igraph Reference Manual

For using the igraph C library

Chapter 25. Spectral Coarse Graining

1. Introduction

The SCG functions provide a framework, called Spectral Coarse Graining (SCG), for reducing large graphs while preserving their spectral-related features, that is features closely related with the eigenvalues and eigenvectors of a graph matrix (which for now can be the adjacency, the stochastic, or the Laplacian matrix).

Common examples of such features comprise the first-passage-time of random walkers on Markovian graphs, thermodynamic properties of lattice models in statistical physics (e.g. Ising model), and the epidemic threshold of epidemic network models (SIR and SIS models).

SCG differs from traditional clustering schemes by producing a coarse-grained graph (not just a partition of the vertices), representative of the original one. As shown in [1], Principal Component Analysis can be viewed as a particular SCG, called exact SCG, where the matrix to be coarse-grained is the covariance matrix of some data set.

SCG should be of interest to practitioners of various fields dealing with problems where matrix eigenpairs play an important role, as for instance is the case of dynamical processes on networks.

1.1. SCG in brief

The main idea of SCG is to operate on a matrix a shrinkage operation specifically designed to preserve some of the matrix eigenpairs while not altering other important matrix features (such as its structure). Mathematically, this idea was expressed as follows. Consider a (complex) n x n matrix M and form the product

M'=LMR*,

where n' < n and L, R are from C[n'xn]} and are such that LR*=I[n'] (R* denotes the conjugate transpose of R). Under these assumptions, it can be shown that P=R*L is an n'-rank projector and that, if (lambda, v) is a (right) eigenpair of M (i.e. Mv=lambda v} and P is orthogonal, there exists an eigenvalue lambda' of M' such that

|lambda-lambda'| <= const ||e[P](v)|| [1+O(||e[P](v)||2)],

where ||e[P](v)||=||v-Pv||. Hence, if P (or equivalently L, R) is chosen so as to make ||e[P](v)|| as small as possible, one can preserve to any desired level the original eigenvalue lambda in the coarse-grained matrix M'; under extra assumptions on M, this result can be generalized to eigenvectors [1]. This leads to the following generic definition of a SCG problem.

Given M (C[nxn]) and (lambda, v), a (right) eigenpair of M to be preserved by the coarse graining, the problem is to find a projector P' solving

min(||e[P](v)||, p in Omega),

where Omega is a set of projectors in C[nxn] described by some ad hoc constraints c[1], ..., c[r] (e.g. c[1]: P in R[nxn], c[2]: P=t(P), c[3]: P[i,j] >= 0}, etc).

Choosing pertinent constraints to solve the SCG problem is of great importance in applications. For instance, in the absence of constraints the SCG problem is solved trivially by P'=vv* (v is assumed normalized). We have designed a particular constraint, called homogeneous mixing, which ensures that vertices belonging to the same group are merged consistently from a physical point of view (see [1] for details). Under this constraint the SCG problem reduces to finding the partition of 1, ..., n (labeling the original vertices) minimizing

||e[P](v)||2 = sum([v(i)-(Pv)(i)]2; alpha=1,...,n', i in alpha),

where alpha denotes a group (i.e. a block) in a partition of {1, ..., n}, and |alpha| is the number of elements in alpha.

If M is symmetric or stochastic, for instance, then it may be desirable (or mandatory) to choose L, R so that M' is symmetric or stochastic as well. This structural constraint has led to the construction of particular semi-projectors for symmetric [1], stochastic [3] and Laplacian [2] matrices, that are made available.

In short, the coarse graining of matrices and graphs involves:

  1. Retrieving a matrix or a graph matrix M from the problem.

  2. Computing the eigenpairs of M to be preserved in the coarse-grained graph or matrix.

  3. Setting some problem-specific constraints (e.g. dimension of the coarse-grained object).

  4. Solving the constrained SCG problem, that is finding P'.

  5. Computing from P' two semi-projectors L' and R' (e.g. following the method proposed in [1]).

  6. Working out the product M'=L'MR'* and, if needed, defining from M' a coarse-grained graph.

1.2. Functions for performing SCG

The main functions are igraph_scg_adjacency(), igraph_scg_laplacian() and igraph_scg_stochastic(). These functions handle all the steps involved in the Spectral Coarse Graining (SCG) of some particular matrices and graphs as described above and in reference [1]. In more details, they compute some prescribed eigenpairs of a matrix or a graph matrix, (for now adjacency, Laplacian and stochastic matrices are available), work out an optimal partition to preserve the eigenpairs, and finally output a coarse-grained matrix or graph along with other useful information.

These steps can also be carried out independently: (1) Use igraph_get_adjacency(), igraph_get_sparsemat(), igraph_laplacian(), igraph_get_stochastic() or igraph_get_stochastic_sparsemat() to compute a matrix M. (2) Work out some prescribed eigenpairs of M e.g. by means of igraph_arpack_rssolve() or igraph_arpack_rnsolve(). (3) Invoke one the four algorithms of the function igraph_scg_grouping() to get a partition that will preserve the eigenpairs in the coarse-grained matrix. (4) Compute the semi-projectors L and R using igraph_scg_semiprojectors() and from there the coarse-grained matrix M'=LMR*. If necessary, construct a coarse-grained graph from M' (e.g. as in [1]).

1.3. References

[1] D. Morton de Lachapelle, D. Gfeller, and P. De Los Rios, Shrinking Matrices while Preserving their Eigenpairs with Application to the Spectral Coarse Graining of Graphs. Submitted to SIAM Journal on Matrix Analysis and Applications, 2008. http://people.epfl.ch/david.morton

[2] D. Gfeller, and P. De Los Rios, Spectral Coarse Graining and Synchronization in Oscillator Networks. Physical Review Letters, 100(17), 2008. http://arxiv.org/abs/0708.2055

[3] D. Gfeller, and P. De Los Rios, Spectral Coarse Graining of Complex Networks, Physical Review Letters, 99(3), 2007. http://arxiv.org/abs/0706.0812

2. SCG functions

2.1. igraph_scg_adjacency — Spectral coarse graining, symmetric case.

int igraph_scg_adjacency(const igraph_t *graph,
			 const igraph_matrix_t *matrix,
			 const igraph_sparsemat_t *sparsemat,
			 const igraph_vector_t *ev,
			 igraph_integer_t nt,
			 const igraph_vector_t *nt_vec,
			 igraph_scg_algorithm_t algo,
			 igraph_vector_t *values,
			 igraph_matrix_t *vectors,
			 igraph_vector_t *groups,
			 igraph_bool_t use_arpack,
			 igraph_integer_t maxiter,
			 igraph_t *scg_graph,
			 igraph_matrix_t *scg_matrix,
			 igraph_sparsemat_t *scg_sparsemat,
			 igraph_matrix_t *L,
			 igraph_matrix_t *R,
			 igraph_sparsemat_t *Lsparse,
			 igraph_sparsemat_t *Rsparse);

This function handles all the steps involved in the Spectral Coarse Graining (SCG) of some matrices and graphs as described in the reference below.

