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author | KatolaZ <katolaz@freaknet.org> | 2017-09-27 15:06:31 +0100 |
---|---|---|
committer | KatolaZ <katolaz@freaknet.org> | 2017-09-27 15:06:31 +0100 |
commit | 3aee2fd43e3059a699af2b63c6f2395e5a55e515 (patch) | |
tree | 58c95505a0906ed9cfa694f9dbd319403fd8f01d /src/gn |
First commit on github -- NetBunch 1.0
Diffstat (limited to 'src/gn')
-rw-r--r-- | src/gn/Makefile.am | 5 | ||||
-rw-r--r-- | src/gn/Makefile.in | 578 | ||||
-rw-r--r-- | src/gn/gn.c | 495 |
3 files changed, 1078 insertions, 0 deletions
diff --git a/src/gn/Makefile.am b/src/gn/Makefile.am new file mode 100644 index 0000000..77874be --- /dev/null +++ b/src/gn/Makefile.am @@ -0,0 +1,5 @@ +include ../common.mk +bin_PROGRAMS = gn +gn_SOURCES = gn.c ../utils/utils.c ../include/utils.h +gn_LDADD = -lm + diff --git a/src/gn/Makefile.in b/src/gn/Makefile.in new file mode 100644 index 0000000..85ffa4c --- /dev/null +++ b/src/gn/Makefile.in @@ -0,0 +1,578 @@ +# Makefile.in generated by automake 1.15 from Makefile.am. +# @configure_input@ + +# Copyright (C) 1994-2014 Free Software Foundation, Inc. + +# This Makefile.in is free software; the Free Software Foundation +# gives unlimited permission to copy and/or distribute it, +# with or without modifications, as long as this notice is preserved. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY, to the extent permitted by law; without +# even the implied warranty of MERCHANTABILITY or FITNESS FOR A +# PARTICULAR PURPOSE. + +@SET_MAKE@ + +VPATH = @srcdir@ +am__is_gnu_make = { \ + if test -z '$(MAKELEVEL)'; then \ + false; \ + elif test -n '$(MAKE_HOST)'; then \ + true; \ + elif test -n '$(MAKE_VERSION)' && test -n '$(CURDIR)'; then \ + true; \ + else \ + false; \ + fi; \ +} +am__make_running_with_option = \ + case $${target_option-} in \ + ?) ;; \ + *) echo "am__make_running_with_option: internal error: invalid" \ + "target option '$${target_option-}' specified" >&2; \ + exit 1;; \ + esac; \ + has_opt=no; \ + sane_makeflags=$$MAKEFLAGS; \ + if $(am__is_gnu_make); then \ + sane_makeflags=$$MFLAGS; \ + else \ + case $$MAKEFLAGS in \ + *\\[\ \ ]*) \ + bs=\\; \ + sane_makeflags=`printf '%s\n' "$$MAKEFLAGS" \ + | sed "s/$$bs$$bs[$$bs $$bs ]*//g"`;; \ + esac; \ + fi; \ + skip_next=no; \ + strip_trailopt () \ + { \ + flg=`printf '%s\n' "$$flg" | sed "s/$$1.*$$//"`; \ + }; \ + for flg in $$sane_makeflags; do \ + test $$skip_next = yes && { skip_next=no; continue; }; \ + case $$flg in \ + *=*|--*) continue;; \ + -*I) strip_trailopt 'I'; skip_next=yes;; \ + -*I?*) strip_trailopt 'I';; \ + -*O) strip_trailopt 'O'; skip_next=yes;; \ + -*O?*) strip_trailopt 'O';; \ + -*l) strip_trailopt 'l'; skip_next=yes;; \ + -*l?*) strip_trailopt 'l';; \ + -[dEDm]) skip_next=yes;; \ + -[JT]) skip_next=yes;; \ + esac; \ + case $$flg in \ + *$$target_option*) has_opt=yes; break;; \ + esac; \ + done; \ + test $$has_opt = yes +am__make_dryrun = (target_option=n; $(am__make_running_with_option)) +am__make_keepgoing = (target_option=k; $(am__make_running_with_option)) +pkgdatadir = $(datadir)/@PACKAGE@ +pkgincludedir = $(includedir)/@PACKAGE@ +pkglibdir = $(libdir)/@PACKAGE@ +pkglibexecdir = $(libexecdir)/@PACKAGE@ +am__cd = CDPATH="$${ZSH_VERSION+.