Merge branch 'master' of https://github.com/jmschrei/pomegranate

.github/ISSUE_TEMPLATE/bug_report.md

@@ -12,3 +12,6 @@ A clear and concise description of what the bug is, including what you were expe
 
 **To Reproduce**
 Please provide a snippet of code that can reproduce this error. It is much easier for us to track down bugs and fix them if we have an example script that fails until we're successful.
+
+**Response time**
+Although I will likely respond during weekdays if I am not on vacation, I am not likely to be able to merge PRs or write code until the weekend. 

docs/tutorials/B_Model_Tutorial_4_Hidden_Markov_Models.ipynb

@@ -210,7 +210,7 @@
    "id": "66fb5e21",
    "metadata": {},
    "source": [
-    "It looks like it successfully identified a CG island in the middle (the long stretch of 0's) and another shorter one at the end. More importantly, the model wasn't tricked into thinking that every CG or even pair of CGs was an island. It required many C's and G's to be part of a longer stretch to identify that region as an island. Naturally, the balance of the transition and emission probabilities will heavily influence what regions are detected.\n",
+    "It looks like it successfully identified a CG island in the middle (the long stretch of 1's) and another shorter one at the end. More importantly, the model wasn't tricked into thinking that every CG or even pair of CGs was an island. It required many C's and G's to be part of a longer stretch to identify that region as an island. Naturally, the balance of the transition and emission probabilities will heavily influence what regions are detected.\n",
     "\n",
     "Let's say, though, that we want to get rid of that CG island prediction at the end because we don't believe that real islands can occur at the end of the sequence. We can take care of this by adding in an explicit end state that only the non-island hidden state can get to. We enforce that the model has to end in the end state, and if only the non-island state gets there, the sequence of hidden states must end in the non-island state. Here's how:"
    ]

pomegranate/_utils.py

@@ -355,7 +355,7 @@ def _initialize_centroids(X, k, algorithm='first-k', random_state=None):
 		return selector.fit_transform(X)
 
 
-def partition_sequences(X, sample_weight=None, priors=None):
+def partition_sequences(X, sample_weight=None, priors=None, n_dists=None):
 	"""Partition a set of sequences into blobs of equal length.
 
 	This function will take in a list of sequences, where each sequence is
@@ -391,48 +391,53 @@ def partition_sequences(X, sample_weight=None, priors=None):
 		The input sequence priors for the sequences or None. If None, return
 		None. Default is None.
 
+	n_dists: int or None
+		The expected last dimension of the priors tensor. Must be provided if
+		`priors` is provided. Default is None.
+
 
 	Returns
 	-------
 	X_: list or tensor
 		The partitioned and grouped sequences.
 	"""
-
+	if priors is not None and n_dists is None:
+		raise RuntimeError("If priors are provided, n_dists must be provided as well.")
 	# If a 3D tensor has been passed in, return it
 	try:
 		X = [_check_parameter(_cast_as_tensor(X), "X", ndim=3)]
-
+	except:
+		pass
+	else:
 		if sample_weight is not None:
 			sample_weight = [_check_parameter(_cast_as_tensor(sample_weight),
 				"sample_weight", min_value=0.0)]
 
 		if priors is not None:
 			priors = [_check_parameter(_cast_as_tensor(priors), "priors",
-				ndim=3, shape=X[0].shape)]
+									   ndim=3, shape=(*X[0].shape[:-1], n_dists))]
 
 		return X, sample_weight, priors
-	except:
-		pass
 
 	# Otherwise, cast all elements in the list as a tensor
 	X = [_cast_as_tensor(x) for x in X]
 
 	# If a list of 3D tensors has been passed in, return it
 	try:
 		X = [_check_parameter(x, "X", ndim=3) for x in X]
-
+	except:
+		pass
+	else:
 		if sample_weight is not None:
 			sample_weight = [_check_parameter(_cast_as_tensor(w_),
 				"sample_weight", min_value=0.0) for w_ in sample_weight]
 
 		if priors is not None:
 			priors = [_check_parameter(_cast_as_tensor(p), "priors",
-				ndim=3, shape=X[i].shape) for i, p in enumerate(priors)]
+									   ndim=3, shape=(*X[i].shape[:-1], n_dists)) for i, p in enumerate(priors)]
 
 		if all([x.ndim == 3 for x in X]):
 			return X, sample_weight, priors
-	except:
-		pass
 