Arguments: 

graph:

The input graph. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

matrix:

The input matrix. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

sparsemat:

The input sparse matrix. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

ev:

A vector of positive integers giving the indexes of the eigenpairs to be preserved. 1 designates the eigenvalue with largest algebraic value, 2 the one with second largest algebraic value, etc.

nt:

Positive integer. When algo is IGRAPH_SCG_OPTIMUM, it gives the number of groups to partition each eigenvector separately. When algo is IGRAPH_SCG_INTERV or IGRAPH_SCG_INTERV_KM, it gives the number of intervals to partition each eigenvector. This is ignored when algo is IGRAPH_SCG_EXACT.

nt_vec:

A numeric vector of length one or the length must match the number of eigenvectors given in V, or a NULL pointer. If not NULL, then this argument gives the number of groups or intervals, and nt is ignored. Different number of groups or intervals can be specified for each eigenvector.

algo:

The algorithm to solve the SCG problem. Possible values: IGRAPH_SCG_OPTIMUM, IGRAPH_SCG_INTERV_KM, IGRAPH_SCG_INTERV and IGRAPH_SCG_EXACT. Please see the details about them above.

values:

If this is not NULL and the eigenvectors are re-calculated, then the eigenvalues are stored here.

vectors:

If this is not NULL, and not a zero-length matrix, then it is interpreted as the eigenvectors to use for the coarse-graining. Otherwise the eigenvectors are re-calculated, and they are stored here. (If this is not NULL.)

groups:

If this is not NULL, and not a zero-length vector, then it is interpreted as the vector of group labels. (Group labels are integers from zero and are sequential.) Otherwise group labels are re-calculated and stored here, if this argument is not a null pointer.

use_arpack:

Whether to use ARPACK for solving the eigenproblem. Currently ARPACK is not implemented.

maxiter:

A positive integer giving the number of iterations of the k-means algorithm when algo is IGRAPH_SCG_INTERV_KM. It is ignored in other cases. A reasonable (initial) value for this argument is 100.

scg_graph:

If not a NULL pointer, then the coarse-grained graph is returned here.

scg_matrix:

If not a NULL pointer, then it must be an initialied matrix, and the coarse-grained matrix is returned here.

scg_sparsemat:

If not a NULL pointer, then the coarse grained matrix is returned here, in sparse matrix form.

L:

If not a NULL pointer, then it must be an initialized matrix and the left semi-projector is returned here.

R:

If not a NULL pointer, then it must be an initialized matrix and the right semi-projector is returned here.

Lsparse:

If not a NULL pointer, then the left semi-projector is returned here.

Rsparse:

If not a NULL pointer, then the right semi-projector is returned here.

Returns: 

Error code.

Time complexity: TODO.

See also: 

Example 25.1.  File examples/simple/scg.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  igraph_t g;
  igraph_vector_t ev;
  igraph_t scg_graph;
  igraph_matrix_t scg_matrix;
  igraph_sparsemat_t scg_sparsemat;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t input_matrix;
  igraph_vector_t groups;
  igraph_vector_t eval;
  igraph_matrix_t evec;
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_vector_init(&ev, 1);
  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&scg_matrix, 0, 0);
  igraph_vector_init(&groups, 0);
  igraph_vector_init(&eval, 0);
  igraph_matrix_init(&evec, 0, 0);

#define CALLSYM(algo) do {						\
    igraph_vector_clear(&eval);						\
    igraph_matrix_resize(&evec, 0, 0);					\
    igraph_scg_adjacency(&g, /*matrix=*/ 0, /*sparsemat=*/ 0, &ev,	\
			 /* intervals= */ 3, /* intervals_vector= */ 0,	\
			 /* algorithm= */ algo, &eval, &evec,		\
			 /* groups= */ &groups, /* use_arpack= */ 0,	\
			 /* maxiter= */ 0, &scg_graph, &scg_matrix,	\
			 &scg_sparsemat, &L, &R,			\
			 &Lsparse, &Rsparse); } while(0)

  
#define PRINTRES()						\
  do {								\
    printf("------------------------------------\n");		\
    igraph_write_graph_edgelist(&scg_graph, stdout);		\
    printf("---\n");						\
    igraph_vector_print(&groups);				\
    printf("---\n");						\
    igraph_vector_print(&eval);					\
    igraph_matrix_print(&evec);					\
    printf("---\n");						\
    igraph_sparsemat_print(&scg_sparsemat, stdout);		\
    printf("---\n");						\
    igraph_sparsemat_print(&Lsparse, stdout);			\
    printf("---\n");						\
    igraph_sparsemat_print(&Rsparse, stdout);			\
    printf("---\n");						\
  } while (0)

  VECTOR(ev)[0] = 1;
  CALLSYM(IGRAPH_SCG_EXACT);
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  VECTOR(ev)[0] = 3;
  CALLSYM(IGRAPH_SCG_EXACT);
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_vector_resize(&ev, 2);
  VECTOR(ev)[0] = 1; VECTOR(ev)[1] = 3;
  CALLSYM(IGRAPH_SCG_EXACT);
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

