Source code for graspy.embed.omni

# omni.py
# Created by Jaewon Chung on 2018-09-10.
# Email: j1c@jhu.edu
# Copyright (c) 2018. All rights reserved.
import warnings

import numpy as np
from sklearn.utils.validation import check_is_fitted

from .base import BaseEmbed
from .svd import selectSVD
from ..utils import import_graph, get_lcc, is_fully_connected


def _check_valid_graphs(graphs):
    """
    Checks if all graphs in list have same shapes.

    Raises an ValueError if there are more than one shape in the input list,
    or if the list is empty or has one element.

    Parameters
    ----------
    graphs : list
        List of array-like with shapes (n_vertices, n_vertices).

    Raises
    ------
    ValueError
        If all graphs do not have same shape, or input list is empty or has 
        one element.
    """
    if len(graphs) <= 1:
        msg = "Omnibus embedding requires more than one graph."
        raise ValueError(msg)

    shapes = set(map(np.shape, graphs))

    if len(shapes) > 1:
        msg = "There are {} different sizes of graphs.".format(len(shapes))
        raise ValueError(msg)


def _get_omni_matrix(graphs):
    """
    Helper function for creating the omnibus matrix.

    Parameters
    ----------
    graphs : list
        List of array-like with shapes (n_vertices, n_vertices).

    Returns
    -------
    out : 2d-array
        Array of shape (n_vertices * n_graphs, n_vertices * n_graphs)
    """
    shape = graphs[0].shape
    n = shape[0]  # number of vertices
    m = len(graphs)  # number of graphs

    A = np.array(graphs, copy=False, ndmin=3)

    # Do some numpy broadcasting magic.
    # We do sum in 4d arrays and reduce to 2d array.
    # Super fast and efficient
    out = (A[:, :, None, :] + A.transpose(1, 0, 2)[None, :, :, :]).reshape(n * m, -1)

    # Averaging
    out /= 2

    return out


[docs]class OmnibusEmbed(BaseEmbed): r""" Omnibus embedding of arbitrary number of input graphs with matched vertex sets. Given :math:`A_1, A_2, ..., A_m` a collection of (possibly weighted) adjacency matrices of a collection :math:`m` undirected graphs with matched vertices. Then the :math:`(mn \times mn)` omnibus matrix, :math:`M`, has the subgraph where :math:`M_{ij} = \frac{1}{2}(A_i + A_j)`. The omnibus matrix is then embedded using adjacency spectral embedding. Parameters ---------- n_components : int or None, default = None Desired dimensionality of output data. If "full", n_components must be <= min(X.shape). Otherwise, n_components must be < min(X.shape). If None, then optimal dimensions will be chosen by ``select_dimension`` using ``n_elbows`` argument. n_elbows : int, optional, default: 2 If `n_compoents=None`, then compute the optimal embedding dimension using `select_dimension`. Otherwise, ignored. algorithm : {'full', 'truncated' (default), 'randomized'}, optional SVD solver to use: - 'full' Computes full svd using ``scipy.linalg.svd`` - 'truncated' Computes truncated svd using ``scipy.sparse.linalg.svd`` - 'randomized' Computes randomized svd using ``sklearn.utils.extmath.randomized_svd`` n_iter : int, optional (default = 5) Number of iterations for randomized SVD solver. Not used by 'full' or 'truncated'. The default is larger than the default in randomized_svd to handle sparse matrices that may have large slowly decaying spectrum. Attributes ---------- n_graphs_ : int Number of graphs n_vertices_ : int Number of vertices in each graph latent_left_ : array, shape (n_samples, n_components) Estimated left latent positions of the graph. latent_right_ : array, shape (n_samples, n_components), or None Only computed when the graph is directed, or adjacency matrix is asymmetric. Estimated right latent positions of the graph. Otherwise, None. singular_values_ : array, shape (n_components) Singular values associated with the latent position matrices. indices_ : array, or None If ``lcc`` is True, these are the indices of the vertices that were kept. See Also -------- graspy.embed.selectSVD graspy.embed.select_dimension """ def __init__(self, n_components=None, n_elbows=2, algorithm="randomized", n_iter=5): super().__init__( n_components=n_components, n_elbows=n_elbows, algorithm=algorithm, n_iter=n_iter, )
[docs] def fit(self, graphs, y=None): """ Fit the model with graphs. Parameters ---------- graphs : list of graphs, or array-like List of array-like, (n_vertices, n_vertices), or list of networkx.Graph. If array-like, the shape must be (n_graphs, n_vertices, n_vertices) y : Ignored Returns ------- self : returns an instance of self. """ # Convert input to np.arrays graphs = [import_graph(g) for g in graphs] # Check if the input is valid _check_valid_graphs(graphs) # Save attributes self.n_graphs_ = len(graphs) self.n_vertices_ = graphs[0].shape[0] graphs = np.stack(graphs) # Check if Abar is connected if not is_fully_connected(graphs.mean(axis=0)): msg = r"""Input graphs are not fully connected. Results may not \ be optimal. You can compute the largest connected component by \ using ``graspy.utils.get_multigraph_union_lcc``.""" warnings.warn(msg, UserWarning) # Create omni matrix omni_matrix = _get_omni_matrix(graphs) # Embed self._reduce_dim(omni_matrix) return self
[docs] def fit_transform(self, graphs, y=None): """ Fit the model with graphs and apply the embedding on graphs. n_dimension is either automatically determined or based on user input. Parameters ---------- graphs : list of graphs List of array-like, (n_vertices, n_vertices), or list of networkx.Graph. y : Ignored Returns ------- out : array-like, shape (n_vertices * n_graphs, n_dimension) if input graphs were symmetric. If graphs were directed, returns tuple of two arrays (same shape as above) where the first corresponds to the left latent positions, and the right to the right latent positions """ return self._fit_transform(graphs)