adding greenkhorn

Author: arakotom

ot/bregman.py

@@ -47,7 +47,7 @@ def sinkhorn(a, b, M, reg, method='sinkhorn', numItermax=1000,
     reg : float
         Regularization term >0
     method : str
-        method used for the solver either 'sinkhorn',  'sinkhorn_stabilized' or
+        method used for the solver either 'sinkhorn', 'greenkhorn', 'sinkhorn_stabilized' or
         'sinkhorn_epsilon_scaling', see those function for specific parameters
     numItermax : int, optional
         Max number of iterations
@@ -103,6 +103,10 @@ def sinkhorn(a, b, M, reg, method='sinkhorn', numItermax=1000,
         def sink():
             return sinkhorn_knopp(a, b, M, reg, numItermax=numItermax,
                                   stopThr=stopThr, verbose=verbose, log=log, **kwargs)
+    if method.lower() == 'greenkhorn':
+        def sink():
+            return greenkhorn(a, b, M, reg, numItermax=numItermax,
+                                  stopThr=stopThr, verbose=verbose, log=log)
     elif method.lower() == 'sinkhorn_stabilized':
         def sink():
             return sinkhorn_stabilized(a, b, M, reg, numItermax=numItermax,
@@ -197,13 +201,16 @@ def sinkhorn2(a, b, M, reg, method='sinkhorn', numItermax=1000,
 
     .. [10] Chizat, L., Peyré, G., Schmitzer, B., & Vialard, F. X. (2016). Scaling algorithms for unbalanced transport problems. arXiv preprint arXiv:1607.05816.
 
+       [21] Altschuler J., Weed J., Rigollet P. : Near-linear time approximation algorithms for optimal transport via Sinkhorn iteration, Advances in Neural Information Processing Systems (NIPS) 31, 2017
+
 
 
     See Also
     --------
     ot.lp.emd : Unregularized OT
     ot.optim.cg : General regularized OT
     ot.bregman.sinkhorn_knopp : Classic Sinkhorn [2]
+    ot.bregman.greenkhorn : Greenkhorn [21]
     ot.bregman.sinkhorn_stabilized: Stabilized sinkhorn [9][10]
     ot.bregman.sinkhorn_epsilon_scaling: Sinkhorn with epslilon scaling [9][10]
 
@@ -410,6 +417,148 @@ def sinkhorn_knopp(a, b, M, reg, numItermax=1000,
             return u.reshape((-1, 1)) * K * v.reshape((1, -1))
 