#define CALLSYM2(algo) do {						\
    igraph_vector_clear(&eval);						\
    igraph_matrix_resize(&evec, 0, 0);					\
    igraph_scg_adjacency(/* graph=*/ 0, &input_matrix, /*sparsemat=*/ 0, \
			 &ev, /* intervals= */ 3,			\
			 /* intervals_vector= */ 0,			\
			 /* algorithm= */ algo, &eval, &evec,		\
			 /* groups= */ &groups, /* use_arpack= */ 0,	\
			 /* maxiter= */ 0, &scg_graph, &scg_matrix,	\
			 &scg_sparsemat, &L, &R,			\
			 &Lsparse, &Rsparse); } while (0)

  igraph_matrix_init(&input_matrix, 0, 0);
  igraph_get_adjacency(&g, &input_matrix, IGRAPH_GET_ADJACENCY_BOTH, 
		       /* eids= */ 0);

  igraph_vector_resize(&ev, 1);
  VECTOR(ev)[0] = 1;
  CALLSYM2(IGRAPH_SCG_EXACT);
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  VECTOR(ev)[0] = 3;
  CALLSYM2(IGRAPH_SCG_EXACT);
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_vector_resize(&ev, 2);
  VECTOR(ev)[0] = 1; VECTOR(ev)[1] = 3;
  CALLSYM2(IGRAPH_SCG_EXACT);
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_matrix_destroy(&evec);
  igraph_vector_destroy(&eval);
  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&input_matrix);
  igraph_matrix_destroy(&scg_matrix);
  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_vector_destroy(&ev);
  igraph_destroy(&g);

  /* -------------------------------------------------------------------- */

  return 0;
}


2.2. igraph_scg_stochastic — Spectral coarse graining, stochastic case.

int igraph_scg_stochastic(const igraph_t *graph,
			  const igraph_matrix_t *matrix,
			  const igraph_sparsemat_t *sparsemat,
			  const igraph_vector_t *ev,
			  igraph_integer_t nt,
			  const igraph_vector_t *nt_vec,
			  igraph_scg_algorithm_t algo,
			  igraph_scg_norm_t norm,
			  igraph_vector_complex_t *values,
			  igraph_matrix_complex_t *vectors,
			  igraph_vector_t *groups,
			  igraph_vector_t *p,
			  igraph_bool_t use_arpack,
			  igraph_integer_t maxiter,
			  igraph_t *scg_graph,
			  igraph_matrix_t *scg_matrix,
			  igraph_sparsemat_t *scg_sparsemat,
			  igraph_matrix_t *L,
			  igraph_matrix_t *R,
			  igraph_sparsemat_t *Lsparse,
			  igraph_sparsemat_t *Rsparse);

This function handles all the steps involved in the Spectral Coarse Graining (SCG) of some matrices and graphs as described in the reference below.

Arguments: 

graph:

The input graph. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

matrix:

The input matrix. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

sparsemat:

The input sparse matrix. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

ev:

A vector of positive integers giving the indexes of the eigenpairs to be preserved. 1 designates the eigenvalue with largest magnitude, 2 the one with second largest magnitude, etc.

nt:

Positive integer. When algo is IGRAPH_SCG_OPTIMUM, it gives the number of groups to partition each eigenvector separately. When algo is IGRAPH_SCG_INTERV or IGRAPH_SCG_INTERV_KM, it gives the number of intervals to partition each eigenvector. This is ignored when algo is IGRAPH_SCG_EXACT.

nt_vec:

A numeric vector of length one or the length must match the number of eigenvectors given in V, or a NULL pointer. If not NULL, then this argument gives the number of groups or intervals, and nt is ignored. Different number of groups or intervals can be specified for each eigenvector.

algo:

The algorithm to solve the SCG problem. Possible values: IGRAPH_SCG_OPTIMUM, IGRAPH_SCG_INTERV_KM, IGRAPH_SCG_INTERV and IGRAPH_SCG_EXACT. Please see the details about them above.

norm:

Either IGRAPH_SCG_NORM_ROW or IGRAPH_SCG_NORM_COL. Specifies whether the rows or the columns of the stochastic matrix sum up to one.

values:

If this is not NULL and the eigenvectors are re-calculated, then the eigenvalues are stored here.

vectors:

If this is not NULL, and not a zero-length matrix, then it is interpreted as the eigenvectors to use for the coarse-graining. Otherwise the eigenvectors are re-calculated, and they are stored here. (If this is not NULL.)

groups:

If this is not NULL, and not a zero-length vector, then it is interpreted as the vector of group labels. (Group labels are integers from zero and are sequential.) Otherwise group labels are re-calculated and stored here, if this argument is not a null pointer.

p:

If this is not NULL, and not zero length, then it is interpreted as the stationary probability distribution of the Markov chain corresponding to the input matrix/graph. Its length must match the number of vertices in the input graph (or number of rows in the input matrix). If not given, then the stationary distribution is calculated and stored here. (Unless this argument is a NULL pointer, in which case it is not stored.)

use_arpack:

Whether to use ARPACK for solving the eigenproblem. Currently ARPACK is not implemented.

maxiter:

A positive integer giving the number of iterations of the k-means algorithm when algo is IGRAPH_SCG_INTERV_KM. It is ignored in other cases. A reasonable (initial) value for this argument is 100.

scg_graph:

If not a NULL pointer, then the coarse-grained graph is returned here.

scg_matrix:

If not a NULL pointer, then it must be an initialied matrix, and the coarse-grained matrix is returned here.

scg_sparsemat:

If not a NULL pointer, then the coarse grained matrix is returned here, in sparse matrix form.

L:

If not a NULL pointer, then it must be an initialized matrix and the left semi-projector is returned here.

R:

If not a NULL pointer, then it must be an initialized matrix and the right semi-projector is returned here.

Lsparse:

If not a NULL pointer, then the left semi-projector is returned here.

Rsparse:

If not a NULL pointer, then the right semi-projector is returned here.

Returns: 

Error code.

Time complexity: TODO.

