partial entropic fgw solvers

ot/gromov/__init__.py

@@ -107,6 +107,8 @@
     solve_partial_gromov_linesearch,
     entropic_partial_gromov_wasserstein,
     entropic_partial_gromov_wasserstein2,
+    entropic_partial_fused_gromov_wasserstein,
+    entropic_partial_fused_gromov_wasserstein2,
 )
 
 
@@ -180,4 +182,6 @@
     "solve_partial_gromov_linesearch",
     "entropic_partial_gromov_wasserstein",
     "entropic_partial_gromov_wasserstein2",
+    "entropic_partial_fused_gromov_wasserstein",
+    "entropic_partial_fused_gromov_wasserstein2",
 ]

ot/gromov/_partial.py

@@ -1433,3 +1433,380 @@ def entropic_partial_gromov_wasserstein2(
         return log_gw["partial_gw_dist"], log_gw
     else:
         return log_gw["partial_gw_dist"]
+
+
+def entropic_partial_fused_gromov_wasserstein(
+    M,
+    C1,
+    C2,
+    p=None,
+    q=None,
+    reg=1.0,
+    m=None,
+    loss_fun="square_loss",
+    alpha=0.5,
+    G0=None,
+    numItermax=1000,
+    tol=1e-7,
+    symmetric=None,
+    log=False,
+    verbose=False,
+):
+    r"""
+    Returns the entropic partial Fused Gromov-Wasserstein transport between
+    :math:`(\mathbf{C_1}, \mathbf{F_1}, \mathbf{p})` and
+    :math:`(\mathbf{C_2}, \mathbf{F_2}, \mathbf{q})`, with pairwise
+    distance matrix :math:`\mathbf{M}` between node feature matrices.
+
+    The function solves the following optimization problem:
+
+    .. math::
+        \gamma = \mathop{\arg \min}_{\gamma} \quad (1 - \alpha) \langle \mathbf{T}, \mathbf{M} \rangle_F +
+        + \alpha \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{M}`: metric cost matrix between features across domains
+    - :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 FGW problem has been proposed in
+    :ref:`[24] <references-entropic-partial-fused-gromov-wasserstein>` and the
+    partial GW in :ref:`[29] <references-entropic-partial-fused-gromov-wasserstein>`
+
+    Parameters
+    ----------
+    M : array-like, shape (ns, nt)
+        Metric cost matrix between features across domains
+    C1 : array-like, shape (ns, ns)
+        Metric cost matrix in the source space
+    C2 : array-like, shape (nt, nt)
+        Metric cost matrix in the target space
+    p : array-like, shape (ns,), optional
+        Distribution in the source space.
+        If let to its default value None, uniform distribution is taken.
+    q : array-like, shape (nt,), optional
+        Distribution in the target space.
+        If let to its default value None, uniform distribution is taken.
+    reg: float, optional. Default is 1.
+        entropic regularization parameter
+    m : float, optional
+        Amount of mass to be transported (default:
+        :math:`\min\{\|\mathbf{p}\|_1, \|\mathbf{q}\|_1\}`)
+    loss_fun : str, optional
+        Loss function used for the solver either 'square_loss' or 'kl_loss'.
+    alpha : float, optional
+        Trade-off parameter (0 < alpha < 1)
+    G0 : array-like, shape (ns, nt), optional
+        Initialization of the transportation matrix
+    numItermax : int, optional
+        Max number of iterations
+    tol : float, optional
+        Stop threshold on error (>0)
+    symmetric : bool, optional
+        Either C1 and C2 are to be assumed symmetric or not.
+        If let to its default None value, a symmetry test will be conducted.
+        Else if set to True (resp. False), C1 and C2 will be assumed symmetric (resp. asymmetric).
+    log : bool, optional
+        return log if True
+    verbose : bool, optional
+        Print information along iterations
+
+    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-fused-gromov-wasserstein:
+    References
+    ----------
+    .. [24] Vayer Titouan, Chapel Laetitia, Flamary Rémi, Tavenard Romain
