# -*- coding: utf-8 -*-
"""
Partial OT solvers
"""
# Author: Laetitia Chapel <laetitia.chapel@irisa.fr>
# Yikun Bai < yikun.bai@vanderbilt.edu >
# Cédric Vincent-Cuaz <cedvincentcuaz@gmail.com>
from .utils import list_to_array
from .backend import get_backend
from .lp import emd
import numpy as np
import warnings
# License: MIT License
[docs]
def partial_wasserstein_lagrange(
a, b, M, reg_m=None, nb_dummies=1, log=False, **kwargs
):
r"""
Solves the partial optimal transport problem for the quadratic cost
and returns the OT plan
The function considers the following problem:
.. math::
\gamma = \mathop{\arg \min}_\gamma \quad \langle \gamma, (\mathbf{M} - \lambda) \rangle_F
.. math::
s.t. \ \gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\gamma &\geq 0
\mathbf{1}^T \gamma^T \mathbf{1} = m &
\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
or equivalently (see Chizat, L., Peyré, G., Schmitzer, B., & Vialard, F. X.
(2018). An interpolating distance between optimal transport and Fisher–Rao
metrics. Foundations of Computational Mathematics, 18(1), 1-44.)
.. math::
\gamma = \mathop{\arg \min}_\gamma \quad \langle \gamma, \mathbf{M} \rangle_F +
\sqrt{\frac{\lambda}{2} (\|\gamma \mathbf{1} - \mathbf{a}\|_1 + \|\gamma^T \mathbf{1} - \mathbf{b}\|_1)}
s.t. \ \gamma \geq 0
where :
- :math:`\mathbf{M}` is the metric cost matrix
- :math:`\mathbf{a}` and :math:`\mathbf{b}` are source and target unbalanced distributions
- :math:`\lambda` is the lagrangian cost. Tuning its value allows attaining
a given mass to be transported `m`
The formulation of the problem has been proposed in
:ref:`[28] <references-partial-wasserstein-lagrange>`
Parameters
----------
a : np.ndarray (dim_a,)
Unnormalized histogram of dimension `dim_a`
b : np.ndarray (dim_b,)
Unnormalized histograms of dimension `dim_b`
M : np.ndarray (dim_a, dim_b)
cost matrix for the quadratic cost
reg_m : float, optional
Lagrangian cost
nb_dummies : int, optional, default:1
number of reservoir points to be added (to avoid numerical
instabilities, increase its value if an error is raised)
log : bool, optional
record log if True
**kwargs : dict
parameters can be directly passed to the emd solver
.. warning::
When dealing with a large number of points, the EMD solver may face
some instabilities, especially when the mass associated to the dummy
point is large. To avoid them, increase the number of dummy points
(allows a smoother repartition of the mass over the points).
Returns
-------
gamma : (dim_a, dim_b) ndarray
Optimal transportation matrix for the given parameters
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> a = [.1, .2]
>>> b = [.1, .1]
>>> M = [[0., 1.], [2., 3.]]
>>> np.round(partial_wasserstein_lagrange(a,b,M), 2)
array([[0.1, 0. ],
[0. , 0.1]])
>>> np.round(partial_wasserstein_lagrange(a,b,M,reg_m=2), 2)
array([[0.1, 0. ],
[0. , 0. ]])
.. _references-partial-wasserstein-lagrange:
References
----------
.. [28] Caffarelli, L. A., & McCann, R. J. (2010) Free boundaries in
optimal transport and Monge-Ampere obstacle problems. Annals of
mathematics, 673-730.
