Simple stick breaking (Formerly #3620)

pymc3/distributions/transforms.py

@@ -1,3 +1,5 @@
+import warnings
+
 import theano
 import theano.tensor as tt
 
@@ -14,6 +16,7 @@
 __all__ = [
     "transform",
     "stick_breaking",
+    "stick_breaking2",
     "logodds",
     "interval",
     "log_exp_m1",
@@ -510,6 +513,62 @@ def t_stick_breaking(eps):
     return StickBreaking(eps)
 
 
+class StickBreaking2(Transform):
+    """
+    Transforms K - 1 dimensional simplex space (k values in [0,1] and that sum to 1) to a K - 1 vector of real values.
+    """
+
+    name = "stickbreaking"
+
+    def __init__(self, eps=None):
+        if eps is not None:
+            warnings.warn("The argument `eps` is depricated and will not be used.",
+                          DeprecationWarning)
+
+    def forward(self, x_):
+        x = x_.T
+        n = x.shape[0]
+        lx = tt.log(x)
+        shift = tt.sum(lx, 0, keepdims=True) / n
+        y = lx[:-1] - shift
+        return floatX(y.T)
+
+    def forward_val(self, x_):
+        x = x_.T
+        n = x.shape[0]
+        lx = np.log(x)
+        shift = np.sum(lx, 0, keepdims=True) / n
+        y = lx[:-1] - shift
+        return floatX(y.T)
+
+    def backward(self, y_):
+        y = y_.T
+        y = tt.concatenate([y, -tt.sum(y, 0, keepdims=True)])
+        # "softmax" with vector support and no deprication warning:
+        e_y = tt.exp(y - tt.max(y, 0, keepdims=True))
+        x = e_y / tt.sum(e_y, 0, keepdims=True)
+        return floatX(x.T)
+
+    def backward_val(self, y_):
+        y = y_.T
+        y = np.concatenate([y, -np.sum(y, 0, keepdims=True)])
+        x = np.exp(y)/np.sum(np.exp(y), 0, keepdims=True)
+        return floatX(x.T)
+
+    def jacobian_det(self, y_):
+        y = y_.T
+        Km1 = y.shape[0]
+        sy = tt.sum(y, 0, keepdims=True)
+        r = tt.concatenate([y+sy, tt.zeros(sy.shape)])
+        # stable according to: http://deeplearning.net/software/theano_versions/0.9.X/NEWS.html
+        sr = tt.log(tt.sum(tt.exp(r), 0, keepdims=True))
+        d = tt.log(Km1) + (Km1*sy) - (Km1*sr)
+        return tt.sum(d, 0).T
+
+
+stick_breaking2 = StickBreaking2()
+
+
 class Circular(ElemwiseTransform):
     """Transforms a linear space into a circular one.
     """

pymc3/tests/test_transforms.py

@@ -70,15 +70,15 @@ def check_jacobian_det(transform, domain,
             computed_ljd(yval), tol)
 
 
-def test_simplex():
+def test_stickbreaking():
     check_vector_transform(tr.stick_breaking, Simplex(2))
     check_vector_transform(tr.stick_breaking, Simplex(4))
 
     check_transform(tr.stick_breaking, MultiSimplex(
         3, 2), constructor=tt.dmatrix, test=np.zeros((2, 2)))
 
 
-def test_simplex_bounds():
+def test_stickbreaking_bounds():
     vals = get_values(tr.stick_breaking, Vector(R, 2),
                       tt.dvector, np.array([0, 0]))
 
@@ -90,6 +90,27 @@ def test_simplex_bounds():
         R, 2), tt.dvector, np.array([0, 0]), lambda x: x[:-1])
 
 
+def test_stickbreaking2():
+    check_vector_transform(tr.stick_breaking2, Simplex(2))
+    check_vector_transform(tr.stick_breaking2, Simplex(4))
+
+    check_transform(tr.stick_breaking2, MultiSimplex(
+        3, 2), constructor=tt.dmatrix, test=np.zeros((2, 2)))
+
+
+def test_stickbreaking2_bounds():
+    vals = get_values(tr.stick_breaking2, Vector(R, 2),
+                      tt.dvector, np.array([0, 0]))
+
+    close_to(vals.sum(axis=1), 1, tol)
+    close_to_logical(vals > 0, True, tol)
+    close_to_logical(vals < 1, True, tol)
+
+    check_jacobian_det(tr.stick_breaking2, Vector(R, 2),
+                       tt.dvector, np.array([0, 0]),
+                       lambda x: x[:-1])
+
+
 def test_sum_to_1():
     check_vector_transform(tr.sum_to_1, Simplex(2))
     check_vector_transform(tr.sum_to_1, Simplex(4))