finish jit-able speciate function

next time i'll create a new branch

algorithms/neat/genome/utils.py

@@ -76,6 +76,12 @@ def fetch_random(rand_key, mask, default=I_INT) -> Array:
     return fetch_first(mask, default)
 
 
+@jit
+def argmin_with_mask(arr: Array, mask: Array) -> Array:
+    masked_arr = jnp.where(mask, arr, jnp.inf)
+    min_idx = jnp.argmin(masked_arr)
+    return min_idx
+
 if __name__ == '__main__':
 
     a = jnp.array([1, 2, 3, 4, 5])

algorithms/neat/jitable_speciate.py

@@ -1,4 +1,109 @@
-from jax import jit
+from functools import partial
+
+import jax
+import jax.numpy as jnp
+from jax import jit, vmap
+
+from jax import Array
+
+from .genome import distance
+from .genome.utils import I_INT, fetch_first, argmin_with_mask
+
+
 @jit
-def jitable_speciate():
-    pass
+def jitable_speciate(pop_nodes: Array, pop_cons: Array, spe_center_nodes: Array, spe_center_cons: Array,
+                     disjoint_coe: float = 1., compatibility_coe: float = 0.5, compatibility_threshold=3.0
+                     ):
+    """
+    args:
+        pop_nodes: (pop_size, N, 5)
+        pop_cons: (pop_size, C, 4)
+        spe_center_nodes: (species_size, N, 5)
+        spe_center_cons: (species_size, C, 4)
+    """
+    pop_size, species_size = pop_nodes.shape[0], spe_center_nodes.shape[0]
+
+    # prepare distance functions
+    distance_with_args = partial(distance, disjoint_coe=disjoint_coe, compatibility_coe=compatibility_coe)
+    o2p_distance_func = vmap(distance_with_args, in_axes=(None, None, 0, 0))
+    s2p_distance_func = vmap(
+        o2p_distance_func, in_axes=(0, 0, None, None)
+    )
+
+    idx2specie = jnp.full((pop_size,), I_INT, dtype=jnp.int32)  # I_INT means not assigned to any species
+
+    # the distance between each species' center and each genome in population
+    s2p_distance = s2p_distance_func(spe_center_nodes, spe_center_cons, pop_nodes, pop_cons)
+
+    def continue_execute_while(carry):
+        i, i2s, scn, scc = carry
+        not_all_assigned = ~jnp.all(i2s != I_INT)
+        not_reach_species_upper_bounds = i < species_size
+        return not_all_assigned & not_reach_species_upper_bounds
+
+    def deal_with_each_center_genome(carry):
+        i, i2s, scn, scc = carry  # scn is short for spe_center_nodes, scc is short for spe_center_cons
+        center_nodes, center_cons = spe_center_nodes[i], spe_center_cons[i]
+
+        i2s, scn, scc = jax.lax.cond(
+            jnp.all(jnp.isnan(center_nodes)),  # whether the center genome is valid
+            create_new_specie,  # if not valid, create a new specie
+            update_exist_specie,  # if valid, update the specie
+            (i, i2s, scn, scc)
+        )
+
+        return i + 1, i2s, scn, scc
+
+    def create_new_specie(carry):
+        i, i2s, scn, scc = carry
+        # pick the first one who has not been assigned to any species
+        idx = fetch_first(i2s == I_INT)
+
+        # assign it to new specie
+        i2s = i2s.at[idx].set(i)
+
+        # update center genomes
+        scn = scn.at[i].set(pop_nodes[idx])
+        scc = scc.at[i].set(pop_cons[idx])
+
+        i2s, scn, scc = speciate_by_threshold((i, i2s, scn, scc))
+        return i2s, scn, scc
+
+    def update_exist_specie(carry):
+        i, i2s, scn, scc = carry
+
+        # find new center
+        idx = argmin_with_mask(s2p_distance[i], mask=i2s == I_INT)
+
+        # update new center
+        i2s = i2s.at[idx].set(i)
+
+        # update center genomes
+        scn = scn.at[i].set(pop_nodes[idx])
+        scc = scc.at[i].set(pop_cons[idx])
+
+        i2s, scn, scc = speciate_by_threshold((i, i2s, scn, scc))
+        return i2s, scn, scc
+
+    def speciate_by_threshold(carry):
+        i, i2s, scn, scc = carry
+        # distance between such center genome and ppo genomes
+        o2p_distance = o2p_distance_func(scn[i], scc[i], pop_nodes, pop_cons)
+        close_enough_mask = o2p_distance < compatibility_threshold
+
+        # when it is close enough, assign it to the species, remember not to update genome has already been assigned
+        i2s = jnp.where(close_enough_mask & (i2s == I_INT), i, i2s)
+        return i2s, scn, scc
+
+    # update idx2specie
+    _, idx2specie, spe_center_nodes, spe_center_cons = jax.lax.while_loop(
+        continue_execute_while,
+        deal_with_each_center_genome,
+        (0, idx2specie, spe_center_nodes, spe_center_cons)
+    )
+
+    # if there are still some pop genomes not assigned to any species, add them to the last genome
+    # this condition seems to be only happened when the number of species is reached species upper bounds
+    idx2specie = jnp.where(idx2specie == I_INT, species_size - 1, idx2specie)
+
+    return idx2specie, spe_center_nodes, spe_center_cons