vf1D getWeights(DSL_network &network, string &childName) {
int childIdx = network.FindNode(childName.c_str());
DSL_node* node = network.GetNode(childIdx);
int handle = node->Handle();
DSL_nodeDefinition *def = node->Definition();
const DSL_Dmatrix &cpt = *def->GetMatrix();
const DSL_intArray &parents = network.GetParents(handle);
int parentCount = parents.NumItems();
DSL_intArray coords;
unsigned int colSize = def->GetNumberOfOutcomes();
unsigned int rowSize = cpt.GetSize() / colSize;
vf1D weights(rowSize, 0.0);
unsigned int rowIdx = 0;
for (int elemIdx = 0; elemIdx < cpt.GetSize(); elemIdx += colSize) {
cpt.IndexToCoordinates(elemIdx, coords);
double mult = 1.0;
for (int parentIdx = 0; parentIdx < parentCount; parentIdx ++) {
DSL_node *parentNode = network.GetNode(parents[parentIdx]);
const DSL_Dmatrix &parent_cpt = *parentNode->Definition()->GetMatrix();
mult *= parent_cpt[coords[parentIdx]];
}
weights[rowIdx++] = mult;
}
return weights;
}
vf2D getCPTArray(DSL_network &network, string &childName) {
//DSL_network* net = node->Network(); // node network
int childIdx = network.FindNode(childName.c_str());
DSL_node* node = network.GetNode(childIdx);
DSL_nodeDefinition *def = node->Definition();
const DSL_Dmatrix &cpt = *def->GetMatrix();
DSL_intArray coords;
unsigned int colSize = def->GetNumberOfOutcomes();
unsigned int rowSize = cpt.GetSize() / colSize;
vf2D cpt2(rowSize , vf1D(colSize, 0.0));
unsigned int colIdx = 0;
unsigned int rowIdx = 0;
for (int elemIdx = 0; elemIdx < cpt.GetSize(); elemIdx ++) {
cpt2[rowIdx][colIdx] = cpt[elemIdx];
++colIdx;
if(colIdx == colSize) {
colIdx = 0;
++rowIdx;
}
}
return cpt2;
}
CBNet* ConvertFromDSLNet(const std::string& filename)
{
DSL_network dslNet;
if( dslNet.ReadFile(const_cast<char*>(dslFilename(filename).c_str()))
!= DSL_OKAY )
{
std::cout << " can't read DSL model file named "
<< dslFilename(filename).c_str() << std::endl;
return NULL;
}
// Convert DSL to PNL
DSLPNLConverter DPConverter;
CBNet* pnlNet;
pnlNet = DPConverter.CreateBNet(dslNet);
if( pnlNet == NULL )
{
std::cout << " Conversion DSL->PNL failed. " << std::endl;
return NULL;
}
return pnlNet;
}
int main(int argc, char* argv[]) {
ios_base::sync_with_stdio(0);
string data_infile = string(argv[1]);
string network_infile = string(argv[2]);
string child_name = string("C1");
if (argv[3] == string("EM") || argv[3] == string("Smile")) {
DSL_network net = LearnParamsEM(data_infile, network_infile, child_name);
int childIdx = net.FindNode(child_name.c_str());
DSL_node* childNode = net.GetNode(childIdx);
if (argv[3] == string("Smile")) {
childNode->ChangeType(DSL_NOISY_MAX);
}
//printCPT(childNode);
} else if (argv[3] == string("Naive")) {
DSL_network net = LearnParamsNaive(data_infile, network_infile, child_name);
//int childIdx = net.FindNode(child_name.c_str());
//DSL_node* childNode = net.GetNode(childIdx);
//printCPT(childNode);
} else if (argv[3] == string("Gauss")) {
DSL_network net = LearnParamsGaussJordan(data_infile, network_infile, child_name);
//int childIdx = net.FindNode(child_name.c_str());
//DSL_node* childNode = net.GetNode(childIdx);
//printCPT(childNode);
} else if (argv[3] == string("NvGJ")) {
DSL_network netGJ = LearnParamsGaussJordan(data_infile, network_infile, child_name);
DSL_network netNaive = LearnParamsNaive(data_infile, network_infile, child_name);
DSL_network netEM = LearnParamsEM(data_infile, network_infile, child_name);
DSL_network netOriginal = OpenNetwork(network_infile);
