import os import numpy as np from .arpack import _arpack # type: ignore[attr-defined] from . import eigsh from scipy._lib._util import check_random_state from scipy.sparse.linalg._interface import LinearOperator, aslinearoperator from scipy.sparse.linalg._eigen.lobpcg import lobpcg # type: ignore[no-redef] if os.environ.get("SCIPY_USE_PROPACK"): from scipy.sparse.linalg._svdp import _svdp HAS_PROPACK = True else: HAS_PROPACK = False from scipy.linalg import svd arpack_int = _arpack.timing.nbx.dtype __all__ = ['svds'] def _herm(x): return x.T.conj() def _iv(A, k, ncv, tol, which, v0, maxiter, return_singular, solver, random_state): # input validation/standardization for `solver` # out of order because it's needed for other parameters solver = str(solver).lower() solvers = {"arpack", "lobpcg", "propack"} if solver not in solvers: raise ValueError(f"solver must be one of {solvers}.") # input validation/standardization for `A` A = aslinearoperator(A) # this takes care of some input validation if not (np.issubdtype(A.dtype, np.complexfloating) or np.issubdtype(A.dtype, np.floating)): message = "`A` must be of floating or complex floating data type." raise ValueError(message) if np.prod(A.shape) == 0: message = "`A` must not be empty." raise ValueError(message) # input validation/standardization for `k` kmax = min(A.shape) if solver == 'propack' else min(A.shape) - 1 if int(k) != k or not (0 < k <= kmax): message = "`k` must be an integer satisfying `0 < k < min(A.shape)`." raise ValueError(message) k = int(k) # input validation/standardization for `ncv` if solver == "arpack" and ncv is not None: if int(ncv) != ncv or not (k < ncv < min(A.shape)): message = ("`ncv` must be an integer satisfying " "`k < ncv < min(A.shape)`.") raise ValueError(message) ncv = int(ncv) # input validation/standardization for `tol` if tol < 0 or not np.isfinite(tol): message = "`tol` must be a non-negative floating point value." raise ValueError(message) tol = float(tol) # input validation/standardization for `which` which = str(which).upper() whichs = {'LM', 'SM'} if which not in whichs: raise ValueError(f"`which` must be in {whichs}.") # input validation/standardization for `v0` if v0 is not None: v0 = np.atleast_1d(v0) if not (np.issubdtype(v0.dtype, np.complexfloating) or np.issubdtype(v0.dtype, np.floating)): message = ("`v0` must be of floating or complex floating " "data type.") raise ValueError(message) shape = (A.shape[0],) if solver == 'propack' else (min(A.shape),) if v0.shape != shape: message = f"`v0` must have shape {shape}." raise ValueError(message) # input validation/standardization for `maxiter` if maxiter is not None and (int(maxiter) != maxiter or maxiter <= 0): message = "`maxiter` must be a positive integer." raise ValueError(message) maxiter = int(maxiter) if maxiter is not None else maxiter # input validation/standardization for `return_singular_vectors` # not going to be flexible with this; too complicated for little gain rs_options = {True, False, "vh", "u"} if return_singular not in rs_options: raise ValueError(f"`return_singular_vectors` must be in {rs_options}.") random_state = check_random_state(random_state) return (A, k, ncv, tol, which, v0, maxiter, return_singular, solver, random_state) def svds(A, k=6, ncv=None, tol=0, which='LM', v0=None, maxiter=None, return_singular_vectors=True, solver='arpack', random_state=None, options=None): """ Partial singular value decomposition of a sparse matrix. Compute the