+        and Courty Nicolas "Optimal Transport for structured data with
+        application on graphs", International Conference on Machine Learning
+        (ICML). 2019.
+
+    .. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
+        Transport with Applications on Positive-Unlabeled Learning".
+        NeurIPS.
+
+    See Also
+    --------
+    ot.gromov.partial_fused_gromov_wasserstein: exact Partial Fused Gromov-Wasserstein
+    """
+
+    arr = [M, C1, C2, G0]
+    if p is not None:
+        p = list_to_array(p)
+        arr.append(p)
+    if q is not None:
+        q = list_to_array(q)
+        arr.append(q)
+
+    nx = get_backend(*arr)
+
+    if p is None:
+        p = nx.ones(C1.shape[0], type_as=C1) / C1.shape[0]
+    if q is None:
+        q = nx.ones(C2.shape[0], type_as=C2) / C2.shape[0]
+
+    if m is None:
+        m = min(nx.sum(p), nx.sum(q))
+    elif m < 0:
+        raise ValueError("Problem infeasible. Parameter m should be greater" " than 0.")
+    elif m > min(nx.sum(p), nx.sum(q)):
+        raise ValueError(
+            "Problem infeasible. Parameter m should lower or"
+            " equal than min(|a|_1, |b|_1)."
+        )
+
+    if G0 is None:
+        G0 = (
+            nx.outer(p, q) * m / (nx.sum(p) * nx.sum(q))
+        )  # make sure |G0|=m, G01_m\leq p, G0.T1_n\leq q.
+
+    else:
+        # Check marginals of G0
+        assert nx.any(nx.sum(G0, 1) <= p)
+        assert nx.any(nx.sum(G0, 0) <= q)
+
+    if symmetric is None:
+        symmetric = np.allclose(C1, C1.T, atol=1e-10) and np.allclose(
+            C2, C2.T, atol=1e-10
+        )
+
+    # Setup gradient computation
+    fC1, fC2, hC1, hC2 = _transform_matrix(C1, C2, loss_fun, nx)
+    fC2t = fC2.T
+    if not symmetric:
+        fC1t, hC1t, hC2t = fC1.T, hC1.T, hC2.T
+
+    ones_p = nx.ones(p.shape[0], type_as=p)
+    ones_q = nx.ones(q.shape[0], type_as=q)
+
+    def f(G):
+        pG = nx.sum(G, 1)
+        qG = nx.sum(G, 0)
+        constC1 = nx.outer(nx.dot(fC1, pG), ones_q)
+        constC2 = nx.outer(ones_p, nx.dot(qG, fC2t))
+        return alpha * gwloss(constC1 + constC2, hC1, hC2, G, nx) + (
+            1 - alpha
+        ) * nx.sum(G * M)
+
+    if symmetric:
+
+        def df(G):
+            pG = nx.sum(G, 1)
+            qG = nx.sum(G, 0)
+            constC1 = nx.outer(nx.dot(fC1, pG), ones_q)
+            constC2 = nx.outer(ones_p, nx.dot(qG, fC2t))
+            return alpha * gwggrad(constC1 + constC2, hC1, hC2, G, nx) + (
+                1 - alpha
+            ) * nx.sum(G * M)
+    else:
+
+        def df(G):
+            pG = nx.sum(G, 1)
+            qG = nx.sum(G, 0)
+            constC1 = nx.outer(nx.dot(fC1, pG), ones_q)
+            constC2 = nx.outer(ones_p, nx.dot(qG, fC2t))
+            constC1t = nx.outer(nx.dot(fC1t, pG), ones_q)
+            constC2t = nx.outer(ones_p, nx.dot(qG, fC2))
+
+            return 0.5 * alpha * (
+                gwggrad(constC1 + constC2, hC1, hC2, G, nx)
+                + gwggrad(constC1t + constC2t, hC1t, hC2t, G, nx)
+            ) + (1 - alpha) * nx.sum(G * M)
+
+    cpt = 0
+    err = 1
+
+    loge = {"err": []}
+
+    while err > tol and cpt < numItermax:
+        Gprev = G0
+        M_entr = df(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, f(G0)))
+
+        cpt += 1
+
+    if log:
+        loge["partial_fgw_dist"] = f(G0)
+        return G0, loge
+    else:
+        return G0
+
+
+def entropic_partial_fused_gromov_wasserstein2(
+    M,
+    C1,
+    C2,
+    p=None,
+    q=None,
+    reg=1.0,
+    m=None,
+    loss_fun="square_loss",
+    alpha=0.5,
+    G0=None,
+    numItermax=1000,
+    tol=1e-7,
+    symmetric=None,
+    log=False,
+    verbose=False,