vf1D weights = getWeights(netOriginal, child_name);
vf2D cptGJ = getCPTArray(netGJ, child_name);
vf2D cptNaive = getCPTArray(netNaive, child_name);
vf2D cptEM = getCPTArray(netEM, child_name);
vf2D cptOriginal = getCPTArray(netOriginal, child_name);
cout << "Gauss:" << EuclidianDistance( cptOriginal, cptGJ, weights) << endl;
cout << "Naive:" << EuclidianDistance( cptOriginal, cptNaive, weights) << endl;
cout << "EM:" << EuclidianDistance( cptOriginal, cptEM, weights) << endl;
//cout << "Euclidian distance (orig vs GJ): " << EuclidianDistance(original, netGJ, child_name) << endl;
//cout << "Euclidian distance (orig vs Naive): " << EuclidianDistance(original, netNaive, child_name) << endl;
//int childIdx = net.FindNode(child_name.c_str());
}
return 0;
}
DSL_network OpenNetwork(string network_infile) {
DSL_network originalNet;
if (originalNet.ReadFile(network_infile.c_str(), DSL_XDSL_FORMAT) != DSL_OKAY) {
cout << "Cannot read network... exiting." << endl;
exit(1);
}
return originalNet;
}
void generateDatafile(int n, string inname) {
DSL_network theNet;
theNet.ReadFile(inname.c_str());
int cancer = theNet.FindNode("LungCancer");
DSL_node *node = theNet.GetNode(cancer);
cptMap cpt1 = get_cptmap(node);
keyMap km1;
km1[string("Smoker")] = string("True");
km1[string("Genetic")] = string("True");
km1[string("CoalWorker")] = string("True");
km1[string("BadDiet")] = string("True");
printMap(km1);
cout << "SIZE: "<< cpt1.size() << endl;
cout << cpt1[km1]["True"];
}
DSL_network LearnParamsEM(string data_infile, string network_infile, string child_name) {
DSL_dataset ds;
if (ds.ReadFile(data_infile.c_str()) != DSL_OKAY) {
cout << "Cannot read data file... exiting." << endl;
exit(1);
}
DSL_network originalNet;
if (originalNet.ReadFile(network_infile.c_str(), DSL_XDSL_FORMAT) != DSL_OKAY) {
cout << "Cannot read network... exiting." << endl;
exit(1);
}
int childIdx = originalNet.FindNode(child_name.c_str());
originalNet.GetNode(childIdx)->ChangeType(DSL_CPT);
vector<DSL_datasetMatch> matches;
string err;
if (ds.MatchNetwork(originalNet, matches, err) != DSL_OKAY) {
cout << "Cannot match network... exiting." << endl;
exit(1);
}
DSL_em em;
em.SetUniformizeParameters(true);
em.SetRandomizeParameters(true);
em.SetSeed(0);
em.SetEquivalentSampleSize(1);
if (em.Learn(ds, originalNet, matches) != DSL_OKAY) {
cout << "Cannot learn parameters... exiting." << endl;
exit(1);
}
return originalNet;
}
void printCPT(DSL_node *node) {
DSL_network* net = node->Network(); // node network
int handle = node->Handle();
DSL_nodeDefinition *def = node->Definition();
const DSL_Dmatrix &cpt = *def->GetMatrix();
const DSL_idArray &outcomes = *def->GetOutcomesNames();
const DSL_intArray &parents = net->GetParents(handle);
int parentCount = parents.NumItems();
DSL_intArray coords;
// for (int elemIdx = 0; elemIdx < cpt.GetSize(); elemIdx ++) { for (int parentIdx = 0; parentIdx < parentCount; parentIdx ++){ } }
for (int elemIdx = 0; elemIdx < cpt.GetSize(); elemIdx ++) {
string name = "";
cpt.IndexToCoordinates(elemIdx, coords);
//cout << "P(" << node->GetId() << " = " << outcomes[coords[parentCount]] << " | ";
for (int parentIdx = 0; parentIdx < parentCount; parentIdx ++) {
DSL_node *parentNode = net->GetNode(parents[parentIdx]);
if(elemIdx == 0) {
cout << parentNode->GetId()<< " ";
if(parentIdx == parentCount-1) {
cout<< node->GetId() <<endl;
}
}
const DSL_idArray &parentStates = *parentNode->Definition()->GetOutcomesNames();