See Also
--------
ot.partial.partial_wasserstein : Partial Wasserstein with fixed mass
"""
a, b, M = list_to_array(a, b, M)
nx = get_backend(a, b, M)
if nx.sum(a) > 1 + 1e-15 or nx.sum(b) > 1 + 1e-15: # 1e-15 for numerical errors
raise ValueError("Problem infeasible. Check that a and b are in the " "simplex")
if reg_m is None:
reg_m = float(nx.max(M)) + 1
if reg_m < -nx.max(M):
return nx.zeros((len(a), len(b)), type_as=M)
a0, b0, M0 = a, b, M
# convert to humpy
a, b, M = nx.to_numpy(a, b, M)
eps = 1e-20
M = np.asarray(M, dtype=np.float64)
b = np.asarray(b, dtype=np.float64)
a = np.asarray(a, dtype=np.float64)
M_star = M - reg_m # modified cost matrix
# trick to fasten the computation: select only the subset of columns/lines
# that can have marginals greater than 0 (that is to say M < 0)
idx_x = np.where(np.min(M_star, axis=1) < eps)[0]
idx_y = np.where(np.min(M_star, axis=0) < eps)[0]
# extend a, b, M with "reservoir" or "dummy" points
M_extended = np.zeros((len(idx_x) + nb_dummies, len(idx_y) + nb_dummies))
M_extended[: len(idx_x), : len(idx_y)] = M_star[np.ix_(idx_x, idx_y)]
a_extended = np.append(
a[idx_x], [(np.sum(a) - np.sum(a[idx_x]) + np.sum(b)) / nb_dummies] * nb_dummies
)
b_extended = np.append(
b[idx_y], [(np.sum(b) - np.sum(b[idx_y]) + np.sum(a)) / nb_dummies] * nb_dummies
)
gamma_extended, log_emd = emd(
a_extended, b_extended, M_extended, log=True, **kwargs
)
gamma = np.zeros((len(a), len(b)))
gamma[np.ix_(idx_x, idx_y)] = gamma_extended[:-nb_dummies, :-nb_dummies]
# convert back to backend
gamma = nx.from_numpy(gamma, type_as=M0)
if log_emd["warning"] is not None:
raise ValueError(
"Error in the EMD resolution: try to increase the" " number of dummy points"
)
log_emd["cost"] = nx.sum(gamma * M0)
log_emd["u"] = nx.from_numpy(log_emd["u"], type_as=a0)
log_emd["v"] = nx.from_numpy(log_emd["v"], type_as=b0)
if log:
return gamma, log_emd
else:
return gamma
[docs]
def partial_wasserstein(a, b, M, m=None, nb_dummies=1, log=False, **kwargs):
r"""
Solves the partial optimal transport problem for the quadratic cost
and returns the OT plan
The function considers the following problem:
.. math::
\gamma = \mathop{\arg \min}_\gamma \quad \langle \gamma, \mathbf{M} \rangle_F
.. math::
s.t. \ \gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\gamma &\geq 0
\mathbf{1}^T \gamma^T \mathbf{1} = m &\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
where :
- :math:`\mathbf{M}` is the metric cost matrix
- :math:`\mathbf{a}` and :math:`\mathbf{b}` are source and target unbalanced distributions
- `m` is the amount of mass to be transported
Parameters
----------
a : np.ndarray (dim_a,)
Unnormalized histogram of dimension `dim_a`
b : np.ndarray (dim_b,)
Unnormalized histograms of dimension `dim_b`
M : np.ndarray (dim_a, dim_b)
cost matrix for the quadratic cost
m : float, optional
amount of mass to be transported
nb_dummies : int, optional, default:1
number of reservoir points to be added (to avoid numerical
instabilities, increase its value if an error is raised)
log : bool, optional
record log if True
**kwargs : dict
parameters can be directly passed to the emd solver
.. warning::
When dealing with a large number of points, the EMD solver may face
some instabilities, especially when the mass associated to the dummy
point is large. To avoid them, increase the number of dummy points
(allows a smoother repartition of the mass over the points).
Returns
-------
gamma : (dim_a, dim_b) ndarray
Optimal transportation matrix for the given parameters
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> a = [.1, .2]
>>> b = [.1, .1]
>>> M = [[0., 1.], [2., 3.]]
>>> np.round(partial_wasserstein(a,b,M), 2)
array([[0.1, 0. ],
[0. , 0.1]])
>>> np.round(partial_wasserstein(a,b,M,m=0.1), 2)
array([[0.1, 0. ],
[0. , 0. ]])
References
----------
.. [28] Caffarelli, L. A., & McCann, R. J. (2010) Free boundaries in
optimal transport and Monge-Ampere obstacle problems. Annals of
mathematics, 673-730.
.. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
Transport with Applications on Positive-Unlabeled Learning".
NeurIPS.
See Also
--------
ot.partial.partial_wasserstein_lagrange: Partial Wasserstein with
regularization on the marginals
ot.partial.entropic_partial_wasserstein: Partial Wasserstein with a
entropic regularization parameter
"""
a, b, M = list_to_array(a, b, M)
nx = get_backend(a, b, M)
dim_a, dim_b = M.shape
if len(a) == 0:
a = nx.ones(dim_a, type_as=a) / dim_a
if len(b) == 0:
b = nx.ones(dim_b, type_as=b) / dim_b
if m is None:
return partial_wasserstein_lagrange(a, b, M, log=log, **kwargs)
elif m < 0:
raise ValueError("Problem infeasible. Parameter m should be greater" " than 0.")
elif m > nx.min(nx.stack((nx.sum(a), nx.sum(b)))):
raise ValueError(
"Problem infeasible. Parameter m should lower or"
" equal than min(|a|_1, |b|_1)."
