copy from SVN

COPYING

@@ -631,8 +631,8 @@ to attach them to the start of each source file to most effectively
 state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
-    {one line to give the program's name and a brief idea of what it does.}
-    Copyright (C) {year}  {name of author}
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
 
     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
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    {project}  Copyright (C) {year}  {fullname}
+    <program>  Copyright (C) <year>  <name of author>
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.
@@ -672,4 +672,3 @@ may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
 <http://www.gnu.org/philosophy/why-not-lgpl.html>.
-

README.md

@@ -5,6 +5,23 @@ Matlab.  It is part of the KONECT project (Koblenz Network Collection)
 
 http://konect.uni-koblenz.de/
 
+## Installation
+
+The toolbox consists entirely of *.m files.  To use it, add this
+directory to the Matlab path, e.g., using addpath().  
+
+## Requirements
+
+Some functions need BGL, the Boost Graph Library. 
+
+Installation of BGL:
+* Download version 4.0.1 from website (newer versions may not work)
+* unzip it
+* (on some systems:  install libstdc++5 from http://packages.debian.org/stable/base/libstdc++5)
+* symlink the unzipped matlab_bgl to here
+
+## License
+
 Written by Jérome Kunegis at the University of Koblenz-Landau.
 
 The KONECT Toolbox is free software: you can redistribute it and/or modify it under the

m/@konect_timer/konect_timer.m

@@ -0,0 +1,100 @@
+%
+% Timer class.  This is used to output the remaining time on the log
+% of a long computation.  See konect_clusco.m for example usage. 
+%
+% Note: it is important to assign the result of konect_timer_tick()
+% to the timer object. 
+%
+% ABOUT 
+%	This file is part of the KONECT Matlab Toolbox version 0.3.
+%	konect.uni-koblenz.de
+%	(c) Jerome Kunegis 2014; this is Free Software released under
+%	the GPLv3, see COPYING. 
+%
+
+classdef konect_timer
+
+    properties
+        time_begin
+        time_last
+	time_threshold
+        n 
+        count_my;   
+    end
+
+    methods
+
+        % Create a timer with N iterations. 
+        function this = konect_timer(n)
+            persistent count; 
+
+            if (n < 0)
+                count = count - 1; 
+                return; 
+            end
+
+            this.time_begin = clock; 
+            this.time_last = this.time_begin; 
+            this.n = n; 
+            if ~size(count), count = 0; end;
+            this.count_my = count; 
+            count = count + 1; 
+            this.time_threshold = 10; % seconds
+        end
+
+        function this = konect_timer_tick(this, i)
+
+            assert(i >= 0); 
+
+            time_now = clock; 
+
+            time_diff = etime(time_now, this.time_last); 
+            if (time_diff < this.time_threshold)
+                return; 
+            end
+
+            this.time_last = time_now; 
+
+            time_diff = etime(time_now, this.time_begin); 
+            left = time_diff * (this.n - i + 1) / (i - 1); 
+            text = konect_timer_text(this, left);
+            if this.count_my > 0 
+                fprintf(1, '%d of %d {%s left}\n', i - 1, this.n, text); 
+            else
+                fprintf(1, '%d of %d [%s left]\n', i - 1, this.n, text); 
+            end
+        end
+
+        function text = konect_timer_text(this, t)
+            if t < 60
+                text = sprintf('%ds', floor(t));   
+            elseif t < 3600
+                text = sprintf('%d:%02d', floor(t/60), mod(floor(t), 60)); 
+            elseif t < 3600 * 24
+                text = sprintf('%d:%02d:%02d', floor(t/3600), mod(floor(t/60), 60), mod(floor(t), 60)); 
+            else
+                text = sprintf('%dd %02d:%02d:%02d', floor(t/3600/24), mod(floor(t/3600), 24), mod(floor(t/60), 60), mod(floor(t), 60)); 
+            end
+        end 
+
+        function this = konect_timer_end(this)
+            e = etime(this.time_last, this.time_begin);
+            if e ~= 0
+                text = konect_timer_text(this, 0); 
+                if this.count_my > 0 
+                    fprintf(1, '%d of %d {%s left}\n', this.n, this.n, text); 
+                else
+                    fprintf(1, '%d of %d [%s left]\n', this.n, this.n, text); 
+                end
+            end
+            konect_timer(-1); 
+        end
+
+        % Set new value of N, i.e. of the total number of
+        % iterations 
+        function this = konect_timer_set(this, n_new)
+            this.n = n_new; 
+        end
+
+    end
+end

m/konect_absx.m

@@ -0,0 +1,26 @@
+%
+% Wrapper for abs() that also accepts sparse logical matrices and just
+% returns them, as opposed to abs() which does not work for logical
+% matrices. 
+%
+% RESULT 
+%	ret	Absolute value of the argument matrix 
+%
+% PARAMETERS 
+%	A	Matrix of which the absolute value is to be computed;
+%		may be a logical matrix
+%
+% ABOUT 
+%	This file is part of the KONECT Matlab Toolbox version 0.3.
+%	konect.uni-koblenz.de
+%	(c) Jerome Kunegis 2014; this is Free Software released under
+%	the GPLv3, see COPYING. 
+%
+
+function ret = konect_absx(A)
+
+if islogical(A)
+    ret = A;
+else
+    ret = abs(A);
+end

m/konect_ap.m

@@ -0,0 +1,47 @@
+%
+% Compute the average precision. 
+%
+% If target is not a 0/1 vector, its values are rounded to 0 or 1. 
+%
+% PARAMETERS 
+%	prediction	(e*1) Prediction scores
+%	target		(e*1) Correct scores
+%			
+% RESULT 
+%	ret		The average precision
+%
+% ABOUT 
+%	This file is part of the KONECT Matlab Toolbox version 0.3.
+%	konect.uni-koblenz.de
+%	(c) Jerome Kunegis 2014; this is Free Software released under
+%	the GPLv3, see COPYING. 
+%
+
+function ret = konect_ap(prediction, target)
+
+if length(prediction) ~= length(target), error('*** both vectors must have same length'); end; 
+
+e = length(prediction); 
+
+% Round target to 0/1
+target = target > 0; 
+
+% Randomize order 
+p = randperm(e);
+prediction = prediction(p); 
+target = target(p); 
+
+% Compte MAP
+[tmp,i] = sort(-prediction);
+a = target(i); 
+p_sum = 0;  
+nz = 0;
+
+for j = 1 : e
+    if a(j) ~= 0
+        nz = nz + a(j);  
+        p_sum = p_sum + a(j) * nz / j;
+    end;
+end;
+
+ret = p_sum / nz;

m/konect_ap_sorted.m

@@ -0,0 +1,17 @@
+%
+% Compute the average precision, given only the 0/1 vector sorted by
+% scores, which don't have to be given. 
+%
+% PARAMETERS 
+%	t	(e*1) The 0/1 vector, ranked by descending scores
+%
+% ABOUT 
+%	This file is part of the KONECT Matlab Toolbox version 0.3.
+%	konect.uni-koblenz.de
+%	(c) Jerome Kunegis 2014; this is Free Software released under
+%	the GPLv3, see COPYING. 
+%
+
+function ap = konect_ap_sorted(t)
+
+ap = mean((1:sum(t))' ./ find(t)); 

m/konect_auc.m

@@ -0,0 +1,56 @@
+%
+% The area under the ROC curve, i.e. the AUC.
+%
+% If target is not a 0/1 vector, its values are rounded to 0 or 1. 
+%
+% PARAMETERS 
+%	prediction	(e*1) vector of predicted scores
+%	target		(e*1) vector of values to be predicted 
+%
+% RESULT 
+%	ret		The AUC
+%
+% ABOUT 
+%	This file is part of the KONECT Matlab Toolbox version 0.3.
+%	konect.uni-koblenz.de
+%	(c) Jerome Kunegis 2014; this is Free Software released under
+%	the GPLv3, see COPYING. 
+%
+
+function ret = konect_auc(prediction, target)
+
+assert(length(prediction) == length(target)); 
+
+% All values passed are finite 
+assert(sum(~isfinite(prediction)) == 0);
+assert(sum(~isfinite(target)) == 0);
+
+target = target > 0; 
+
+e = length(prediction);
+k = sum(target);
+
+if k == e | k == 0
+    ret = 0;  
+    return; 
+end 
+
+% Randomize order 
+p = randperm(e);
+prediction = prediction(p);
+target = target(p); 
+
+[tmp,x] = sort(prediction, 'descend');
+a = target(x);
+
+s = 0;
+c = e-k;
+for i = 1 : e
+    if a(i) == 0
+        c = c - 1;
+    else
+        s = s + c;
+    end
+end
+
+ret = s / (k * (e-k));