 	# Otherwise, group together same-sized examples
 	X_dict = collections.defaultdict(list)
@@ -453,7 +458,7 @@ def partition_sequences(X, sample_weight=None, priors=None):
 
 		if priors is not None:
 			p = _check_parameter(_cast_as_tensor(priors[i]), "priors",
-				ndim=2, shape=x.shape)
+								 ndim=2, shape=(*x.shape[:-1], n_dists))
 
 			priors_dict[n].append(p)
 

pomegranate/hmm/_base.py

@@ -565,7 +565,7 @@ def fit(self, X, sample_weight=None, priors=None):
 			Prior probabilities of assigning each symbol to each node. If not
 			provided, do not include in the calculations (conceptually
 			equivalent to a uniform probability, but without scaling the
-			probabilities). This can be used to assign labels to observatons
+			probabilities). This can be used to assign labels to observations
 			by setting one of the probabilities for an observation to 1.0.
 			Note that this can be used to assign hard labels, but does not
 			have the same semantics for soft labels, in that it only
@@ -580,7 +580,7 @@ def fit(self, X, sample_weight=None, priors=None):
 		"""
 
 		X, sample_weight, priors = partition_sequences(X, 
-			sample_weight=sample_weight, priors=priors)
+			sample_weight=sample_weight, priors=priors, n_dists=self.k)
 
 		# Initialize by concatenating across sequences
 		if not self._initialized:

tests/hmm/test_dense_hmm.py

@@ -1626,3 +1626,22 @@ def test_masked_fit(X, X_masked):
 	assert_array_almost_equal(d2.scales, [2.8777, 2.3498, 2.1939], 4)
 	assert_array_almost_equal(d2._w_sum, [0., 0., 0.])
 	assert_array_almost_equal(d2._xw_sum, [0., 0., 0.])
+
+
+@pytest.mark.parametrize("n_states", [2, 3, 4])
+def test_priors_in_fit_valid(n_states):
+	funcs = (lambda x: x, tuple, numpy.array,
+		lambda x: torch.from_numpy(numpy.array(x)))
+
+	# Data here is a 3D array of lists
+	_data = [[[1, 2, 3], [4, 5, 6], [7, 8, 9]],
+		[[10, 11, 12], [13, 14, 15], [16, 17, 18]],
+		[[19, 20, 21], [22, 23, 24], [25, 26, 27]]]
+
+	for func in funcs:
+		model = DenseHMM(distributions=[Exponential() for _ in range(n_states)])
+		data = func(_data)
+
+		priors = torch.ones((*numpy.array(data).shape[:-1], n_states)) / n_states
+
+		model.fit(data, priors=priors)

tests/test_utils.py

@@ -641,7 +641,7 @@ def test_partition_3d_Xp(X1, p1):
 		lambda x: torch.from_numpy(numpy.array(x)))
 
 	for func in funcs:
-		y, w, p = partition_sequences(func(X1), priors=func(p1))
+		y, w, p = partition_sequences(func(X1), priors=func(p1), n_dists=2)
 
 		assert isinstance(y, list)
 		assert len(y) == 1
@@ -667,8 +667,8 @@ def test_partition_3d_Xwp(X1, w1, p1):
 		lambda x: torch.from_numpy(numpy.array(x)))
 
 	for func in funcs:
-		y, w, p = partition_sequences(func(X1), sample_weight=func(w1), 
-			priors=func(p1))
+		y, w, p = partition_sequences(func(X1), sample_weight=func(w1),
+									  priors=func(p1), n_dists=2)
 
 		assert isinstance(y, list)
 		assert len(y) == 1
@@ -753,25 +753,6 @@ def test_partition_3ds_X(X2):
 			assert_array_almost_equal(y_, X2[i])
 