)
b_extension = nx.ones(nb_dummies, type_as=b) * (nx.sum(a) - m) / nb_dummies
b_extended = nx.concatenate((b, b_extension))
a_extension = nx.ones(nb_dummies, type_as=a) * (nx.sum(b) - m) / nb_dummies
a_extended = nx.concatenate((a, a_extension))
M_extension = nx.ones((nb_dummies, nb_dummies), type_as=M) * nx.max(M) * 2
M_extended = nx.concatenate(
(
nx.concatenate((M, nx.zeros((M.shape[0], M_extension.shape[1]))), axis=1),
nx.concatenate(
(nx.zeros((M_extension.shape[0], M.shape[1])), M_extension), axis=1
),
),
axis=0,
)
gamma, log_emd = emd(a_extended, b_extended, M_extended, log=True, **kwargs)
gamma = gamma[: len(a), : len(b)]
if log_emd["warning"] is not None:
raise ValueError(
"Error in the EMD resolution: try to increase the" " number of dummy points"
)
log_emd["partial_w_dist"] = nx.sum(M * gamma)
log_emd["u"] = log_emd["u"][: len(a)]
log_emd["v"] = log_emd["v"][: len(b)]
if log:
return gamma, log_emd
else:
return gamma
[docs]
def partial_wasserstein2(a, b, M, m=None, nb_dummies=1, log=False, **kwargs):
r"""
Solves the partial optimal transport problem for the quadratic cost
and returns the partial GW discrepancy
The function considers the following problem:
.. math::
\gamma = \min_\gamma \quad \langle \gamma, \mathbf{M} \rangle_F
.. math::
s.t. \ \gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\gamma &\geq 0
\mathbf{1}^T \gamma^T \mathbf{1} = m &\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
where :
- :math:`\mathbf{M}` is the metric cost matrix
- :math:`\mathbf{a}` and :math:`\mathbf{b}` are source and target unbalanced distributions
- `m` is the amount of mass to be transported
Parameters
----------
a : np.ndarray (dim_a,)
Unnormalized histogram of dimension `dim_a`
b : np.ndarray (dim_b,)
Unnormalized histograms of dimension `dim_b`
M : np.ndarray (dim_a, dim_b)
cost matrix for the quadratic cost
m : float, optional
amount of mass to be transported
nb_dummies : int, optional, default:1
number of reservoir points to be added (to avoid numerical
instabilities, increase its value if an error is raised)
log : bool, optional
record log if True
**kwargs : dict
parameters can be directly passed to the emd solver
.. warning::
When dealing with a large number of points, the EMD solver may face
some instabilities, especially when the mass associated to the dummy
point is large. To avoid them, increase the number of dummy points
(allows a smoother repartition of the mass over the points).
Returns
-------
GW: float
partial GW discrepancy
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> a=[.1, .2]
>>> b=[.1, .1]
>>> M=[[0., 1.], [2., 3.]]
>>> np.round(partial_wasserstein2(a, b, M), 1)
0.3
>>> np.round(partial_wasserstein2(a,b,M,m=0.1), 1)
0.0
References
----------
.. [28] Caffarelli, L. A., & McCann, R. J. (2010) Free boundaries in
optimal transport and Monge-Ampere obstacle problems. Annals of
mathematics, 673-730.
.. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
Transport with Applications on Positive-Unlabeled Learning".
NeurIPS.
"""
a, b, M = list_to_array(a, b, M)
nx = get_backend(a, b, M)
partial_gw, log_w = partial_wasserstein(a, b, M, m, nb_dummies, log=True, **kwargs)
log_w["T"] = partial_gw
if log:
return nx.sum(partial_gw * M), log_w
else:
return nx.sum(partial_gw * M)
[docs]
def entropic_partial_wasserstein(
a, b, M, reg, m=None, numItermax=1000, stopThr=1e-100, verbose=False, log=False
):
r"""
Solves the partial optimal transport problem
and returns the OT plan
The function considers the following problem:
.. math::
\gamma = \mathop{\arg \min}_\gamma \quad \langle \gamma,
\mathbf{M} \rangle_F + \mathrm{reg} \cdot\Omega(\gamma)
s.t. \gamma \mathbf{1} &\leq \mathbf{a} \\
\gamma^T \mathbf{1} &\leq \mathbf{b} \\
\gamma &\geq 0 \\
\mathbf{1}^T \gamma^T \mathbf{1} = m
&\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\} \\
where :
- :math:`\mathbf{M}` is the metric cost matrix
- :math:`\Omega` is the entropic regularization term,
:math:`\Omega=\sum_{i,j} \gamma_{i,j}\log(\gamma_{i,j})`
- :math:`\mathbf{a}` and :math:`\mathbf{b}` are the sample weights
- `m` is the amount of mass to be transported
The formulation of the problem has been proposed in
:ref:`[3] <references-entropic-partial-wasserstein>` (prop. 5)
Parameters
----------
a : np.ndarray (dim_a,)
Unnormalized histogram of dimension `dim_a`
b : np.ndarray (dim_b,)
Unnormalized histograms of dimension `dim_b`
M : np.ndarray (dim_a, dim_b)
cost matrix
reg : float
Regularization term > 0
m : float, optional
Amount of mass to be transported
numItermax : int, optional
Max number of iterations
stopThr : float, optional
Stop threshold on error (>0)
verbose : bool, optional
Print information along iterations
log : bool, optional
record log if True
Returns
-------
gamma : (dim_a, dim_b) ndarray
Optimal transportation matrix for the given parameters
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> a = [.1, .2]
>>> b = [.1, .1]
>>> M = [[0., 1.], [2., 3.]]
