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-rw-r--r--src/betweenness/Makefile.am7
-rw-r--r--src/betweenness/Makefile.in590
-rw-r--r--src/betweenness/README8
-rw-r--r--src/betweenness/bet_dependency.c224
-rw-r--r--src/betweenness/betweenness.c316
5 files changed, 1145 insertions, 0 deletions
diff --git a/src/betweenness/Makefile.am b/src/betweenness/Makefile.am
new file mode 100644
index 0000000..6adf93f
--- /dev/null
+++ b/src/betweenness/Makefile.am
@@ -0,0 +1,7 @@
+include ../common.mk
+bin_PROGRAMS = betweenness bet_dependency
+betweenness_SOURCES = betweenness.c ../utils/utils.c ../include/utils.h
+betweenness_LDADD = -lm
+bet_dependency_SOURCES = bet_dependency.c ../utils/utils.c ../include/utils.h
+bet_dependency_LDADD = -lm
+
diff --git a/src/betweenness/Makefile.in b/src/betweenness/Makefile.in
new file mode 100644
index 0000000..776f7a1
--- /dev/null
+++ b/src/betweenness/Makefile.in
@@ -0,0 +1,590 @@
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+ @echo "This command is intended for maintainers to use"
+ @echo "it deletes files that may require special tools to rebuild."
+clean: clean-am
+
+clean-am: clean-binPROGRAMS clean-generic mostlyclean-am
+
+distclean: distclean-am
+ -rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+ -rm -f Makefile
+distclean-am: clean-am distclean-compile distclean-generic \
+ distclean-tags
+
+dvi: dvi-am
+
+dvi-am:
+
+html: html-am
+
+html-am:
+
+info: info-am
+
+info-am:
+
+install-data-am:
+
+install-dvi: install-dvi-am
+
+install-dvi-am:
+
+install-exec-am: install-binPROGRAMS
+
+install-html: install-html-am
+
+install-html-am:
+
+install-info: install-info-am
+
+install-info-am:
+
+install-man:
+
+install-pdf: install-pdf-am
+
+install-pdf-am:
+
+install-ps: install-ps-am
+
+install-ps-am:
+
+installcheck-am:
+
+maintainer-clean: maintainer-clean-am
+ -rm -rf ../utils/$(DEPDIR) ./$(DEPDIR)
+ -rm -f Makefile
+maintainer-clean-am: distclean-am maintainer-clean-generic
+
+mostlyclean: mostlyclean-am
+
+mostlyclean-am: mostlyclean-compile mostlyclean-generic
+
+pdf: pdf-am
+
+pdf-am:
+
+ps: ps-am
+
+ps-am:
+
+uninstall-am: uninstall-binPROGRAMS
+
+.MAKE: install-am install-strip
+
+.PHONY: CTAGS GTAGS TAGS all all-am check check-am clean \
+ clean-binPROGRAMS clean-generic cscopelist-am ctags ctags-am \
+ distclean distclean-compile distclean-generic distclean-tags \
+ distdir dvi dvi-am html html-am info info-am install \
+ install-am install-binPROGRAMS install-data install-data-am \
+ install-dvi install-dvi-am install-exec install-exec-am \
+ install-html install-html-am install-info install-info-am \
+ install-man install-pdf install-pdf-am install-ps \
+ install-ps-am install-strip installcheck installcheck-am \
+ installdirs maintainer-clean maintainer-clean-generic \
+ mostlyclean mostlyclean-compile mostlyclean-generic pdf pdf-am \
+ ps ps-am tags tags-am uninstall uninstall-am \
+ uninstall-binPROGRAMS
+
+.PRECIOUS: Makefile
+
+
+# Tell versions [3.59,3.63) of GNU make to not export all variables.
+# Otherwise a system limit (for SysV at least) may be exceeded.
+.NOEXPORT:
diff --git a/src/betweenness/README b/src/betweenness/README
new file mode 100644
index 0000000..c41e3d1
--- /dev/null
+++ b/src/betweenness/README
@@ -0,0 +1,8 @@
+- bet_dependency computes the contribution to betweenness of each node in the graph
+ restricted to shortest paths originating from a range of nodes
+
+ --- TODO ---
+
+- make a multi-threaded version
+- make an MPI implementation
+- make a version which considers only X% of the nodes, sampled at random
diff --git a/src/betweenness/bet_dependency.c b/src/betweenness/bet_dependency.c
new file mode 100644
index 0000000..2b55543
--- /dev/null
+++ b/src/betweenness/bet_dependency.c
@@ -0,0 +1,224 @@
+/**
+ * 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 3 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, 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 computes the betweenness dependency of all the nodes
+ * of a graph, using Brandes' algorithm, and counting all the
+ * shortest paths originating from a set of nodes (potentially the
+ * whole set of vertices).
+ *
+ * References:
+ * U. Brandes. "A Faster Algorithm for Betweenness
+ * Centrality". J. Math. Sociol. 25 (2001), 163-177.