//cout << parentNode->GetId() << " = " << parentStates[coords[parentIdx]];
name += parentStates[coords[parentIdx]];
name += " ";
}
name += outcomes[coords[parentCount]];
cout << name << " " << cpt[elemIdx] << endl;
//cout << ") = " << cpt[elemIdx] << endl;
}
}
cptMap get_cptmap(DSL_node *node) {
DSL_network* net = node->Network(); // node network
int handle = node->Handle();
DSL_nodeDefinition *def = node->Definition();
const DSL_Dmatrix &cpt = *def->GetMatrix();
const DSL_idArray &outcomes = *def->GetOutcomesNames();
const DSL_intArray &parents = net->GetParents(handle);
int parentCount = parents.NumItems();
DSL_intArray coords;
cptMap cptmap;
for (int elemIdx = 0; elemIdx < cpt.GetSize(); elemIdx ++) {
cpt.IndexToCoordinates(elemIdx, coords);
//cout << "P(" << node->GetId() << " = " << outcomes[coords[parentCount]] << " | ";
keyMap km;
for (int parentIdx = 0; parentIdx < parentCount; parentIdx ++) {
// if (parentIdx > 0) cout << ", ";
DSL_node *parentNode = net->GetNode(parents[parentIdx]);
const DSL_idArray &parentStates = *parentNode->Definition()->GetOutcomesNames();
km[string(parentNode->GetId())] = string(parentStates[coords[parentIdx]]);
//cout << parentNode->GetId() << " = " << parentStates[coords[parentIdx]];
}
//printMap(km);
if (cptmap.count(km) == 0){
valMap vm;
vm[string(outcomes[coords[parentCount]])] = cpt[elemIdx];
cptmap[km] = vm;
} else {
cptmap[km][string(outcomes[coords[parentCount]])] = cpt[elemIdx];
}
//cout << ") = " << cpt[elemIdx] << endl;
}
return cptmap;
}
string unrollNetwork(string theNet, int stepNumber){
DSL_network net;
net.ReadFile(theNet.c_str());
// Unroll DBN for user specific timestep number
net.SetNumberOfSlices(stepNumber);
// Save unrolled DBN to a file.
DSL_network unrolled;
std::vector< int > dontcare;
net.UnrollNetwork(unrolled,dontcare);
string resNet = theNet.insert(theNet.find_last_of("."), "_Unrolled");
unrolled.WriteFile(resNet.c_str());
return resNet;
}
LearningInfo(string data_infile, string network_infile, string child_name) {
if (dataSet.ReadFile(data_infile.c_str()) != DSL_OKAY) {
cout << "Cannot read data file... exiting." << endl;
exit(1);
}
if (originalNet.ReadFile(network_infile.c_str(), DSL_XDSL_FORMAT) != DSL_OKAY) {
cout << "Cannot read network... exiting." << endl;
exit(1);
}
string err;
if (dataSet.MatchNetwork(originalNet, matches, err) != DSL_OKAY) {
cout << "Cannot match network... exiting." << endl;
exit(1);
}
for(unsigned int i=0 ; i < matches.size() ; ++i) {
matchNetToData[matches[i].node] = matches[i].column;
matchDataToNet[matches[i].column] = matches[i].node;
}
childIdx = originalNet.FindNode(child_name.c_str());
childNode = originalNet.GetNode(childIdx);
if (childNode->Definition()->GetType() != (DSL_CHANCE | DSL_DISCRETE | DSL_NOISY_MAX) ) {
cout << "Child should be a NoisyMAX... exiting" << endl;
// ewentualnie zmienic na noisy-max ręcznie
exit(1);
}
childMAXDefinition = new DSL_noisyMAX(*(childNode->Definition()));
DSL_intArray &parents = originalNet.GetParents(childNode->Handle());
numberOfParents = parents.NumItems();
parentIndices = vector<int>(numberOfParents, 0);
for(int i=0; i<numberOfParents; ++i)
parentIndices[i] = parents[i];
childDimension = childNode->Definition()->GetNumberOfOutcomes();
parentDimensions = vector<int>(numberOfParents, 0);
sumParentDimensions = 0;
parentOutcomesStrengths = vector<DSL_intArray>(numberOfParents);
minimalNumberOfParameters = 1; // minimal number of unique parameters to calculate (count leak right away)
