int main(int argc, char* argv[]) {
LogisticRegression lr;
LogisticRegressionScoreTest lrst;
LogisticRegressionPermutationTest lrpt;
Vector y;
Matrix x;
Matrix cov;
LoadVector("input.y", y);
LoadMatrix("input.x", x);
LoadMatrix("input.cov", cov);
Matrix xall;
xall = x;
xall.StackRight(cov); // 1 + x + cov
if (lr.FitLogisticModel(xall, y, 100) == false) {
fprintf(stderr, "Fitting failed!\n");
return -1;
}
Vector& beta = lr.GetCovEst();
Matrix& v = lr.GetCovB();
Vector& pWald = lr.GetAsyPvalue();
fprintf(stdout, "wald_beta\t");
Print(beta);
fputc('\n', stdout);
fprintf(stdout, "wald_vcov\t");
Print(v);
fputc('\n', stdout);
fprintf(stdout, "wald_p\t");
Print(pWald[1]);
fputc('\n', stdout);
if (lrpt.FitLogisticModelCov(xall, 1, y, 2000, -1) == false) {
fprintf(stderr, "Fitting failed!\n");
return -1;
}
fprintf(stdout, "permutation_p\t");
double permu_p = lrpt.getPvalue();
Print(permu_p);
fputc('\n', stdout);
if (lrst.FitLogisticModel(xall, y, 1, 100) == false) {
fprintf(stderr, "Fitting failed!\n");
return -1;
}
fprintf(stdout, "score_p\t");
double score_p = lrst.GetPvalue();
Print(score_p);
fputc('\n', stdout);
return 0;
};
TEST_F(LR_Separable_Test, test_separable) {
LogisticRegression lr;
int separableColumn = lr.dataIsSeparable(cov, response);
ASSERT_EQ( separableColumn, 0);
}
int main (void)
{
cout << "Hello world for Logistic Regression" << endl;
LogisticRegression toDo;
toDo.Test ();
return 0;
}
int main(int argc, char *argv[])
{
time_t now = time(0);
printf("chisq p = 0.05 cutoff = %f",chidist(3.84, 1.0));
printf("Start analysis at %s \n", ctime(&now));
/*
Matrix a(2,2);
a[0][0] = 1.0;
a[1][1] = 1.0;
a[0][1] = a[1][0] = 0.5;
SVD svd;
svd.InvertInPlace(a);
for (int i = 0; i < a.rows; i ++) {
for (int j = 0; j < a.cols; j ++) {
std::cout << "a[" << i << "]" << "[" << j << "]" << a[i][j] << "\t";
}
std::cout << "\n";
}
return 0;
*/
Matrix X;
String Xinput = "ExampleX.test";
Vector Y;
String Yinput = "ExampleY.test";
if (loadMatrix(X,Xinput) || loadVector(Y, Yinput)) {
fprintf(stderr, "Data loading problem!\n");
exit(1);
}
LogisticRegression lr;
if (lr.FitLogisticModel(X, Y, 30) ) {
printf("fit all right!\n");
} else {
printf("fit failed\n");
}
now = time(0);
printf("Finsihed analysis at %s \n", ctime(&now));
LogisticRegressionScoreTest lrst;
int Xcol = 1;
lrst.FitLogisticModel(X,Y,Xcol,30);
printf("score p-value is: %lf \n", lrst.getPvalue());
Vector& pvalue = lr.GetAsyPvalue();
printf("wald p-value is: %lf \n", pvalue[Xcol]);
return 0;
}
int main()
{
double alpha = 0.001;
int iters = 10000;
LogisticRegression lr;
lr.readData("input.txt");
lr.gradientDescent(alpha, iters);
int n = _getch();
return 1;
}
void PosteriorEstimator::estimate(vector<pair<double, bool> >& combined,
LogisticRegression& lr) {
// switch sorting order
if (!reversed) {
reverse(combined.begin(), combined.end());
}
vector<double> medians;
vector<unsigned int> negatives, sizes;
binData(combined, medians, negatives, sizes);
lr.setData(medians, negatives, sizes);
lr.roughnessPenaltyIRLS();
// restore sorting order
if (!reversed) {
reverse(combined.begin(), combined.end());
}
}
void PosteriorEstimator::estimatePEP(
vector<pair<double, bool> >& combined,
double pi0, vector<double>& peps,
bool include_negative) {
// Logistic regression on the data
size_t nTargets = 0, nDecoys = 0;
LogisticRegression lr;
estimate(combined, lr);
vector<double> xvals(0);
vector<pair<double, bool> >::const_iterator elem = combined.begin();