>>> np.round(entropic_partial_wasserstein(a, b, M, 1, 0.1), 2)
array([[0.06, 0.02],
[0.01, 0. ]])
.. _references-entropic-partial-wasserstein:
References
----------
.. [3] Benamou, J. D., Carlier, G., Cuturi, M., Nenna, L., & Peyré, G.
(2015). Iterative Bregman projections for regularized transportation
problems. SIAM Journal on Scientific Computing, 37(2), A1111-A1138.
See Also
--------
ot.partial.partial_wasserstein: exact Partial Wasserstein
"""
a, b, M = list_to_array(a, b, M)
nx = get_backend(a, b, M)
dim_a, dim_b = M.shape
dx = nx.ones(dim_a, type_as=a)
dy = nx.ones(dim_b, type_as=b)
if len(a) == 0:
a = nx.ones(dim_a, type_as=a) / dim_a
if len(b) == 0:
b = nx.ones(dim_b, type_as=b) / dim_b
if m is None:
m = nx.min(nx.stack((nx.sum(a), nx.sum(b)))) * 1.0
if m < 0:
raise ValueError("Problem infeasible. Parameter m should be greater" " than 0.")
if m > nx.min(nx.stack((nx.sum(a), nx.sum(b)))):
raise ValueError(
"Problem infeasible. Parameter m should lower or"
" equal than min(|a|_1, |b|_1)."
)
log_e = {"err": []}
if nx.__name__ == "numpy":
# Next 3 lines equivalent to K=nx.exp(-M/reg), but faster to compute
K = np.empty(M.shape, dtype=M.dtype)
np.divide(M, -reg, out=K)
np.exp(K, out=K)
np.multiply(K, m / np.sum(K), out=K)
else:
K = nx.exp(-M / reg)
K = K * m / nx.sum(K)
err, cpt = 1, 0
q1 = nx.ones(K.shape, type_as=K)
q2 = nx.ones(K.shape, type_as=K)
q3 = nx.ones(K.shape, type_as=K)
while err > stopThr and cpt < numItermax:
Kprev = K
K = K * q1
K1 = nx.dot(nx.diag(nx.minimum(a / nx.sum(K, axis=1), dx)), K)
q1 = q1 * Kprev / K1
K1prev = K1
K1 = K1 * q2
K2 = nx.dot(K1, nx.diag(nx.minimum(b / nx.sum(K1, axis=0), dy)))
q2 = q2 * K1prev / K2
K2prev = K2
K2 = K2 * q3
K = K2 * (m / nx.sum(K2))
q3 = q3 * K2prev / K
if nx.any(nx.isnan(K)) or nx.any(nx.isinf(K)):
print("Warning: numerical errors at iteration", cpt)
break
if cpt % 10 == 0:
err = nx.norm(Kprev - K)
if log:
log_e["err"].append(err)
if verbose:
if cpt % 200 == 0:
print("{:5s}|{:12s}".format("It.", "Err") + "\n" + "-" * 11)
print("{:5d}|{:8e}|".format(cpt, err))
cpt = cpt + 1
log_e["partial_w_dist"] = nx.sum(M * K)
if log:
return K, log_e
else:
return K
[docs]
def gwgrad_partial(C1, C2, T):
"""Compute the GW gradient. Note: we can not use the trick in :ref:`[12] <references-gwgrad-partial>`
as the marginals may not sum to 1.
.. note:: This function will be deprecated in a near future, please use
`ot.gromov.gwggrad` instead.
Parameters
----------
C1: array of shape (n_p,n_p)
intra-source (P) cost matrix
C2: array of shape (n_u,n_u)
intra-target (U) cost matrix
T : array of shape(n_p+nb_dummies, n_u) (default: None)
Transport matrix
Returns
-------
numpy.array of shape (n_p+nb_dummies, n_u)
gradient
.. _references-gwgrad-partial:
References
----------
.. [12] Peyré, Gabriel, Marco Cuturi, and Justin Solomon,
"Gromov-Wasserstein averaging of kernel and distance matrices."
International Conference on Machine Learning (ICML). 2016.
"""
warnings.warn(
"This function will be deprecated in a near future, please use "
"ot.gromov.gwggrad` instead.",
stacklevel=2,
)
cC1 = np.dot(C1**2 / 2, np.dot(T, np.ones(C2.shape[0]).reshape(-1, 1)))
cC2 = np.dot(np.dot(np.ones(C1.shape[0]).reshape(1, -1), T), C2**2 / 2)
constC = cC1 + cC2
A = -np.dot(C1, T).dot(C2.T)
tens = constC + A
return tens * 2
[docs]
def gwloss_partial(C1, C2, T):
"""Compute the GW loss.
.. note:: This function will be deprecated in a near future, please use
`ot.gromov.gwloss` instead.