 
+
+def greenkhorn(a, b, M, reg, numItermax=10000, stopThr=1e-9, verbose=False, log = False):
+    """
+    Solve the entropic regularization optimal transport problem and return the OT matrix
+    
+    The algorithm used is based on the paper
+        
+    Near-linear time approximation algorithms for optimal transport via Sinkhorn iteration
+        by Jason Altschuler, Jonathan Weed, Philippe Rigollet
+        appeared at NIPS 2017
+        
+    which is a stochastic version of the Sinkhorn-Knopp algorithm [2].
+
+    The function solves the following optimization problem:
+
+    .. math::
+        \gamma = arg\min_\gamma <\gamma,M>_F + reg\cdot\Omega(\gamma)
+
+        s.t. \gamma 1 = a
+
+             \gamma^T 1= b
+
+             \gamma\geq 0
+    where :
+
+    - M is the (ns,nt) metric cost matrix
+    - :math:`\Omega` is the entropic regularization term :math:`\Omega(\gamma)=\sum_{i,j} \gamma_{i,j}\log(\gamma_{i,j})`
+    - a and b are source and target weights (sum to 1)
+
+
+
+    Parameters
+    ----------
+    a : np.ndarray (ns,)
+        samples weights in the source domain
+    b : np.ndarray (nt,) or np.ndarray (nt,nbb)
+        samples in the target domain, compute sinkhorn with multiple targets
+        and fixed M if b is a matrix (return OT loss + dual variables in log)
+    M : np.ndarray (ns,nt)
+        loss matrix
+    reg : float
+        Regularization term >0
+    numItermax : int, optional
+        Max number of iterations
+    stopThr : float, optional
+        Stop threshol on error (>0)
+    log : bool, optional
+        record log if True
+
+
+    Returns
+    -------
+    gamma : (ns x nt) ndarray
+        Optimal transportation matrix for the given parameters
+    log : dict
+        log dictionary return only if log==True in parameters
+
+    Examples
+    --------
+
+    >>> import ot
+    >>> a=[.5,.5]
+    >>> b=[.5,.5]
+    >>> M=[[0.,1.],[1.,0.]]
+    >>> ot.sinkhorn(a,b,M,1)
+    array([[ 0.36552929,  0.13447071],
+           [ 0.13447071,  0.36552929]])
+
+
+    References
+    ----------
+
+    .. [2] M. Cuturi, Sinkhorn Distances : Lightspeed Computation of Optimal Transport, Advances in Neural Information Processing Systems (NIPS) 26, 2013
+       [21] J. Altschuler, J.Weed, P. Rigollet : Near-linear time approximation algorithms for optimal transport via Sinkhorn iteration, Advances in Neural Information Processing Systems (NIPS) 31, 2017
+
+
+    See Also
+    --------
+    ot.lp.emd : Unregularized OT
+    ot.optim.cg : General regularized OT
+
+    """
+    
+    i = 0
+    
+    n = a.shape[0]
+    m = b.shape[0]
+    
+    # Next 3 lines equivalent to K= np.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)
+    
+    u = np.ones(n)/n
+    v = np.ones(m)/m
+    G = np.diag(u)@K@np.diag(v)
+    
+    one_n = np.ones(n)
+    one_m = np.ones(m)
+    viol = G@one_m - a
+    viol_2 = G.T@one_n - b
+    stopThr_val = 1
+    if log:
+        log['u'] = u
+        log['v'] = v
+
+    while i < numItermax and stopThr_val > stopThr:
+        i +=1
+        i_1 = np.argmax(np.abs(viol))
+        i_2 = np.argmax(np.abs(viol_2))
+        m_viol_1 = np.abs(viol[i_1])
+        m_viol_2 = np.abs(viol_2[i_2])
+        stopThr_val = np.maximum(m_viol_1,m_viol_2)
+    
+        if m_viol_1 > m_viol_2:
+            old_u = u[i_1]
+            u[i_1] = a[i_1]/(K[i_1,:]@v)
+            G[i_1,:] = u[i_1]*K[i_1,:]*v
+
+            viol[i_1] = u[i_1]*K[i_1,:]@v - a[i_1]
+            viol_2 = viol_2 + ( K[i_1,:].T*(u[i_1] - old_u)*v) 
+
+        else:
+            old_v = v[i_2]
+            v[i_2] = b[i_2]/(K[:,i_2].T@u)
+            G[:,i_2] = u*K[:,i_2]*v[i_2]
+            #aviol = (G@one_m - a)
+            #aviol_2 = (G.T@one_n - b)
+            viol = viol + ( -old_v + v[i_2])*K[:,i_2]*u
+            viol_2[i_2] = v[i_2]*K[:,i_2]@u - b[i_2]
+            
+            #print('b',np.max(abs(aviol -viol)),np.max(abs(aviol_2 - viol_2)))
+            
+        if log:
+            log['u'] = u
+            log['v'] = v
+    
+    if log:
+        return G,log
+    else:
+        return G
+
 def sinkhorn_stabilized(a, b, M, reg, numItermax=1000, tau=1e3, stopThr=1e-9,
                         warmstart=None, verbose=False, print_period=20, log=False, **kwargs):
     """

test/test_bregman.py

@@ -71,12 +71,14 @@ def test_sinkhorn_variants():
     Ges = ot.sinkhorn(
         u, u, M, 1, method='sinkhorn_epsilon_scaling', stopThr=1e-10)
     Gerr = ot.sinkhorn(u, u, M, 1, method='do_not_exists', stopThr=1e-10)
+    G_green = ot.sinkhorn(u, u, M, 1, method='greenkhorn', stopThr=1e-10)
 
     # check values
     np.testing.assert_allclose(G0, Gs, atol=1e-05)
     np.testing.assert_allclose(G0, Ges, atol=1e-05)
     np.testing.assert_allclose(G0, Gerr)
-
+    np.testing.assert_allclose(G0, G_green, atol =  1e-32)
+    print(G0,G_green)
 
 def test_bary():