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+ printf("********************************************************************\n"
+ "** **\n"
+ "** -*- bet_dependency -*- **\n"
+ "** **\n"
+ "** Compute the betweenness dependency of all the nodes of a **\n"
+ "** network due to the shortest paths originating from a set **\n"
+ "** of initial nodes. If no start node is specified, compute **\n"
+ "** the dependency due to all the nodes of the graph. If no end **\n"
+ "** node is specified, compute the dependency due to the nodes **\n"
+ "** between node_start and the last node of the graph. **\n"
+ "** **\n"
+ "** The dependency of each node is printed on standard output. **\n"
+ "** **\n"
+ "** **\n"
+ "********************************************************************\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"
+ " (c) Vincenzo Nicosia 2009-2017 (katolaz@yahoo.it)\n\n");
+ printf("Usage: %s <graph_in> [<node_start> [<node_end>]]\n\n" , argv[0]);
+}
+
+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;
+}
+
+
+
+/*
+ * Returns a list of dependencies
+ */
+double* compute_bet_dependency(unsigned int N, unsigned int *J_slap, unsigned int *r_slap,
+ unsigned int n_start, unsigned int n_end){
+
+ int i, j, k, w, idx, cur_node;
+ unsigned int *marked, **preds, *dist, *nj;
+ double *delta, *cB;
+ unsigned int d;
+ unsigned int n, nd, ndp;
+
+ dist = malloc(N * sizeof(unsigned int));
+ marked = malloc(N * sizeof(unsigned int));
+ preds = malloc(N * sizeof(unsigned int *));
+
+ nj = malloc(N * sizeof(unsigned int));
+ delta = malloc(N * sizeof(double));
+ cB = malloc(N * sizeof(double));
+
+ for (i=0; i<N; i++){
+ cB[i] = 0;
+ preds[i] = NULL;
+ }
+
+ for (j=n_start; j<=n_end && j<N; j++){
+ for(i=0; i<N; i ++){
+ dist[i] = N;
+ if (! preds[i]){
+ 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 ( 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];
+ delta[i] += 1.0 * nj[i] / nj[w] * (1 + delta[w]);
+ }
+ cB[w] += delta[w];
+ }
+ }
+ free(dist);
+ free(marked);
+ for (i=0; i<N; i++){
+ free(preds[i]);
+ }
+ free(preds);
+ free(nj);
+ free(delta);
+
+ return cB;
+}
+
+
+
+void dump_cB(double *cB, unsigned int N){
+
+ unsigned int i;
+ for (i=0; i<N; i++){
+ printf("%g\n", cB[i]);
+ }
+}
+
+
+int main(int argc, char *argv[]){
+
+ unsigned int *J_slap=NULL, *r_slap=NULL;
+ unsigned int K, N;
+ unsigned int n_start, n_end;
+ double *cB;
+ FILE *filein;
+
+ n_start = 0;
+ n_end = -1;
+
+ switch (argc){
+
+ case 4:
+ n_end = atoi(argv[3]);
+ case 3:
+ n_start = atoi(argv[2]);
+ case 2:
+ break;
+ default:
+ usage(argv);
+ exit(1);
+ break;
+ }
+
+ 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);
+ if (n_end == -1)
+ n_end = N-1;
+ cB = compute_bet_dependency(N, J_slap, r_slap, n_start, n_end);
+ dump_cB(cB, N);
+
+ free(cB);
+ free(J_slap);
+ free(r_slap);
+
+}
diff --git a/src/betweenness/betweenness.c b/src/betweenness/betweenness.c
new file mode 100644
index 0000000..5e37747
--- /dev/null
+++ b/src/betweenness/betweenness.c
@@ -0,0 +1,316 @@
+/**
+ * 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 3 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, 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 computes the betweenness of all the nodes of a graph,
+ * using Brandes' algorithm, and counting all the shortest paths
+ * originating from a set of nodes (potentially the whole set of
+ * vertices).
+ *
+ * References:
+ * U. Brandes. "A Faster Algorithm for Betweenness
+ * Centrality". J. Math. Sociol. 25 (2001), 163-177.
