From: Francois Fleuret <fleuret@moose.fleuret.org>
Date: Sun, 14 Dec 2008 21:46:20 +0000 (+0100)
Subject: automatic commit
X-Git-Url: https://fleuret.org/cgi-bin/gitweb/gitweb.cgi?a=commitdiff_plain;h=713c683d77fc94a4257c4031b0c51ef4669a3d4a;p=mlp.git

automatic commit
---

diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..48ecf1b
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,42 @@
+
+#  mlp-mnist is an implementation of a multi-layer neural network.
+#
+#  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+#  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+#
+#  This file is part of mlp-mnist.
+#
+#  mlp-mnist is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License version 3 as
+#  published by the Free Software Foundation.
+#
+#  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+
+ifeq ($(DEBUG),yes)
+ CXXFLAGS = -Wall -g
+else
+ # Optimized compilation
+ CXXFLAGS = -Wall -ffast-math -fcaller-saves -finline-functions -funroll-all-loops -O3
+endif
+
+all: ann
+
+ann: ann.o misc.o images.o neural.o
+	$(CXX) $(CXXFLAGS) -o $@ $^ $(LDFLAGS)
+
+Makefile.depend: *.h *.cc Makefile
+	$(CC) -M *.cc > Makefile.depend
+
+clean:
+	\rm ann *.o Makefile.depend
+
+archive:
+	cd .. ; tar zcvf mlp-mnist.tgz mlp-mnist/{*.{cc,h,txt,sh},Makefile}
+
+-include Makefile.depend
diff --git a/README.txt b/README.txt
new file mode 100644
index 0000000..cfae48b
--- /dev/null
+++ b/README.txt
@@ -0,0 +1,49 @@
+
+You can run the whole script with "./doit --download-mnist" or just
+"./doit.sh" if you already have the MNIST database in the current
+directory.
+
+You should get the following output (this takes a few hours on a
+1.2Ghz Pentium-M):
+
+----------------------------------------------------------------------
+Loading the data file ... done.
+Database contains 60000 images of resolution 28x28 divided into 10 objects.
+Creating a new network (layers of sizes 784 200 10).
+Training the network with 20000 training and 20000 validation examples.
+0 TRAINING 12235.8 (8.58%) TESTING 13030 (9.405%)
+1 TRAINING 8839.31 (6.69%) TESTING 10132.9 (7.71%)
+2 TRAINING 6502.38 (4.575%) TESTING 8268.75 (6.235%)
+3 TRAINING 5656.71 (3.975%) TESTING 7637.6 (5.75%)
+4 TRAINING 5456.68 (3.56%) TESTING 7683.5 (5.6%) [1]
+5 TRAINING 4167.26 (2.64%) TESTING 6557.84 (4.82%)
+6 TRAINING 4320.34 (2.7%) TESTING 6796.09 (4.89%) [2]
+7 TRAINING 3725.38 (2.435%) TESTING 6307.99 (4.52%)
+8 TRAINING 3946.58 (2.49%) TESTING 6614.6 (4.53%) [3]
+9 TRAINING 3773.16 (2.24%) TESTING 6698.8 (4.67%) [4]
+10 TRAINING 3485.74 (2.13%) TESTING 6539.64 (4.54%)
+11 TRAINING 5903.21 (3.53%) TESTING 8881.58 (5.905%) [5]
+12 TRAINING 3165.84 (1.89%) TESTING 6366.87 (4.385%)
+13 TRAINING 3288.64 (2%) TESTING 6520.78 (4.5%) [6]
+14 TRAINING 2849.94 (1.615%) TESTING 6201.43 (4.215%)
+15 TRAINING 2693.19 (1.555%) TESTING 5991.35 (4.235%)
+16 TRAINING 2827.86 (1.575%) TESTING 6181.83 (4.235%) [7]
+17 TRAINING 2374.73 (1.355%) TESTING 5668.65 (3.77%)
+18 TRAINING 2194.12 (1.255%) TESTING 5572.82 (3.705%)
+19 TRAINING 2114.23 (1.155%) TESTING 5587.74 (3.71%) [8]
+20 TRAINING 1909.78 (1.15%) TESTING 5377.6 (3.64%)
+21 TRAINING 3064.62 (1.705%) TESTING 6642.78 (4.36%) [9]
+22 TRAINING 1832.23 (1.04%) TESTING 5386.12 (3.575%)
+23 TRAINING 1695.47 (0.95%) TESTING 5342.3 (3.61%)
+24 TRAINING 1699.28 (0.935%) TESTING 5331.84 (3.46%)
+25 TRAINING 1478.36 (0.835%) TESTING 5075.09 (3.335%)
+26 TRAINING 1528.62 (0.865%) TESTING 5221.1 (3.41%) [10]
+Saving network simple.mlp ... done.
+Loading the data file ... done.
+Database contains 10000 images of resolution 28x28 divided into 10 objects.
+Loading network simple.mlp ... done (layers of sizes 784 200 10)
+Error rate 2599.54 (3.42%)
+----------------------------------------------------------------------
+
+The computation produces a file simple.mlp containing the learnt
+perceptron.
diff --git a/ann.cc b/ann.cc
new file mode 100644
index 0000000..c3e9e98
--- /dev/null
+++ b/ann.cc
@@ -0,0 +1,320 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+// LeCun et al. 1998:
+
+// 2-layer NN, 300 hidden units, mean square error  4.70%
+// 2-layer NN, 1000 hidden units                    4.50%
+// 3-layer NN, 300+100 hidden units                 3.05%
+// 3-layer NN, 500+150 hidden units                 2.95%
+
+/*********************************************************************
+
+   This program, trained on 20,000 (+ 20,000 for the stopping
+   criterion), tested on the 10,000 of the MNIST test set 100 hidden
+   neurons, basic network, 3.48%
+
+   TRAINING
+
+    ./ann --nb-training-examples 20000 --nb-validation-examples 20000 \
+        --mlp-structure 784,200,10 \
+        --data-files ${DATA_DIR}/train-images-idx3-ubyte ${DATA_DIR}/train-labels-idx1-ubyte \
+        --save-mlp simple.mlp
+
+   TEST
+
+    ./ann --load-mlp simple.mlp \
+        --data-files ${DATA_DIR}/t10k-images-idx3-ubyte ${DATA_DIR}/t10k-labels-idx1-ubyte \
+        --nb-test-examples 10000
+
+*********************************************************************/
+
+#include <iostream>
+#include <fstream>
+#include <cmath>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+using namespace std;
+
+#include "images.h"
+#include "neural.h"
+
+#define SMALL_BUFFER_SIZE 1024
+
+//////////////////////////////////////////////////////////////////////
+// Global Variables
+//////////////////////////////////////////////////////////////////////
+
+int nb_experiment = 0;
+int nb_training_examples = 0;
+int nb_validation_examples = 0;
+int nb_test_examples = 0;
+bool save_data = false;
+
+char images_filename[SMALL_BUFFER_SIZE] = "\0";
+char labels_filename[SMALL_BUFFER_SIZE] = "\0";
+char opt_load_filename[SMALL_BUFFER_SIZE] = "\0";
+char opt_save_filename[SMALL_BUFFER_SIZE] = "\0";
+char opt_layer_sizes[SMALL_BUFFER_SIZE] = "\0";
+
+char *next_word(char *buffer, char *r, int buffer_size) {
+  char *s;
+  s = buffer;
+  if(r != NULL)
+    {
+      if(*r == '"') {
+        r++;
+        while((*r != '"') && (*r != '\0') &&
+              (s<buffer+buffer_size-1))
+          *s++ = *r++;
+        if(*r == '"') r++;
+      } else {
+        while((*r != '\r') && (*r != '\n') && (*r != '\0') &&
+              (*r != '\t') && (*r != ' ') && (*r != ',') &&
+              (s<buffer+buffer_size-1))
+          *s++ = *r++;
+      }
+
+      while((*r == ' ') || (*r == '\t') || (*r == ',')) r++;
+      if((*r == '\0') || (*r=='\r') || (*r=='\n')) r = NULL;
+    }
+  *s = '\0';
+  return r;
+}
+
+//////////////////////////////////////////////////////////////////////
+// Simple routine to check we have enough parameters
+//////////////////////////////////////////////////////////////////////
+
+void check_opt(int argc, char **argv, int n_opt, int n, const char *help) {
+  if(n_opt + n >= argc) {
+    cerr << "Missing argument for " << argv[n_opt] << ".\n";
+    cerr << "Expecting " << help << ".\n";
+    exit(1);
+  }
+}
+
+void print_help_and_exit(int e) {
+  cout << "ANN. Written by François Fleuret.\n";
+  cout << "$Id: ann.cc,v 1.1 2005-12-13 17:19:11 fleuret Exp $\n";
+  cout<< "\n";
+  exit(e);
+}
+
+int main(int argc, char **argv) {
+
+  if(argc == 1) print_help_and_exit(1);
+
+  nice(10);
+
+  // Parsing the command line parameters ///////////////////////////////
+
+  int i = 1;
+
+  while(i < argc) {
+
+    if(argc == 1 || strcmp(argv[i], "--help") == 0) print_help_and_exit(0);
+
+    else if(strcmp(argv[i], "--data-files") == 0) {
+      check_opt(argc, argv, i, 2, "<string: pixel filename> <string: label filename>");
+      strncpy(images_filename, argv[i+1], SMALL_BUFFER_SIZE);
+      strncpy(labels_filename, argv[i+2], SMALL_BUFFER_SIZE);
+      i += 3;
+    }
+
+    else if(strcmp(argv[i], "--load-mlp") == 0) {
+      check_opt(argc, argv, i, 1, "<string: mlp filename>");
+      strncpy(opt_load_filename, argv[i+1], SMALL_BUFFER_SIZE);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--mlp-structure") == 0) {
+      check_opt(argc, argv, i, 1, "<int: input layer size>,<int: first hidden layer size>,[...,]<int: output layer size>");
+      strncpy(opt_layer_sizes, argv[i+1], SMALL_BUFFER_SIZE);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--save-mlp") == 0) {
+      check_opt(argc, argv, i, 1, "<string: mlp filename>");
+      strncpy(opt_save_filename, argv[i+1], SMALL_BUFFER_SIZE);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--nb-experiment") == 0) {
+      check_opt(argc, argv, i, 1, "<int: number of the experiment>");
+      nb_experiment = atoi(argv[i+1]);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--nb-training-examples") == 0) {
+      check_opt(argc, argv, i, 1, "<int: number of examples for the training>");
+      nb_training_examples = atoi(argv[i+1]);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--nb-validation-examples") == 0) {
+      check_opt(argc, argv, i, 1, "<int: number of examples for the validation>");
+      nb_validation_examples = atoi(argv[i+1]);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--nb-test-examples") == 0) {
+      check_opt(argc, argv, i, 1, "<int: number of examples for the test>");
+      nb_test_examples = atoi(argv[i+1]);
+      i += 2;
+    }
+
+    else if(strcmp(argv[i], "--save-data") == 0) {
+      save_data = true;
+      i++;
+    }
+
+    else {
+      cerr << "Unknown option " << argv[i] << "\n";
+      print_help_and_exit(1);
+    }
+  }
+
+  ImageSet image_set;
+  cout << "Loading the data file ..."; cout.flush();
+  image_set.load_mnist_format(images_filename, labels_filename);
+  cout << " done.\n"; cout.flush();
+
+  cout << "Database contains " << image_set.nb_pics()
+       << " images of resolution " << image_set.width() << "x" << image_set.height()
+       << " divided into " << image_set.nb_obj() << " objects.\n";
+
+  srand48(nb_experiment);
+
+  int nb_layers = 0;
+  int *layer_sizes = 0;
+
+  if(opt_layer_sizes[0]) {
+    char *s = opt_layer_sizes;
+    char token[SMALL_BUFFER_SIZE];
+    while(s) { s = next_word(token, s, SMALL_BUFFER_SIZE); nb_layers++; }
+
+    if(nb_layers < 2) {
+      cerr << "Need at least two layers.\n";
+      exit(1);
+    }
+
+    layer_sizes = new int[nb_layers];
+    s = opt_layer_sizes;
+    int n = 0;
+    while(s) { s = next_word(token, s, SMALL_BUFFER_SIZE); layer_sizes[n++] = atoi(token); }
+  }
+
+  // Loading or creating a perceptron from scratch /////////////////////
+
+  MultiLayerPerceptron *mlp = 0;
+
+  if(opt_load_filename[0]) {
+
+    ifstream stream(opt_load_filename);
+    if(stream.fail()) {
+      cerr << "Can not read " << opt_load_filename << ".\n";
+      exit(1);
+    }
+
+    cout << "Loading network " << opt_load_filename << " ... "; cout.flush();
+    mlp = new MultiLayerPerceptron(stream);
+    cout << "done (layers of sizes";
+    for(int l = 0; l < mlp->nb_layers(); l++) cout << " " << mlp->layer_size(l);
+    cout << ")\n"; cout.flush();
+
+  } else if(nb_layers > 0) {
+
+    if(layer_sizes[0] != image_set.width() * image_set.height() ||
+       layer_sizes[nb_layers-1] != image_set.nb_obj()) {
+      cerr << "For this data set, the input layer has to be of size " << image_set.width() * image_set.height() << ",\n";
+      cerr << "and the output has to be of size " << image_set.nb_obj() << ".\n";
+      exit(1);
+    }
+
+    cout << "Creating a new network (layers of sizes";
+    for(int i = 0; i < nb_layers; i++) cout << " " << layer_sizes[i];
+    cout << ").\n";
+
+    mlp = new MultiLayerPerceptron(nb_layers, layer_sizes);
+    mlp->init_random_weights(1e-1);
+  }
+
+  // Training the perceptron ///////////////////////////////////////////
+
+  ImageSet training_set, validation_set, test_set;
+
+  if(nb_training_examples > 0)
+    training_set.extract_unused_pictures(image_set, nb_training_examples);
+
+  if(nb_validation_examples > 0)
+    validation_set.extract_unused_pictures(image_set, nb_validation_examples);
+
+  if(save_data && mlp) mlp->save_data();
+
+  if(nb_training_examples > 0) {
+    if(validation_set.nb_pics() == 0) {
+      cerr << "We need validation pictures for training.\n";
+      exit(1);
+    }
+    cout << "Training the network with " << nb_training_examples << " training and " << nb_validation_examples << " validation examples.\n"; cout.flush();
+    mlp->train(&training_set, &validation_set);
+  }
+
+  // Saving the perceptron /////////////////////////////////////////////
+
+  if(opt_save_filename[0]) {
+    if(!mlp) {
+      cerr << "No perceptron to save.\n";
+      exit(1);
+    }
+
+    ofstream stream(opt_save_filename);
+    if(stream.fail()) {
+      cerr << "Can not write " << opt_save_filename << ".\n";
+      exit(1);
+    }
+
+    cout << "Saving network " << opt_save_filename << " ... "; cout.flush();
+    mlp->save(stream);
+    cout << "done.\n"; cout.flush();
+  }
+
+  // Testing the perceptron ////////////////////////////////////////////
+
+  if(nb_test_examples > 0) {
+    test_set.extract_unused_pictures(image_set, nb_test_examples);
+    cout << "Error rate " << mlp->error(&test_set) << " (" << mlp->classification_error(&test_set)*100 << "%)\n";
+
+    // This is to test the analytical gradient
+    //     scalar_t gradient[mlp->nb_weights()], numerical_gradient[mlp->nb_weights()];
+    //     mlp->compute_gradient(&test_set, gradient);
+    //     mlp->compute_numerical_gradient(&test_set, numerical_gradient);
+    //     for(int i = 0; i < mlp->nb_weights(); i++) cout << "TEST " << gradient[i] << " " << numerical_gradient[i] << "\n";
+  }
+
+  // Flushing the log //////////////////////////////////////////////////
+
+  delete[] layer_sizes;
+}
diff --git a/doit.sh b/doit.sh
new file mode 100755
index 0000000..bd6f195
--- /dev/null
+++ b/doit.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+#  mlp-mnist is an implementation of a multi-layer neural network.
+#
+#  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+#  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+#
+#  This file is part of mlp-mnist.
+#
+#  mlp-mnist is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License version 3 as
+#  published by the Free Software Foundation.
+#
+#  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+
+make -k ann
+
+if [[ $1 == "--download-mnist" ]]; then
+    for f in train-images-idx3-ubyte train-labels-idx1-ubyte t10k-images-idx3-ubyte t10k-labels-idx1-ubyte; do
+        if [[ ! -f "./$f" ]]; then
+            echo "Could not find $f, downloading it."
+            wget http://yann.lecun.com/exdb/mnist/$f.gz
+            gunzip $f.gz
+        fi
+    done
+fi
+
+for f in train-images-idx3-ubyte train-labels-idx1-ubyte t10k-images-idx3-ubyte t10k-labels-idx1-ubyte; do
+    if [[ -f "./$f" ]]; then
+        echo "Found $f, good."
+    else
+        echo "File $f is missing. Try $0 --download-mnist."
+        exit 1
+    fi
+done
+
+./ann --nb-training-examples 20000 --nb-validation-examples 20000 \
+    --mlp-structure 784,200,10 \
+    --data-files ./train-images-idx3-ubyte ./train-labels-idx1-ubyte \
+    --save-mlp simple.mlp
+
+./ann --load-mlp simple.mlp \
+    --data-files ./t10k-images-idx3-ubyte ./t10k-labels-idx1-ubyte \
+    --nb-test-examples 10000
diff --git a/gpl-3.0.txt b/gpl-3.0.txt
new file mode 100644
index 0000000..94a9ed0
--- /dev/null
+++ b/gpl-3.0.txt
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
+free programs, and that you know you can do these things.
+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must pass on to the recipients the same
+freedoms that you received.  You must make sure that they, too, receive
+or can get the source code.  And you must show them these terms so they
+know their rights.
+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
+authors' sake, the GPL requires that modified versions be marked as
+changed, so that their problems will not be attributed erroneously to
+authors of previous versions.
+
+  Some devices are designed to deny users access to install or run
+modified versions of the software inside them, although the manufacturer
+can do so.  This is fundamentally incompatible with the aim of
+protecting users' freedom to change the software.  The systematic
+pattern of such abuse occurs in the area of products for individuals to
+use, which is precisely where it is most unacceptable.  Therefore, we
+have designed this version of the GPL to prohibit the practice for those
+products.  If such problems arise substantially in other domains, we
+stand ready to extend this provision to those domains in future versions
+of the GPL, as needed to protect the freedom of users.
+
+  Finally, every program is threatened constantly by software patents.
+States should not allow patents to restrict development and use of
+software on general-purpose computers, but in those that do, we wish to
+avoid the special danger that patents applied to a free program could
+make it effectively proprietary.  To prevent this, the GPL assures that
+patents cannot be used to render the program non-free.
+
+  The precise terms and conditions for copying, distribution and
+modification follow.
+
+                       TERMS AND CONDITIONS
+
+  0. Definitions.
+
+  "This License" refers to version 3 of the GNU General Public License.
+
+  "Copyright" also means copyright-like laws that apply to other kinds of
+works, such as semiconductor masks.
+
+  "The Program" refers to any copyrightable work licensed under this
+License.  Each licensee is addressed as "you".  "Licensees" and
+"recipients" may be individuals or organizations.
+
+  To "modify" a work means to copy from or adapt all or part of the work
+in a fashion requiring copyright permission, other than the making of an
+exact copy.  The resulting work is called a "modified version" of the
+earlier work or a work "based on" the earlier work.
+
+  A "covered work" means either the unmodified Program or a work based
+on the Program.
+
+  To "propagate" a work means to do anything with it that, without
+permission, would make you directly or secondarily liable for
+infringement under applicable copyright law, except executing it on a
+computer or modifying a private copy.  Propagation includes copying,
+distribution (with or without modification), making available to the
+public, and in some countries other activities as well.
+
+  To "convey" a work means any kind of propagation that enables other
+parties to make or receive copies.  Mere interaction with a user through
+a computer network, with no transfer of a copy, is not conveying.
+
+  An interactive user interface displays "Appropriate Legal Notices"
+to the extent that it includes a convenient and prominently visible
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diff --git a/images.cc b/images.cc
new file mode 100644
index 0000000..e1b07b4
--- /dev/null
+++ b/images.cc
@@ -0,0 +1,153 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include "images.h"
+#include <stdlib.h>
+
+PixelMaps::PixelMaps(int size) : _nb_ref(0),_core(new unsigned char[size]) {}
+PixelMaps::~PixelMaps() { delete[] _core; }
+PixelMaps *PixelMaps::add_ref() { _nb_ref++; return this; }
+void PixelMaps::del_ref() { _nb_ref--; if(_nb_ref == 0) delete this; }
+
+const unsigned int mnist_pictures_magic = 0x00000803;
+const unsigned int mnist_labels_magic = 0x00000801;
+
+inline unsigned int read_high_endian_int(istream &is) {
+  unsigned int result;
+  char *s = (char *) &result;
+  char c;
+  is.read(s, sizeof(result));
+  c = s[0]; s[0] = s[3]; s[3] = c;
+  c = s[1]; s[1] = s[2]; s[2] = c;
+  return result;
+}
+
+ImageSet::ImageSet() : _nb_pics(-1), _nb_obj(0), _width(-1), _height(-1),
+                       _pixel_maps(0), _pixels(0), _labels(0), _used_picture(0) { }
+
+ImageSet::~ImageSet() {
+  if(_pixel_maps) _pixel_maps->del_ref();
+  delete[] _pixels;
+  delete[] _labels;
+  delete[] _used_picture;
+}
+
+void ImageSet::reset_used_pictures() {
+  for(int p = 0; p < _nb_pics; p++) _used_picture[p] = false;
+}
+
+int ImageSet::nb_unused_pictures() {
+  int n = 0;
+  for(int p = 0; p < _nb_pics; p++) if(!_used_picture[p]) n++;
+  return n;
+}
+
+int ImageSet::pick_unused_picture() {
+  int m;
+  do { m = int(drand48() * _nb_pics); } while(_used_picture[m]);
+  _used_picture[m] = true;
+  return m;
+}
+
+void ImageSet::extract_unused_pictures(ImageSet &is, int nb) {
+  if(nb > is.nb_unused_pictures()) {
+    cerr << "Trying to extract " << nb << " pictures from a set of " << is.nb_unused_pictures() << "\n";
+    exit(1);
+  }
+
+  _nb_pics = nb;
+  _width = is._width;
+  _height = is._height;
+  _nb_obj = is._nb_obj;
+  _pixel_maps = is._pixel_maps->add_ref();
+  _pixels = new unsigned char *[_nb_pics];
+  _labels = new unsigned char[_nb_pics];
+  _used_picture = new bool[_nb_pics];
+  for(int n = 0; n < _nb_pics; n++) {
+    int m = is.pick_unused_picture();
+    _pixels[n] = is._pixels[m];
+    _labels[n] = is._labels[m];
+  }
+
+  reset_used_pictures();
+}
+
+void ImageSet::load_mnist_format(char *picture_file_name, char *label_file_name) {
+  unsigned int magic;
+
+  ifstream picture_is(picture_file_name);
+
+  if(picture_is.fail()) {
+    cerr << "Can not open file [" << picture_file_name << "].\n";
+    exit(1);
+  }
+
+  magic = read_high_endian_int(picture_is);
+  if(magic != mnist_pictures_magic) {
+    cerr << "Invalid magic for picture, file [" << picture_file_name << "] number [" << magic << "]\n";
+    exit(1);
+  }
+
+  _nb_pics = read_high_endian_int(picture_is);
+  _width = read_high_endian_int(picture_is);
+  _height = read_high_endian_int(picture_is);
+
+  ifstream label_is(label_file_name);
+  if(label_is.fail()) {
+    cerr << "Can not open file [" << label_file_name << "].\n";
+    exit(1);
+  }
+
+  magic = read_high_endian_int(label_is);
+  if(magic != mnist_labels_magic) {
+    cerr << "Invalid magic for labels, file [" << label_file_name << "] number [" << magic << "]\n";
+    exit(1);
+  }
+
+  int nb_pics_labels = read_high_endian_int(label_is);
+
+  if(nb_pics_labels != _nb_pics) {
+    cerr << "Inconsistency between the number of pictures in [" << picture_file_name << "] (" << _nb_pics << ")"
+         << " and the number of labels in [" << label_file_name << "] (" << nb_pics_labels << ").\n";
+    exit(1);
+  }
+
+  PixelMaps *pm = new PixelMaps(_nb_pics * _width * _height);
+  _pixel_maps = pm->add_ref();
+  _pixels = new unsigned char *[_nb_pics];
+  _labels = new unsigned char[_nb_pics];
+  _used_picture = new bool[_nb_pics];
+
+  picture_is.read((char *) _pixel_maps->_core, _nb_pics * _width * _height);
+  label_is.read((char *) _labels, _nb_pics);
+
+  for(int i = 0; i < _nb_pics * _width * _height; i++) _pixel_maps->_core[i] = 255 - _pixel_maps->_core[i];
+
+  _nb_obj = 0;
+  for(int n = 0; n < _nb_pics; n++) {
+    _pixels[n] = _pixel_maps->_core + n * _width * _height;
+    if(_labels[n] > _nb_obj) _nb_obj = _labels[n];
+  }
+  _nb_obj++;
+
+  reset_used_pictures();
+}
diff --git a/images.h b/images.h
new file mode 100644
index 0000000..71e0440
--- /dev/null
+++ b/images.h
@@ -0,0 +1,75 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+// $Id: images.h,v 1.1 2005-12-13 17:19:11 fleuret Exp $
+
+#ifndef IMAGES_H
+#define IMAGES_H
+
+#include <iostream>
+#include <fstream>
+#include <stdint.h>
+
+using namespace std;
+
+#include "features.h"
+
+class PixelMaps {
+public:
+  unsigned int _nb_ref;
+  unsigned char *_core;
+  PixelMaps(int size);
+  ~PixelMaps();
+  PixelMaps *add_ref();
+  void del_ref();
+};
+
+class ImageSet {
+  int _nb_pics, _nb_obj;
+  int _width, _height;
+  PixelMaps *_pixel_maps;
+  unsigned char **_pixels, *_labels;
+  bool *_used_picture;
+
+public:
+  ImageSet();
+  ~ImageSet();
+
+  inline int nb_pics() { return _nb_pics; }
+  inline int nb_obj() { return _nb_obj; }
+  inline int width() { return _width; }
+  inline int height() { return _height; }
+  inline unsigned char *pixels(int p) { return _pixels[p]; }
+  inline unsigned char pixel(int p, int x, int y) { return _pixels[p][x + y * _width]; }
+  inline unsigned char label(int p) { return _labels[p]; }
+
+  void reset_used_pictures();
+  int nb_unused_pictures();
+  int pick_unused_picture();
+
+  void load_mnist_format(char *picture_file_name, char *label_file_name);
+
+  void extract_unused_pictures(ImageSet &is, int nb);
+
+};
+
+#endif
diff --git a/misc.cc b/misc.cc
new file mode 100644
index 0000000..2f6fa3d
--- /dev/null
+++ b/misc.cc
@@ -0,0 +1,37 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+// $Id: misc.cc,v 1.1 2005-12-13 17:19:11 fleuret Exp $
+
+#include "misc.h"
+
+int compare_couple(const void *a, const void *b) {
+  if(((Couple *) a)->value < ((Couple *) b)->value) return -1;
+  else if(((Couple *) a)->value > ((Couple *) b)->value) return 1;
+  else return 0;
+}
+
+int factorial(int k) {
+  int n = 1;
+  for(int l = 1; l <= k; l++) n *= l;
+  return n;
+}
diff --git a/misc.h b/misc.h
new file mode 100644
index 0000000..3a8b43d
--- /dev/null
+++ b/misc.h
@@ -0,0 +1,47 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef MISC_H
+#define MISC_H
+
+#ifdef DEBUG
+#define ASSERT(x, s) if(!(x)) { std::cerr << "ASSERT FAILED IN " << __FILE__ << ":" << __LINE__ << " [" << (s) << "]\n"; abort(); }
+#else
+#define ASSERT(x, s)
+#endif
+
+typedef float scalar_t;
+
+template<class T> T sq(T x) { return x*x; }
+
+template<class T> T pos(T x) { if(x < 0) return 0.0; else return x; }
+
+struct Couple {
+  int index;
+  double value;
+};
+
+int compare_couple(const void *a, const void *b);
+
+int factorial(int k);
+
+#endif
diff --git a/neural.cc b/neural.cc
new file mode 100644
index 0000000..275ad7e
--- /dev/null
+++ b/neural.cc
@@ -0,0 +1,412 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#include <string.h>
+
+#include "neural.h"
+
+const scalar_t MultiLayerPerceptron::output_amplitude = 0.95;
+
+// I won't comment the natural elegance of C++ in that kind of
+// situation. IT SUCKS.
+
+MultiLayerPerceptron::MultiLayerPerceptron(const MultiLayerPerceptron &mlp) {
+  _nb_layers = mlp._nb_layers;
+  _layer_sizes = new int[_nb_layers];
+  _frozen_layers = new bool[_nb_layers-1];
+  memcpy((void *) _frozen_layers, (void *) mlp._frozen_layers, _nb_layers * sizeof(bool));
+  _activations_index = new int[_nb_layers];
+  _weights_index = new int[_nb_layers];
+
+  _nb_activations = 0;
+  _nb_weights = 0;
+
+  for(int n = 0; n < _nb_layers; n++) _layer_sizes[n] = mlp._layer_sizes[n];
+
+  for(int n = 0; n < _nb_layers; n++) {
+    _activations_index[n] = _nb_activations;
+    _nb_activations += _layer_sizes[n];
+    if(n < _nb_layers - 1) {
+      _frozen_layers[n] = false;
+      _weights_index[n] = _nb_weights;
+      _nb_weights += (_layer_sizes[n] + 1) * _layer_sizes[n+1];
+    }
+  }
+
+  _activations = new scalar_t[_nb_activations];
+  _pre_sigma_activations = new scalar_t[_nb_activations];
+
+  _weights = new scalar_t[_nb_weights];
+  memcpy((void *) _weights, (void *) mlp._weights, _nb_weights * sizeof(scalar_t));
+}
+
+MultiLayerPerceptron::MultiLayerPerceptron(int nb_layers, int *layer_sizes) {
+  _nb_layers = nb_layers;
+  _layer_sizes = new int[_nb_layers];
+  _frozen_layers = new bool[_nb_layers-1];
+  _activations_index = new int[_nb_layers];
+  _weights_index = new int[_nb_layers];
+
+  _nb_activations = 0;
+  _nb_weights = 0;
+
+  for(int n = 0; n < _nb_layers; n++) _layer_sizes[n] = layer_sizes[n];
+
+  for(int n = 0; n < _nb_layers; n++) {
+    _activations_index[n] = _nb_activations;
+    _nb_activations += _layer_sizes[n];
+    if(n < _nb_layers - 1) {
+      _frozen_layers[n] = false;
+      _weights_index[n] = _nb_weights;
+      _nb_weights += (_layer_sizes[n] + 1) * _layer_sizes[n+1];
+    }
+  }
+
+  _activations = new scalar_t[_nb_activations];
+  _pre_sigma_activations = new scalar_t[_nb_activations];
+
+  _weights = new scalar_t[_nb_weights];
+}
+
+MultiLayerPerceptron::MultiLayerPerceptron(istream &is) {
+  is >> _nb_layers;
+
+  _layer_sizes = new int[_nb_layers];
+  _frozen_layers = new bool[_nb_layers - 1];
+  _activations_index = new int[_nb_layers];
+  _weights_index = new int[_nb_layers];
+
+  _nb_activations = 0;
+  _nb_weights = 0;
+
+  for(int n = 0; n < _nb_layers; n++) is >> _layer_sizes[n];
+
+  for(int n = 0; n < _nb_layers; n++) {
+    _activations_index[n] = _nb_activations;
+    _nb_activations += _layer_sizes[n];
+    if(n < _nb_layers - 1) {
+      _frozen_layers[n] = false;
+      _weights_index[n] = _nb_weights;
+      _nb_weights += (_layer_sizes[n] + 1) * _layer_sizes[n+1];
+    }
+  }
+
+  _activations = new scalar_t[_nb_activations];
+  _pre_sigma_activations = new scalar_t[_nb_activations];
+
+  _weights = new scalar_t[_nb_weights];
+
+  for(int l = 0; l < _nb_layers - 1; l++) {
+    int ll;
+    is >> ll;
+    if(l != ll) {
+      cerr << "Inconsistent layer number during loading!\n";
+      cerr.flush();
+      exit(1);
+    }
+    for(int j = 0; j < _layer_sizes[l]; j++)
+      for(int i = 0; i < _layer_sizes[l+1]; i++)
+        is >> _weights[_weights_index[l] + i * (_layer_sizes[l] + 1) + j];
+  }
+}
+
+MultiLayerPerceptron::~MultiLayerPerceptron() {
+  delete[] _weights;
+  delete[] _activations;
+  delete[] _pre_sigma_activations;
+
+  delete[] _layer_sizes;
+  delete[] _frozen_layers;
+  delete[] _weights_index;
+  delete[] _activations_index;
+}
+
+void MultiLayerPerceptron::save(ostream &os) {
+  os << _nb_layers << "\n";
+  for(int n = 0; n < _nb_layers; n++) os << _layer_sizes[n] << (n < _nb_layers - 1 ? " " : "\n");
+  for(int l = 0; l < _nb_layers - 1; l++) {
+    os << l << "\n";
+    for(int j = 0; j < _layer_sizes[l]; j++) {
+      for(int i = 0; i < _layer_sizes[l+1]; i++)
+        os << _weights[_weights_index[l] + i * (_layer_sizes[l] + 1) + j] << (i < _layer_sizes[l+1] - 1 ? " " : "\n");
+    }
+  }
+}
+
+void MultiLayerPerceptron::save_data() {
+  for(int i = 0; i < _layer_sizes[1]; i++) {
+    char buffer[256];
+    sprintf(buffer, "/tmp/hidden_%03d.dat", i);
+    ofstream stream(buffer);
+    for(int j = 0; j < _layer_sizes[0]; j++) {
+      if(j%28 == 0) stream << "\n";
+      stream << j%28 << " " << j/28 << " " << _weights[i * (_layer_sizes[0] + 1) + j] << "\n";
+    }
+  }
+}
+
+void MultiLayerPerceptron::init_random_weights(scalar_t stdd) {
+  for(int w = 0; w < _nb_weights; w++) _weights[w] = normal_sample() * stdd;
+}
+
+void MultiLayerPerceptron::compute_gradient_1s(ImageSet *is, int p, scalar_t *gradient_1s) {
+  scalar_t dactivations[_nb_activations];
+
+  compute_activations_1s(is, p);
+
+  int nb_unfrozen = 0;
+  for(int l = 0; l < _nb_layers - 1; l++) if(!_frozen_layers[l]) nb_unfrozen++;
+
+  for(int i = 0; i < _layer_sizes[_nb_layers - 1]; i++) {
+    scalar_t correct;
+    if(is->label(p) == i) correct =   output_amplitude;
+    else                  correct = - output_amplitude;
+    dactivations[_activations_index[_nb_layers - 1] + i] = 2 * (_activations[_activations_index[_nb_layers - 1] + i] - correct);
+  }
+
+  for(int l = _nb_layers - 2; (l >= 0) && (nb_unfrozen > 0); l--) {
+    int ai0 = _activations_index[l], ai1 = _activations_index[l+1],
+      wi0 = _weights_index[l], ls0p1 = _layer_sizes[l] + 1;
+
+    int j;
+    for(j = 0; j < _layer_sizes[l]; j++) {
+      scalar_t s = 0.0;
+      for(int i = 0; i < _layer_sizes[l+1]; i++) {
+        scalar_t alpha = dactivations[ai1 + i] * dsigma(_pre_sigma_activations[ai1 + i]);
+        s += alpha * _weights[wi0 + i * ls0p1 + j];
+        gradient_1s[wi0 + i * ls0p1 + j] = alpha * _activations[ai0 + j];
+      }
+      dactivations[ai0 + j] = s;
+    }
+
+    for(int i = 0; i < _layer_sizes[l+1]; i++) {
+      scalar_t alpha = dactivations[ai1 + i] * dsigma(_pre_sigma_activations[ai1 + i]);
+      gradient_1s[wi0 + i * ls0p1 + j] = alpha;
+    }
+    if(!_frozen_layers[l]) nb_unfrozen--;
+  }
+}
+
+void MultiLayerPerceptron::compute_gradient(ImageSet *is, scalar_t *gradient) {
+  scalar_t gradient_1s[_nb_weights];
+  for(int w = 0; w < _nb_weights; w++) gradient[w] = 0.0;
+  for(int p = 0; p < is->nb_pics(); p++) {
+    compute_gradient_1s(is, p, gradient_1s);
+    for(int w = 0; w < _nb_weights; w++) gradient[w] += gradient_1s[w];
+  }
+}
+
+void MultiLayerPerceptron::compute_numerical_gradient(ImageSet *is, scalar_t *gradient) {
+  const scalar_t eps = 1e-3;
+  scalar_t error_plus, error_minus, ref;
+  for(int w = 0; w < _nb_weights; w++) {
+    ref = _weights[w];
+    _weights[w] = ref + eps;
+    error_plus = error(is);
+    _weights[w] = ref - eps;
+    error_minus = error(is);
+    _weights[w] = ref;
+    gradient[w] = (error_plus - error_minus) / (2 * eps);
+  }
+}
+
+void MultiLayerPerceptron::print_gradient(ostream &os, scalar_t *gradient) {
+  for(int w = 0; w < _nb_weights; w++) os << gradient[w] << "\n";
+}
+
+void MultiLayerPerceptron::move_on_line(scalar_t *origin, scalar_t *gradient, scalar_t lambda) {
+  for(int l = 0; l < _nb_layers-1; l++) if(!_frozen_layers[l]) {
+    for(int i = 0; i < (_layer_sizes[l] + 1) * _layer_sizes[l+1]; i++)
+      _weights[_weights_index[l] + i] =
+        origin[_weights_index[l] + i] + lambda * gradient[_weights_index[l] + i];
+  }
+}
+
+void MultiLayerPerceptron::one_step_basic_gradient(ImageSet *is, scalar_t dt) {
+  scalar_t gradient_1s[_nb_weights];
+  for(int p = 0; p < is->nb_pics(); p++) {
+    if(p%1000 == 0) {
+      int n = (p*50)/is->nb_pics();
+      int j;
+      for(j = 0; j < n; j++) cout << "X";
+      for(; j < 50; j++) cout << ((j%5 == 0) ? "+" : "-");
+      cout << "\r";
+      cout.flush();
+    }
+    compute_gradient_1s(is, p, gradient_1s);
+    move_on_line(_weights, gradient_1s, -dt);
+  }
+  cout << "                                                            \r"; cout.flush();
+}
+
+void MultiLayerPerceptron::one_step_global_gradient(ImageSet *is, scalar_t *xi, scalar_t *g, scalar_t *h) {
+  scalar_t origin[_nb_weights];
+  for(int w = 0; w < _nb_weights; w++) origin[w] = _weights[w];
+
+  scalar_t l = 1e-8;
+  scalar_t e, pe;
+
+  e = error(is);
+
+  do {
+    pe = e;
+    l *= 2;
+    move_on_line(origin, xi, l);
+    e = error(is);
+  } while(e < pe);
+
+  scalar_t dl = - l / 4;
+
+  while(abs(dl) > 1e-6) {
+    move_on_line(origin, xi, l);
+    e = error(is);
+    do {
+      pe = e;
+      l  += dl;
+      move_on_line(origin, xi, l);
+      e = error(is);
+    } while(e < pe);
+    dl = - dl / 4;
+  }
+
+  compute_gradient(is, xi);
+
+  scalar_t gg = 0, gxi = 0, xixi = 0;
+
+  // Polak-Ribiere
+
+  for(int w = 0; w < _nb_weights; w++) {
+    gg += sq(g[w]);
+    gxi += g[w] * xi[w];
+    xixi += sq(xi[w]);
+  }
+
+  scalar_t gamma = (xixi + gxi)/gg;
+
+  // Set gamma to 0 for standard gradient descente
+  //   gamma = 0.0;
+
+  for(int w = 0; w < _nb_weights; w++) {
+    g[w] = -xi[w];
+    h[w] = g[w] + gamma * h[w];
+    xi[w] = h[w];
+  }
+}
+
+void MultiLayerPerceptron::train(ImageSet *training_set, ImageSet *validation_set) {
+  scalar_t prev_validation_error = 1.0, validation_error = 1.0, training_error;
+  int l = 0, nb_increases = 0;
+  do {
+// #warning horrible debugging
+//     {
+//       char buffer[1024];
+//       sprintf(buffer, "tmp_%04d.mlp", l);
+//       ofstream stream(buffer);
+//       save(stream);
+//       stream.flush();
+//     }
+    prev_validation_error = validation_error;
+    //     one_step_global_gradient(training_set, xi, g, h);
+    one_step_basic_gradient(training_set, 1e-2);
+    training_error = error(training_set);
+    validation_error = error(validation_set);
+    cout << l
+         << " TRAINING " << training_error << " (" << classification_error(training_set)*100 << "%)"
+         << " VALIDATION " << validation_error << " (" << classification_error(validation_set)*100 << "%)";
+    if(l > 0 && validation_error >= prev_validation_error) {
+      nb_increases++;
+      cout << " [" << nb_increases << "]";
+    }
+    cout << "\n";
+    cout.flush();
+    l++;
+  } while(nb_increases < 10);
+
+}
+
+void MultiLayerPerceptron::compute_activations_1s(ImageSet *is, int p) {
+  ASSERT(_layer_sizes[0] == is->width() * is->height(), "The first layer has to have as many units as there are pixels!");
+
+  scalar_t *a = _activations;
+  scalar_t *w = _weights;
+
+  for(int y = 0; y < is->height(); y++) for(int x = 0; x < is->width(); x++)
+    *(a++) = 2.0 * (scalar_t(is->pixel(p, x, y)) / 255.0) - 1.0;
+
+  scalar_t *pa = _pre_sigma_activations + _activations_index[1];
+  scalar_t *b = _activations, *b2 = 0;
+
+  for(int l = 0; l < _nb_layers - 1; l++) {
+    for(int i = 0; i < _layer_sizes[l+1]; i++) {
+      scalar_t s = 0;
+      b2 = b;
+      for(int j = 0; j < _layer_sizes[l]; j++) s += *(w++) * *(b2++);
+      s += *(w++);
+      *(pa++) = s;
+      *(a++) = sigma(s);
+    }
+    b = b2;
+  }
+}
+
+void MultiLayerPerceptron::test(ImageSet *is, scalar_t *responses) {
+  for(int p = 0; p < is->nb_pics(); p++) {
+    compute_activations_1s(is, p);
+    for(int i = 0; i < _layer_sizes[_nb_layers - 1]; i++)
+      responses[p * _layer_sizes[_nb_layers - 1] + i] = _activations[_activations_index[_nb_layers - 1] + i];
+  }
+}
+
+scalar_t MultiLayerPerceptron::error(ImageSet *is) {
+  scalar_t error = 0;
+
+  for(int p = 0; p < is->nb_pics(); p++) {
+    compute_activations_1s(is, p);
+    for(int i = 0; i < _layer_sizes[_nb_layers - 1]; i++) {
+      scalar_t correct;
+      if(is->label(p) == i) correct =   output_amplitude;
+      else                  correct = - output_amplitude;
+      error += sq(_activations[_activations_index[_nb_layers - 1] + i] - correct);
+    }
+  }
+
+  return error;
+}
+
+scalar_t MultiLayerPerceptron::classification_error(ImageSet *is) {
+  int nb_error = 0;
+
+  for(int p = 0; p < is->nb_pics(); p++) {
+    compute_activations_1s(is, p);
+    scalar_t max = -1;
+    int i_max = -1;
+    for(int i = 0; i < _layer_sizes[_nb_layers - 1]; i++) {
+      if(i_max < 0 || _activations[_activations_index[_nb_layers - 1] + i] > max) {
+        i_max = i;
+        max = _activations[_activations_index[_nb_layers - 1] + i];
+      }
+    }
+    if(is->label(p) != i_max) nb_error++;
+  }
+
+  return scalar_t(nb_error)/scalar_t(is->nb_pics());
+}
diff --git a/neural.h b/neural.h
new file mode 100644
index 0000000..6843212
--- /dev/null
+++ b/neural.h
@@ -0,0 +1,118 @@
+/*
+ *  mlp-mnist is an implementation of a multi-layer neural network.
+ *
+ *  Copyright (c) 2008 Idiap Research Institute, http://www.idiap.ch/
+ *  Written by Francois Fleuret <francois.fleuret@idiap.ch>
+ *
+ *  This file is part of mlp-mnist.
+ *
+ *  mlp-mnist is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License version 3 as
+ *  published by the Free Software Foundation.
+ *
+ *  mlp-mnist 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 mlp-mnist.  If not, see <http://www.gnu.org/licenses/>.
+ *
+ */
+
+#ifndef NEURAL_H
+#define NEURAL_H
+
+#include <cmath>
+#include <stdlib.h>
+
+#include "misc.h"
+#include "images.h"
+
+inline scalar_t normal_sample() {
+  scalar_t a = drand48();
+  scalar_t b = drand48();
+  return cos(2 * M_PI * a) * sqrt(-2 * log(b));
+}
+
+class MultiLayerPerceptron {
+protected:
+  static const scalar_t output_amplitude;
+
+  int _nb_layers;
+  int *_layer_sizes;
+  int _nb_activations, _nb_weights;
+
+  // We can 'freeze' certain layers and let the learning only change
+  // the others
+  bool *_frozen_layers;
+
+  // Tell us where the layers begin
+  int *_weights_index, *_activations_index;
+
+  scalar_t *_activations, *_pre_sigma_activations;
+  scalar_t *_weights;
+
+public:
+  MultiLayerPerceptron(const MultiLayerPerceptron &mlp);
+  MultiLayerPerceptron(int nb_layers, int *layer_sizes);
+  MultiLayerPerceptron(istream &is);
+  ~MultiLayerPerceptron();
+
+  void save(ostream &os);
+
+  void save_data();
+
+  inline int nb_layers() { return _nb_layers; }
+  inline int layer_size(int l) { return _layer_sizes[l]; }
+  inline int nb_weights() { return _nb_weights; }
+  inline void freeze(int l, bool f) { _frozen_layers[l] = f; }
+  scalar_t sigma(scalar_t x) { return 2 / (1 + exp(- x)) - 1; }
+  scalar_t dsigma(scalar_t x) { scalar_t e = exp(- x); return 2 * e / sq(1 + e); }
+
+  // Init all the weights with a normal distribution of given standard
+  // deviation
+  void init_random_weights(scalar_t stdd);
+
+  // Compute the gradient based on one single sample
+  void compute_gradient_1s(ImageSet *is, int p, scalar_t *gradient_1s);
+  // Compute the gradient based on all samples from the set
+  void compute_gradient(ImageSet *is, scalar_t *gradient);
+
+  // Compute the same gradient numerically (to check the one above)
+  void compute_numerical_gradient(ImageSet *is, scalar_t *gradient);
+
+  // Print the gradient
+  void print_gradient(ostream &os, scalar_t *gradient);
+
+  // Move all weights to origin + lambda * gradient
+  void move_on_line(scalar_t *origin, scalar_t *gradient, scalar_t lambda);
+
+  // The 'basic' gradient just goes through all samples and add dt
+  // time the gradient on each one
+  void one_step_basic_gradient(ImageSet *is, scalar_t dt);
+
+  // The global gradient uses a conjugate gradient to minmize the
+  // global quadratic error
+  void one_step_global_gradient(ImageSet *is, scalar_t *xi, scalar_t *g, scalar_t *h);
+
+  // Performs gradient descent until the test error as increased
+  // during 5 steps
+  void train(ImageSet *training_set, ImageSet *validation_set);
+
+  // Compute the activation of the network from one sample. The input
+  // layer has to be as large as the number of pixels in the images.
+  void compute_activations_1s(ImageSet *is, int p);
+
+  // Compute the activation of the network on all samples. The
+  // responses array has to be as large as the number of samples in is
+  // time the dimension of the output layer
+  void test(ImageSet *is, scalar_t *responses);
+
+  // Compute the quadratic error
+  scalar_t error(ImageSet *is);
+  // Compute the classification error
+  scalar_t classification_error(ImageSet *is);
+};
+
+#endif