See also: 

Example 25.2.  File examples/simple/scg2.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  igraph_t g;
  igraph_vector_t ev;
  igraph_t scg_graph;
  igraph_matrix_t scg_matrix;
  igraph_sparsemat_t scg_sparsemat;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_vector_t p;
  igraph_vector_t groups;
  igraph_vector_complex_t eval;
  igraph_matrix_complex_t evec;
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_vector_init(&ev, 1);
  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&scg_matrix, 0, 0);
  igraph_vector_init(&p, 0);
  igraph_vector_init(&groups, 0);
  igraph_vector_complex_init(&eval, 0);
  igraph_matrix_complex_init(&evec, 0, 0);

#define CALLSTO() do {							 \
    igraph_vector_resize(&p, 0);					 \
    igraph_vector_resize(&groups, 0);					 \
    igraph_vector_complex_resize(&eval, 0);				 \
    igraph_matrix_complex_resize(&evec, 0, 0);				 \
    igraph_scg_stochastic(&g, /*matrix=*/ 0, /*sparsemat=*/ 0, &ev,	 \
			  /* intervals= */ 2, /* intervals_vector= */ 0, \
			  /* algorithm= */ IGRAPH_SCG_EXACT,		 \
			  IGRAPH_SCG_NORM_ROW, &eval, &evec, 		 \
			  &groups, &p, /* use_arpack= */ 0,		 \
			  /* maxiter= */ 0, &scg_graph, &scg_matrix,	 \
			  &scg_sparsemat, &L, &R,			 \
			  &Lsparse, &Rsparse);				 \
} while (0)

#define PRINTRES()						\
  do {								\
    printf("--------------------------------\n");		\
    igraph_vector_print(&groups);				\
    printf("---\n");						\
    igraph_vector_complex_print(&eval);				\
    igraph_matrix_complex_print(&evec);				\
    printf("---\n");						\
    igraph_write_graph_edgelist(&scg_graph, stdout);		\
    printf("---\n");						\
    igraph_sparsemat_print(&scg_sparsemat, stdout);		\
    printf("---\n");						\
    igraph_sparsemat_print(&Lsparse, stdout);			\
    printf("---\n");						\
    igraph_sparsemat_print(&Rsparse, stdout);			\
    printf("---\n");						\
  } while (0)
  
  VECTOR(ev)[0] = 1;
  CALLSTO();
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  VECTOR(ev)[0] = 3;
  CALLSTO();
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_vector_resize(&ev, 2);
  VECTOR(ev)[0] = 1; VECTOR(ev)[1] = 3;
  CALLSTO();
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_matrix_complex_destroy(&evec);
  igraph_vector_complex_destroy(&eval);
  igraph_vector_destroy(&groups);
  igraph_vector_destroy(&p);
  igraph_matrix_destroy(&scg_matrix);
  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_vector_destroy(&ev);
  igraph_destroy(&g);

  /* -------------------------------------------------------------------- */

#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}


2.3. igraph_scg_laplacian — Spectral coarse graining, laplacian matrix.

int igraph_scg_laplacian(const igraph_t *graph,
			 const igraph_matrix_t *matrix,
			 const igraph_sparsemat_t *sparsemat,
			 const igraph_vector_t *ev,
			 igraph_integer_t nt,
			 const igraph_vector_t *nt_vec,
			 igraph_scg_algorithm_t algo,
			 igraph_scg_norm_t norm,
			 igraph_scg_direction_t direction,
			 igraph_vector_complex_t *values,
			 igraph_matrix_complex_t *vectors,
			 igraph_vector_t *groups,
			 igraph_bool_t use_arpack,
			 igraph_integer_t maxiter,
			 igraph_t *scg_graph,
			 igraph_matrix_t *scg_matrix,
			 igraph_sparsemat_t *scg_sparsemat,
			 igraph_matrix_t *L,
			 igraph_matrix_t *R,
			 igraph_sparsemat_t *Lsparse,
			 igraph_sparsemat_t *Rsparse);

This function handles all the steps involved in the Spectral Coarse Graining (SCG) of some matrices and graphs as described in the reference below.

Arguments: 

graph:

The input graph. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

matrix:

The input matrix. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

sparsemat:

The input sparse matrix. Exactly one of graph, matrix and sparsemat must be given, the other two must be NULL pointers.

ev:

A vector of positive integers giving the indexes of the eigenpairs to be preserved. 1 designates the eigenvalue with largest magnitude, 2 the one with second largest magnitude, etc.

nt:

Positive integer. When algo is IGRAPH_SCG_OPTIMUM, it gives the number of groups to partition each eigenvector separately. When algo is IGRAPH_SCG_INTERV or IGRAPH_SCG_INTERV_KM, it gives the number of intervals to partition each eigenvector. This is ignored when algo is IGRAPH_SCG_EXACT.

nt_vec:

A numeric vector of length one or the length must match the number of eigenvectors given in V, or a NULL pointer. If not NULL, then this argument gives the number of groups or intervals, and nt is ignored. Different number of groups or intervals can be specified for each eigenvector.

algo:

The algorithm to solve the SCG problem. Possible values: IGRAPH_SCG_OPTIMUM, IGRAPH_SCG_INTERV_KM, IGRAPH_SCG_INTERV and IGRAPH_SCG_EXACT. Please see the details about them above.

norm:

Either IGRAPH_SCG_NORM_ROW or IGRAPH_SCG_NORM_COL. Specifies whether the rows or the columns of the Laplacian matrix sum up to zero.

direction:

Whether to work with left or right eigenvectors. Possible values: IGRAPH_SCG_DIRECTION_DEFAULT, IGRAPH_SCG_DIRECTION_LEFT, IGRAPH_SCG_DIRECTION_RIGHT. This argument is currently ignored and right eigenvectors are always used.

values:

If this is not NULL and the eigenvectors are re-calculated, then the eigenvalues are stored here.

vectors:

If this is not NULL, and not a zero-length matrix, then it is interpreted as the eigenvectors to use for the coarse-graining. Otherwise the eigenvectors are re-calculated, and they are stored here. (If this is not NULL.)

groups:

If this is not NULL, and not a zero-length vector, then it is interpreted as the vector of group labels. (Group labels are integers from zero and are sequential.) Otherwise group labels are re-calculated and stored here, if this argument is not a null pointer.

use_arpack:

Whether to use ARPACK for solving the eigenproblem. Currently ARPACK is not implemented.

maxiter:

A positive integer giving the number of iterations of the k-means algorithm when algo is IGRAPH_SCG_INTERV_KM. It is ignored in other cases. A reasonable (initial) value for this argument is 100.

scg_graph:

If not a NULL pointer, then the coarse-grained graph is returned here.

scg_matrix:

If not a NULL pointer, then it must be an initialied matrix, and the coarse-grained matrix is returned here.

scg_sparsemat:

If not a NULL pointer, then the coarse grained matrix is returned here, in sparse matrix form.