for(int parentIdx = 0 ; parentIdx < numberOfParents ; ++parentIdx) {
DSL_node *parentNode = originalNet.GetNode(parentIndices[parentIdx]);
sumParentDimensions += (parentDimensions[parentIdx] = parentNode->Definition()->GetNumberOfOutcomes()); //parent dimension is equal to the number of outcomes
parentOutcomesStrengths[parentIdx] = childMAXDefinition->GetParentOutcomeStrengths(parentIdx);
//for (int stateIdx=0 ; stateIdx < parentDimensions[parentIdx] ; ++stateIdx)
// cout << parentOutcomesStrengths[parentIdx][stateIdx] << " ";
//cout << endl;
minimalNumberOfParameters += parentDimensions[parentIdx] - 1; // (each parent dimension reduced by one) because we don't count distinguished states of parents
distinguishedStates[parentIdx] = parentOutcomesStrengths[parentIdx][parentDimensions[parentIdx] - 1];
}
int sumOffset = 0;
parameterRowOffset = vi1D(numberOfParents + 1, 0); // +1 so we know the offset for LEAK column
for(int parentIdx = 0; parentIdx < numberOfParents ; ++parentIdx) {
parameterRowOffset[parentIdx] = sumOffset;
sumOffset += parentDimensions[parentIdx] - 1;
}
parameterRowOffset[numberOfParents] = sumOffset;
parametersRowLength = minimalNumberOfParameters;
minimalNumberOfParameters *= (childDimension - 1); // number of unique rows, last row is always 1.0 - sum
// DEBUG(minimalNumberOfParameters);
// DEBUG(childDimension);
// DEBUGV(parentDimensions);
// DEBUGV(parameterRowOffset);
//for(int j=0; j< 7 ; ++j) {
// DSL_datasetVarInfo vi = ds.GetVariableInfo(j);
// cout << "discreete:" << vi.discrete << " id:" << vi.id << endl << " missingInt:" << vi.missingInt << " mF:" << vi.missingFloat << "snames:"<< endl;
// for(int i=0;i<vi.stateNames.size(); ++i)
// cout << vi.stateNames[i]<< " ";
// cout <<endl;
//}
//for(int i = 0; i < ds.GetNumberOfRecords(); ++i) {
// vector<int> row(ds.GetNumberOfVariables(), 0);
// int sum_ones = 0;
// for(int j = 0; j < ds.GetNumberOfVariables(); ++j) {
// sum_ones += (row[j] = ds.GetInt(j,i));
// }
//}
//vector<int> rd = ds.GetIntData(0);
//cout <<"RDSize:"<<rd.size()<< endl;
//for(int i=0;i<rd.size();++i) {
// cout << vi.stateNames[rd[i]] << endl;
//}
//
}
void DSLPNLConverter::CreateFactors(DSL_network& dslNet, CBNet* pnlBNet)
{
int i,j,k;
// Read number of nodes in the net
int numberOfNodes = dslNet.GetNumberOfNodes();
// This is a way PNL likes it
pnlBNet->AllocFactors();
DSL_Dmatrix* dslMatrix;
CCPD* pnlCPD;
for (i=0;i<numberOfNodes;i++)
{
// Get parents of the ith node
// IMPORTANT -- we should preserve order from DSL_network, since
// probabilities will be according DSL ordering
DSL_intArray dslParents;
dslParents = dslNet.GetParents(dslNet.FindNode(theIds[i]));
// establish sizes and allocate memory
int numberOfNodesInDomain = dslParents.NumItems() + 1;
int* domain = new int[numberOfNodesInDomain];
CNodeType** nodeTypes = new CNodeType*[numberOfNodesInDomain];
// establish members of the domain
for (j=0;j<numberOfNodesInDomain-1;j++)
domain[j] = dslParents[j];
domain[numberOfNodesInDomain-1] = i;
// Fill up node types
for (j=0;j<numberOfNodesInDomain;j++)
nodeTypes[j] = const_cast <CNodeType*> (pnlBNet->GetNodeType(domain[j]));
// Read CPT from SMILE
dslNet.GetNode(dslNet.FindNode(theIds[i]))->Definition()->GetDefinition(&dslMatrix);
// Alloc space for CPT
int sizeOfCPT = dslMatrix->GetSize();
float* flatCPT = new float[sizeOfCPT];
// Here we convert 'copy' numbers from SMILE to PNL
// The painful part is convert double to float.