 
-def test_partition_3ds_X(X2):
-	funcs = (lambda x: x, tuple, numpy.array, 
-		lambda x: torch.from_numpy(numpy.array(x)))
-
-	for func in funcs:
-		X2_ = [func(x) for x in X2]
-
-		y, _, _ = partition_sequences(X2_)
-
-		assert isinstance(y, list)
-		assert len(y) == 2
-
-		for i, y_ in enumerate(y):
-			assert isinstance(y_, torch.Tensor)
-			assert y_.ndim == 3
-			assert y_.shape == (2, i+2, 2)
-			assert_array_almost_equal(y_, X2[i])
-
-
 def test_partition_3ds_Xw(X2, w2):
 	funcs = (lambda x: x, tuple, numpy.array, 
 		lambda x: torch.from_numpy(numpy.array(x)))
@@ -811,7 +792,7 @@ def test_partition_3ds_Xp(X2, p2):
 		X2_ = [func(x) for x in X2]
 		p2_ = [func(p) for p in p2]
 
-		y, w, p = partition_sequences(X2_, priors=p2_) 
+		y, w, p = partition_sequences(X2_, priors=p2_, n_dists=2)
 
 		assert isinstance(y, list)
 		assert len(y) == 2
@@ -843,7 +824,8 @@ def test_partition_3ds_Xwp(X2, w2, p2):
 		w2_ = [func(w) for w in w2]
 		p2_ = [func(p) for p in p2]
 
-		y, w, p = partition_sequences(X2_, sample_weight=w2_, priors=p2_) 
+		y, w, p = partition_sequences(X2_,
+			sample_weight=w2_, priors=p2_, n_dists=2)
 
 		assert isinstance(y, list)
 		assert len(y) == 2
@@ -1025,7 +1007,7 @@ def test_partition_2ds_Xp(X3, p3):
 		X3_ = [func(x) for x in X3]
 		p3_ = [func(p) for p in p3]
 
-		y, w, p = partition_sequences(X3_, priors=p3_) 
+		y, w, p = partition_sequences(X3_, priors=p3_, n_dists=2)
 
 		assert isinstance(y, list)
 		assert len(y) == 3
@@ -1056,7 +1038,7 @@ def test_partition_2ds_Xwp(X3, w3, p3):
 		w3_ = [func(w) for w in w3]
 		p3_ = [func(p) for p in p3]
 
-		y, w, p = partition_sequences(X3_, sample_weight=w3_, priors=p3_) 
+		y, w, p = partition_sequences(X3_, sample_weight=w3_, priors=p3_, n_dists=2)
 
 		assert isinstance(y, list)
 		assert len(y) == 3
@@ -1081,3 +1063,14 @@ def test_partition_2ds_Xwp(X3, w3, p3):
 			assert isinstance(p_, torch.Tensor)
 			assert p_.ndim == 3
 			assert p_.shape == ([1, 3, 2][i], i+1, 2)
+
+
+@pytest.mark.parametrize("X", [torch.ones((1, 10, 2)), [torch.ones((1, 10, 2)), torch.ones((2, 10, 2))]])
+@pytest.mark.parametrize("invalid", ["sample_weight", "priors"])
+def test_dont_hide_errors_for_priors_and_sample_weight(X, invalid):
+	"""Test that we get the correct error message when we don't pass data in case 3."""
+
+	with pytest.raises(ValueError) as excinfo:
+		partition_sequences(X, **{invalid: numpy.zeros((1, 1)) - 1}, n_dists=10)
+
+	assert invalid in str(excinfo.value)