L:

If not a NULL pointer, then it must be an initialized matrix and the left semi-projector is returned here.

R:

If not a NULL pointer, then it must be an initialized matrix and the right semi-projector is returned here.

Lsparse:

If not a NULL pointer, then the left semi-projector is returned here.

Rsparse:

If not a NULL pointer, then the right semi-projector is returned here.

Returns: 

Error code.

Time complexity: TODO.

See also: 

Example 25.3.  File examples/simple/scg3.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  igraph_t g;
  igraph_vector_t ev;
  igraph_t scg_graph;
  igraph_matrix_t scg_matrix;
  igraph_sparsemat_t scg_sparsemat;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_vector_t groups;
  igraph_vector_complex_t eval;
  igraph_matrix_complex_t evec;
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_vector_init(&ev, 1);
  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&scg_matrix, 0, 0);
  igraph_vector_init(&groups, 0);
  igraph_vector_complex_init(&eval, 0);
  igraph_matrix_complex_init(&evec, 0, 0);

#define CALLLAP() do {							 \
    igraph_vector_resize(&groups, 0);					 \
    igraph_vector_complex_resize(&eval, 0);				 \
    igraph_matrix_complex_resize(&evec, 0, 0);				 \
    igraph_scg_laplacian(&g, /*matrix=*/ 0, /*sparsemat=*/ 0, &ev,	 \
			 /* intervals= */ 2, /* intervals_vector= */ 0, \
			 /* algorithm= */ IGRAPH_SCG_EXACT,		\
			 IGRAPH_SCG_NORM_ROW,				\
			 IGRAPH_SCG_DIRECTION_DEFAULT, &eval, &evec,	\
			 &groups, /* use_arpack= */ 0,			\
			 /* maxiter= */ 0, &scg_graph, &scg_matrix,	\
			 &scg_sparsemat, &L, &R,			\
			 &Lsparse, &Rsparse);				\
} while (0)

#define PRINTRES()						\
  do {								\
    printf("--------------------------------\n");		\
    igraph_vector_print(&groups);				\
    printf("---\n");						\
    igraph_vector_complex_print(&eval);				\
    igraph_matrix_complex_print(&evec);				\
    printf("---\n");						\
    igraph_write_graph_edgelist(&scg_graph, stdout);		\
    printf("---\n");						\
    igraph_sparsemat_print(&scg_sparsemat, stdout);		\
    printf("---\n");						\
    igraph_sparsemat_print(&Lsparse, stdout);			\
    printf("---\n");						\
    igraph_sparsemat_print(&Rsparse, stdout);			\
    printf("---\n");						\
  } while (0)

  VECTOR(ev)[0] = 1;
  CALLLAP();
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  VECTOR(ev)[0] = 3;
  CALLLAP();
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_vector_resize(&ev, 2);
  VECTOR(ev)[0] = 1; VECTOR(ev)[1] = 3;
  CALLLAP();
  PRINTRES();
  igraph_destroy(&scg_graph);
  igraph_sparsemat_destroy(&scg_sparsemat);
  igraph_sparsemat_destroy(&Lsparse);
  igraph_sparsemat_destroy(&Rsparse);

  igraph_matrix_complex_destroy(&evec);
  igraph_vector_complex_destroy(&eval);
  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&scg_matrix);
  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_vector_destroy(&ev);
  igraph_destroy(&g);

  /* -------------------------------------------------------------------- */

#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
  


2.4. igraph_scg_grouping — SCG problem solver

int igraph_scg_grouping(const igraph_matrix_t *V, 
			igraph_vector_t *groups,
			igraph_integer_t nt,
			const igraph_vector_t *nt_vec,
			igraph_scg_matrix_t mtype,
			igraph_scg_algorithm_t algo,
			const igraph_vector_t *p,
			igraph_integer_t maxiter);

This function solves the Spectral Coarse Graining (SCG) problem; either exactly, or approximately but faster.

The algorithm IGRAPH_SCG_OPTIMUM solves exactly the SCG problem for each eigenvector in V. The running time of this algorithm is O(max(nt) m^2) for the symmetric and laplacian matrix problems It is O(m^3) for the stochastic problem. Here m is the number of rows in V. In all three cases, the memory usage is O(m^2).

The algorithms IGRAPH_SCG_INTERV and IGRAPH_SCG_INTERV_KM solve approximately the SCG problem by performing a (for now) constant binning of the components of the eigenvectors, that is nt VECTOR(nt_vec)[i] ) constant-size bins are used to partition V[,i] . When algo is IGRAPH_SCG_INTERV_KM, the (Lloyd) k-means algorithm is run on each partition obtained by IGRAPH_SCG_INTERV to improve accuracy.

Once a minimizing partition (either exact or approximate) has been found for each eigenvector, the final grouping is worked out as follows: two vertices are grouped together in the final partition if they are grouped together in each minimizing partition. In general the size of the final partition is not known in advance when the number of columns in V is larger than one.

Finally, the algorithm IGRAPH_SCG_EXACT groups the vertices with equal components in each eigenvector. The last three algorithms essentially have linear running time and memory load.