+ *
+ */
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include <time.h>
+
+#include "utils.h"
+
+
+void usage(char *argv[]){
+ printf("********************************************************************\n"
+ "** **\n"
+ "** -*- betweenness -*- **\n"
+ "** **\n"
+ "** Compute the betweenness of all the nodes and edges of a **\n"
+ "** network due to the shortest paths originating from a set **\n"
+ "** of initial nodes. The set can be either a sequence of **\n"
+ "** nodes (if the second argument is 'SEQ') or a random sample **\n"
+ "** from the set of all the nodes (if it is 'RND'). **\n"
+ "** **\n"
+ "** The input file is an edge-list (use '-' to read from STDIN). **\n"
+ "** **\n"
+ "** With 'SEQ': **\n"
+ "** If <node_start> is not specified, computes the betweenness **\n"
+ "** using shortest paths from *all* the nodes (WARNING: This can **\n"
+ "** be slow for large graphs!). If <node_end> is not specified, **\n"
+ "** use shortest paths from all the nodes between <node_start> **\n"
+ "** and the node with the largest label. **\n"
+ "** **\n"
+ "** With 'RND': **\n"
+ "** Compute the betweenness based on the shortest paths from **\n"
+ "** <num> nodes sampled uniformly at random. **\n"
+ "** **\n"
+ "** When called with just <graph_in>, use all the nodes. **\n"
+ "** **\n"
+ "** The betweenness of all the nodes is printed on standard **\n"
+ "** output (STDOUT), while the edge betweenness is printed on **\n"
+ "** standard error (STDERR) **\n"
+ "** **\n"
+ "********************************************************************\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"
+ " (c) Vincenzo Nicosia 2009-2017 (v.nicosia@qmul.ac.uk)\n\n");
+ printf("Usage: %s <graph_in> [SEQ <node_start> [<node_end>]]\n" , argv[0]);
+ printf("Usage: %s <graph_in> [RND <num>]\n" , argv[0]);
+
+}
+
+/*
+ * Add a node the a list of predecessors
+ */
+
+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(unsigned int N, unsigned int *J_slap, unsigned int *r_slap,
+ unsigned int *nlist, unsigned int num, double *edge_bet){
+
+ int i, j, k, w, idx, cur_node, m;
+ unsigned int *marked, **preds, *dist, *nj;
+ double *delta, *cB, val;
+ unsigned int d;
+ unsigned int n, nd, ndp;
+ unsigned int edge_pos;
+
+ dist = malloc(N * sizeof(unsigned int));
+ marked = malloc(N * sizeof(unsigned int));
+ preds = malloc(N * sizeof(unsigned int *));
+
+ nj = malloc(N * sizeof(unsigned int));
+ delta = malloc(N * sizeof(double));
+ cB = malloc(N * sizeof(double));
+
+ for (i=0; i<N; i++){
+ cB[i] = 0;
+ preds[i] = NULL;
+ }
+
+ for (m=0; m<num; m++){
+ /* We start from the m-th node in nlist*/
+ j = nlist[m];
+
+ for(i=0; i<N; i ++){
+ dist[i] = N;
+ if (! preds[i]){
+ 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 ( 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(dist);
+ free(marked);
+ for (i=0; i<N; i++){
+ free(preds[i]);
+ }
+ free(preds);
+ free(nj);
+ free(delta);
+ return cB;
+}
+
+
+
+/*
+ * print of STDOUT the betweenness of each node
+ */
+void dump_cB(double *cB, unsigned int N){
+
+ unsigned int i;
+ for (i=0; i<N; i++){
+ printf("%g\n", cB[i]);
+ }
+}
+
+/*
+ * print on STDERR the betweenness of each edge
+ */
+
+void dump_edge_bet(unsigned int *J_slap, unsigned int *r_slap, unsigned int N,
+ double *v, FILE *fout){
+
+ unsigned int i, j;
+
+ for(i=0; i<N; i++){
+ for (j=r_slap[i]; j<r_slap[i+1]; j++)
+ fprintf(fout, "%d %d %g\n", i, J_slap[j], v[j]);
+ }
+}
+
+
+
+int main(int argc, char *argv[]){
+
+ unsigned int *J_slap=NULL, *r_slap=NULL;
+ unsigned int K, N, i;
+ unsigned int n_start, n_end;
+ unsigned int *nlist=NULL;
+ unsigned int num;
+ double *edge_bet = NULL;
+ double *cB;
+ FILE *filein;
+
+
+ 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);
+
+ nlist = malloc(N * sizeof(unsigned int));
+
+ for(i=0; i<N; i++){
+ nlist[i] = i;
+ }
+
+ n_start = 0;
+ n_end = N-1;
+ num = N;
+
+
+ if (argc > 3){
+ if(!my_strcasecmp(argv[2], "SEQ")){
+ n_start = atoi(argv[3]);
+ if (n_start > N-1)
+ n_start = 0;
+ if (argc > 4){
+ n_end = atoi(argv[4]);
+ }
+ else{
+ n_end = N-1;
+ }
+ num = n_end - n_start + 1;
+ }
+ else if (!my_strcasecmp(argv[2], "RND")){
+ num = atoi(argv[3]);
+ n_start = 0;
+ n_end = num-1;
+ if (num > N || num < 1)
+ num = N;
+ shuffle_vector(nlist, N);
+ }
+ }
+
+ sort_neighbours(J_slap, r_slap, N);
+ edge_bet = malloc(K * sizeof(double));
+ memset(edge_bet, 0, K * sizeof(double));
+ cB = compute_bet_dependency(N, J_slap, r_slap, nlist+n_start, num, edge_bet);
+
+ dump_cB(cB, N);
+ dump_edge_bet(J_slap, r_slap, N, edge_bet, stderr);
+
+ free(cB);
+ free(J_slap);
+ free(r_slap);
+ free(edge_bet);
+ free(nlist);
+
+}