largest or smallest `k` singular values and corresponding singular vectors of a sparse matrix `A`. The order in which the singular values are returned is not guaranteed. In the descriptions below, let ``M, N = A.shape``. Parameters ---------- A : ndarray, sparse matrix, or LinearOperator Matrix to decompose of a floating point numeric dtype. k : int, default: 6 Number of singular values and singular vectors to compute. Must satisfy ``1 <= k <= kmax``, where ``kmax=min(M, N)`` for ``solver='propack'`` and ``kmax=min(M, N) - 1`` otherwise. ncv : int, optional When ``solver='arpack'``, this is the number of Lanczos vectors generated. See :ref:`'arpack' ` for details. When ``solver='lobpcg'`` or ``solver='propack'``, this parameter is ignored. tol : float, optional Tolerance for singular values. Zero (default) means machine precision. which : {'LM', 'SM'} Which `k` singular values to find: either the largest magnitude ('LM') or smallest magnitude ('SM') singular values. v0 : ndarray, optional The starting vector for iteration; see method-specific documentation (:ref:`'arpack' `, :ref:`'lobpcg' `), or :ref:`'propack' ` for details. maxiter : int, optional Maximum number of iterations; see method-specific documentation (:ref:`'arpack' `, :ref:`'lobpcg' `), or :ref:`'propack' ` for details. return_singular_vectors : {True, False, "u", "vh"} Singular values are always computed and returned; this parameter controls the computation and return of singular vectors. - ``True``: return singular vectors. - ``False``: do not return singular vectors. - ``"u"``: if ``M <= N``, compute only the left singular vectors and return ``None`` for the right singular vectors. Otherwise, compute all singular vectors. - ``"vh"``: if ``M > N``, compute only the right singular vectors and return ``None`` for the left singular vectors. Otherwise, compute all singular vectors. If ``solver='propack'``, the option is respected regardless of the matrix shape. solver : {'arpack', 'propack', 'lobpcg'}, optional The solver used. :ref:`'arpack' `, :ref:`'lobpcg' `, and :ref:`'propack' ` are supported. Default: `'arpack'`. random_state : {None, int, `numpy.random.Generator`, `numpy.random.RandomState`}, optional Pseudorandom number generator state used to generate resamples. If `random_state` is ``None`` (or `np.random`), the `numpy.random.RandomState` singleton is used. If `random_state` is an int, a new ``RandomState`` instance is used, seeded with `random_state`. If `random_state` is already a ``Generator`` or ``RandomState`` instance then that instance is used. options : dict, optional A dictionary of solver-specific options. No solver-specific options are currently supported; this parameter is reserved for future use. Returns ------- u : ndarray, shape=(M, k) Unitary matrix having left singular vectors as columns. s : ndarray, shape=(k,) The singular values. vh : ndarray, shape=(k, N) Unitary matrix having right singular vectors as rows. Notes ----- This is a naive implementation using ARPACK or LOBPCG as an eigensolver on the matrix ``A.conj().T @ A`` or ``A @ A.conj().T``, depending on which one is smaller size, followed by the Rayleigh-Ritz method as postprocessing; see Using the normal matrix, in Rayleigh-Ritz method, (2022, Nov. 19), Wikipedia, https://w.wiki/4zms. Alternatively, the PROPACK solver can be called. ``form="array"`` Choices of the input matrix ``A`` numeric dtype may be limited. Only ``solver="lobpcg"`` supports all floating