Parameters
----------
C1: array of shape (n_p,n_p)
intra-source (P) cost matrix
C2: array of shape (n_u,n_u)
intra-target (U) cost matrix
T : array of shape(n_p+nb_dummies, n_u) (default: None)
Transport matrix
Returns
-------
GW loss
"""
warnings.warn(
"This function will be deprecated in a near future, please use "
"ot.gromov.gwloss` instead.",
stacklevel=2,
)
g = gwgrad_partial(C1, C2, T) * 0.5
return np.sum(g * T)
[docs]
def partial_gromov_wasserstein(
C1,
C2,
p,
q,
m=None,
nb_dummies=1,
G0=None,
thres=1,
numItermax=1000,
tol=1e-7,
log=False,
verbose=False,
**kwargs,
):
r"""
Solves the partial optimal transport problem
and returns the OT plan
The function considers the following problem:
.. math::
\gamma = \mathop{\arg \min}_\gamma \quad \langle \gamma, \mathbf{M} \rangle_F
.. math::
s.t. \ \gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\gamma &\geq 0
\mathbf{1}^T \gamma^T \mathbf{1} = m &\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
where :
- :math:`\mathbf{M}` is the metric cost matrix
- :math:`\Omega` is the entropic regularization term, :math:`\Omega(\gamma) = \sum_{i,j} \gamma_{i,j}\log(\gamma_{i,j})`
- :math:`\mathbf{a}` and :math:`\mathbf{b}` are the sample weights
- `m` is the amount of mass to be transported
The formulation of the problem has been proposed in
:ref:`[29] <references-partial-gromov-wasserstein>`
.. note:: This function will be deprecated in a near future, please use
`ot.gromov.partial_gromov_wasserstein` instead.
Parameters
----------
C1 : ndarray, shape (ns, ns)
Metric cost matrix in the source space
C2 : ndarray, shape (nt, nt)
Metric costfr matrix in the target space
p : ndarray, shape (ns,)
Distribution in the source space
q : ndarray, shape (nt,)
Distribution in the target space
m : float, optional
Amount of mass to be transported
(default: :math:`\min\{\|\mathbf{p}\|_1, \|\mathbf{q}\|_1\}`)
nb_dummies : int, optional
Number of dummy points to add (avoid instabilities in the EMD solver)
G0 : ndarray, shape (ns, nt), optional
Initialization of the transportation matrix
thres : float, optional
quantile of the gradient matrix to populate the cost matrix when 0
(default: 1)
numItermax : int, optional
Max number of iterations
tol : float, optional
tolerance for stopping iterations
log : bool, optional
return log if True
verbose : bool, optional
Print information along iterations
**kwargs : dict
parameters can be directly passed to the emd solver
Returns
-------
gamma : (dim_a, dim_b) ndarray
Optimal transportation matrix for the given parameters
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> import scipy as sp
>>> a = np.array([0.25] * 4)
>>> b = np.array([0.25] * 4)
>>> x = np.array([1,2,100,200]).reshape((-1,1))
>>> y = np.array([3,2,98,199]).reshape((-1,1))
>>> C1 = sp.spatial.distance.cdist(x, x)
>>> C2 = sp.spatial.distance.cdist(y, y)
>>> np.round(partial_gromov_wasserstein(C1, C2, a, b),2)
array([[0. , 0.25, 0. , 0. ],
[0.25, 0. , 0. , 0. ],
[0. , 0. , 0.25, 0. ],
[0. , 0. , 0. , 0.25]])
>>> np.round(partial_gromov_wasserstein(C1, C2, a, b, m=0.25),2)
array([[0. , 0. , 0. , 0. ],
[0. , 0. , 0. , 0. ],
[0. , 0. , 0.25, 0. ],
[0. , 0. , 0. , 0. ]])
.. _references-partial-gromov-wasserstein:
References
----------
.. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
Transport with Applications on Positive-Unlabeled Learning".
NeurIPS.
"""
warnings.warn(
"This function will be deprecated in a near future, please use "
"ot.gromov.partial_gromov_wasserstein` instead.",
stacklevel=2,
)
if m is None:
m = np.min((np.sum(p), np.sum(q)))
elif m < 0:
raise ValueError("Problem infeasible. Parameter m should be greater" " than 0.")
elif m > np.min((np.sum(p), np.sum(q))):
raise ValueError(
"Problem infeasible. Parameter m should lower or"
" equal than min(|a|_1, |b|_1)."
)
if G0 is None:
G0 = (
np.outer(p, q) * m / (np.sum(p) * np.sum(q))
) # make sure |G0|=m, G01_m\leq p, G0.T1_n\leq q.
