create function_factory.py, use to manage functions

algorithms/neat/function_factory.py

@@ -0,0 +1,215 @@
+"""
+Lowers, compiles, and creates functions used in the NEAT pipeline.
+"""
+from functools import partial
+
+import numpy as np
+from jax import jit, vmap
+
+from .genome import act_name2key, agg_name2key
+from .genome.genome import initialize_genomes
+from .genome.mutate import mutate
+from .genome.distance import distance
+from .genome.crossover import crossover
+
+
+class FunctionFactory:
+    def __init__(self, config, debug=False):
+        self.config = config
+        self.debug = debug
+
+        self.init_N = config.basic.init_maximum_nodes
+        self.expand_coe = config.basic.expands_coe
+        self.precompile_times = config.basic.pre_compile_times
+        self.compiled_function = {}
+
+        self.load_config_vals(config)
+        self.precompile()
+        pass
+
+    def load_config_vals(self, config):
+        self.pop_size = config.neat.population.pop_size
+        self.init_N = config.basic.init_maximum_nodes
+
+        self.disjoint_coe = config.neat.genome.compatibility_disjoint_coefficient
+        self.compatibility_coe = config.neat.genome.compatibility_weight_coefficient
+
+        self.num_inputs = config.basic.num_inputs
+        self.num_outputs = config.basic.num_outputs
+        self.input_idx = np.arange(self.num_inputs)
+        self.output_idx = np.arange(self.num_inputs, self.num_inputs + self.num_outputs)
+
+        bias = config.neat.gene.bias
+        self.bias_mean = bias.init_mean
+        self.bias_std = bias.init_stdev
+        self.bias_mutate_strength = bias.mutate_power
+        self.bias_mutate_rate = bias.mutate_rate
+        self.bias_replace_rate = bias.replace_rate
+
+        response = config.neat.gene.response
+        self.response_mean = response.init_mean
+        self.response_std = response.init_stdev
+        self.response_mutate_strength = response.mutate_power
+        self.response_mutate_rate = response.mutate_rate
+        self.response_replace_rate = response.replace_rate
+
+        weight = config.neat.gene.weight
+        self.weight_mean = weight.init_mean
+        self.weight_std = weight.init_stdev
+        self.weight_mutate_strength = weight.mutate_power
+        self.weight_mutate_rate = weight.mutate_rate
+        self.weight_replace_rate = weight.replace_rate
+
+        activation = config.neat.gene.activation
+        self.act_default = act_name2key[activation.default]
+        self.act_list = np.array([act_name2key[name] for name in activation.options])
+        self.act_replace_rate = activation.mutate_rate
+
+        aggregation = config.neat.gene.aggregation
+        self.agg_default = agg_name2key[aggregation.default]
+        self.agg_list = np.array([agg_name2key[name] for name in aggregation.options])
+        self.agg_replace_rate = aggregation.mutate_rate
+
+        enabled = config.neat.gene.enabled
+        self.enabled_reverse_rate = enabled.mutate_rate
+
+        genome = config.neat.genome
+        self.add_node_rate = genome.node_add_prob
+        self.delete_node_rate = genome.node_delete_prob
+        self.add_connection_rate = genome.conn_add_prob
+        self.delete_connection_rate = genome.conn_delete_prob
+        self.single_structure_mutate = genome.single_structural_mutation
+
+    def create_initialize(self):
+        func = partial(
+            initialize_genomes,
+            pop_size=self.pop_size,
+            N=self.init_N,
+            num_inputs=self.num_inputs,
+            num_outputs=self.num_outputs,
+            default_bias=self.bias_mean,
+            default_response=self.response_mean,
+            default_act=self.act_default,
+            default_agg=self.agg_default,
+            default_weight=self.weight_mean
+        )
+        if self.debug:
+            return lambda *args: func(*args)
+        else:
+            return func
+
+    def precompile(self):
+        self.create_mutate_with_args()
+        self.create_distance_with_args()
+        self.create_crossover_with_args()
+        n = self.init_N
+        print("start precompile")
+        for _ in range(self.precompile_times):
+            self.compile_mutate(n)
+            self.compile_distance(n)
+            self.compile_crossover(n)
+            n = int(self.expand_coe * n)
+        print("end precompile")
+
+    def create_mutate_with_args(self):
+        func = partial(
+            mutate,
+            input_idx=self.input_idx,
+            output_idx=self.output_idx,
+            bias_mean=self.bias_mean,
+            bias_std=self.bias_std,
