double GeneralPathSuffStatMultipleMatrixMixtureProfileProcess::ProfileSuffStatLogProb(int cat, int l) {
double total = 0;
SubMatrix* mat = matrixarray[cat][l];
if (! mat) {
cerr << "error : null matrix\n";
cerr << cat << '\t' << Ncomponent << '\n';
cerr << occupancy[cat] << '\n';
exit(1);
}
const double* stat = mat->GetStationary();
for (map<int,int>::iterator i = profilerootcount[cat][l].begin(); i!= profilerootcount[cat][l].end(); i++) {
total += i->second * log(stat[i->first]);
}
for (map<int,double>::iterator i = profilewaitingtime[cat][l].begin(); i!= profilewaitingtime[cat][l].end(); i++) {
total += i->second * (*mat)(i->first,i->first);
}
for (map<pair<int,int>, int>::iterator i = profilepaircount[cat][l].begin(); i!= profilepaircount[cat][l].end(); i++) {
total += i->second * log((*mat)(i->first.first, i->first.second));
}
if (isnan(total)) {
cerr << "error: in GPSSMultipleMat ProfileSuffStatLogProb: nan\n";
exit(1);
}
return total;
}
SpdMatrix::SpdMatrix(const SubMatrix &rhs, bool check)
{
if(check){
if(rhs.nrow() != rhs.ncol()){
report_error("SpdMatrix constructor was supplied a non-square"
"SubMatrix argument");
}
}
operator=(rhs);
}
void LMAT::add_to(SubMatrix block)const {
if(block.nrow() != 3 || block.ncol() !=3) {
report_error("block is the wrong size in LMAT::add_to");
}
double phi = phi_->value();
block(0,0) += 1;
block(0,1) += 1;
block(1,1) += phi;
block(1,2) += 1-phi;
block(2,2) += 1;
}
BorderMatrix matrix2DFinder(int** matrix, int sizeX,int sizeY, int ignValue, int radius)
{
BorderMatrix bm;
VectorQueue vctQ,tmpQ;
SubMatrix sb;
sb.radius=radius;
int xMax,yMax,xMin,yMin;
vector<SubMatrix> subMatrixVect;
int i,j,k;
i=j=k=0;
while(i<sizeY)
{
while(j<sizeX)
{
if((matrix[j][i]!= ignValue) && (matrix[j][i]>0))
{
while(!vctQ.isEmpty())
vctQ.pop();
vctQ.push(j,i,0);
matrix[j][i]-=2*matrix[j][i];
tmpQ=neighbour2D(matrix,ignValue, radius,vctQ, sizeX,sizeY);
xMax=sb.getMax(tmpQ.x);
yMax=sb.getMax(tmpQ.y);
xMin=sb.getMin(tmpQ.x);
yMin=sb.getMin(tmpQ.y);
bm.push(xMax,xMin,yMax,yMin,0,0);
k++;
}
++j;
}
j=0;
++i;
}
BorderMatrix tmp;
for(int l=0;l<k;l++)
{
tmp.push(bm.xMax.front(),bm.xMin.front(),bm.yMax.front(),bm.yMin.front(),0,0);
matrixAbs2D(matrix,bm.xMax.front(),bm.xMin.front(),bm.yMax.front(),bm.yMin.front(), 2*radius);
bm.pop();
}
return tmp;
}
double GeneralPathSuffStatMultipleMatrixMixtureProfileProcess::LogStatProb(int site, int cat) {
double total = 0;
int l = GetSubAlloc(site);
SubMatrix* mat = matrixarray[cat][l];
const double* stat = mat->GetStationary();
int rootstate = GetSiteRootState(site);
if (rootstate != -1) {
total += log(stat[GetSiteRootState(site)]);
map<int,double>& waitingtime = GetSiteWaitingTime(site);
for (map<int,double>::iterator i = waitingtime.begin(); i!= waitingtime.end(); i++) {
total += i->second * (*mat)(i->first,i->first);
}
map<pair<int,int>, int>& paircount = GetSitePairCount(site);
for (map<pair<int,int>, int>::iterator i = paircount.begin(); i!= paircount.end(); i++) {
total += i->second * log((*mat)(i->first.first, i->first.second));
