modify pipeline for "update_by_data";

fix bug in speciate. currently, node_delete and conn_delete can successfully work

tensorneat/algorithm/base.py

@@ -19,9 +19,15 @@ class BaseAlgorithm:
         """transform the genome into a neural network"""
         raise NotImplementedError
 
+    def restore(self, state, transformed):
+        raise NotImplementedError
+
     def forward(self, state, inputs, transformed):
         raise NotImplementedError
 
+    def update_by_batch(self, state, batch_input, transformed):
+        raise NotImplementedError
+
     @property
     def num_inputs(self):
         raise NotImplementedError

tensorneat/algorithm/neat/ga/mutation/default.py

@@ -178,18 +178,25 @@ class DefaultMutation(BaseMutation):
         def no(key_, nodes_, conns_):
             return nodes_, conns_
 
-        nodes, conns = jax.lax.cond(
+        if self.node_add > 0:
-            r1 < self.node_add, mutate_add_node, no, k1, nodes, conns
+            nodes, conns = jax.lax.cond(
-        )
+                r1 < self.node_add, mutate_add_node, no, k1, nodes, conns
-        nodes, conns = jax.lax.cond(
+            )
-            r2 < self.node_delete, mutate_delete_node, no, k2, nodes, conns
+
-        )
+        if self.node_delete > 0:
-        nodes, conns = jax.lax.cond(
+            nodes, conns = jax.lax.cond(
-            r3 < self.conn_add, mutate_add_conn, no, k3, nodes, conns
+                r2 < self.node_delete, mutate_delete_node, no, k2, nodes, conns
-        )
+            )
-        nodes, conns = jax.lax.cond(
+
-            r4 < self.conn_delete, mutate_delete_conn, no, k4, nodes, conns
+        if self.conn_add > 0:
-        )
+            nodes, conns = jax.lax.cond(
+                r3 < self.conn_add, mutate_add_conn, no, k3, nodes, conns
+            )
+
+        if self.conn_delete > 0:
+            nodes, conns = jax.lax.cond(
+                r4 < self.conn_delete, mutate_delete_conn, no, k4, nodes, conns
+            )
 
         return nodes, conns
 

tensorneat/algorithm/neat/genome/default.py

@@ -117,7 +117,9 @@ class DefaultGenome(BaseGenome):
 
             def hit():
                 batch_ins, new_conn_attrs = jax.vmap(
-                    self.conn_gene.update_by_batch, in_axes=(None, 1, 1), out_axes=(1, 1)
+                    self.conn_gene.update_by_batch,
+                    in_axes=(None, 1, 1),
+                    out_axes=(1, 1),
                 )(state, u_conns_[:, :, i], batch_values)
                 batch_z, new_node_attrs = self.node_gene.update_by_batch(
                     state,
@@ -132,12 +134,12 @@ class DefaultGenome(BaseGenome):
                     u_conns_.at[:, :, i].set(new_conn_attrs),
                 )
 
+            # the val of input nodes is obtained by the task, not by calculation
             (batch_values, nodes_attrs_, u_conns_) = jax.lax.cond(
                 jnp.isin(i, self.input_idx),
                 lambda: (batch_values, nodes_attrs_, u_conns_),
                 hit,
             )
-            # the val of input nodes is obtained by the task, not by calculation
 
             return batch_values, nodes_attrs_, u_conns_, idx + 1
 

tensorneat/algorithm/neat/neat.py

@@ -44,9 +44,15 @@ class NEAT(BaseAlgorithm):
         nodes, conns = individual
         return self.genome.transform(state, nodes, conns)
 
+    def restore(self, state, transformed):
+        return self.genome.restore(state, transformed)
+
     def forward(self, state, inputs, transformed):
         return self.genome.forward(state, inputs, transformed)
 
+    def update_by_batch(self, state, batch_input, transformed):
+        return self.genome.update_by_batch(state, batch_input, transformed)
+
     @property
     def num_inputs(self):
         return self.genome.num_inputs

tensorneat/algorithm/neat/species/default.py

@@ -113,6 +113,9 @@ class DefaultSpecies(BaseSpecies):
         return state.pop_nodes, state.pop_conns
 
     def update_species(self, state, fitness):
+        # set nan to -inf
+        fitness = jnp.where(jnp.isnan(fitness), -jnp.inf, fitness)
+
         # update the fitness of each species
         state, species_fitness = self.update_species_fitness(state, fitness)
 
