Example notebook with PMAP sampling of RBMs trained on MNIST digits (#80

)

* Special indexing for 1D variable array

* RBM notebook

* Clean up RBM notebook; include data

* Get coverage back to 100%

* Add unit test for running examples

* Fix imports

* Address comments; disable RBM test for speed

* Make notebooks work again

examples/rbm.py

@@ -0,0 +1,71 @@
+# ---
+# jupyter:
+#   jupytext:
+#     formats: ipynb,py:percent
+#     text_representation:
+#       extension: .py
+#       format_name: percent
+#       format_version: '1.3'
+#       jupytext_version: 1.11.4
+#   kernelspec:
+#     display_name: Python 3
+#     language: python
+#     name: python3
+# ---
+
+# %%
+# %matplotlib inline
+import itertools
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from pgmax.fg import graph, groups
+
+# %%
+# Load parameters
+params = np.load("example_data/rbm_mnist.npz")
+bv = params["bv"]
+bh = params["bh"]
+W = params["W"]
+nv = bv.shape[0]
+nh = bh.shape[0]
+
+# %%
+# Build factor graph
+visible_variables = groups.NDVariableArray(variable_size=2, shape=(nv,))
+hidden_variables = groups.NDVariableArray(variable_size=2, shape=(nh,))
+fg = graph.FactorGraph(
+    variables=dict(visible=visible_variables, hidden=hidden_variables),
+)
+for ii in range(nh):
+    for jj in range(nv):
+        fg.add_factor(
+            [("hidden", ii), ("visible", jj)],
+            np.array(list(itertools.product(np.arange(2), repeat=2))),
+            np.array([0, 0, 0, W[ii, jj]]),
+        )
+
+# %%
+# Set evidence
+init_msgs = fg.get_init_msgs()
+init_msgs.evidence["hidden"] = np.stack(
+    [np.zeros_like(bh), bh + np.random.logistic(size=bh.shape)], axis=1
+)
+init_msgs.evidence["visible"] = np.stack(
+    [np.zeros_like(bv), bv + np.random.logistic(size=bv.shape)], axis=1
+)
+
+# %%
+# Run inference and decode
+msgs = fg.run_bp(100, 0.5, init_msgs)
+map_states = fg.decode_map_states(msgs)
+
+# %%
+# Visualize decodings
+img = np.zeros(bv.shape)
+for ii in range(nv):
+    img[ii] = map_states[("visible", ii)]
+
+img = img.reshape((28, 28))
+plt.imshow(img)

pgmax/fg/groups.py

@@ -257,15 +257,19 @@ class NDVariableArray(VariableGroup):
     variable_size: int
     shape: Tuple[int, ...]
 
-    def _get_keys_to_vars(self) -> Dict[Tuple[int, ...], nodes.Variable]:
+    def _get_keys_to_vars(self) -> Dict[Union[int, Tuple[int, ...]], nodes.Variable]:
         """Function that generates a dictionary mapping keys to variables.
 
         Returns:
             a dictionary mapping all possible keys to different variables.
         """
-        keys_to_vars: Dict[Tuple[int, ...], nodes.Variable] = {}
+        keys_to_vars: Dict[Union[int, Tuple[int, ...]], nodes.Variable] = {}
         for key in itertools.product(*[list(range(k)) for k in self.shape]):
-            keys_to_vars[key] = nodes.Variable(self.variable_size)
+            if len(key) == 1:
+                keys_to_vars[key[0]] = nodes.Variable(self.variable_size)
+            else:
+                keys_to_vars[key] = nodes.Variable(self.variable_size)
+
         return keys_to_vars
 
     def get_vars_to_evidence(

tests/fg/test_groups.py

@@ -1,7 +1,7 @@
 import numpy as np
 import pytest
 
-from pgmax.fg import groups
+from pgmax.fg import groups, nodes
 
 
 def test_vargroup_list_idx():
@@ -33,6 +33,11 @@ def test_composite_vargroup_evidence():
         assert (arr == np.zeros(3, dtype=float)).all()
 
 
+def test_1dvararray_indexing():
+    v_group = groups.NDVariableArray(2, (1,))
+    assert isinstance(v_group[0], nodes.Variable)
+
+
 def test_ndvararray_evidence_error():
     v_group = groups.NDVariableArray(3, (2, 2))
     with pytest.raises(ValueError) as verror:

tests/test_examples.py

@@ -0,0 +1,22 @@
+import os
+import subprocess
+import sys
+
+import pytest
+
+EXAMPLES_DIR = os.path.abspath(
+    os.path.join(os.path.dirname(os.path.dirname(__file__)), "examples")
+)
+EXAMPLES = [
+    #  "heretic_example.py",
+    "ising_model.py",
+    #  "rbm.py",
+    "sanity_check_example.py",
+]
+
+
+@pytest.mark.parametrize("example", EXAMPLES)
+def test_example(example):
+    print(f"Running:\npython examples/{example}")
+    filename = os.path.join(EXAMPLES_DIR, example)
+    subprocess.check_call([sys.executable, filename])