}$(PATH_SEPARATOR)" && cd +install_sh_DATA = $(install_sh) -c -m 644 +install_sh_PROGRAM = $(install_sh) -c +install_sh_SCRIPT = $(install_sh) -c +INSTALL_HEADER = $(INSTALL_DATA) +transform = $(program_transform_name) +NORMAL_INSTALL = : +PRE_INSTALL = : +POST_INSTALL = : +NORMAL_UNINSTALL = : +PRE_UNINSTALL = : +POST_UNINSTALL = : +bin_PROGRAMS = gn$(EXEEXT) +subdir = src/gn +ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 +am__aclocal_m4_deps = $(top_srcdir)/configure.ac +am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \ + $(ACLOCAL_M4) +DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON) +mkinstalldirs = $(install_sh) -d +CONFIG_HEADER = $(top_builddir)/config.h +CONFIG_CLEAN_FILES = +CONFIG_CLEAN_VPATH_FILES = +am__installdirs = "$(DESTDIR)$(bindir)" +PROGRAMS = $(bin_PROGRAMS) +am__dirstamp = $(am__leading_dot)dirstamp +am_gn_OBJECTS = gn.$(OBJEXT) ../utils/utils.$(OBJEXT) +gn_OBJECTS = $(am_gn_OBJECTS) +gn_DEPENDENCIES = +AM_V_P = $(am__v_P_@AM_V@) +am__v_P_ = $(am__v_P_@AM_DEFAULT_V@) +am__v_P_0 = false +am__v_P_1 = : +AM_V_GEN = $(am__v_GEN_@AM_V@) +am__v_GEN_ = $(am__v_GEN_@AM_DEFAULT_V@) +am__v_GEN_0 = @echo " GEN " $@; +am__v_GEN_1 = +AM_V_at = $(am__v_at_@AM_V@) +am__v_at_ = $(am__v_at_@AM_DEFAULT_V@) +am__v_at_0 = @ +am__v_at_1 = +DEFAULT_INCLUDES = -I.@am__isrc@ -I$(top_builddir) +depcomp = $(SHELL) $(top_srcdir)/depcomp +am__depfiles_maybe = depfiles +am__mv = mv -f +COMPILE = $(CC) $(DEFS) $(DEFAULT_INCLUDES) $(INCLUDES) $(AM_CPPFLAGS) \ + $(CPPFLAGS) $(AM_CFLAGS) $(CFLAGS) +AM_V_CC = $(am__v_CC_@AM_V@) +am__v_CC_ = $(am__v_CC_@AM_DEFAULT_V@) +am__v_CC_0 = @echo " CC " $@; +am__v_CC_1 = +CCLD = $(CC) +LINK = $(CCLD) $(AM_CFLAGS) $(CFLAGS) $(AM_LDFLAGS) $(LDFLAGS) -o $@ +AM_V_CCLD = $(am__v_CCLD_@AM_V@) +am__v_CCLD_ = $(am__v_CCLD_@AM_DEFAULT_V@) +am__v_CCLD_0 = @echo " CCLD " $@; +am__v_CCLD_1 = +SOURCES = $(gn_SOURCES) +DIST_SOURCES = $(gn_SOURCES) +am__can_run_installinfo = \ + case $$AM_UPDATE_INFO_DIR in \ + n|no|NO) false;; \ + *) (install-info --version) >/dev/null 2>&1;; \ + esac +am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP) +# Read a list of newline-separated strings from the standard input, +# and print each of them once, without duplicates. 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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, see + * <http://www.gnu.org/licenses/>. + * + * (c) Vincenzo Nicosia 2009-2017 -- <v.nicosia@qmul.ac.uk> + * + * This file is part of NetBunch, a package for complex network + * analysis and modelling. For more information please visit: + * + * http://www.complex-networks.net/ + * + * If you use this software, please add a reference to + * + * V. Latora, V. Nicosia, G. Russo + * "Complex Networks: Principles, Methods and Applications" + * Cambridge University Press (2017) + * ISBN: 9781107103184 + * + *********************************************************************** + * + * This program implements the Girvan-Newman algorithm for community + * detection, based on the removal of edges with largest betweenness. + * + * + * References: + * + * [1] M. Girvan and M. E. J. Newman. "Community structure in social + * and biological networks". P. Natl. Acad. Sci. USA 99 (2002), + * 7821--7826. + * + */ + + +#include <stdio.h> +#include <stdlib.h> +#include <string.h> +#include <time.h> +#include <math.h> + +#include "utils.h" + +void usage(char *argv[]){ + + printf("********************************************************************\n" + "** **\n" + "** -*- gn -*- **\n" + "** **\n" + "** Find the communities of the input graph 'graph_in' using **\n" + "** the Girvan-Newman algorithm (successive removal of edges **\n" + "** with high betweeneess). **\n" + "** **\n" + "** The input file 'graph_in' is an edge-list: **\n" + "** **\n" + "** I_1 J_1 **\n" + "** I_2 J_2 **\n" + "** I_3 J_3 **\n" + "** ... ... **\n" + "** I_K J_K **\n" + "** **\n" + "** If 'graph_in' is equal to '-' (dash), read the file from **\n" + "** the standard input (STDIN). **\n" + "** **\n" + "** The program prints on STDOUT the partition corresponding **\n" + "** to the largest value of modularity, in the format: **\n" + "** **\n" + "** node_1 comm_1 **\n" + "** node_2 comm_2 **\n" + "** node_3 comm_3 **\n" + "** ..... **\n" + "** **\n" + "** where 'comm_1' is the community to which 'node_1' belongs. **\n" + "** **\n" + "** The program prints on STDERR the number of communities and **\n" + "** the value of modularity obtained after the removal of each **\n" + "** edge, in the format: **\n" + "** **\n" + "** **\n" + "** ## nc: NUM_COMM Q_max: Q_MAX **\n" + "** nc_1 Q_1 **\n" + "** nc_2 Q_2 **\n" + "** nc_3 Q_3 **\n" + "** ... **\n" + "** **\n" + "** where 'nc_1', 'nc_2', 'nc_3', etc. is the number of **\n" + "** communities (connected components) remaining after the **\n" + "** 1st, 2nd, 3rd, etc. edge has been removed, and 'Q_1', **\n" + "** 'Q_2', 'Q_3', etc. are the value of the modularity **\n" + "** function of the corresponding node partition. The first **\n" + "** output line reports the number of communities NUM_COMM **\n" + "** and corresponding value of modularity Q_MAX of the best **\n" + "** partition found. **\n" + "** **\n" + "********************************************************************\n" + " This is Free Software - You can use and distribute it under \n" + " the terms of the GNU General Public License, version 3 or later\n\n" + " Please visit http://www.complex-networks.net for more information\n\n" + " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n" + "********************************************************************\n\n" + ); + printf("Usage: %s <graph_in>\n", argv[0]); + exit(1); +} + + +void add_predecessor(unsigned int **pred, unsigned int k){ + + (*pred)[0] += 1; + *pred = realloc(*pred, ((*pred)[0] + 1) * sizeof(unsigned int)); + (*pred)[ (*pred)[0] ] = k; +} + + + +/* + * + * Compute node and edge betweenness, based on shortest paths + * originating on the "num" nodes specified in "nlist". "edge_bet" + * should be an appropriately allocated (and initialised to zero!!!!) + * vector of length equal to J_slap, and will contain the values of + * edge betweenness. + * + */ +double* compute_bet_dependency_active(unsigned int N, unsigned int *J_slap, unsigned int *r_slap, + double *edge_bet, char *active){ + + static unsigned int *marked, **preds, *dist, *nj; + static double *delta, *cB; + int i, j, k, w, idx, cur_node; + double val; + unsigned int d; + unsigned int n, nd, ndp; + unsigned int edge_pos; + + if (!dist) + dist = malloc(N * sizeof(unsigned int)); + if (!marked) + marked = malloc(N * sizeof(unsigned int)); + if (!preds) + preds = malloc(N * sizeof(unsigned int *)); + if (!nj) + nj = malloc(N * sizeof(unsigned int)); + if (!delta) + delta = malloc(N * sizeof(double)); + if (!cB) + cB = malloc(N * sizeof(double)); + + for (i=0; i<N; i++){ + cB[i] = 0; + preds[i] = NULL; + } + + for (j=0; j<N; j++){ + for(i=0; i<N; i++){ + dist[i] = N; + if (preds[i] == NULL){ + preds[i] = malloc(sizeof(unsigned int)); + } + preds[i][0] = 0; /* The list of predecessors is now empty! */ + + nj[i] = 0; + delta[i]= 0; + } + dist[j] = 0; + nj[j] = 1; + marked[0] = j; + d = 0; + n = 0; + nd = 1; + ndp = 0; + while (d<N && nd > 0){ + for(i = n; i< n+nd; i ++){ + cur_node = marked[i]; + for (k=r_slap[cur_node]; k<r_slap[cur_node +1] ; k++){ + w = J_slap[k]; + if (!active[k]) + /* discard inactive links */ + continue; + + if ( dist[w] == d+1){ + add_predecessor((unsigned int **)(preds + w), cur_node); + nj[w] += nj[cur_node]; + } + if ( dist[w] == N){ + dist[w] = d+1; + marked[n + nd + ndp] = w; + add_predecessor(preds + w, cur_node); + ndp +=1; + nj[w] += nj[cur_node]; + } + } + } + n = n + nd; + nd = ndp; + ndp = 0; + d += 1; + } + for (k= n-1; k>=1; k--){ + w = marked[k]; + for (idx=1; idx <= preds[w][0]; idx ++ ){ + i = preds[w][idx]; + val = 1.0 * nj[i] / nj[w] * (1 + delta[w]); + delta[i] += val; + /* Now we should update the betweenness of the edge (i,w) in + the appropriate position of the vector edge_bet*/ + find_neigh_in_Jslap(J_slap, r_slap, N, i, w, &edge_pos); + edge_bet[edge_pos] += val; + find_neigh_in_Jslap(J_slap, r_slap, N, w, i, &edge_pos); + edge_bet[edge_pos] += val; + } + cB[w] += delta[w]; + } + } + //free(marked); + return cB; +} + + + +/** + * + * Depth-First search on the node i.... + * + */ +int dfs_active(unsigned int i, unsigned int *J_slap, unsigned int *r_slap, + unsigned int N, unsigned int nc, unsigned int *ic, unsigned int *f, + char reset, char *active){ + + static unsigned int time; + unsigned int j, s; + + if(reset){ + time = 0; + } + + ic[i] = nc; + s = 1; + time += 1; + + for(j=r_slap[i]; j<r_slap[i+1]; j++){ + if (ic[J_slap[j]] == 0 && active[j]){ + s += dfs_active(J_slap[j], J_slap, r_slap, N, nc, ic, f, 0, active); + } + } + time += 1; + f[i] = time; + return s; +} + +/** + * + * Find all the components of the given graph + * + */ + +int components(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, + unsigned int *ic, unsigned int *f, unsigned int *sizes, + char *active){ + + unsigned int nc, s; + unsigned int i; + + + for(i=0; i<N; i++){ + ic[i] = 0; + f[i] = 0; + } + nc = 0; + for(i=0; i<N; i++){ + while( i<N && ic[i] != 0) + i += 1; + if (i == N) + break; + nc += 1; + s = dfs_active(i, J_slap, r_slap, N, nc, ic, f, 1, active); + sizes[nc] = s; + } + return nc; +} + + +/** + * find the position of the element in v with maximal value. If there + * are more than one element with the same value, return the position + * of the last one found. In order to introduce randomness, the search + * starts from a position sampled uniformly at random + * + */ +unsigned int find_pos_max_rand(double *v, unsigned int K, char *active){ + + unsigned int i; + double max; + unsigned int base, pos_max; + + base = rand() % K; + while(! active[base] ) + base = (base + 1) % K; + max = v[base]; + pos_max = base; + + for(i=base; i<base + K; i++){ + if (v[i % K] >= max && active[i % K]){ + max = v[i % K]; + pos_max = i % K; + } + } + return pos_max; +} + + +unsigned int find_pos_max(double *v, unsigned int K, char *active){ + + unsigned int i; + double max; + unsigned int base, pos_max; + + base = 0; + while(! active[base] ) + base = (base + 1) % K; + max = v[base]; + pos_max = base; + + for(i=base; i<base + K; i++){ + if (v[i % K] >= max && active[i % K]){ + max = v[i % K]; + pos_max = i % K; + } + } + return pos_max; +} + + +/* This function compute the modularity function of the partition + 'part'...