@@ -121,6 +124,7 @@ class DefaultSpecies(BaseSpecies):
 
         # sort species_info by their fitness. (also push nan to the end)
         sort_indices = jnp.argsort(species_fitness)[::-1]
+
         state = state.update(
             species_keys=state.species_keys[sort_indices],
             best_fitness=state.best_fitness[sort_indices],

tensorneat/examples/func_fit/xor.py

@@ -21,11 +21,11 @@ if __name__ == "__main__":
                     mutation=DefaultMutation(
                         node_add=0.05,
                         conn_add=0.05,
-                        node_delete=0,
+                        node_delete=0.05,
-                        conn_delete=0,
+                        conn_delete=0.05,
                     ),
                 ),
-                pop_size=100,
+                pop_size=1000,
                 species_size=20,
                 compatibility_threshold=2,
                 survival_threshold=0.01,  # magic

tensorneat/pipeline.py

@@ -1,11 +1,11 @@
-from functools import partial
-
 import jax, jax.numpy as jnp
 import time
 import numpy as np
 
 from algorithm import BaseAlgorithm
 from problem import BaseProblem
+from problem.rl_env import RLEnv
+from problem.func_fit import FuncFit
 from utils import State
 
 
@@ -17,6 +17,8 @@ class Pipeline:
         seed: int = 42,
         fitness_target: float = 1,
         generation_limit: int = 1000,
+        pre_update: bool = False,
+        update_batch_size: int = 10000,
     ):
         assert problem.jitable, "Currently, problem must be jitable"
 
@@ -37,10 +39,30 @@ class Pipeline:
         self.best_genome = None
         self.best_fitness = float("-inf")
         self.generation_timestamp = None
+        self.pre_update = pre_update
+        self.update_batch_size = update_batch_size
+        if pre_update:
+            if isinstance(problem, RLEnv):
+                assert problem.record_episode, "record_episode must be True"
+                self.fetch_data = lambda episode: episode["obs"]
+            elif isinstance(problem, FuncFit):
+                assert problem.return_data, "return_data must be True"
+                self.fetch_data = lambda data: data
+            else:
+                raise NotImplementedError
 
     def setup(self, state=State()):
         print("initializing")
         state = state.register(randkey=jax.random.PRNGKey(self.seed))
+
+        if self.pre_update:
+            # initial with mean = 0 and std = 1
+            state = state.register(
+                data=jax.random.normal(
+                    state.randkey, (self.update_batch_size, self.algorithm.num_inputs)
+                )
+            )
+
         state = self.algorithm.setup(state)
         state = self.problem.setup(state)
         print("initializing finished")
@@ -57,9 +79,42 @@ class Pipeline:
             state, pop
         )
 
-        fitnesses = jax.vmap(self.problem.evaluate, in_axes=(None, 0, None, 0))(
+        if self.pre_update:
-            state, keys, self.algorithm.forward, pop_transformed
+            # update the population
-        )
+            _, pop_transformed = jax.vmap(
+                self.algorithm.update_by_batch, in_axes=(None, None, 0)
+            )(state, state.data, pop_transformed)
+
+            # raw_data: (Pop, Batch, num_inputs)
+            fitnesses, raw_data = jax.vmap(
+                self.problem.evaluate, in_axes=(None, 0, None, 0)
+            )(state, keys, self.algorithm.forward, pop_transformed)
+
+            data = self.fetch_data(raw_data)
+            assert (
+                data.ndim == 3
+                and data.shape[0] == self.pop_size
+                and data.shape[2] == self.algorithm.num_inputs
+            )
+            # reshape to (Pop * Batch, num_inputs)
+            data = data.reshape(
+                data.shape[0] * data.shape[1], self.algorithm.num_inputs
+            )
+            # shuffle
+            data = jax.random.permutation(randkey_, data, axis=0)
+            # cutoff or expand
+            if data.shape[0] >= self.update_batch_size:
+                data = data[: self.update_batch_size]  # cutoff
+            else:
+                data = (
+                    jnp.full(state.data.shape, jnp.nan).at[: data.shape[0]].set(data)
+                )  # expand
+            state = state.update(data=data)
+
+        else:
+            fitnesses = jax.vmap(self.problem.evaluate, in_axes=(None, 0, None, 0))(
+                state, keys, self.algorithm.forward, pop_transformed
+            )
 
         state = self.algorithm.tell(state, fitnesses)
 