for (; elem != combined.end(); ++elem)
if (elem->second) {
xvals.push_back(elem->first);
++nTargets;
} else {
if (include_negative) {
xvals.push_back(elem->first);
}
++nDecoys;
}
lr.predict(xvals, peps);
#define OUTPUT_DEBUG_FILES
#undef OUTPUT_DEBUG_FILES
#ifdef OUTPUT_DEBUG_FILES
ofstream drFile("decoyRate.all", ios::out), xvalFile("xvals.all", ios::out);
ostream_iterator<double> drIt(drFile, "\n"), xvalIt(xvalFile, "\n");
copy(peps.begin(), peps.end(), drIt);
copy(xvals.begin(), xvals.end(), xvalIt);
#endif
double factor = pi0 * ((double)nTargets / (double)nDecoys);
double top = min(1.0, factor
* exp(*max_element(peps.begin(), peps.end())));
vector<double>::iterator pep = peps.begin();
bool crap = false;
for (; pep != peps.end(); ++pep) {
if (crap) {
*pep = top;
continue;
}
*pep = factor * exp(*pep);
if (*pep >= top) {
*pep = top;
crap = true;
}
}
partial_sum(peps.rbegin(), peps.rend(), peps.rbegin(), mymin);
}
int main(int argc,char **argv)
{
if(argc!=6)
{
cerr<<"usage: ";
cout<<argv[0]<<" train_feature_data test_feature_data regularization_parameter bias_parameter feature_config"<<endl;
return -1;
}
int rank,size;
MPI_Init(&argc,&argv);
MPI_Comm_rank(MPI_COMM_WORLD,&rank);
MPI_Comm_size(MPI_COMM_WORLD,&size);
// string train_data=string(argv[1])+string(".")+CommonTool::to_string(rank);
// string test_data=string(argv[2])+string(".")+CommonTool::to_string(rank);
bool split=true;
string train_data=string(argv[1]);
string test_data=string(argv[2]);
LogisticRegression LR;
LR.set_mpirank(rank);
LR.set_mpisize(size);
if(rank==0)
{
cerr<<" mpi rank="<<rank<<" mpi size="<<size<<endl;
time_t t=time(0);
cerr<<"start process:"<<asctime(localtime(&t))<<endl;
}
// LR.read_dataset("data/train.feature.filter","conf/overall.conf");
// LR.init_data_buffer("data/train.feature.filter");
LR.init_data_buffer(train_data,test_data,split);
string parameters;
float lambda=atof(argv[3]);
float bias=atof(argv[4]);
string feature_conf(argv[5]);
int status=LR.optimize(feature_conf,string("model/para"),parameters,lambda,bias);
if(rank==0)
{
cerr<<"LBFGS status:"<<status<<endl;
time_t t=time(0);
cerr<<"end process:"<<asctime(localtime(&t))<<endl;
}
MPI_Finalize();
return 0;
}
void PosteriorEstimator::estimatePEPGeneralized(
vector<pair<double, bool> >& combined,
vector<double>& peps,
bool include_negative) {
// Logistic regression on the data
size_t nTargets = 0, nDecoys = 0;
LogisticRegression lr;
estimate(combined, lr);
vector<double> xvals(0);
vector<pair<double, bool> >::const_iterator elem = combined.begin();
for (; elem != combined.end(); ++elem) {
xvals.push_back(elem->first);
if (elem->second) {
++nTargets;
} else {
if (include_negative) {
xvals.push_back(elem->first);
}
++nDecoys;
}
}
lr.predict(xvals, peps);
#ifdef OUTPUT_DEBUG_FILES
ofstream drFile("decoyRate.all", ios::out), xvalFile("xvals.all", ios::out);
ostream_iterator<double> drIt(drFile, "\n"), xvalIt(xvalFile, "\n");
copy(peps.begin(), peps.end(), drIt);
copy(xvals.begin(), xvals.end(), xvalIt);
#endif
double top = exp(*max_element(peps.begin(), peps.end()));
top = top/(1+top);
bool crap = false;
vector<double>::iterator pep = peps.begin();
for (; pep != peps.end(); ++pep) {
if (crap) {
*pep = top;
continue;
}
// eg = p/(1-p)
// eg - egp = p
// p = eg/(1+eg)
double eg = exp(*pep);
*pep = eg/(1+eg);
if (*pep >= top) {
*pep = top;
crap = true;
}
}
partial_sum(peps.rbegin(), peps.rend(), peps.rbegin(), mymin);