dim_G_extended = (len(p) + nb_dummies, len(q) + nb_dummies)
q_extended = np.append(q, [(np.sum(p) - m) / nb_dummies] * nb_dummies)
p_extended = np.append(p, [(np.sum(q) - m) / nb_dummies] * nb_dummies)
cpt = 0
err = 1
if log:
log = {"err": []}
while err > tol and cpt < numItermax:
Gprev = np.copy(G0)
M = 0.5 * gwgrad_partial(
C1, C2, G0
) # rescaling the gradient with 0.5 for line-search while not changing Gc
M_emd = np.zeros(dim_G_extended)
M_emd[: len(p), : len(q)] = M
M_emd[-nb_dummies:, -nb_dummies:] = np.max(M) * 1e2
M_emd = np.asarray(M_emd, dtype=np.float64)
Gc, logemd = emd(p_extended, q_extended, M_emd, log=True, **kwargs)
if logemd["warning"] is not None:
raise ValueError(
"Error in the EMD resolution: try to increase the"
" number of dummy points"
)
G0 = Gc[: len(p), : len(q)]
if cpt % 10 == 0: # to speed up the computations
err = np.linalg.norm(G0 - Gprev)
if log:
log["err"].append(err)
if verbose:
if cpt % 200 == 0:
print(
"{:5s}|{:12s}|{:12s}".format("It.", "Err", "Loss")
+ "\n"
+ "-" * 31
)
print("{:5d}|{:8e}|{:8e}".format(cpt, err, gwloss_partial(C1, C2, G0)))
deltaG = G0 - Gprev
a = gwloss_partial(C1, C2, deltaG)
b = 2 * np.sum(M * deltaG)
if b > 0: # due to numerical precision
gamma = 0
cpt = numItermax
elif a > 0:
gamma = min(1, np.divide(-b, 2.0 * a))
else:
if (a + b) < 0:
gamma = 1
else:
gamma = 0
cpt = numItermax
G0 = Gprev + gamma * deltaG
cpt += 1
if log:
log["partial_gw_dist"] = gwloss_partial(C1, C2, G0)
return G0[: len(p), : len(q)], log
else:
return G0[: len(p), : len(q)]
[docs]
def partial_gromov_wasserstein2(
C1,
C2,
p,
q,
m=None,
nb_dummies=1,
G0=None,
thres=1,
numItermax=1000,
tol=1e-7,
log=False,
verbose=False,
**kwargs,
):
r"""
Solves the partial optimal transport problem
and returns the partial Gromov-Wasserstein discrepancy
The function considers the following problem:
.. math::
GW = \min_\gamma \quad \langle \gamma, \mathbf{M} \rangle_F
.. math::
s.t. \ \gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\gamma &\geq 0
\mathbf{1}^T \gamma^T \mathbf{1} = m
&\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
where :
- :math:`\mathbf{M}` is the metric cost matrix
- :math:`\Omega` is the entropic regularization term,
:math:`\Omega(\gamma) = \sum_{i,j} \gamma_{i,j}\log(\gamma_{i,j})`
- :math:`\mathbf{a}` and :math:`\mathbf{b}` are the sample weights
- `m` is the amount of mass to be transported
The formulation of the problem has been proposed in
:ref:`[29] <references-partial-gromov-wasserstein2>`
.. note:: This function will be deprecated in a near future, please use
`ot.gromov.partial_gromov_wasserstein2` instead.
Parameters
----------
C1 : ndarray, shape (ns, ns)
Metric cost matrix in the source space
C2 : ndarray, shape (nt, nt)
Metric cost matrix in the target space
p : ndarray, shape (ns,)
Distribution in the source space
q : ndarray, shape (nt,)
Distribution in the target space
m : float, optional
Amount of mass to be transported
(default: :math:`\min\{\|\mathbf{p}\|_1, \|\mathbf{q}\|_1\}`)
nb_dummies : int, optional
Number of dummy points to add (avoid instabilities in the EMD solver)
G0 : ndarray, shape (ns, nt), optional
Initialization of the transportation matrix
thres : float, optional
quantile of the gradient matrix to populate the cost matrix when 0
(default: 1)
numItermax : int, optional
Max number of iterations
tol : float, optional
tolerance for stopping iterations
log : bool, optional
return log if True
verbose : bool, optional
Print information along iterations
**kwargs : dict
parameters can be directly passed to the emd solver
.. warning::
When dealing with a large number of points, the EMD solver may face
some instabilities, especially when the mass associated to the dummy
point is large. To avoid them, increase the number of dummy points
(allows a smoother repartition of the mass over the points).
Returns
-------
partial_gw_dist : float
partial GW discrepancy
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> import scipy as sp
>>> a = np.array([0.25] * 4)
>>> b = np.array([0.25] * 4)
>>> x = np.array([1,2,100,200]).reshape((-1,1))
>>> y = np.array([3,2,98,199]).reshape((-1,1))
>>> C1 = sp.spatial.distance.cdist(x, x)
>>> C2 = sp.spatial.distance.cdist(y, y)
>>> np.round(partial_gromov_wasserstein2(C1, C2, a, b),2)
1.69
>>> np.round(partial_gromov_wasserstein2(C1, C2, a, b, m=0.25),2)
0.0
.. _references-partial-gromov-wasserstein2:
References
----------
.. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
Transport with Applications on Positive-Unlabeled Learning".
NeurIPS.