+            bias_mutate_strength=self.bias_mutate_strength,
+            bias_mutate_rate=self.bias_mutate_rate,
+            bias_replace_rate=self.bias_replace_rate,
+            response_mean=self.response_mean,
+            response_std=self.response_std,
+            response_mutate_strength=self.response_mutate_strength,
+            response_mutate_rate=self.response_mutate_rate,
+            response_replace_rate=self.response_replace_rate,
+            weight_mean=self.weight_mean,
+            weight_std=self.weight_std,
+            weight_mutate_strength=self.weight_mutate_strength,
+            weight_mutate_rate=self.weight_mutate_rate,
+            weight_replace_rate=self.weight_replace_rate,
+            act_default=self.act_default,
+            act_list=self.act_list,
+            act_replace_rate=self.act_replace_rate,
+            agg_default=self.agg_default,
+            agg_list=self.agg_list,
+            agg_replace_rate=self.agg_replace_rate,
+            enabled_reverse_rate=self.enabled_reverse_rate,
+            add_node_rate=self.add_node_rate,
+            delete_node_rate=self.delete_node_rate,
+            add_connection_rate=self.add_connection_rate,
+            delete_connection_rate=self.delete_connection_rate,
+            single_structure_mutate=self.single_structure_mutate
+        )
+        self.mutate_with_args = func
+
+    def compile_mutate(self, n):
+        func = self.mutate_with_args
+        rand_key_lower = np.zeros((self.pop_size, 2), dtype=np.uint32)
+        nodes_lower = np.zeros((self.pop_size, n, 5))
+        connections_lower = np.zeros((self.pop_size, 2, n, n))
+        new_node_key_lower = np.zeros((self.pop_size,), dtype=np.int32)
+        batched_mutate_func = jit(vmap(func)).lower(rand_key_lower, nodes_lower,
+                                                    connections_lower, new_node_key_lower).compile()
+        self.compiled_function[('mutate', n)] = batched_mutate_func
+
+    def create_mutate(self, n):
+        key = ('mutate', n)
+        if key not in self.compiled_function:
+            self.compile_mutate(n)
+        return self.compiled_function[key]
+
+    def create_distance_with_args(self):
+        func = partial(
+            distance,
+            disjoint_coe=self.disjoint_coe,
+            compatibility_coe=self.compatibility_coe
+        )
+        self.distance_with_args = func
+
+    def compile_distance(self, n):
+        func = self.distance_with_args
+        o2o_nodes1_lower = np.zeros((n, 5))
+        o2o_connections1_lower = np.zeros((2, n, n))
+        o2o_nodes2_lower = np.zeros((n, 5))
+        o2o_connections2_lower = np.zeros((2, n, n))
+        o2o_distance = jit(func).lower(o2o_nodes1_lower, o2o_connections1_lower,
+                                       o2o_nodes2_lower, o2o_connections2_lower).compile()
+
+        o2m_nodes2_lower = np.zeros((self.pop_size, n, 5))
+        o2m_connections2_lower = np.zeros((self.pop_size, 2, n, n))
+        o2m_distance = jit(vmap(func, in_axes=(None, None, 0, 0))).lower(o2o_nodes1_lower, o2o_connections1_lower,
+                                                                         o2m_nodes2_lower,
+                                                                         o2m_connections2_lower).compile()
+
+        self.compiled_function[('o2o_distance', n)] = o2o_distance
+        self.compiled_function[('o2m_distance', n)] = o2m_distance
+
+    def create_distance(self, n):
+        key1, key2 = ('o2o_distance', n), ('o2m_distance', n)
+        if key1 not in self.compiled_function:
+            self.compile_distance(n)
+        return self.compiled_function[key1], self.compiled_function[key2]
+
+    def create_crossover_with_args(self):
+        self.crossover_with_args = crossover
+
+    def compile_crossover(self, n):
+        func = self.crossover_with_args
+        randkey_lower = np.zeros((self.pop_size, 2), dtype=np.uint32)
+        nodes1_lower = np.zeros((self.pop_size, n, 5))
+        connections1_lower = np.zeros((self.pop_size, 2, n, n))
+        nodes2_lower = np.zeros((self.pop_size, n, 5))
+        connections2_lower = np.zeros((self.pop_size, 2, n, n))
+        func = jit(vmap(func)).lower(randkey_lower, nodes1_lower, connections1_lower,
+                                     nodes2_lower, connections2_lower).compile()
+        self.compiled_function[('crossover', n)] = func
+
+    def create_crossover(self, n):
+        key = ('crossover', n)
+        if key not in self.compiled_function:
+            self.compile_crossover(n)
+        return self.compiled_function[key]