Arguments: 

V:

The matrix of eigenvectors to be preserved by coarse graining, each column is an eigenvector.

groups:

Pointer to an initialized vector, the result of the SCG is stored here.

nt:

Positive integer. When algo is IGRAPH_SCG_OPTIMUM, it gives the number of groups to partition each eigenvector separately. When algo is IGRAPH_SCG_INTERV or IGRAPH_SCG_INTERV_KM, it gives the number of intervals to partition each eigenvector. This is ignored when algo is IGRAPH_SCG_EXACT.

nt_vec:

A numeric vector of length one or the length must match the number of eigenvectors given in V, or a NULL pointer. If not NULL, then this argument gives the number of groups or intervals, and nt is ignored. Different number of groups or intervals can be specified for each eigenvector.

mtype:

The type of semi-projectors used in the SCG. Possible values are IGRAPH_SCG_SYMMETRIC, IGRAPH_SCG_STOCHASTIC and IGRAPH_SCG_LAPLACIAN.

algo:

The algorithm to solve the SCG problem. Possible values: IGRAPH_SCG_OPTIMUM, IGRAPH_SCG_INTERV_KM, IGRAPH_SCG_INTERV and IGRAPH_SCG_EXACT. Please see the details about them above.

p:

A probability vector, or NULL. This argument must be given if mtype is IGRAPH_SCG_STOCHASTIC, but it is ignored otherwise. For the stochastic case it gives the stationary probability distribution of a Markov chain, the one specified by the graph/matrix under study.

maxiter:

A positive integer giving the number of iterations of the k-means algorithm when algo is IGRAPH_SCG_INTERV_KM. It is ignored in other cases. A reasonable (initial) value for this argument is 100.

Returns: 

Error code.

Time complexity: see description above.

See also: 

Example 25.4.  File examples/simple/igraph_scg_grouping.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge, MA, 02138 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

#define SIZE (1000)

int main() {

  igraph_matrix_t M, M2;
  igraph_vector_t lambda;
  igraph_matrix_t V;
  igraph_vector_t groups;
  igraph_vector_t ivec;
  int i, j;
  int n;

  igraph_rng_seed(igraph_rng_default(), 42);

  /* Symmetric matrix, exponentially distributed elements */

  igraph_matrix_init(&M, SIZE, SIZE);
  n=igraph_matrix_nrow(&M);
  for (i=0; i<n; i++) {
    for (j=0; j<n; j++) {
      MATRIX(M, i, j) = igraph_rng_get_exp(igraph_rng_default(), 1);
    }
  }
  igraph_matrix_init(&M2, n, n);
  igraph_matrix_update(&M2, &M);
  igraph_matrix_transpose(&M2);
  igraph_matrix_add(&M, &M2);
  igraph_matrix_scale(&M, 0.5);
  igraph_matrix_destroy(&M2);

  /* Get first (most positive) two eigenvectors */

  igraph_vector_init(&lambda, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_lapack_dsyevr(&M, IGRAPH_LAPACK_DSYEV_SELECT, /*vl=*/ 0, /*vu=*/ 0, 
		       /*vestimate=*/ 0, /*il=*/ n-1, /*iu=*/ n, 
		       /*abstol=*/ 0.0, /*values=*/ &lambda, /*vectors=*/ &V, 
		       /*support=*/ 0);
  
  /* Grouping */
  
  igraph_vector_init(&groups, 0);
  igraph_vector_init(&ivec, 2);
  VECTOR(ivec)[0] = 2; VECTOR(ivec)[1] = 3;  
  igraph_scg_grouping(&V, &groups, /*invervals=*/ 0, 
		      /*intervals_vector=*/ &ivec, IGRAPH_SCG_SYMMETRIC, 
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 100);
  
  igraph_vector_print(&groups);

  igraph_vector_destroy(&ivec);
  igraph_vector_destroy(&groups);
  igraph_vector_destroy(&lambda);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&M);

  return 0;
}


Example 25.5.  File examples/simple/igraph_scg_grouping2.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  igraph_t g;
  igraph_matrix_t adj, V;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_matrix_init(&adj, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_vector_init(&groups, 0);
    
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);

  igraph_get_adjacency(&g, &adj, IGRAPH_GET_ADJACENCY_BOTH, /*eids=*/ 0);

  which.pos=IGRAPH_EIGEN_LM;
  which.howmany=1;
  igraph_eigen_matrix_symmetric(&adj, /*sparsemat=*/ 0, /*fun=*/ 0, 
				igraph_vcount(&g), /*extra=*/ 0, 
				/*algorithm=*/ IGRAPH_EIGEN_LAPACK,
				&which, /*options=*/ 0, /*storage=*/ 0,
				/*values=*/ 0, &V);
  
  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);
  

  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&adj);
  igraph_destroy(&g);
  
  return 0;
}
    


Example 25.6.  File examples/simple/igraph_scg_grouping3.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  const int nodes=10;
  igraph_t g;
  igraph_matrix_t V, V3;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t stochastic, stochasticT;
  igraph_vector_t groups;
  igraph_eigen_which_t which;
  igraph_vector_t p, selcol;

  igraph_tree(&g, nodes, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);

  igraph_sparsemat_init(&stochastic, nodes, nodes, igraph_ecount(&g)*2);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_matrix_init(&V3, 0, 0);
  igraph_vector_init(&groups, 0);
  igraph_vector_init(&p, 0);
  igraph_vector_init(&selcol, 1);  
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_get_stochastic_sparsemat(&g, &stochastic, /*column-wise=*/ 0);
  igraph_sparsemat_transpose(&stochastic, &stochasticT, /*values=*/ 1);

  which.pos=IGRAPH_EIGEN_LR;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &stochasticT, /*fun=*/ 0, nodes,
		      /*extra=*/ 0, /*1algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);

  /* `p' is always the eigenvector corresponding to the 1-eigenvalue */
  igraph_matrix_get_col(&V, &p, 0);
  igraph_vector_print(&p);

  which.howmany=3;
  igraph_eigen_matrix(/*matrix=*/ 0, &stochastic, /*fun=*/ 0, nodes,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V3);
  VECTOR(selcol)[0]=2;
  igraph_matrix_select_cols(&V3, &V, &selcol);

  /* ------------ */
  
  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_OPTIMUM, &p, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_INTERV_KM, &p, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_INTERV, &p, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_EXACT, &p, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */  

  igraph_vector_destroy(&p);
  igraph_vector_destroy(&selcol);
  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&V3);
  igraph_matrix_complex_destroy(&V2);
  igraph_sparsemat_destroy(&stochasticT);
  igraph_sparsemat_destroy(&stochastic);
  igraph_destroy(&g);
  