@@ -89,24 +144,18 @@ class Pipeline:
                 print("Fitness limit reached!")
                 return state, self.best_genome
 
-            # node = previous_pop[0][0][:, 0]
-            # node_count = jnp.sum(~jnp.isnan(node))
-            # conn = previous_pop[1][0][:, 0]
-            # conn_count = jnp.sum(~jnp.isnan(conn))
-            # if (w % 5 == 0):
-            #     print("node_count", node_count)
-            #     print("conn_count", conn_count)
-
         print("Generation limit reached!")
         return state, self.best_genome
 
     def analysis(self, state, pop, fitnesses):
 
+        valid_fitnesses = fitnesses[~np.isnan(fitnesses)]
+
         max_f, min_f, mean_f, std_f = (
-            max(fitnesses),
+            max(valid_fitnesses),
-            min(fitnesses),
+            min(valid_fitnesses),
-            np.mean(fitnesses),
+            np.mean(valid_fitnesses),
-            np.std(fitnesses),
+            np.std(valid_fitnesses),
         )
 
         new_timestamp = time.time()
@@ -122,9 +171,9 @@ class Pipeline:
         species_sizes = [int(i) for i in member_count if i > 0]
 
         print(
-            f"Generation: {self.algorithm.generation(state)}",
+            f"Generation: {self.algorithm.generation(state)}, Cost time: {cost_time * 1000:.2f}ms\n",
-            f"species: {len(species_sizes)}, {species_sizes}",
+            f"\tspecies: {len(species_sizes)}, {species_sizes}\n",
-            f"fitness: {max_f:.6f}, {min_f:.6f}, {mean_f:.6f}, {std_f:.6f}, Cost time: {cost_time * 1000:.6f}ms",
+            f"\tfitness: valid cnt: {len(valid_fitnesses)}, max: {max_f:.4f}, min: {min_f:.4f}, mean: {mean_f:.4f}, std: {std_f:.4f}\n",
         )
 
     def show(self, state, best, *args, **kwargs):

tensorneat/problem/func_fit/func_fit.py

@@ -49,7 +49,10 @@ class FuncFit(BaseProblem):
             state, self.inputs, params
         )
         inputs, target, predict = jax.device_get([self.inputs, self.targets, predict])
-        loss = self.evaluate(state, randkey, act_func, params)
+        if self.return_data:
+            loss, _ = self.evaluate(state, randkey, act_func, params)
+        else:
+            loss = self.evaluate(state, randkey, act_func, params)
         loss = -loss
 
         msg = ""

tensorneat/problem/func_fit/xor.py

@@ -4,14 +4,19 @@ from .func_fit import FuncFit
 
 
 class XOR(FuncFit):
-
     @property
     def inputs(self):
-        return np.array([[0, 0], [0, 1], [1, 0], [1, 1]])
+        return np.array(
+            [[0, 0], [0, 1], [1, 0], [1, 1]],
+            dtype=np.float32,
+        )
 
     @property
     def targets(self):
-        return np.array([[0], [1], [1], [0]])
+        return np.array(
+            [[0], [1], [1], [0]],
+            dtype=np.float32,
+        )
 
     @property
     def input_shape(self):

tensorneat/problem/func_fit/xor3d.py

@@ -16,12 +16,16 @@ class XOR3d(FuncFit):
                 [1, 0, 1],
                 [1, 1, 0],
                 [1, 1, 1],
-            ]
+            ],
+            dtype=np.float32,
         )
 
     @property
     def targets(self):
-        return np.array([[0], [1], [1], [0], [1], [0], [0], [1]])
+        return np.array(
+            [[0], [1], [1], [0], [1], [0], [0], [1]],
+            dtype=np.float32,
+        )
 
     @property
     def input_shape(self):

tensorneat/problem/rl_env/__init__.py

@@ -1,2 +1,3 @@
 from .gymnax_env import GymNaxEnv
 from .brax_env import BraxEnv
+from .rl_jit import RLEnv

tensorneat/utils/__init__.py

@@ -1,5 +1,5 @@
-from .activation import Act, act
+from .activation import Act, act, ACT_ALL
-from .aggregation import Agg, agg
+from .aggregation import Agg, agg, AGG_ALL
 from .tools import *
 from .graph import *
 from .state import State