algorithms/neat/genome/__init__.py

@@ -3,3 +3,5 @@ from .distance import create_distance_function
 from .mutate import create_mutate_function
 from .forward import create_forward_function
 from .crossover import create_crossover_function
+from .activations import act_name2key
+from .aggregations import agg_name2key

algorithms/neat/genome/distance.py

@@ -33,9 +33,6 @@ def create_distance_function(N, config, type: str, debug: bool = False):
         else:
             return res_func
 
-        # return lambda nodes1, connections1, nodes2, connections2: \
-        #     distance_numpy(nodes1, connections1, nodes2, connections2, disjoint_coe, compatibility_coe)
-
     elif type == 'o2m':
         vmap_func = vmap(distance_with_args, in_axes=(None, None, 0, 0))
         pop_size = config.neat.population.pop_size

algorithms/neat/genome/genome.py

@@ -45,7 +45,8 @@ def create_initialize_function(config):
 
 def initialize_genomes(pop_size: int,
                        N: int,
-                       num_inputs: int, num_outputs: int,
+                       num_inputs: int,
+                       num_outputs: int,
                        default_bias: float = 0.0,
                        default_response: float = 1.0,
                        default_act: int = 0,

algorithms/neat/genome/mutate.py

@@ -113,13 +113,11 @@ def mutate(rand_key: Array,
            new_node_key: int,
            input_idx: Array,
            output_idx: Array,
-           bias_default: float = 0,
            bias_mean: float = 0,
            bias_std: float = 1,
            bias_mutate_strength: float = 0.5,
            bias_mutate_rate: float = 0.7,
            bias_replace_rate: float = 0.1,
-           response_default: float = 1,
            response_mean: float = 1.,
            response_std: float = 0.,
            response_mutate_strength: float = 0.,
@@ -147,8 +145,6 @@ def mutate(rand_key: Array,
     :param input_idx:
     :param agg_default:
     :param act_default:
-    :param response_default:
-    :param bias_default:
     :param rand_key:
     :param nodes: (N, 5)
     :param connections: (2, N, N)
@@ -186,7 +182,7 @@ def mutate(rand_key: Array,
         return n, c
 
     def m_add_node(rk, n, c):
-        return mutate_add_node(rk, new_node_key, n, c, bias_default, response_default, act_default, agg_default)
+        return mutate_add_node(rk, new_node_key, n, c, bias_mean, response_mean, act_default, agg_default)
 
     def m_delete_node(rk, n, c):
         return mutate_delete_node(rk, n, c, input_idx, output_idx)

algorithms/neat/pipeline.py

@@ -2,13 +2,13 @@ from typing import List, Union, Tuple, Callable
 import time
 
 import jax
-import jax.numpy as jnp
 import numpy as np
 
 from .species import SpeciesController
 from .genome import expand, expand_single
 from .genome import create_initialize_function, create_mutate_function, create_forward_function, \
     create_distance_function, create_crossover_function
+from .function_factory import FunctionFactory
 
 
 class Pipeline:
@@ -17,17 +17,18 @@ class Pipeline:
     """
 
     def __init__(self, config, seed=42):
-        self.generation_timestamp = time.time()
         self.randkey = jax.random.PRNGKey(seed)
         np.random.seed(seed)
 
         self.config = config
+        self.function_factory = FunctionFactory(config)
+
         self.N = config.basic.init_maximum_nodes
         self.expand_coe = config.basic.expands_coe
         self.pop_size = config.neat.population.pop_size
 
         self.species_controller = SpeciesController(config)
-        self.initialize_func = create_initialize_function(config)
+        self.initialize_func = self.function_factory.create_initialize()
         self.pop_nodes, self.pop_connections, self.input_idx, self.output_idx = self.initialize_func()
 
         self.compile_functions(debug=True)
@@ -36,6 +37,7 @@ class Pipeline:
         self.species_controller.init_speciate(self.pop_nodes, self.pop_connections)
 
         self.best_fitness = float('-inf')
+        self.generation_timestamp = time.time()
 
     def ask(self, batch: bool):
         """
@@ -140,10 +142,9 @@ class Pipeline:
             self.compile_functions(debug=True)
 
     def compile_functions(self, debug=False):
-        self.mutate_func = create_mutate_function(self.N, self.config, batch=True, debug=debug)
+        self.mutate_func = self.function_factory.create_mutate(self.N)
-        self.crossover_func = create_crossover_function(self.N, self.config, batch=True, debug=debug)
+        self.crossover_func = self.function_factory.create_crossover(self.N)
-        self.o2o_distance = create_distance_function(self.N, self.config, type='o2o', debug=debug)
+        self.o2o_distance, self.o2m_distance = self.function_factory.create_distance(self.N)
-        self.o2m_distance = create_distance_function(self.N, self.config, type='o2m', debug=debug)
 
     def default_analysis(self, fitnesses):
         max_f, min_f, mean_f, std_f = max(fitnesses), min(fitnesses), np.mean(fitnesses), np.std(fitnesses)

utils/default_config.json

@@ -2,8 +2,9 @@
     "basic": {
         "num_inputs": 2,
         "num_outputs": 1,
-        "init_maximum_nodes": 30,
+        "init_maximum_nodes": 10,
-        "expands_coe": 2
+        "expands_coe": 2,
+        "pre_compile_times": 3
     },
     "neat": {
         "population": {