complete HyperNEAT!

algorithm/hyperneat/substrate/__init__.py

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+from .base import BaseSubstrate
+from .tools import analysis_substrate

algorithm/hyperneat/substrate/base.py

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+import numpy as np
+
+
+class BaseSubstrate:
+
+    @staticmethod
+    def setup(state, config):
+        return state.update(
+            input_coors=np.asarray(config['input_coors'], dtype=np.float32),
+            output_coors=np.asarray(config['output_coors'], dtype=np.float32),
+            hidden_coors=np.asarray(config['hidden_coors'], dtype=np.float32),
+        )

algorithm/hyperneat/substrate/tools.py

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+from typing import Type
+
+import numpy as np
+
+from .base import BaseSubstrate
+
+
+def analysis_substrate(state):
+    cd = state.input_coors.shape[1]  # coordinate dimensions
+    si = state.input_coors.shape[0]  # input coordinate size
+    so = state.output_coors.shape[0]  # output coordinate size
+    sh = state.hidden_coors.shape[0]  # hidden coordinate size
+
+    input_idx = np.arange(si)
+    output_idx = np.arange(si, si + so)
+    hidden_idx = np.arange(si + so, si + so + sh)
+
+    total_conns = si * sh + sh * sh + sh * so
+    query_coors = np.zeros((total_conns, cd * 2))
+    correspond_keys = np.zeros((total_conns, 2))
+
+    # connect input to hidden
+    aux_coors, aux_keys = cartesian_product(input_idx, hidden_idx, state.input_coors, state.hidden_coors)
+    query_coors[0: si * sh, :] = aux_coors
+    correspond_keys[0: si * sh, :] = aux_keys
+
+    # connect hidden to hidden
+    aux_coors, aux_keys = cartesian_product(hidden_idx, hidden_idx, state.hidden_coors, state.hidden_coors)
+    query_coors[si * sh: si * sh + sh * sh, :] = aux_coors
+    correspond_keys[si * sh: si * sh + sh * sh, :] = aux_keys
+
+    # connect hidden to output
+    aux_coors, aux_keys = cartesian_product(hidden_idx, output_idx, state.hidden_coors, state.output_coors)
+    query_coors[si * sh + sh * sh:, :] = aux_coors
+    correspond_keys[si * sh + sh * sh:, :] = aux_keys
+
+    return input_idx, output_idx, hidden_idx, query_coors, correspond_keys
+
+
+def cartesian_product(keys1, keys2, coors1, coors2):
+    len1 = keys1.shape[0]
+    len2 = keys2.shape[0]
+
+    repeated_coors1 = np.repeat(coors1, len2, axis=0)
+    repeated_keys1 = np.repeat(keys1, len2)
+
+    tiled_coors2 = np.tile(coors2, (len1, 1))
+    tiled_keys2 = np.tile(keys2, len1)
+
+    new_coors = np.concatenate((repeated_coors1, tiled_coors2), axis=1)
+    correspond_keys = np.column_stack((repeated_keys1, tiled_keys2))
+
+    return new_coors, correspond_keys