#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
    


Example 25.7.  File examples/simple/igraph_scg_grouping4.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  const int nodes=10;
  igraph_t g;
  igraph_matrix_t V;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t laplacian;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_tree(&g, nodes, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);

  igraph_sparsemat_init(&laplacian, nodes, nodes, igraph_ecount(&g)*2);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_vector_init(&groups, 0);
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_sparsemat_init(&laplacian, 0, 0, 0);
  igraph_laplacian(&g, /*res=*/ 0, /*sparseres=*/ &laplacian, 
		   /*normalized=*/ 0, /*weights=*/ 0);

  which.pos=IGRAPH_EIGEN_LR;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &laplacian, /*fun=*/ 0, nodes,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);

  /* ------------ */
  
  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  igraph_vector_print(&groups);

  /* ------------ */  

  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&V);
  igraph_matrix_complex_destroy(&V2);
  igraph_sparsemat_destroy(&laplacian);
  igraph_destroy(&g);

#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}


2.5. igraph_scg_semiprojectors — Compute SCG semi-projectors for a given partition

int igraph_scg_semiprojectors(const igraph_vector_t *groups,
			      igraph_scg_matrix_t mtype,
			      igraph_matrix_t *L,
			      igraph_matrix_t *R,
			      igraph_sparsemat_t *Lsparse,
			      igraph_sparsemat_t *Rsparse, 
			      const igraph_vector_t *p,
			      igraph_scg_norm_t norm);

The three types of semi-projectors are defined as follows. Let gamma(j) label the group of vertex j in a partition of all the vertices.

The symmetric semi-projectors are defined as

L[alpha,j] = R[alpha,j] = 1/sqrt(|alpha|) delta[alpha,gamma(j)],

the (row) Laplacian semi-projectors as

L[alpha,j] = 1/|alpha| delta[alpha,gamma(j)]

and

R[alpha,j] = delta[alpha,gamma(j)],

and the (row) stochastic semi-projectors as

L[alpha,j] = p[1][j] / sum(p[1][k]; k in gamma(j)) delta[alpha,gamma(j)]

and

R[alpha,j] = delta[alpha,gamma(j)],

where p[1] is the (left) eigenvector associated with the one-eigenvalue of the stochastic matrix. L and R are defined in a symmetric way when norm is IGRAPH_SCG_NORM_COL. All these semi-projectors verify various properties described in the reference.

Arguments: 

groups:

A vector of integers, giving the group label of every vertex in the partition. Group labels should start at zero and should be sequential.

mtype:

The type of semi-projectors. For now IGRAPH_SCG_SYMMETRIC, IGRAPH_SCG_STOCHASTIC and IGRAP_SCG_LAPLACIAN are supported.

L:

If not a NULL pointer, then it must be a pointer to an initialized matrix. The left semi-projector is stored here.

R:

If not a NULL pointer, then it must be a pointer to an initialized matrix. The right semi-projector is stored here.

Lsparse:

If not a NULL pointer, then it must be a pointer to an uninitialized sparse matrix. The left semi-projector is stored here.

Rsparse:

If not a NULL pointer, then it must be a pointer to an uninitialized sparse matrix. The right semi-projector is stored here.

p:

NULL, or a probability vector of the same length as groups. p is the stationary probability distribution of a Markov chain when mtype is IGRAPH_SCG_STOCHASTIC. This argument is ignored in all other cases.

norm:

Either IGRAPH_SCG_NORM_ROW or IGRAPH_SCG_NORM_COL. Specifies whether the rows or the columns of the Laplacian matrix sum up to zero, or whether the rows or the columns of the stochastic matrix sum up to one.

Returns: 

Error code.

Time complexity: TODO.

See also: 

Example 25.8.  File examples/simple/igraph_scg_semiprojectors.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  igraph_t g;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t adj, V;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&adj, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_vector_init(&groups, 0);
    
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_get_adjacency(&g, &adj, IGRAPH_GET_ADJACENCY_BOTH, /*eids=*/ 0);

  which.pos=IGRAPH_EIGEN_LM;
  which.howmany=1;
  igraph_eigen_matrix_symmetric(&adj, /*sparsemat=*/ 0, /*fun=*/ 0,
				igraph_vcount(&g), /*extra=*/ 0, 
				/*algorithm=*/ IGRAPH_EIGEN_LAPACK,
				&which, /*options=*/ 0, /*storage=*/ 0, 
				/*values=*/ 0, &V);

#define SEMI()								\
  do {									\
    igraph_scg_semiprojectors(&groups, IGRAPH_SCG_SYMMETRIC, &L, &R,	\
			      &Lsparse, &Rsparse, /*p=*/ 0,		\
			      IGRAPH_SCG_NORM_ROW);			\
  } while(0)

#define PRINTRES()				\
  do {						\
    printf("----------------------\n");		\
    igraph_matrix_print(&L);			\
    printf("---\n");				\
    igraph_matrix_print(&R);			\
    printf("---\n");				\
  } while (0)

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_SYMMETRIC,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&adj);
  igraph_destroy(&g);
  
  return 0;
}
    


Example 25.9.  File examples/simple/igraph_scg_semiprojectors2.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  int nodes=10;
  igraph_t g;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t V, V3;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t stochastic, stochasticT;
  igraph_vector_t groups;
  igraph_eigen_which_t which;
  igraph_vector_t p, selcol;

  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_matrix_init(&V3, 0, 0);
  igraph_vector_init(&groups, 0);
  igraph_vector_init(&selcol, 1);
    
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_sparsemat_init(&stochastic, nodes, nodes, igraph_ecount(&g)*2);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_vector_init(&p, 0);
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_get_stochastic_sparsemat(&g, &stochastic, /*column-wise=*/ 0);
  igraph_sparsemat_transpose(&stochastic, &stochasticT, /*values=*/ 1);

  which.pos=IGRAPH_EIGEN_LR;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &stochasticT, /*fun=*/ 0, 10,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);
  /* `p' is always the eigenvector corresponding to the 1-eigenvalue */
  igraph_matrix_get_col(&V, &p, 0);

  which.howmany=3;
  igraph_eigen_matrix(/*matrix=*/ 0, &stochastic, /*fun=*/ 0, 10,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V3);
  VECTOR(selcol)[0]=2;
  igraph_matrix_select_cols(&V3, &V, &selcol);