}
}
return total;
}
vector<SubMatrix> matrix3DFinder(int*** matrix, int sizeX,int sizeY, int sizeZ, int ignValue, int radius)
{
VectorQueue vctQ,tmpQ;
SubMatrix sb;
int xMax,yMax,zMax,xMin,yMin,zMin;
vector<SubMatrix> subMatrixVect;
int i,j,k;
i=j=k=0;
int subSizeX;
int subSizeY;
int subSizeZ;
while (k<sizeZ)
{
while(i<sizeY)
{
while(j<sizeX)
{
if((matrix[j][i][k]!= ignValue) && (matrix[j][i][k]>0))
{
while(!vctQ.isEmpty())
vctQ.pop();
vctQ.push(j,i,k);
matrix[j][i][k]-=2*matrix[j][i][k];
tmpQ=neighbour3D(matrix,ignValue, radius,vctQ);
xMax=sb.getMax(tmpQ.x);
yMax=sb.getMax(tmpQ.y);
zMax=sb.getMax(tmpQ.z);
xMin=sb.getMin(tmpQ.x);
yMin=sb.getMin(tmpQ.y);
zMin=sb.getMin(tmpQ.z);
sb.xPos=xMin;
sb.yPos=yMin;
sb.zPos=zMin;
subSizeX=xMax-xMin+1+2*radius;
subSizeY=yMax-yMin+1+2*radius;
subSizeZ=zMax-zMin+1+2*radius;
sb.size=subSizeX*subSizeY*subSizeZ;
sb.xSize=subSizeX;
sb.ySize=subSizeY;
sb.zSize=subSizeZ;
sb.subMatrixCreation3D(matrix,subSizeX,subSizeY,subSizeZ,xMin,yMin,zMin,tmpQ,ignValue,radius);
subMatrixVect.push_back(sb);
}
++j;
}
j=0;
++i;
}
i=0;
k++;
}
return subMatrixVect;
}
int main( int argc, char** argv ) {
if ( argc == 6 || argc == 7 ) {
const char* config = argv[1];
const char* model = argv[2];
const char* data = argv[3];
int order = atoi( argv[4] );
int batch = atoi( argv[5] );
float lnZ = 0.0f;
if ( argc > 6 ) {
lnZ = atof( argv[6] );
ASSERT( lnZ > 0.0f );
}
BatchConstructor bc( data, order, batch, 0, false );
Network network( config );
network.LoadParam( model );
Matrix placeholder;
Matrix buffer;
double loss = 0.0;
int nExample = 0;
while( bc.HasNext() ) {
bc.PrepareNext();
const SubMatrix input = bc.GetInput();
const SubMatrix target = bc.GetTarget();
ExtraInfo info( input.Rows(),
bc.GetSentenceLength(),
false,
target, // actually not used
placeholder ); // not used either
network.Prepare( info );
const MatrixBase& output = network.Compute( input );
if ( lnZ == 0.0f ) {
loss += output.Xent( target );
nExample += output.Rows();
}
else {
buffer.Reshape( output.Rows(), output.Columns() );
buffer.Copy( output );
buffer.Shift( -lnZ );
buffer.Exp( buffer );
loss += buffer.Xent( target );
nExample += output.Rows();
}
}
double avgLoss = loss / (double)nExample;
double ppl = exp(avgLoss);
cout << right
<< CurrentTime() << ") average cross-entropy loss of " << nExample
<< " examples: " << KGRN << avgLoss << KNRM << " or "
<< KGRN << ppl << KNRM << " in PPL " << endl;
return EXIT_SUCCESS;
}
else {
cerr << KRED;
cerr << "Usag: " << argv[0] << " <config> <model> <numeric-data> <order> <batch-size> [lnZ]" << endl;
cerr << " <config> : network configuration" << endl;
cerr << " <model> : trained model corresponding to config" << endl;
cerr << " <numeric-data> : data set to be evaluated, in numeric form" << endl;
cerr << " <order> : length of context window" << endl;
cerr << " <batch-size> : mini-batch size" << endl;
cerr << " [lnZ] : optional, if set, softmax is not applied" << endl;
cerr << KNRM;
exit( EXIT_FAILURE );
}
}