double high = *max_element(peps.begin(), peps.end());
double low = *min_element(peps.begin(), peps.end());
assert(high>low);
if (VERB > 2) {
cerr << "Highest generalized decoy rate =" << high
<< ", low rate = " << low << endl;
}
pep = peps.begin();
for (; pep != peps.end(); ++pep) {
*pep = (*pep - low)/(high-low);
}
}
bool train( CommandLineParser &parser ){
infoLog << "Training regression model..." << endl;
string trainDatasetFilename = "";
string modelFilename = "";
string defaultFilename = "linear-regression-model.grt";
bool removeFeatures = false;
bool defaultRemoveFeatures = false;
//Get the filename
if( !parser.get("filename",trainDatasetFilename) ){
errorLog << "Failed to parse filename from command line! You can set the filename using the -f." << endl;
printUsage();
return false;
}
//Get the model filename
parser.get("model-filename",modelFilename,defaultFilename);
//Load the training data to train the model
RegressionData trainingData;
infoLog << "- Loading Training Data..." << endl;
if( !trainingData.load( trainDatasetFilename ) ){
errorLog << "Failed to load training data!\n";
return false;
}
const unsigned int N = trainingData.getNumInputDimensions();
const unsigned int T = trainingData.getNumTargetDimensions();
infoLog << "- Num training samples: " << trainingData.getNumSamples() << endl;
infoLog << "- Num input dimensions: " << N << endl;
infoLog << "- Num target dimensions: " << T << endl;
//Create a new regression instance
LogisticRegression regression;
regression.setMaxNumEpochs( 500 );
regression.setMinChange( 1.0e-5 );
regression.setUseValidationSet( true );
regression.setValidationSetSize( 20 );
regression.setRandomiseTrainingOrder( true );
regression.enableScaling( true );
//Create a new pipeline that will hold the regression algorithm
GestureRecognitionPipeline pipeline;
//Add a multidimensional regression instance and set the regression algorithm to Linear Regression
pipeline.setRegressifier( MultidimensionalRegression( regression, true ) );
infoLog << "- Training model...\n";
//Train the classifier
if( !pipeline.train( trainingData ) ){
errorLog << "Failed to train model!" << endl;
return false;
}
infoLog << "- Model trained!" << endl;
infoLog << "- Saving model to: " << modelFilename << endl;
//Save the pipeline
if( pipeline.save( modelFilename ) ){
infoLog << "- Model saved." << endl;
}else warningLog << "Failed to save model to file: " << modelFilename << endl;
infoLog << "- TrainingTime: " << pipeline.getTrainingTime() << endl;
return true;
}
/**
* Run a single likelihood ratio test. Assumes covariates and phenotype are set as global variables.
* The test is performed on the haps vector.
*
* @param haps Haplotype variable. H_0 is that this vector is independant.
* @param ones Set of ones. Precomputed for speed.
* @return ZaykingStatsInfo should contain all information for this likelihood ratio test.
*/
ZaykinStatsInfo Zaykin::runLikelihoodRatio(const vector<double> &haps, const vector<double> &ones){
ZaykinStatsInfo stats;
vector<vector<double> > testVecWithout = cov;
vector<vector<double> > testVecWith; // wait to fill this one.
testVecWithout.push_back(ones);
LogisticRegression lrWith, lrWithout;
vector<vector<double> > inv_infmatrixWithOut, inv_infmatrixWith;
vector<double> betasWith, betasWithOut;
inv_infmatrixWithOut = vecops::getDblVec(testVecWithout.size() , testVecWithout.size());
int retry = 0;
double startVal = 0; // value to start betas with.