point dtypes real: 'np.single', 'np.double', 'np.longdouble' and complex: 'np.csingle', 'np.cdouble', 'np.clongdouble'. The ``solver="arpack"`` supports only 'np.single', 'np.double', and 'np.cdouble'. Examples -------- Construct a matrix ``A`` from singular values and vectors. >>> import numpy as np >>> from scipy.stats import ortho_group >>> from scipy.sparse.linalg import svds >>> from scipy.sparse import csr_matrix >>> rng = np.random.default_rng() Construct a dense matrix ``A`` from singular values and vectors. >>> orthogonal = ortho_group.rvs(10, random_state=rng) >>> s = [1e-3, 1, 2, 3, 4] # non-zero singular values >>> u = orthogonal[:, :5] # left singular vectors >>> vT = orthogonal[:, 5:].T # right singular vectors >>> A = u @ np.diag(s) @ vT With only four singular values/vectors, the SVD approximates the original matrix. >>> u4, s4, vT4 = svds(A, k=4) >>> A4 = u4 @ np.diag(s4) @ vT4 >>> np.allclose(A4, A, atol=1e-3) True With all five non-zero singular values/vectors, we can reproduce the original matrix more accurately. >>> u5, s5, vT5 = svds(A, k=5) >>> A5 = u5 @ np.diag(s5) @ vT5 >>> np.allclose(A5, A) True The singular values match the expected singular values. >>> np.allclose(s5, s) True Since the singular values are not close to each other in this example, every singular vector matches as expected up to a difference in sign. >>> (np.allclose(np.abs(u5), np.abs(u)) and ... np.allclose(np.abs(vT5), np.abs(vT))) True The singular vectors are also orthogonal. >>> (np.allclose(u5.T @ u5, np.eye(5)) and ... np.allclose(vT5 @ vT5.T, np.eye(5))) True If there are (nearly) multiple singular values, the corresponding individual singular vectors may be unstable, but the whole invariant subspace containing all such singular vectors is computed accurately as can be measured by angles between subspaces via 'subspace_angles'. >>> from scipy.linalg import subspace_angles as s_a >>> rng = np.random.default_rng() >>> s = [1, 1 + 1e-6] # non-zero singular values >>> u, _ = np.linalg.qr(rng.standard_normal((99, 2))) >>> v, _ = np.linalg.qr(rng.standard_normal((99, 2))) >>> vT = v.T >>> A = u @ np.diag(s) @ vT >>> A = A.astype(np.float32) >>> u2, s2, vT2 = svds(A, k=2) >>> np.allclose(s2, s) True The angles between the individual exact and computed singular vectors are not so small. >>> s_a(u2[:, :1], u[:, :1]) + s_a(u2[:, 1:], u[:, 1:]) > 1e-3 True >>> (s_a(vT2[:1, :].T, vT[:1, :].T) + ... s_a(vT2[1:, :].T, vT[1:, :].T)) > 1e-3 True As opposed to the angles between the 2-dimensional invariant subspaces that these vectors span, which are small for rights singular vectors >>> s_a(u2, u).sum() < 1e-6 True as well as for left singular vectors. >>> s_a(vT2.T, vT.T).sum() < 1e-6 True The next example follows that of 'sklearn.decomposition.TruncatedSVD'. >>> rng = np.random.RandomState(0) >>> X_dense = rng.random(size=(100, 100)) >>> X_dense[:, 2 * np.arange(50)] = 0 >>> X = csr_matrix(X_dense) >>> _, singular_values, _ = svds(X, k=5) >>> print(singular_values) [ 4.3293... 4.4491... 4.5420... 4.5987... 