"""
warnings.warn(
"This function will be deprecated in a near future, please use "
"ot.gromov.partial_gromov_wasserstein2` instead.",
stacklevel=2,
)
partial_gw, log_gw = partial_gromov_wasserstein(
C1, C2, p, q, m, nb_dummies, G0, thres, numItermax, tol, True, verbose, **kwargs
)
log_gw["T"] = partial_gw
if log:
return log_gw["partial_gw_dist"], log_gw
else:
return log_gw["partial_gw_dist"]
[docs]
def entropic_partial_gromov_wasserstein(
C1,
C2,
p,
q,
reg,
m=None,
G0=None,
numItermax=1000,
tol=1e-7,
log=False,
verbose=False,
):
r"""
Returns the partial Gromov-Wasserstein transport between
:math:`(\mathbf{C_1}, \mathbf{p})` and :math:`(\mathbf{C_2}, \mathbf{q})`
The function solves the following optimization problem:
.. math::
\gamma = \mathop{\arg \min}_{\gamma} \quad \sum_{i,j,k,l}
L(\mathbf{C_1}_{i,k}, \mathbf{C_2}_{j,l})\cdot
\gamma_{i,j}\cdot\gamma_{k,l} + \mathrm{reg} \cdot\Omega(\gamma)
.. math::
s.t. \ \gamma &\geq 0
\gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\mathbf{1}^T \gamma^T \mathbf{1} = m
&\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
where :
- :math:`\mathbf{C_1}` is the metric cost matrix in the source space
- :math:`\mathbf{C_2}` is the metric cost matrix in the target space
- :math:`\mathbf{p}` and :math:`\mathbf{q}` are the sample weights
- `L`: quadratic loss function
- :math:`\Omega` is the entropic regularization term,
:math:`\Omega=\sum_{i,j} \gamma_{i,j}\log(\gamma_{i,j})`
- `m` is the amount of mass to be transported
The formulation of the GW problem has been proposed in
:ref:`[12] <references-entropic-partial-gromov-wasserstein>` and the
partial GW in :ref:`[29] <references-entropic-partial-gromov-wasserstein>`
.. note:: This function will be deprecated in a near future, please use
`ot.gromov.entropic_partial_gromov_wasserstein` instead.
Parameters
----------
C1 : ndarray, shape (ns, ns)
Metric cost matrix in the source space
C2 : ndarray, shape (nt, nt)
Metric cost matrix in the target space
p : ndarray, shape (ns,)
Distribution in the source space
q : ndarray, shape (nt,)
Distribution in the target space
reg: float
entropic regularization parameter
m : float, optional
Amount of mass to be transported (default:
:math:`\min\{\|\mathbf{p}\|_1, \|\mathbf{q}\|_1\}`)
G0 : ndarray, shape (ns, nt), optional
Initialization of the transportation matrix
numItermax : int, optional
Max number of iterations
tol : float, optional
Stop threshold on error (>0)
log : bool, optional
return log if True
verbose : bool, optional
Print information along iterations
Examples
--------
>>> import ot
>>> import scipy as sp
>>> a = np.array([0.25] * 4)
>>> b = np.array([0.25] * 4)
>>> x = np.array([1,2,100,200]).reshape((-1,1))
>>> y = np.array([3,2,98,199]).reshape((-1,1))
>>> C1 = sp.spatial.distance.cdist(x, x)
>>> C2 = sp.spatial.distance.cdist(y, y)
>>> np.round(entropic_partial_gromov_wasserstein(C1, C2, a, b, 50), 2)
array([[0.12, 0.13, 0. , 0. ],
[0.13, 0.12, 0. , 0. ],
[0. , 0. , 0.25, 0. ],
[0. , 0. , 0. , 0.25]])
>>> np.round(entropic_partial_gromov_wasserstein(C1, C2, a, b, 50,0.25), 2)
array([[0.02, 0.03, 0. , 0.03],
[0.03, 0.03, 0. , 0.03],
[0. , 0. , 0.03, 0. ],
[0.02, 0.02, 0. , 0.03]])
Returns
-------
:math: `gamma` : (dim_a, dim_b) ndarray
Optimal transportation matrix for the given parameters
log : dict
log dictionary returned only if `log` is `True`
.. _references-entropic-partial-gromov-wasserstein:
References
----------
.. [12] Peyré, Gabriel, Marco Cuturi, and Justin Solomon,
"Gromov-Wasserstein averaging of kernel and distance matrices."
International Conference on Machine Learning (ICML). 2016.
.. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
Transport with Applications on Positive-Unlabeled Learning".
NeurIPS.
See Also
--------
ot.partial.partial_gromov_wasserstein: exact Partial Gromov-Wasserstein
"""
warnings.warn(
"This function will be deprecated in a near future, please use "
"ot.gromov.entropic_partial_gromov_wasserstein` instead.",
stacklevel=2,
)
if G0 is None:
G0 = np.outer(p, q)
if m is None:
m = np.min((np.sum(p), np.sum(q)))
elif m < 0:
raise ValueError("Problem infeasible. Parameter m should be greater" " than 0.")
elif m > np.min((np.sum(p), np.sum(q))):
raise ValueError(
"Problem infeasible. Parameter m should lower or"
" equal than min(|a|_1, |b|_1)."
)
cpt = 0
err = 1
loge = {"err": []}
while err > tol and cpt < numItermax:
Gprev = G0
M_entr = gwgrad_partial(C1, C2, G0)
G0 = entropic_partial_wasserstein(p, q, M_entr, reg, m)
if cpt % 10 == 0: # to speed up the computations
err = np.linalg.norm(G0 - Gprev)
if log:
loge["err"].append(err)
if verbose:
if cpt % 200 == 0:
print(
"{:5s}|{:12s}|{:12s}".format("It.", "Err", "Loss")
+ "\n"
+ "-" * 31
)
print("{:5d}|{:8e}|{:8e}".format(cpt, err, gwloss_partial(C1, C2, G0)))
cpt += 1
if log:
loge["partial_gw_dist"] = gwloss_partial(C1, C2, G0)
return G0, loge
else:
return G0
[docs]
def entropic_partial_gromov_wasserstein2(
C1,
C2,
p,
q,
reg,
m=None,
G0=None,
numItermax=1000,
tol=1e-7,
log=False,
verbose=False,
):
r"""
Returns the partial Gromov-Wasserstein discrepancy between
:math:`(\mathbf{C_1}, \mathbf{p})` and :math:`(\mathbf{C_2}, \mathbf{q})`
The function solves the following optimization problem:
.. math::
GW = \min_{\gamma} \quad \sum_{i,j,k,l} L(\mathbf{C_1}_{i,k},
\mathbf{C_2}_{j,l})\cdot
\gamma_{i,j}\cdot\gamma_{k,l} + \mathrm{reg} \cdot\Omega(\gamma)
.. math::
s.t. \ \gamma &\geq 0
\gamma \mathbf{1} &\leq \mathbf{a}
\gamma^T \mathbf{1} &\leq \mathbf{b}
\mathbf{1}^T \gamma^T \mathbf{1} = m &\leq \min\{\|\mathbf{a}\|_1, \|\mathbf{b}\|_1\}
where :
- :math:`\mathbf{C_1}` is the metric cost matrix in the source space
- :math:`\mathbf{C_2}` is the metric cost matrix in the target space
- :math:`\mathbf{p}` and :math:`\mathbf{q}` are the sample weights
- `L` : quadratic loss function
- :math:`\Omega` is the entropic regularization term,
:math:`\Omega=\sum_{i,j} \gamma_{i,j}\log(\gamma_{i,j})`
- `m` is the amount of mass to be transported
The formulation of the GW problem has been proposed in
:ref:`[12] <references-entropic-partial-gromov-wasserstein2>` and the
partial GW in :ref:`[29] <references-entropic-partial-gromov-wasserstein2>`
.. note:: This function will be deprecated in a near future, please use
`ot.gromov.entropic_partial_gromov_wasserstein2` instead.
Parameters
----------
C1 : ndarray, shape (ns, ns)
Metric cost matrix in the source space
C2 : ndarray, shape (nt, nt)
Metric cost matrix in the target space
p : ndarray, shape (ns,)
Distribution in the source space
q : ndarray, shape (nt,)
Distribution in the target space
reg: float
entropic regularization parameter
m : float, optional
Amount of mass to be transported (default:
:math:`\min\{\|\mathbf{p}\|_1, \|\mathbf{q}\|_1\}`)
G0 : ndarray, shape (ns, nt), optional
Initialization of the transportation matrix
numItermax : int, optional
Max number of iterations
tol : float, optional
Stop threshold on error (>0)
log : bool, optional
return log if True
verbose : bool, optional
Print information along iterations
Returns
-------
partial_gw_dist: float
Gromov-Wasserstein distance
log : dict
log dictionary returned only if `log` is `True`
Examples
--------
>>> import ot
>>> import scipy as sp
>>> a = np.array([0.25] * 4)
>>> b = np.array([0.25] * 4)
>>> x = np.array([1,2,100,200]).reshape((-1,1))
>>> y = np.array([3,2,98,199]).reshape((-1,1))
>>> C1 = sp.spatial.distance.cdist(x, x)
>>> C2 = sp.spatial.distance.cdist(y, y)
>>> np.round(entropic_partial_gromov_wasserstein2(C1, C2, a, b,50), 2)
1.87
.. _references-entropic-partial-gromov-wasserstein2:
References
----------
.. [12] Peyré, Gabriel, Marco Cuturi, and Justin Solomon,
"Gromov-Wasserstein averaging of kernel and distance matrices."
International Conference on Machine Learning (ICML). 2016.
.. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
Transport with Applications on Positive-Unlabeled Learning".
NeurIPS.
"""
warnings.warn(
"This function will be deprecated in a near future, please use "
"ot.gromov.entropic_partial_gromov_wasserstein2` instead.",
stacklevel=2,
)
partial_gw, log_gw = entropic_partial_gromov_wasserstein(
C1, C2, p, q, reg, m, G0, numItermax, tol, True, verbose
)
log_gw["T"] = partial_gw
if log:
return log_gw["partial_gw_dist"], log_gw
else:
return log_gw["partial_gw_dist"]
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