change repo structure; modify readme

tensorneat/algorithm/neat/genome/recurrent.py

@@ -0,0 +1,60 @@
+import jax, jax.numpy as jnp
+from utils import unflatten_conns
+
+from . import BaseGenome
+from ..gene import BaseNodeGene, BaseConnGene, DefaultNodeGene, DefaultConnGene
+
+
+class RecurrentGenome(BaseGenome):
+    """Default genome class, with the same behavior as the NEAT-Python"""
+
+    network_type = 'recurrent'
+
+    def __init__(self,
+                 num_inputs: int,
+                 num_outputs: int,
+                 max_nodes: int,
+                 max_conns: int,
+                 node_gene: BaseNodeGene = DefaultNodeGene(),
+                 conn_gene: BaseConnGene = DefaultConnGene(),
+                 activate_time: int = 10,
+                 ):
+        super().__init__(num_inputs, num_outputs, max_nodes, max_conns, node_gene, conn_gene)
+        self.activate_time = activate_time
+
+    def transform(self, nodes, conns):
+        u_conns = unflatten_conns(nodes, conns)
+
+        # remove un-enable connections and remove enable attr
+        conn_enable = u_conns[0] == 1
+        u_conns = jnp.where(conn_enable, u_conns[1:, :], jnp.nan)
+
+        return nodes, u_conns
+
+    def forward(self, inputs, transformed):
+        nodes, conns = transformed
+
+        N = nodes.shape[0]
+        vals = jnp.full((N,), jnp.nan)
+        nodes_attrs = nodes[:, 1:]
+
+        def body_func(_, values):
+            # set input values
+            values = values.at[self.input_idx].set(inputs)
+
+            # calculate connections
+            node_ins = jax.vmap(
+                jax.vmap(
+                    self.conn_gene.forward,
+                    in_axes=(1, None)
+                ),
+                in_axes=(1, 0)
+            )(conns, values)
+
+            # calculate nodes
+            values = jax.vmap(self.node_gene.forward)(nodes_attrs, node_ins.T)
+            return values
+
+        vals = jax.lax.fori_loop(0, self.activate_time, body_func, vals)
+
+        return vals[self.output_idx]