35.2410...] The function can be called without the transpose of the input matrix ever explicitly constructed. >>> from scipy.linalg import svd >>> from scipy.sparse import rand >>> from scipy.sparse.linalg import aslinearoperator >>> rng = np.random.RandomState(0) >>> G = rand(8, 9, density=0.5, random_state=rng) >>> Glo = aslinearoperator(G) >>> _, singular_values_svds, _ = svds(Glo, k=5) >>> _, singular_values_svd, _ = svd(G.toarray()) >>> np.allclose(singular_values_svds, singular_values_svd[-4::-1]) True The most memory efficient scenario is where neither the original matrix, nor its transpose, is explicitly constructed. Our example computes the smallest singular values and vectors of 'LinearOperator' constructed from the numpy function 'np.diff' used column-wise to be consistent with 'LinearOperator' operating on columns. >>> from scipy.sparse.linalg import LinearOperator, aslinearoperator >>> diff0 = lambda a: np.diff(a, axis=0) Let us create the matrix from 'diff0' to be used for validation only. >>> n = 5 # The dimension of the space. >>> M_from_diff0 = diff0(np.eye(n)) >>> print(M_from_diff0.astype(int)) [[-1 1 0 0 0] [ 0 -1 1 0 0] [ 0 0 -1 1 0] [ 0 0 0 -1 1]] The matrix 'M_from_diff0' is bi-diagonal and could be alternatively created directly by >>> M = - np.eye(n - 1, n, dtype=int) >>> np.fill_diagonal(M[:,1:], 1) >>> np.allclose(M, M_from_diff0) True Its transpose >>> print(M.T) [[-1 0 0 0] [ 1 -1 0 0] [ 0 1 -1 0] [ 0 0 1 -1] [ 0 0 0 1]] can be viewed as the incidence matrix; see Incidence matrix, (2022, Nov. 19), Wikipedia, https://w.wiki/5YXU, of a linear graph with 5 vertices and 4 edges. The 5x5 normal matrix 'M.T @ M' thus is >>> print(M.T @ M) [[ 1 -1 0 0 0] [-1 2 -1 0 0] [ 0 -1 2 -1 0] [ 0 0 -1 2 -1] [ 0 0 0 -1 1]] the graph Laplacian, while the actually used in 'svds' smaller size 4x4 normal matrix 'M @ M.T' >>> print(M @ M.T) [[ 2 -1 0 0] [-1 2 -1 0] [ 0 -1 2 -1] [ 0 0 -1 2]] is the so-called edge-based Laplacian; see Symmetric Laplacian via the incidence matrix, in Laplacian matrix, (2022, Nov. 19), Wikipedia, https://w.wiki/5YXW. The 'LinearOperator' setup needs the options 'rmatvec' and 'rmatmat' of multiplication by the matrix transpose 'M.T', but we want to be matrix-free to save memory, so knowing how 'M.T' looks like, we manually construct the following function to be used in 'rmatmat=diff0t'. >>> def diff0t(a): ... if a.ndim == 1: ... a = a[:,np.newaxis] # Turn 1D into 2D array ... d = np.zeros((a.shape[0] + 1, a.shape[1]), dtype=a.dtype) ... d[0, :] = - a[0, :] ... d[1:-1, :] = a[0:-1, :] - a[1:, :] ... d[-1, :] = a[-1, :] ... return d We check that our function 'diff0t' for the matrix transpose is valid. >>> np.allclose(M.T, diff0t(np.eye(n-1))) True Now we setup our matrix-free 'LinearOperator' called 'diff0_func_aslo' and for validation the matrix-based 'diff0_matrix_aslo'. >>> def diff0_func_aslo_def(n): ... return LinearOperator(matvec=diff0, ... matmat=diff0, ... rmatvec=diff0t, ... rmatmat=diff0t, ... shape=(n - 1, n)) >>> diff0_func_aslo = diff0_func_aslo_def(n) >>> diff0_matrix_aslo = aslinearoperator(M_from_diff0) And validate both the matrix and its transpose in 'LinearOperator'. >>> np.allclose(diff0_func_aslo(np.eye(n)), ... diff0_matrix_aslo(np.eye(n))) True >>> np.allclose(diff0_func_aslo.T(np.eye(n-1)), ... diff0_matrix_aslo.T(np.eye(n-1))) True Having the 'LinearOperator' setup validated, we run the solver. >>> n = 100 >>> diff0_func_aslo = diff0_func_aslo_def(n) >>> u, s, vT = svds(diff0_func_aslo, k=3, which='SM') The singular values squared and the singular vectors are known explicitly; see Pure Dirichlet boundary conditions, in Eigenvalues and eigenvectors of the second derivative, (2022, Nov. 19), Wikipedia, https://w.wiki/5YX6, since 'diff' corresponds to first derivative, and its smaller size n-1 x n-1 normal matrix 'M @ M.T' represent the discrete second derivative with the Dirichlet boundary conditions. We use these analytic expressions for validation. >>> se = 2. * np.sin(np.pi * np.arange(1, 4) / (2. * n)) >>> ue = np.sqrt(2 / n) * np.sin(np.pi * np.outer(np.arange(1, n), ... np.arange(1, 4)) / n) >>> np.allclose(s, se, atol=1e-3) True >>> print(np.allclose(np.abs(u), np.abs(ue), atol=1e-6)) True """ args = _iv(A, k, ncv, tol, which, v0, maxiter, return_singular_vectors, solver, random_state) (A, k, ncv, tol, which, v0, maxiter, return_singular_vectors, solver, random_state) = args largest = (which == 'LM') n, m = A.shape if n >= m: X_dot = A.matvec X_matmat = A.matmat XH_dot = A.rmatvec XH_mat = A.rmatmat transpose = False else: X_dot = A.rmatvec X_matmat = A.rmatmat XH_dot = A.matvec XH_mat = A.matmat transpose = True dtype = getattr(A, 'dtype', None) if dtype is None: dtype = A.dot(np.zeros([m, 1])).dtype def matvec_XH_X(x): return XH_dot(X_dot(x)) def matmat_XH_X(x): return XH_mat(X_matmat(x)) XH_X = LinearOperator(matvec=matvec_XH_X, dtype=A.dtype, matmat=matmat_XH_X, shape=(min(A.shape), min(A.shape))) # Get a low rank approximation of the implicitly defined gramian matrix. # This is not a stable way to approach the problem. if solver == 'lobpcg': if k == 1 and v0 is not None: X = np.reshape(v0, (-1, 1)) else: X = random_state.standard_normal(size=(min(A.shape), k)) _, eigvec = lobpcg(XH_X, X, tol=tol ** 2, maxiter=maxiter, largest=largest) # lobpcg does not guarantee exactly orthonormal eigenvectors # until after gh-16320 is merged eigvec, _ = np.linalg.qr(eigvec) elif solver == 'propack': if not HAS_PROPACK: raise ValueError("`solver='propack'` is opt-in due " "to potential issues on Windows, " "it can be enabled by setting the " "`SCIPY_USE_PROPACK` environment " "variable before importing scipy") jobu = return_singular_vectors in {True, 'u'} jobv = return_singular_vectors in {True, 'vh'} irl_mode = (which == 'SM') res = _svdp(A, k=k, tol=tol**2, which=which, maxiter=None, compute_u=jobu, compute_v=jobv, irl_mode=irl_mode, kmax=maxiter, v0=v0, random_state=random_state) u, s, vh, _ = res # but we'll ignore bnd, the last output # PROPACK order appears to be largest first. `svds` output order is not # guaranteed, according to documentation, but for ARPACK and LOBPCG # they actually are ordered smallest to largest, so reverse for # consistency. s = s[::-1] u = u[:, ::-1] vh = vh[::-1] u = u if jobu else None vh = vh if jobv else None if return_singular_vectors: return u, s, vh else: return s elif solver == 'arpack' or solver is None: if v0 is None: v0 = random_state.standard_normal(size=(min(A.shape),)) _, eigvec = eigsh(XH_X, k=k, tol=tol ** 2, maxiter=maxiter, ncv=ncv, which=which, v0=v0) # arpack do not guarantee exactly orthonormal eigenvectors # for clustered eigenvalues, especially in complex arithmetic eigvec, _ = np.linalg.qr(eigvec) # the eigenvectors eigvec must be orthonomal here; see gh-16712 Av = X_matmat(eigvec) if not return_singular_vectors: s = svd(Av, compute_uv=False, overwrite_a=True) return s[::-1] # compute the left singular vectors of X and update the right ones # accordingly u, s, vh = svd(Av, full_matrices=False, overwrite_a=True) u = u[:, ::-1] s = s[::-1] vh = vh[::-1] jobu = return_singular_vectors in {True, 'u'} jobv = return_singular_vectors in {True, 'vh'} if transpose: u_tmp = eigvec @ _herm(vh) if jobu else None vh = _herm(u) if jobv else None u = u_tmp else: if not jobu: u = None vh = vh @ _herm(eigvec) if jobv else None return u, s, vh