#define SEMI()								\
  do {									\
    igraph_scg_semiprojectors(&groups, IGRAPH_SCG_STOCHASTIC, &L, &R,	\
			      &Lsparse, &Rsparse, &p,			\
			      IGRAPH_SCG_NORM_ROW);			\
  } while(0)

#define PRINTRES()				\
  do {						\
    printf("----------------------\n");		\
    igraph_matrix_print(&L);			\
    printf("---\n");				\
    igraph_matrix_print(&R);			\
    printf("---\n");				\
  } while (0)

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_OPTIMUM, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_INTERV_KM, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_INTERV, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_STOCHASTIC,
		      IGRAPH_SCG_EXACT, &p, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_vector_destroy(&p);
  igraph_vector_destroy(&selcol);
  igraph_vector_destroy(&groups);
  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_matrix_destroy(&V);
  igraph_matrix_destroy(&V3);
  igraph_matrix_complex_destroy(&V2);
  igraph_sparsemat_destroy(&stochasticT);
  igraph_sparsemat_destroy(&stochastic);
  igraph_destroy(&g);
  
#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
    


Example 25.10.  File examples/simple/igraph_scg_semiprojectors3.c

/* -*- mode: C -*-  */
/* 
   IGraph library.
   Copyright (C) 2011-2012  Gabor Csardi <csardi.gabor@gmail.com>
   334 Harvard st, Cambridge MA, 02139 USA
   
   This program is free software; you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation; either version 2 of the License, or
   (at your option) any later version.
   
   This program is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
   
   You should have received a copy of the GNU General Public License
   along with this program; if not, write to the Free Software
   Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 
   02110-1301 USA

*/

#include <igraph.h>

int main() {

  int nodes=10;
  igraph_t g;
  igraph_matrix_t L, R;
  igraph_sparsemat_t Lsparse, Rsparse;
  igraph_matrix_t V;
  igraph_matrix_complex_t V2;
  igraph_sparsemat_t laplacian;
  igraph_vector_t groups;
  igraph_eigen_which_t which;

  igraph_matrix_init(&L, 0, 0);
  igraph_matrix_init(&R, 0, 0);
  igraph_matrix_init(&V, 0, 0);
  igraph_matrix_complex_init(&V2, 0, 0);
  igraph_vector_init(&groups, 0);
    
  igraph_rng_seed(igraph_rng_default(), 42);
  
  igraph_tree(&g, 10, /* children= */ 3, IGRAPH_TREE_UNDIRECTED);
  
  igraph_sparsemat_init(&laplacian, nodes, nodes, igraph_ecount(&g)*2);
  
  igraph_rng_seed(igraph_rng_default(), 42);

  igraph_laplacian(&g, /*res=*/ 0, /*sparseres=*/ &laplacian, 
		   /*normalized=*/ 0, /*weights=*/ 0);

  which.pos=IGRAPH_EIGEN_LM;
  which.howmany=1;

  igraph_eigen_matrix(/*matrix=*/ 0, &laplacian, /*fun=*/ 0, 10,
		      /*extra=*/ 0, /*algorithm=*/ IGRAPH_EIGEN_LAPACK,
		      &which, /*options=*/ 0, /*storage=*/ 0, 
		      /*values=*/ 0, &V2);
  igraph_matrix_complex_real(&V2, &V);

#define SEMI()								\
  do {									\
    igraph_scg_semiprojectors(&groups, IGRAPH_SCG_LAPLACIAN, &L, &R,	\
			      &Lsparse, &Rsparse, /*p=*/ 0,		\
			      IGRAPH_SCG_NORM_ROW);			\
  } while(0)

#define PRINTRES()				\
  do {						\
    printf("----------------------\n");		\
    igraph_matrix_print(&L);			\
    printf("---\n");				\
    igraph_matrix_print(&R);			\
    printf("---\n");				\
  } while (0)

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 3, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_OPTIMUM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV_KM, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*intervals=*/ 2, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_INTERV, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_scg_grouping(&V, &groups, /*(ignored) intervals=*/ 0, 
		      /*intervals_vector=*/ 0, IGRAPH_SCG_LAPLACIAN,
		      IGRAPH_SCG_EXACT, /*p=*/ 0, /*maxiter=*/ 10000);
  SEMI();
  PRINTRES();

  /* -------------- */

  igraph_matrix_destroy(&L);
  igraph_matrix_destroy(&R);
  igraph_matrix_destroy(&V);
  igraph_matrix_complex_destroy(&V2);
  igraph_vector_destroy(&groups);
  igraph_sparsemat_destroy(&laplacian);
  igraph_destroy(&g);
  
#ifdef __APPLE__
  return 0;
#else
  return 77;
#endif
}
    


2.6. igraph_scg_norm_eps — Calculate SCG residuals

int igraph_scg_norm_eps(const igraph_matrix_t *V,
			const igraph_vector_t *groups,
			igraph_vector_t *eps,
			igraph_scg_matrix_t mtype,
			const igraph_vector_t *p,
			igraph_scg_norm_t norm);

Computes |v[i]-Pv[i]|, where v[i] is the i-th eigenvector in V and P is the projector corresponding to the mtype argument.

Arguments: 

V:

The matrix of eigenvectors to be preserved by coarse graining, each column is an eigenvector.

groups:

A vector of integers, giving the group label of every vertex in the partition. Group labels should start at zero and should be sequential.

eps:

Pointer to a real value, the result is stored here.

mtype:

The type of semi-projectors. For now IGRAPH_SCG_SYMMETRIC, IGRAPH_SCG_STOCHASTIC and IGRAP_SCG_LAPLACIAN are supported.

p:

NULL, or a probability vector of the same length as groups. p is the stationary probability distribution of a Markov chain when mtype is IGRAPH_SCG_STOCHASTIC. This argument is ignored in all other cases.

norm:

Either IGRAPH_SCG_NORM_ROW or IGRAPH_SCG_NORM_COL. Specifies whether the rows or the columns of the Laplacian matrix sum up to zero, or whether the rows or the columns of the stochastic matrix sum up to one.

Returns: 

Error code.

Time complexity: TODO.

See also: