void modify_data(DataSequence& data, DataSequence const& old_data)
{
boost::sort(
data,
md::neighbor::inexclusive_cells_neighbor_list_detail::less_()
);
typedef typename DataSequence::iterator data_iterator;
typedef typename DataSequence::const_iterator old_data_iterator;
data_iterator iter = data.begin();
data_iterator const last = data.end();
old_data_iterator old_iter = old_data.begin();
old_data_iterator const old_last = old_data.end();
while (iter != last && old_iter != old_last)
{
if (md::neighbor::inexclusive_cells_neighbor_list_detail::equal_to(
*iter, *old_iter
))
{
*iter = *old_iter;
++iter;
++old_iter;
}
else if (md::neighbor::inexclusive_cells_neighbor_list_detail::less(
*iter, *old_iter
))
++iter;
else
++old_iter;
}
}
typename boost::enable_if<
md::neighbor::meta::is_simple_neighbor<
typename DataSequence::value_type
>,
void>::type update(
DataSequence& data, Length& buffer_length, Length const cutoff_length,
Length const search_length, SquaredLength const squared_search_length,
Particles const& particles, Time const time_step)
{
data.clear();
md::neighbor::inexclusive_cells_neighbor_list_detail::update_impl(
data, squared_search_length, particles
);
buffer_length
= md::neighbor::inexclusive_cells_neighbor_list_detail
::get_buffer_length(
cutoff_length, search_length, particles, time_step
);
}
typename boost::enable_if<
boost::mpl::and_<
typename boost::mpl::not_<
typename md::neighbor::meta::is_simple_neighbor<
typename DataSequence::value_type
>::type
>::type,
typename MD_IS_CONVERTIBLE<
typename std::iterator_traits<
typename DataSequence::iterator
>::iterator_category,
std::random_access_iterator_tag
>::type
>,
void>::type update(
DataSequence& data, Length& buffer_length, Length const cutoff_length,
Length const search_length, SquaredLength const squared_search_length,
Particles1 const& particles1, Particles2 const& particles2,
Time const time_step)
{
DataSequence const old_data(data);
data.clear();
md::neighbor::inexclusive_cells_neighbor_list_detail::update_impl(
data, squared_search_length, particles1, particles2
);
md::neighbor::inexclusive_cells_neighbor_list_detail::modify_data(
data, old_data
);
buffer_length
= md::neighbor::inexclusive_cells_neighbor_list_detail
::get_buffer_length(
cutoff_length, search_length, particles1, particles2, time_step
);
}
int DataSet::load(const char *fileData, const char *fileStateLabels,
const char *fileSeqLabels, const char * fileAdjMat,
const char * fileStatesPerNodes,const char * fileDataSparse)
{
istream* isData = NULL;
istream* isDataSparse = NULL;
istream* isStateLabels = NULL;
istream* isSeqLabels = NULL;
istream* isAdjMat = NULL;
istream* isStatesPerNodes = NULL;
if(fileData != NULL)
{
isData = new ifstream(fileData);
if(!((ifstream*)isData)->is_open())
{
cerr << "Can't find data file: " << fileData << endl;
delete isData;
isData = NULL;
throw BadFileName("Can't find data files");
}
}
if(fileStateLabels != NULL)
{
isStateLabels = new ifstream(fileStateLabels);
if(!((ifstream*)isStateLabels)->is_open())
{
cerr << "Can't find state labels file: " << fileStateLabels << endl;
delete isStateLabels;
isStateLabels = NULL;
throw BadFileName("Can't find state labels file");
}
}
if(fileSeqLabels != NULL)
{
isSeqLabels = new ifstream(fileSeqLabels);
if(!((ifstream*)isSeqLabels)->is_open())
{
cerr << "Can't find sequence labels file: " << fileSeqLabels << endl;
delete isSeqLabels;
isSeqLabels = NULL;
}
}
if(fileAdjMat != NULL)
{
isAdjMat = new ifstream(fileAdjMat);
if(!((ifstream*)isAdjMat)->is_open())
{
cerr << "Can't find adjency matrices file: " << fileAdjMat << endl;
delete isAdjMat;
isAdjMat = NULL;
}
}
if(fileStatesPerNodes != NULL)
{
isStatesPerNodes = new ifstream(fileStatesPerNodes);
if(!((ifstream*)isStatesPerNodes)->is_open())
{
cerr << "Can't find states per nodes file: " << fileStatesPerNodes << endl;
delete isStatesPerNodes;
isStatesPerNodes = NULL;
}
}
if(fileDataSparse != NULL)
{
isDataSparse = new ifstream(fileDataSparse);
if(!((ifstream*)isDataSparse)->is_open())
{
cerr << "Can't find sparse data file: " << fileDataSparse << endl;
delete isDataSparse;
isDataSparse = NULL;
throw BadFileName("Can't find sparse data files");
}
}
DataSequence* seq = new DataSequence;
int seqLabel;
while(seq->load(isData,isStateLabels,isAdjMat,isStatesPerNodes,isDataSparse) == 0)
{
if(isSeqLabels)
{
*isSeqLabels >> seqLabel;
seq->setSequenceLabel(seqLabel);
}
container.insert(container.end(),seq);
seq = new DataSequence;
}
delete seq;
if(isData)
delete isData;
if(isStateLabels)
delete isStateLabels;
if(isSeqLabels)
delete isSeqLabels;
if(isAdjMat)
delete isAdjMat;
if(isStatesPerNodes)
delete isStatesPerNodes;
if(isDataSparse)
delete isDataSparse;
return 0;
}
double Gradient::computeGradient(dVector& vecGradient, Model* m, DataSet* X)
{
double ans = 0.0;
#ifdef _OPENMP
if( nbThreadsMP < 1 )
nbThreadsMP = omp_get_max_threads();
setMaxNumberThreads(nbThreadsMP);
pInfEngine->setMaxNumberThreads(nbThreadsMP);
pFeatureGen->setMaxNumberThreads(nbThreadsMP);
#endif
//Check the size of vecGradient
int nbFeatures = pFeatureGen->getNumberOfFeatures();
if(vecGradient.getLength() != nbFeatures)
vecGradient.create(nbFeatures);
else
vecGradient.set(0);
////////////////////////////////////////////////////////////
// Start of parallel Region
// Some weird stuff in gcc 4.1, with openmp 2.5 support
//
// Note 1: In OpenMP 2.5, the iteration variable in "for" must be
// a signed integer variable type. In OpenMP 3.0 (_OPENMP>=200805),
// it may also be an unsigned integer variable type, a pointer type,
// or a constant-time random access iterator type.
//
// Note 2: schedule(static | dynamic): In the dynamic schedule, there
// is no predictable order in which the loop items are assigned to
// different threads. Each thread asks the OpenMP runtime library for
// an iteration number, then handles it, then asks for the next one.
// It is thus useful when different iterations in the loop may take
// different time to execute.
#pragma omp parallel default(none) \
shared(vecGradient, X, m, ans, nbFeatures, std::cout)
{
// code inside this region runs in parallel
dVector g(nbFeatures, COLVECTOR, 0.0);
#pragma omp for schedule(dynamic) reduction(+:ans)
for(int i=0; (int)i<X->size(); i++) {
DataSequence* x = X->at(i);
if( m->isWeightSequence() && x->getWeightSequence() != 1.0) {
dVector tmp(nbFeatures, COLVECTOR, 0.0);
ans += computeGradient(tmp, m, x) * x->getWeightSequence();
tmp.multiply(x->getWeightSequence());
g.add(tmp);
}
else {
ans += computeGradient(g, m, x);
}
}
// We now put togheter the gradients
// No two threads can execute a critical directive of the same name at the same time
#pragma omp critical (reduce_sum)
{
vecGradient.add(g);
}
}
// End of parallel Region
////////////////////////////////////////////////////////////
vecGradient.negate();
// MaxMargin objective: min L = 0.5*\L2sigma*W*W + Loss()
// MLE objective: min L = 0.5*1/(\L2sigma*\L2sigma)*W*W - log p(y|x)
// Add the regularization term
double scale = (m->isMaxMargin())
? m->getRegL2Sigma()
: 1/(double)(m->getRegL2Sigma()*m->getRegL2Sigma());
if( m->isMaxMargin() )
ans = (1/(double)X->size()) * ans;
if(m->getRegL2Sigma()!=0.0f)
{
for(int f=0; f<nbFeatures; f++)
vecGradient[f] += (*m->getWeights())[f]*scale;
ans += 0.5*scale*m->getWeights()->l2Norm(false);
}
return ans;
}
double Gradient::computeGradient(dVector& vecGradient, Model* m, DataSet* X)
{
//Check the size of vecGradient
int nbFeatures = pFeatureGen->getNumberOfFeatures();
double ans = 0.0;
int TID = 0;
if(vecGradient.getLength() != nbFeatures)
vecGradient.create(nbFeatures);
else
vecGradient.set(0);
// Initialize the buffers (vecFeaturesMP) for each thread
#ifdef _OPENMP
setMaxNumberThreads(omp_get_max_threads());
pInfEngine->setMaxNumberThreads(omp_get_max_threads());
pFeatureGen->setMaxNumberThreads(omp_get_max_threads());
#endif
for(int t=0;t<nbThreadsMP;t++)
{
if(localGrads[t].getLength() != nbFeatures)
localGrads[t].resize(1,nbFeatures,0);
else
localGrads[t].set(0);
}
////////////////////////////////////////////////////////////
// Start of parallel Region
// Some weird stuff in gcc 4.1, with openmp 2.5 support
#if ((_OPENMP == 200505) && __GNUG__)
#pragma omp parallel \
shared(X, m, ans, nbFeatures, std::cout) \
private(TID) \
default(none)
#else
#pragma omp parallel \
shared(vecGradient, X, m, ans, nbFeatures, std::cout) \
private(TID) \
default(none)
#endif
{
#ifdef _OPENMP
TID = omp_get_thread_num();
#endif
// Create a temporary gradient
double localSum = 0;
#ifdef WITH_SEQUENCE_WEIGHTS
dVector tmpVecGradient(nbFeatures);
#endif
#pragma omp for
// we can use unsigned if we have openmp 3.0 support (_OPENMP>=200805).
#ifdef _OPENMP
#if _OPENMP >= 200805
for(unsigned int i = 0; i< X->size(); i++){
#else
for(int i = 0; i< X->size(); i++){
#endif
#else
for(unsigned int i = 0; i< X->size(); i++){
#endif
if (m->getDebugLevel() >=2){
#pragma omp critical(output)
std::cout << "Thread "<<TID<<" computes gradient for sequence "
<< i <<" out of " << (int)X->size()
<< " (Size: " << X->at(i)->length() << ")" << std::endl;
}
DataSequence* x = X->at(i);
#ifdef WITH_SEQUENCE_WEIGHTS
tmpVecGradient.set(0);
localSum += computeGradient(tmpVecGradient, m, x) * x->getWeightSequence();
if(x->getWeightSequence() != 1.0)
tmpVecGradient.multiply(x->getWeightSequence());
localGrads[TID].add(tmpVecGradient);
#else
localSum += computeGradient(localGrads[TID], m, x);// * x->getWeightSequence();
#endif
}
#pragma omp critical (reduce_sum)
// We now put togheter the sums
{
if( m->getDebugLevel() >= 2){
std::cout<<"Thread "<<TID<<" update sums"<<std::endl;
}
ans += localSum;
vecGradient.add(localGrads[TID]);
}
}
// End of parallel Region
////////////////////////////////////////////////////////////
// because we are minimizing -LogP
vecGradient.negate();
// Add the regularization term
double sigmaL2Square = m->getRegL2Sigma()*m->getRegL2Sigma();
if(sigmaL2Square != 0.0f) {
if (m->getDebugLevel() >= 2){
std::cout << "Adding L2 norm gradient\n";
}
for(int f = 0; f < nbFeatures; f++) {
vecGradient[f] += (*m->getWeights())[f]/sigmaL2Square;
}
double weightNorm = m->getWeights()->l2Norm(false);
ans += weightNorm / (2.0*m->getRegL2Sigma()*m->getRegL2Sigma());
}
return ans;
}