// Additionally we check if after conversion they sum-up to 1
int numberOfMyStates = nodeTypes[numberOfNodesInDomain-1]->GetNodeSize();
int iterations = sizeOfCPT/numberOfMyStates;
for (j=0;j<iterations;j++)
{
float sum = 0.0f;
for (k=0;k<numberOfMyStates;k++)
{
flatCPT[j*numberOfMyStates+k] = static_cast <float> (dslMatrix->Subscript(j*numberOfMyStates+k));
sum += flatCPT[j*numberOfMyStates+k];
}
if (sum!=1.0f)
{
for (k=0;k<numberOfMyStates;k++)
flatCPT[j*numberOfMyStates+k] /= sum;
}
}
#ifdef DSLPNL_DEBUG
std::cerr << "Node "<< i << " domain : ";
for (j=0;j<numberOfNodesInDomain;j++)
{
std::cerr << domain[j] << " ";
}
std::cerr << std::endl;
for (j=0;j<sizeOfCPT;j++)
std::cerr << flatCPT[j] << " ";
std::cerr << std::endl;
#endif
CModelDomain* pMD = pnlBNet->GetModelDomain();
pnlCPD = CTabularCPD::Create(domain, numberOfNodesInDomain, pMD, flatCPT);
if (pnlCPD==NULL)
{
std::cout << "We got a problem with creating CPD" << std::endl;
return;
}
pnlBNet->AttachFactor(pnlCPD);
delete[] nodeTypes;
delete[] domain;
delete[] flatCPT;
}
}
string dynamicEMTraining(string theNet, string trainingSet){
// open the data set:
DSL_dataset ds;
if (ds.ReadFile(trainingSet.c_str()) != DSL_OKAY) {
cout << "Cannot read data file... exiting." << endl;
exit(1);
}
// open the network:
DSL_network net;
if (net.ReadFile(theNet.c_str(), DSL_XDSL_FORMAT) != DSL_OKAY) {
cout << "Cannot read network... exiting." << endl;
exit(1);
}
// match the data set and the network (variables):
vector<DSL_datasetMatch> dsMap(ds.GetNumberOfVariables());
int varCnt = 0; // the number of variables occuring both in the data set and the network
for (int i = 0; i < ds.GetNumberOfVariables(); i++) {
string id = ds.GetId(i);
const char* idc = id.c_str();
bool done = false;
for (int j = 0; j < (int) strlen(idc) && !done; j++) {
if (idc[j] == '_') {
char* nodeId = (char*) malloc((j+1) * sizeof(char));
strncpy(nodeId, idc, j);
nodeId[j] = '\0';
int nodeHdl = net.FindNode(nodeId);
if (nodeHdl >= 0) {
DSL_intArray orders;
net.GetTemporalOrders(nodeHdl, orders);
dsMap[varCnt].node = nodeHdl;
dsMap[varCnt].slice = atoi(idc + j + 1);
dsMap[varCnt].column = i;
varCnt++;
free(nodeId);
done = true;
}
}
}
if (!done) {
int nodeHdl = net.FindNode(idc);
if (nodeHdl >= 0) {
dsMap[varCnt].node = nodeHdl;
dsMap[varCnt].slice = 0;
dsMap[varCnt].column = i;
varCnt++;
}
}
}
dsMap.resize(varCnt);
// match the data set and the network (states):
for (int i = 0; i < dsMap.size(); i++) {
DSL_datasetMatch &m = dsMap[i];
int nodeHdl = m.node;
int colIdx = m.column;
DSL_idArray* ids = net.GetNode(nodeHdl)->Definition()->GetOutcomesNames();
const DSL_datasetVarInfo &varInfo = ds.GetVariableInfo(colIdx);
const vector<string> &stateNames = varInfo.stateNames;
vector<int> map(stateNames.size(), -1);
for (int j = 0; j < (int) stateNames.size(); j++) {
const char* id = stateNames[j].c_str();
for (int k = 0; k < ids->NumItems(); k++) {
char* tmpid = (*ids)[k];
if (!strcmp(id, tmpid)) {
map[j] = k;
}
}
}
for (int k = 0; k < ds.GetNumberOfRecords(); k++) {
if (ds.GetInt(colIdx, k) >= 0) {
ds.SetInt(colIdx, k, map[ds.GetInt(colIdx, k)]);
}
}
}
// learn parameters:
DSL_em em;
if (em.Learn(ds, net, dsMap) != DSL_OKAY) {
cout << "Cannot learn parameters... exiting." << endl;
exit(1);
}
net.WriteFile((theNet.insert(theNet.find_last_of("/") + 1, "res_")).c_str(), DSL_XDSL_FORMAT);
return theNet;
}