Move from random seeding to local generators (PythonOT#512)

ot/dr.py

@@ -25,7 +25,7 @@
 import pymanopt.optimizers
 
 from .bregman import sinkhorn as sinkhorn_bregman
-from .utils import dist as dist_utils
+from .utils import dist as dist_utils, check_random_state
 
 
 def dist(x1, x2):
@@ -267,7 +267,7 @@ def proj(X):
     return Popt.point, proj
 
 
-def projection_robust_wasserstein(X, Y, a, b, tau, U0=None, reg=0.1, k=2, stopThr=1e-3, maxiter=100, verbose=0):
+def projection_robust_wasserstein(X, Y, a, b, tau, U0=None, reg=0.1, k=2, stopThr=1e-3, maxiter=100, verbose=0, random_state=None):
     r"""
     Projection Robust Wasserstein Distance :ref:`[32] <references-projection-robust-wasserstein>`
 
@@ -303,6 +303,9 @@ def projection_robust_wasserstein(X, Y, a, b, tau, U0=None, reg=0.1, k=2, stopTh
         Stop threshold on error (>0)
     verbose : int, optional
         Print information along iterations.
+    random_state : int, RandomState instance or None, default=None
+        Determines random number generation for initial value of projection
+        operator when U0 is not given.
 
     Returns
     -------
@@ -332,7 +335,8 @@ def projection_robust_wasserstein(X, Y, a, b, tau, U0=None, reg=0.1, k=2, stopTh
     assert d > k
 
     if U0 is None:
-        U = np.random.randn(d, k)
+        rng = check_random_state(random_state)
+        U = rng.randn(d, k)
         U, _ = np.linalg.qr(U)
     else:
         U = U0

ot/gromov/_dictionary.py

@@ -11,13 +11,13 @@
 import numpy as np
 
 
-from ..utils import unif
+from ..utils import unif, check_random_state
 from ..backend import get_backend
 from ._gw import gromov_wasserstein, fused_gromov_wasserstein
 
 
 def gromov_wasserstein_dictionary_learning(Cs, D, nt, reg=0., ps=None, q=None, epochs=20, batch_size=32, learning_rate=1., Cdict_init=None, projection='nonnegative_symmetric', use_log=True,
-                                           tol_outer=10**(-5), tol_inner=10**(-5), max_iter_outer=20, max_iter_inner=200, use_adam_optimizer=True, verbose=False, **kwargs):
+                                           tol_outer=10**(-5), tol_inner=10**(-5), max_iter_outer=20, max_iter_inner=200, use_adam_optimizer=True, verbose=False, random_state=None, **kwargs):
     r"""
     Infer Gromov-Wasserstein linear dictionary :math:`\{ (\mathbf{C_{dict}[d]}, q) \}_{d \in [D]}`  from the list of structures :math:`\{ (\mathbf{C_s},\mathbf{p_s}) \}_s`
 
@@ -81,6 +81,9 @@ def gromov_wasserstein_dictionary_learning(Cs, D, nt, reg=0., ps=None, q=None, e
         Maximum number of iterations for the Conjugate Gradient. Default is 200.
     verbose : bool, optional
         Print the reconstruction loss every epoch. Default is False.
+    random_state : int, RandomState instance or None, default=None
+        Determines random number generation. Pass an int for reproducible
+        output across multiple function calls.
 
     Returns
     -------
@@ -90,6 +93,7 @@ def gromov_wasserstein_dictionary_learning(Cs, D, nt, reg=0., ps=None, q=None, e
         The dictionary leading to the best loss over an epoch is saved and returned.
     log: dict
         If use_log is True, contains loss evolutions by batches and epochs.
+
     References
     -------
     .. [38] C. Vincent-Cuaz, T. Vayer, R. Flamary, M. Corneli, N. Courty, Online
@@ -110,10 +114,11 @@ def gromov_wasserstein_dictionary_learning(Cs, D, nt, reg=0., ps=None, q=None, e
         q = unif(nt)
     else:
         q = nx.to_numpy(q)
+    rng = check_random_state(random_state)
     if Cdict_init is None:
         # Initialize randomly structures of dictionary atoms based on samples
         dataset_means = [C.mean() for C in Cs]
-        Cdict = np.random.normal(loc=np.mean(dataset_means), scale=np.std(dataset_means), size=(D, nt, nt))
+        Cdict = rng.normal(loc=np.mean(dataset_means), scale=np.std(dataset_means), size=(D, nt, nt))
     else:
         Cdict = nx.to_numpy(Cdict_init).copy()
         assert Cdict.shape == (D, nt, nt)
@@ -141,7 +146,7 @@ def gromov_wasserstein_dictionary_learning(Cs, D, nt, reg=0., ps=None, q=None, e
 
         for _ in range(iter_by_epoch):
             # batch sampling
-            batch = np.random.choice(range(dataset_size), size=batch_size, replace=False)
+            batch = rng.choice(range(dataset_size), size=batch_size, replace=False)
             cumulated_loss_over_batch = 0.
             unmixings = np.zeros((batch_size, D))
             Cs_embedded = np.zeros((batch_size, nt, nt))
@@ -469,7 +474,8 @@ def _linesearch_gromov_wasserstein_unmixing(w, grad_w, x, Cdict, Cembedded, cons
 
 def fused_gromov_wasserstein_dictionary_learning(Cs, Ys, D, nt, alpha, reg=0., ps=None, q=None, epochs=20, batch_size=32, learning_rate_C=1., learning_rate_Y=1.,
                                                  Cdict_init=None, Ydict_init=None, projection='nonnegative_symmetric', use_log=False,
-                                                 tol_outer=10**(-5), tol_inner=10**(-5), max_iter_outer=20, max_iter_inner=200, use_adam_optimizer=True, verbose=False, **kwargs):
+                                                 tol_outer=10**(-5), tol_inner=10**(-5), max_iter_outer=20, max_iter_inner=200, use_adam_optimizer=True, verbose=False,
+                                                 random_state=None, **kwargs):
     r"""
     Infer Fused Gromov-Wasserstein linear dictionary :math:`\{ (\mathbf{C_{dict}[d]}, \mathbf{Y_{dict}[d]}, \mathbf{q}) \}_{d \in [D]}`  from the list of S attributed structures :math:`\{ (\mathbf{C_s}, \mathbf{Y_s},\mathbf{p_s}) \}_s`
 
@@ -548,6 +554,9 @@ def fused_gromov_wasserstein_dictionary_learning(Cs, Ys, D, nt, alpha, reg=0., p
         Maximum number of iterations for the Conjugate Gradient. Default is 200.
     verbose : bool, optional
         Print the reconstruction loss every epoch. Default is False.
+    random_state : int, RandomState instance or None, default=None
+        Determines random number generation. Pass an int for reproducible
+        output across multiple function calls.
 
     Returns
     -------
@@ -560,6 +569,7 @@ def fused_gromov_wasserstein_dictionary_learning(Cs, Ys, D, nt, alpha, reg=0., p
         The dictionary leading to the best loss over an epoch is saved and returned.
     log: dict
         If use_log is True, contains loss evolutions by batches and epochs.
+
     References
     -------
     .. [38] C. Vincent-Cuaz, T. Vayer, R. Flamary, M. Corneli, N. Courty, Online
@@ -583,17 +593,18 @@ def fused_gromov_wasserstein_dictionary_learning(Cs, Ys, D, nt, alpha, reg=0., p
     else:
         q = nx.to_numpy(q)
 
+    rng = check_random_state(random_state)
     if Cdict_init is None:
         # Initialize randomly structures of dictionary atoms based on samples
         dataset_means = [C.mean() for C in Cs]
-        Cdict = np.random.normal(loc=np.mean(dataset_means), scale=np.std(dataset_means), size=(D, nt, nt))
+        Cdict = rng.normal(loc=np.mean(dataset_means), scale=np.std(dataset_means), size=(D, nt, nt))
     else:
         Cdict = nx.to_numpy(Cdict_init).copy()
         assert Cdict.shape == (D, nt, nt)
     if Ydict_init is None:
         # Initialize randomly features of dictionary atoms based on samples distribution by feature component
         dataset_feature_means = np.stack([F.mean(axis=0) for F in Ys])
-        Ydict = np.random.normal(loc=dataset_feature_means.mean(axis=0), scale=dataset_feature_means.std(axis=0), size=(D, nt, d))
+        Ydict = rng.normal(loc=dataset_feature_means.mean(axis=0), scale=dataset_feature_means.std(axis=0), size=(D, nt, d))
     else:
         Ydict = nx.to_numpy(Ydict_init).copy()
         assert Ydict.shape == (D, nt, d)
@@ -626,7 +637,7 @@ def fused_gromov_wasserstein_dictionary_learning(Cs, Ys, D, nt, alpha, reg=0., p
         for _ in range(iter_by_epoch):
 
             # Batch iterations
-            batch = np.random.choice(range(dataset_size), size=batch_size, replace=False)
+            batch = rng.choice(range(dataset_size), size=batch_size, replace=False)
             cumulated_loss_over_batch = 0.
             unmixings = np.zeros((batch_size, D))
             Cs_embedded = np.zeros((batch_size, nt, nt))

ot/stochastic.py

@@ -10,7 +10,7 @@
 # License: MIT License
 
 import numpy as np
-from .utils import dist
+from .utils import dist, check_random_state
 from .backend import get_backend
 
 ##############################################################################
@@ -69,7 +69,7 @@ def coordinate_grad_semi_dual(b, M, reg, beta, i):
     return b - khi
 
 
-def sag_entropic_transport(a, b, M, reg, numItermax=10000, lr=None):
+def sag_entropic_transport(a, b, M, reg, numItermax=10000, lr=None, random_state=None):
     r"""
     Compute the SAG algorithm to solve the regularized discrete measures optimal transport max problem
 
@@ -110,6 +110,9 @@ def sag_entropic_transport(a, b, M, reg, numItermax=10000, lr=None):
         Number of iteration.
     lr : float
         Learning rate.
+    random_state : int, RandomState instance or None, default=None
+        Determines random number generation. Pass an int for reproducible
+        output across multiple function calls.
 
     Returns
     -------
@@ -129,8 +132,9 @@ def sag_entropic_transport(a, b, M, reg, numItermax=10000, lr=None):
     cur_beta = np.zeros(n_target)
     stored_gradient = np.zeros((n_source, n_target))
     sum_stored_gradient = np.zeros(n_target)
+    rng = check_random_state(random_state)
     for _ in range(numItermax):
-        i = np.random.randint(n_source)
+        i = rng.randint(n_source)
         cur_coord_grad = a[i] * coordinate_grad_semi_dual(b, M, reg,
                                                           cur_beta, i)
         sum_stored_gradient += (cur_coord_grad - stored_gradient[i])
@@ -139,7 +143,7 @@ def sag_entropic_transport(a, b, M, reg, numItermax=10000, lr=None):
     return cur_beta
 
 
-def averaged_sgd_entropic_transport(a, b, M, reg, numItermax=300000, lr=None):
+def averaged_sgd_entropic_transport(a, b, M, reg, numItermax=300000, lr=None, random_state=None):
     r'''
     Compute the ASGD algorithm to solve the regularized semi continous measures optimal transport max problem
 
@@ -177,6 +181,9 @@ def averaged_sgd_entropic_transport(a, b, M, reg, numItermax=300000, lr=None):
         Number of iteration.
     lr : float
         Learning rate.
+    random_state : int, RandomState instance or None, default=None
+        Determines random number generation. Pass an int for reproducible
+        output across multiple function calls.
 
     Returns
     -------
@@ -195,9 +202,10 @@ def averaged_sgd_entropic_transport(a, b, M, reg, numItermax=300000, lr=None):
     n_target = np.shape(M)[1]
     cur_beta = np.zeros(n_target)
     ave_beta = np.zeros(n_target)
+    rng = check_random_state(random_state)
     for cur_iter in range(numItermax):
         k = cur_iter + 1
-        i = np.random.randint(n_source)
+        i = rng.randint(n_source)
         cur_coord_grad = coordinate_grad_semi_dual(b, M, reg, cur_beta, i)
         cur_beta += (lr / np.sqrt(k)) * cur_coord_grad
         ave_beta = (1. / k) * cur_beta + (1 - 1. / k) * ave_beta
@@ -422,7 +430,7 @@ def batch_grad_dual(a, b, M, reg, alpha, beta, batch_size, batch_alpha,
     return grad_alpha, grad_beta
 
 
-def sgd_entropic_regularization(a, b, M, reg, batch_size, numItermax, lr):
+def sgd_entropic_regularization(a, b, M, reg, batch_size, numItermax, lr, random_state=None):
     r'''
     Compute the sgd algorithm to solve the regularized discrete measures optimal transport dual problem
 
@@ -460,6 +468,9 @@ def sgd_entropic_regularization(a, b, M, reg, batch_size, numItermax, lr):
         number of iteration
     lr : float
         learning rate
+    random_state : int, RandomState instance or None, default=None
+        Determines random number generation. Pass an int for reproducible
+        output across multiple function calls.
 
     Returns
     -------
@@ -477,10 +488,11 @@ def sgd_entropic_regularization(a, b, M, reg, batch_size, numItermax, lr):
     n_target = np.shape(M)[1]
     cur_alpha = np.zeros(n_source)
     cur_beta = np.zeros(n_target)
+    rng = check_random_state(random_state)
     for cur_iter in range(numItermax):
         k = np.sqrt(cur_iter + 1)
-        batch_alpha = np.random.choice(n_source, batch_size, replace=False)
-        batch_beta = np.random.choice(n_target, batch_size, replace=False)
+        batch_alpha = rng.choice(n_source, batch_size, replace=False)
+        batch_beta = rng.choice(n_target, batch_size, replace=False)
         update_alpha, update_beta = batch_grad_dual(a, b, M, reg, cur_alpha,
                                                     cur_beta, batch_size,
                                                     batch_alpha, batch_beta)

test/test_1d_solver.py

@@ -163,8 +163,8 @@ def test_emd_1d_emd2_1d():
     np.testing.assert_allclose(G, G_1d, atol=1e-15)
 
     # check AssertionError is raised if called on non 1d arrays
-    u = np.random.randn(n, 2)
-    v = np.random.randn(m, 2)
+    u = rng.randn(n, 2)
+    v = rng.randn(m, 2)
     with pytest.raises(AssertionError):
         ot.emd_1d(u, v, [], [])
 

test/test_bregman.py

@@ -298,7 +298,8 @@ def test_sinkhorn_variants(nx):
 def test_sinkhorn_variants_dtype_device(nx, method):
     n = 100
 
-    x = np.random.randn(n, 2)
+    rng = np.random.RandomState(42)
+    x = rng.randn(n, 2)
     u = ot.utils.unif(n)
 
     M = ot.dist(x, x)
@@ -317,7 +318,8 @@ def test_sinkhorn_variants_dtype_device(nx, method):
 def test_sinkhorn2_variants_dtype_device(nx, method):
     n = 100
 
-    x = np.random.randn(n, 2)
+    rng = np.random.RandomState(42)
+    x = rng.randn(n, 2)
     u = ot.utils.unif(n)
 
     M = ot.dist(x, x)
@@ -337,7 +339,8 @@ def test_sinkhorn2_variants_dtype_device(nx, method):
 def test_sinkhorn2_variants_device_tf(method):
     nx = ot.backend.TensorflowBackend()
     n = 100
-    x = np.random.randn(n, 2)
+    rng = np.random.RandomState(42)
+    x = rng.randn(n, 2)
     u = ot.utils.unif(n)
     M = ot.dist(x, x)
 
@@ -690,11 +693,12 @@ def test_barycenter_stabilization(nx):
 
 @pytest.mark.parametrize("method", ["sinkhorn", "sinkhorn_log"])
 def test_wasserstein_bary_2d(nx, method):
+    rng = np.random.RandomState(42)
     size = 20  # size of a square image
-    a1 = np.random.rand(size, size)
+    a1 = rng.rand(size, size)
     a1 += a1.min()
     a1 = a1 / np.sum(a1)
-    a2 = np.random.rand(size, size)
+    a2 = rng.rand(size, size)
     a2 += a2.min()
     a2 = a2 / np.sum(a2)
     # creating matrix A containing all distributions
@@ -724,11 +728,12 @@ def test_wasserstein_bary_2d(nx, method):
 
 @pytest.mark.parametrize("method", ["sinkhorn", "sinkhorn_log"])
 def test_wasserstein_bary_2d_debiased(nx, method):
+    rng = np.random.RandomState(42)
     size = 20  # size of a square image
-    a1 = np.random.rand(size, size)
+    a1 = rng.rand(size, size)
     a1 += a1.min()
     a1 = a1 / np.sum(a1)
-    a2 = np.random.rand(size, size)
+    a2 = rng.rand(size, size)
     a2 += a2.min()
     a2 = a2 / np.sum(a2)
     # creating matrix A containing all distributions

test/test_coot.py

@@ -223,21 +223,22 @@ def test_coot_warmstart(nx):
     xt_nx = nx.from_numpy(xt)
 
     # initialize warmstart
-    init_pi_sample = np.random.rand(n_samples, n_samples)
+    rng = np.random.RandomState(42)
+    init_pi_sample = rng.rand(n_samples, n_samples)
     init_pi_sample = init_pi_sample / np.sum(init_pi_sample)
     init_pi_sample_nx = nx.from_numpy(init_pi_sample)
 
-    init_pi_feature = np.random.rand(2, 2)
+    init_pi_feature = rng.rand(2, 2)
     init_pi_feature /= init_pi_feature / np.sum(init_pi_feature)
     init_pi_feature_nx = nx.from_numpy(init_pi_feature)
 
-    init_duals_sample = (np.random.random(n_samples) * 2 - 1,
-                         np.random.random(n_samples) * 2 - 1)
+    init_duals_sample = (rng.random(n_samples) * 2 - 1,
+                         rng.random(n_samples) * 2 - 1)
     init_duals_sample_nx = (nx.from_numpy(init_duals_sample[0]),
                             nx.from_numpy(init_duals_sample[1]))
 
-    init_duals_feature = (np.random.random(2) * 2 - 1,
-                          np.random.random(2) * 2 - 1)
+    init_duals_feature = (rng.random(2) * 2 - 1,
+                          rng.random(2) * 2 - 1)
     init_duals_feature_nx = (nx.from_numpy(init_duals_feature[0]),
                              nx.from_numpy(init_duals_feature[1]))
 

test/test_da.py

@@ -567,12 +567,11 @@ def test_mapping_transport_class_specific_seed(nx):
     # check that it does not crash when derphi is very close to 0
     ns = 20
     nt = 30
-    np.random.seed(39)
-    Xs, ys = make_data_classif('3gauss', ns)
-    Xt, yt = make_data_classif('3gauss2', nt)
+    rng = np.random.RandomState(39)
+    Xs, ys = make_data_classif('3gauss', ns, random_state=rng)
+    Xt, yt = make_data_classif('3gauss2', nt, random_state=rng)
     otda = ot.da.MappingTransport(kernel="gaussian", bias=False)
     otda.fit(Xs=nx.from_numpy(Xs), Xt=nx.from_numpy(Xt))
-    np.random.seed(None)
 
 
 @pytest.skip_backend("jax")
@@ -712,7 +711,6 @@ def test_jcpot_barycenter(nx):
     nt = 50
 
     sigma = 0.1
-    np.random.seed(1985)
 
     ps1 = .2
     ps2 = .9

test/test_dmmot.py

@@ -10,7 +10,6 @@
 
 
 def create_test_data(nx):
-    np.random.seed(1234)
     n = 4
     a1 = ot.datasets.make_1D_gauss(n, m=20, s=5)
     a2 = ot.datasets.make_1D_gauss(n, m=60, s=8)