+):
+    r"""
+    Returns the entropic partial Fused Gromov-Wasserstein discrepancy between
+    :math:`(\mathbf{C_1}, \mathbf{F_1}, \mathbf{p})` and
+    :math:`(\mathbf{C_2}, \mathbf{F_2}, \mathbf{q})`, with pairwise
+    distance matrix :math:`\mathbf{M}` between node feature matrices.
+
+    The function solves the following optimization problem:
+
+    .. math::
+        PGW = \min_{\gamma} \quad (1 - \alpha) \langle \mathbf{T}, \mathbf{M} \rangle_F +
+        + \alpha \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{M}`: metric cost matrix between features across domains
+    - :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`: Loss function to account for the misfit between the similarity matrices.
+    - :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 FGW problem has been proposed in
+    :ref:`[24] <references-entropic-partial-fused-gromov-wasserstein2>` and the
+    partial GW in :ref:`[29] <references-entropic-partial-fused-gromov-wasserstein2>`
+
+    Parameters
+    ----------
+    M : array-like, shape (ns, nt)
+        Metric cost matrix between features across domains
+    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 : array-like, shape (ns,), optional
+        Distribution in the source space.
+        If let to its default value None, uniform distribution is taken.
+    q : array-like, shape (nt,), optional
+        Distribution in the target space.
+        If let to its default value None, uniform distribution is taken.
+    reg: float
+        entropic regularization parameter
+    m : float, optional
+        Amount of mass to be transported (default:
+        :math:`\min\{\|\mathbf{p}\|_1, \|\mathbf{q}\|_1\}`)
+    loss_fun : str, optional
+        Loss function used for the solver either 'square_loss' or 'kl_loss'.
+    alpha : float, optional
+        Trade-off parameter (0 < alpha < 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)
+    symmetric : bool, optional
+        Either C1 and C2 are to be assumed symmetric or not.
+        If let to its default None value, a symmetry test will be conducted.
+        Else if set to True (resp. False), C1 and C2 will be assumed symmetric (resp. asymmetric).
+    log : bool, optional
+        return log if True
+    verbose : bool, optional
+        Print information along iterations
+
+
+    Returns
+    -------
+    partial_fgw_dist: float
+        Partial Entropic Fused Gromov-Wasserstein discrepancy
+    log : dict
+        log dictionary returned only if `log` is `True`
+
+    .. _references-entropic-partial-fused-gromov-wasserstein2:
+    References
+    ----------
+    .. [24] Vayer Titouan, Chapel Laetitia, Flamary Rémi, Tavenard Romain
+        and Courty Nicolas "Optimal Transport for structured data with
+        application on graphs", International Conference on Machine Learning
+        (ICML). 2019.
+
+    .. [29] Chapel, L., Alaya, M., Gasso, G. (2020). "Partial Optimal
+        Transport with Applications on Positive-Unlabeled Learning".
+        NeurIPS.
+    """
+    nx = get_backend(M, C1, C2)
+
+    T, log_pfgw = entropic_partial_fused_gromov_wasserstein(
+        M,
+        C1,
+        C2,
+        p,
+        q,
+        reg,
+        m,
+        loss_fun,
+        alpha,
+        G0,
+        numItermax,
+        tol,
+        symmetric,
+        True,
+        verbose,
+    )
+
+    log_pfgw["T"] = T
+
+    # setup for ot.solve_gromov
+    lin_term = nx.sum(T * M)
+    log_pfgw["quad_loss"] = log_pfgw["partial_fgw_dist"] - (1 - alpha) * lin_term
+    log_pfgw["lin_loss"] = lin_term * (1 - alpha)
+
+    if log:
+        return log_pfgw["partial_fgw_dist"], log_pfgw
+    else:
+        return log_pfgw["partial_fgw_dist"]