) + abs(n1[1] - n2[1])
+                d += 1 if n1[2] != n2[2] else 0
+                d += 1 if n1[3] != n2[3] else 0
+                nd += d
+
+        max_nodes = max(len(nodes1), len(nodes2))
+        nd = (compatibility_coe * nd + disjoint_coe * disjoint_nodes) / max_nodes
+
+    cd = 0.0
+    if connections1 or connections2:
+        disjoint_connections = 0
+        for k2 in connections2:
+            if k2 not in connections1:
+                disjoint_connections += 1
+
+        for k1, c1 in connections1.items():
+            c2 = connections2.get(k1)
+            if c2 is None:
+                disjoint_connections += 1
+            else:
+                # Homologous genes compute their own distance value.
+                d = abs(c1[0] - c2[0])
+                d += 1 if c1[1] != c2[1] else 0
+                cd += d
+        max_conn = max(len(connections1), len(connections2))
+        cd = (compatibility_coe * cd + disjoint_coe * disjoint_connections) / max_conn
+
+    return nd + cd
+
+
 @jit
 def distance(nodes1: Array, connections1: Array, nodes2: Array, connections2: Array, disjoint_coe: float = 1.,
              compatibility_coe: float = 0.5) -> Array:
@@ -46,7 +135,7 @@ def distance(nodes1: Array, connections1: Array, nodes2: Array, connections2: Ar
 def node_distance(nodes1, nodes2, disjoint_coe=1., compatibility_coe=0.5):
     node_cnt1 = jnp.sum(~jnp.isnan(nodes1[:, 0]))
     node_cnt2 = jnp.sum(~jnp.isnan(nodes2[:, 0]))
-    max_cnt = jnp.maximum(node_cnt1, node_cnt2) - 2
+    max_cnt = jnp.maximum(node_cnt1, node_cnt2)
 
     nodes = jnp.concatenate((nodes1, nodes2), axis=0)
     keys = nodes[:, 0]

examples/xor.py

@@ -23,8 +23,8 @@ def evaluate(forward_func: Callable) -> List[float]:
     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

@@ -9,8 +9,8 @@
         "population": {
             "fitness_criterion": "max",
             "fitness_threshold": 76,
-            "generation_limit": 1000,
-            "pop_size": 200,
+            "generation_limit": 100,
+            "pop_size": 1000,
             "reset_on_extinction": "False"
         },
         "gene": {