*/ +double compute_modularity(unsigned int *J_slap, unsigned int *r_slap, unsigned int N, + unsigned int *part, unsigned int nc){ + static double *e, *a; + + unsigned int i, j, n, K; + unsigned int ci, cj; + double Q; + + if(!e) + e = malloc((N+1) * sizeof(double)); + if(!a) + a = malloc((N+1) * sizeof(double)); + + memset(e, 0, (N+1) * sizeof(double)); + memset(a, 0, (N+1) * sizeof(double)); + + K = r_slap[N]; + + for (i=0; i<N; i++){ + ci = part[i]; + a[ci] += (r_slap[i+1] - r_slap[i]); + for(j=r_slap[i]; j< r_slap[i+1]; j++){ + cj = part[J_slap[j]]; + if (ci == cj){ + e[ci] += 1; + } + } + } + + Q = 0.0; + for (n=1; n<=nc; n++){ + Q += 1.0 * e[n]/(1.0 * K ) - pow(1.0 * a[n]/K, 2); + } + return Q; +} + + +unsigned int* girvan_newman(unsigned int *J_slap, unsigned int *r_slap, unsigned int N){ + + unsigned int K, nc, pos; + double *edge_bet = NULL; + char *active = NULL; + double Q, Q_max; + + unsigned int *ic, *f, *sizes; + unsigned int *best_part; + + int i, j, nc_max; + + K = r_slap[N]; + + ic = malloc((N) * sizeof(unsigned int)); + f = malloc(N * sizeof(unsigned int)); + sizes = malloc((N+1) * sizeof(unsigned int)); + best_part = malloc(N * sizeof(unsigned int)); + + + /* We initialise the vector "active" which idicates active edges */ + + active = malloc(K * sizeof(char)); + for (i=0; i<K; i++){ + active[i] = 1; + } + + edge_bet = malloc(K * sizeof(double)); + nc_max = 0; + Q_max = -1000; + + for(j=0; j<K; j++){ + memset(edge_bet, 0, K * sizeof(double)); + /* compute edge betweenness */ + compute_bet_dependency_active(N, J_slap, r_slap, edge_bet, active); + /* find edge with maximal betweenness... */ + pos = find_pos_max_rand(edge_bet, K, active); + /* and knock it down */ + active[pos] = 0; + /* compute connected components */ + nc = components(J_slap, r_slap, N, ic, f, sizes, active); + /* compute the modularity of the partition induced by components */ + Q = compute_modularity(J_slap, r_slap, N, ic, nc); + fprintf(stderr, "%d %g\n", nc, Q); + /* if Q is maximal, save the current partition */ + if (j > 0){ + if (Q > Q_max){ + Q_max = Q; + nc_max = nc; + memcpy (best_part, ic, N * sizeof(unsigned int)); + } + } + else{ + Q_max = Q; + memcpy(best_part, ic, N*sizeof(unsigned int)); + } + } + /* Return the best partition */ + fprintf(stdout, "### nc: %d Q_max: %g\n", nc_max, Q_max); + free(f); + free(ic); + free(sizes); + free(edge_bet); + free(active); + return best_part; +} + + + +void dump_partition(unsigned int *p, unsigned int N){ + + unsigned int i; + for(i=0; i<N; i++){ + fprintf(stdout, "%d %d\n", i, p[i]); + } +} + + +int main(int argc, char *argv[]){ + + + unsigned int *J_slap=NULL, *r_slap=NULL; + unsigned int K, N; + FILE *filein; + unsigned int *part; + + + if(argc < 2){ + usage(argv); + exit(1); + } + + + srand(time(NULL)); + + if (!strcmp(argv[1], "-")){ + /* take the input from STDIN */ + filein = stdin; + } + else { + filein = openfile_or_exit(argv[1], "r", 2); + } + + read_slap(filein, &K, &N, &J_slap, &r_slap); + sort_neighbours(J_slap, r_slap, N); + fclose(filein); + + part = girvan_newman(J_slap, r_slap, N); + dump_partition(part, N); + free(J_slap); + free(r_slap); + free(part); + +} |