Merge branch 'master' into fix-backend-allocations

Author: rflamary

RELEASES.md

@@ -4,6 +4,7 @@
 
 #### New features
 + Tweaked `get_backend` to ignore `None` inputs (PR # 525)
++ Callbacks for generalized conditional gradient in `ot.da.sinkhorn_l1l2_gl` are now vectorized to improve performance (PR #507)
 
 #### Closed issues
 - Fix line search evaluating cost outside of the interpolation range (Issue #502, PR #504)

ot/backend.py

@@ -460,7 +460,7 @@ def power(self, a, exponents):
         """
         raise NotImplementedError()
 
-    def norm(self, a):
+    def norm(self, a, axis=None, keepdims=False):
         r"""
         Computes the matrix frobenius norm.
 
@@ -680,7 +680,7 @@ def diag(self, a, k=0):
         """
         raise NotImplementedError()
 
-    def unique(self, a):
+    def unique(self, a, return_inverse=False):
         r"""
         Finds unique elements of given tensor.
 
@@ -1140,8 +1140,8 @@ def sqrt(self, a):
     def power(self, a, exponents):
         return np.power(a, exponents)
 
-    def norm(self, a):
-        return np.sqrt(np.sum(np.square(a)))
+    def norm(self, a, axis=None, keepdims=False):
+        return np.linalg.norm(a, axis=axis, keepdims=keepdims)
 
     def any(self, a):
         return np.any(a)
@@ -1217,8 +1217,8 @@ def meshgrid(self, a, b):
     def diag(self, a, k=0):
         return np.diag(a, k)
 
-    def unique(self, a):
-        return np.unique(a)
+    def unique(self, a, return_inverse=False):
+        return np.unique(a, return_inverse=return_inverse)
 
     def logsumexp(self, a, axis=None):
         return special.logsumexp(a, axis=axis)
@@ -1514,8 +1514,8 @@ def sqrt(self, a):
     def power(self, a, exponents):
         return jnp.power(a, exponents)
 
-    def norm(self, a):
-        return jnp.sqrt(jnp.sum(jnp.square(a)))
+    def norm(self, a, axis=None, keepdims=False):
+        return jnp.linalg.norm(a, axis=axis, keepdims=keepdims)
 
     def any(self, a):
         return jnp.any(a)
@@ -1588,8 +1588,8 @@ def meshgrid(self, a, b):
     def diag(self, a, k=0):
         return jnp.diag(a, k)
 
-    def unique(self, a):
-        return jnp.unique(a)
+    def unique(self, a, return_inverse=False):
+        return jnp.unique(a, return_inverse=return_inverse)
 
     def logsumexp(self, a, axis=None):
         return jspecial.logsumexp(a, axis=axis)
@@ -1934,8 +1934,8 @@ def sqrt(self, a):
     def power(self, a, exponents):
         return torch.pow(a, exponents)
 
-    def norm(self, a):
-        return torch.sqrt(torch.sum(torch.square(a)))
+    def norm(self, a, axis=None, keepdims=False):
+        return torch.linalg.norm(a.double(), dim=axis, keepdims=keepdims)
 
     def any(self, a):
         return torch.any(a)
@@ -2039,8 +2039,8 @@ def meshgrid(self, a, b):
     def diag(self, a, k=0):
         return torch.diag(a, diagonal=k)
 
-    def unique(self, a):
-        return torch.unique(a)
+    def unique(self, a, return_inverse=False):
+        return torch.unique(a, return_inverse=return_inverse)
 
     def logsumexp(self, a, axis=None):
         if axis is not None:
@@ -2359,8 +2359,8 @@ def power(self, a, exponents):
     def dot(self, a, b):
         return cp.dot(a, b)
 
-    def norm(self, a):
-        return cp.sqrt(cp.sum(cp.square(a)))
+    def norm(self, a, axis=None, keepdims=False):
+        return cp.linalg.norm(a, axis=axis, keepdims=keepdims)
 
     def any(self, a):
         return cp.any(a)
@@ -2436,8 +2436,8 @@ def meshgrid(self, a, b):
     def diag(self, a, k=0):
         return cp.diag(a, k)
 
-    def unique(self, a):
-        return cp.unique(a)
+    def unique(self, a, return_inverse=False):
+        return cp.unique(a, return_inverse=return_inverse)
 
     def logsumexp(self, a, axis=None):
         # Taken from
@@ -2770,8 +2770,8 @@ def sqrt(self, a):
     def power(self, a, exponents):
         return tnp.power(a, exponents)
 
-    def norm(self, a):
-        return tf.math.reduce_euclidean_norm(a)
+    def norm(self, a, axis=None, keepdims=False):
+        return tf.math.reduce_euclidean_norm(a, axis=axis, keepdims=keepdims)
 
     def any(self, a):
         return tnp.any(a)
@@ -2843,8 +2843,15 @@ def meshgrid(self, a, b):
     def diag(self, a, k=0):
         return tnp.diag(a, k)
 
-    def unique(self, a):
-        return tf.sort(tf.unique(tf.reshape(a, [-1]))[0])
+    def unique(self, a, return_inverse=False):
+        y, idx = tf.unique(tf.reshape(a, [-1]))
+        sort_idx = tf.argsort(y)
+        y_prime = tf.gather(y, sort_idx)
+        if return_inverse:
+            inv_sort_idx = tf.math.invert_permutation(sort_idx)
+            return y_prime, tf.gather(inv_sort_idx, idx)
+        else:
+            return y_prime
 
     def logsumexp(self, a, axis=None):
         return tf.math.reduce_logsumexp(a, axis=axis)

ot/da.py

@@ -148,8 +148,8 @@ def sinkhorn_lpl1_mm(a, labels_a, b, M, reg, eta=0.1, numItermax=10,
 
 
 def sinkhorn_l1l2_gl(a, labels_a, b, M, reg, eta=0.1, numItermax=10,
-                     numInnerItermax=200, stopInnerThr=1e-9, verbose=False,
-                     log=False):
+                     numInnerItermax=200, stopInnerThr=1e-9, eps=1e-12,
+                     verbose=False, log=False):
     r"""
     Solve the entropic regularization optimal transport problem with group
     lasso regularization
@@ -202,6 +202,8 @@ def sinkhorn_l1l2_gl(a, labels_a, b, M, reg, eta=0.1, numItermax=10,
         Max number of iterations (inner sinkhorn solver)
     stopInnerThr : float, optional
         Stop threshold on error (inner sinkhorn solver) (>0)
+    eps: float, optional (default=1e-12)
+        Small value to avoid division by zero
     verbose : bool, optional
         Print information along iterations
     log : bool, optional
@@ -235,25 +237,19 @@ def sinkhorn_l1l2_gl(a, labels_a, b, M, reg, eta=0.1, numItermax=10,
     a, labels_a, b, M = list_to_array(a, labels_a, b, M)
     nx = get_backend(a, labels_a, b, M)
 
-    lstlab = nx.unique(labels_a)
+    labels_u, labels_idx = nx.unique(labels_a, return_inverse=True)
+    n_labels = labels_u.shape[0]
+    unroll_labels_idx = nx.eye(n_labels, type_as=labels_u)[None, labels_idx]
 
     def f(G):
-        res = 0
-        for i in range(G.shape[1]):
-            for lab in lstlab:
-                temp = G[labels_a == lab, i]
-                res += nx.norm(temp)
-        return res
+        G_split = nx.repeat(G.T[:, :, None], n_labels, axis=2)
+        return nx.sum(nx.norm(G_split * unroll_labels_idx, axis=1))
 
     def df(G):
-        W = nx.zeros(G.shape, type_as=G)
-        for i in range(G.shape[1]):
-            for lab in lstlab:
-                temp = G[labels_a == lab, i]
-                n = nx.norm(temp)
-                if n:
-                    W[labels_a == lab, i] = temp / n
-        return W
+        G_split = nx.repeat(G.T[:, :, None], n_labels, axis=2) * unroll_labels_idx
+        W = nx.norm(G_split * unroll_labels_idx, axis=1, keepdims=True)
+        G_norm = G_split / nx.clip(W, eps, None)
+        return nx.sum(G_norm, axis=2).T
 
     return gcg(a, b, M, reg, eta, f, df, G0=None, numItermax=numItermax,
                numInnerItermax=numInnerItermax, stopThr=stopInnerThr,

test/test_backend.py

@@ -412,6 +412,14 @@ def test_func_backends(nx):
         lst_b.append(nx.to_numpy(A))
         lst_name.append('norm')
 
+        A = nx.norm(Mb, axis=1)
+        lst_b.append(nx.to_numpy(A))
+        lst_name.append('norm(M,axis=1)')
+
+        A = nx.norm(Mb, axis=1, keepdims=True)
+        lst_b.append(nx.to_numpy(A))
+        lst_name.append('norm(M,axis=1,keepdims=True)')
+
         A = nx.any(vb > 0)
         lst_b.append(nx.to_numpy(A))
         lst_name.append('any')
@@ -518,6 +526,12 @@ def test_func_backends(nx):
         lst_b.append(nx.to_numpy(A))
         lst_name.append('unique')
 
+        A, A2 = nx.unique(nx.from_numpy(np.stack([M, M]).reshape(-1)), return_inverse=True)
+        lst_b.append(nx.to_numpy(A))
+        lst_name.append('unique(M,return_inverse=True)[0]')
+        lst_b.append(nx.to_numpy(A2))
+        lst_name.append('unique(M,return_inverse=True)[1]')
+
         A = nx.logsumexp(Mb)
         lst_b.append(nx.to_numpy(A))
         lst_name.append('logsumexp')

test/test_da.py

@@ -801,3 +801,52 @@ def test_emd_laplace_class(nx):
     transp_ys = otda.inverse_transform_labels(yt)
     assert_equal(transp_ys.shape[0], ys.shape[0])
     assert_equal(transp_ys.shape[1], len(np.unique(nx.to_numpy(yt))))
+
+
+@pytest.skip_backend("jax")
+@pytest.skip_backend("tf")
+def test_sinkhorn_l1l2_gl_cost_vectorized(nx):
+    n_samples, n_labels = 150, 3
+    rng = np.random.RandomState(42)
+    G = rng.rand(n_samples, n_samples)
+    labels_a = rng.randint(n_labels, size=(n_samples,))
+    G, labels_a = nx.from_numpy(G), nx.from_numpy(labels_a)
+
+    # previously used implementation for the cost estimator
+    lstlab = nx.unique(labels_a)
+
+    def f(G):
+        res = 0
+        for i in range(G.shape[1]):
+            for lab in lstlab:
+                temp = G[labels_a == lab, i]
+                res += nx.norm(temp)
+        return res
+
+    def df(G):
+        W = nx.zeros(G.shape, type_as=G)
+        for i in range(G.shape[1]):
+            for lab in lstlab:
+                temp = G[labels_a == lab, i]
+                n = nx.norm(temp)
+                if n:
+                    W[labels_a == lab, i] = temp / n
+        return W
+
+    # new vectorized implementation for the cost estimator
+    labels_u, labels_idx = nx.unique(labels_a, return_inverse=True)
+    n_labels = labels_u.shape[0]
+    unroll_labels_idx = nx.eye(n_labels, type_as=labels_u)[None, labels_idx]
+
+    def f2(G):
+        G_split = nx.repeat(G.T[:, :, None], n_labels, axis=2)
+        return nx.sum(nx.norm(G_split * unroll_labels_idx, axis=1))
+
+    def df2(G):
+        G_split = nx.repeat(G.T[:, :, None], n_labels, axis=2) * unroll_labels_idx
+        W = nx.norm(G_split * unroll_labels_idx, axis=1, keepdims=True)
+        G_norm = G_split / nx.clip(W, 1e-12, None)
+        return nx.sum(G_norm, axis=2).T
+
+    assert np.allclose(f(G), f2(G))
+    assert np.allclose(df(G), df2(G))