while(retry < 3){
try{
betasWithOut = lrWithout.newtonRaphson(testVecWithout, phenotype, inv_infmatrixWithOut, startVal);
break;
}catch(NewtonRaphsonFailureEx){
handleException(stats, startVal, retry, "Unable to compute reduced model in single haplotype test: Newton-Raphson setup failure.");
}catch(NewtonRaphsonIterationEx){
handleException(stats, startVal, retry, "Unable to compute reduced model in single haplotype test: max iterations hit.");
}catch(SingularMatrixEx){
handleException(stats, startVal, retry, "Unable to compute reduced model in single haplotype test: information matrix was singular.");
}catch(ConditionNumberEx){
LogisticRegression lr;
int separableVariable = lr.dataIsSeparable(testVecWithout, phenotype);
string message;
if (separableVariable < 0){
// Error: poor conditioning.
message = "Unable to compute reduced model in single haplotype test: Poor conditioning in information matrix.";
}else{
message = "Unable to compute reduced model in single haplotype test: Separable data matrix.";
}
handleException(stats, startVal, retry, message);
if (retry >= 3) return stats;
}catch(alglib::ap_error err){
stringstream ss;
ss << "Unable to compute reduced model single haplotype test due to linalg exception: " << err.msg;
handleException(stats, startVal, retry, ss.str());
if (retry >= 3) return stats;
}
}
retry = 0;
startVal = 0; // value to start betas with.
testVecWith = testVecWithout;
testVecWith.push_back(haps);
inv_infmatrixWith = vecops::getDblVec(testVecWith.size() , testVecWith.size());
while(retry < 3){
try{
betasWith = lrWith.newtonRaphson(testVecWith, phenotype, inv_infmatrixWith, startVal);
break;
}catch(NewtonRaphsonFailureEx){
handleException(stats, startVal, retry, "Unable to compute full model in single haplotype test: Newton-Raphson setup failure.");
}catch(NewtonRaphsonIterationEx){
handleException(stats, startVal, retry, "Unable to compute full model in single haplotype test: max iterations hit.");
}catch(SingularMatrixEx){
handleException(stats, startVal, retry, "Unable to compute full model in single haplotype test: information matrix was singular.");
}catch(ConditionNumberEx){
LogisticRegression lr;
int separableVariable = lr.dataIsSeparable(testVecWith, phenotype);
string message;
if (separableVariable < 0){
// Error: poor conditioning.
message = "Unable to compute full model in single haplotype test: Poor conditioning in information matrix.";
}else{
message = "Unable to compute full model in single haplotype test: Separable data matrix.";
}
handleException(stats, startVal, retry, message);
if (retry >= 3) return stats;
}catch(alglib::ap_error err){
stringstream ss;
ss << "Unable to compute full model single haplotype test due to linalg exception: " << err.msg;
handleException(stats, startVal, retry, ss.str());
if (retry >= 3) return stats;
}
}
stats.chiSqStat = lrWith.likelihoodRatio(betasWithOut, testVecWithout, betasWith, testVecWith, phenotype);
stats.degFree = betasWith.size() - betasWithOut.size();
double beta = betasWith.at(betasWith.size() - 1);
double stderr = sqrt(inv_infmatrixWith.at(inv_infmatrixWith.size() - 1).at(inv_infmatrixWith.size() - 1));
stats.OR = exp(beta);
stats.LCI = exp(beta - 1.96*stderr);
stats.UCI = exp(beta + 1.96*stderr);
return stats;
}
/**
* Run the global analysis. Put all data and covariates in a logistic regression model.
*
* Compute likelihood ratio statistic.
* This uses a likelihood statistic where n-1 haplotypes are tested.
*
* @return pvalue.
*/
ZaykinGlobalStatsResults Zaykin::runGlobal(){
ZaykinGlobalStatsResults stats;
vector<vector<double> > haps;
vector<double> ones;
prepHaplotypes(ones, haps);
#if DEBUG_ZAY_PROGRESS
cout << "Zaykin start LR portion" << endl;
#endif
LogisticRegression with(params->getRegressionConditionNumberThreshold()), without(params->getRegressionConditionNumberThreshold());
/*
* Run without the haplotypes:
*/
vector<vector<double> > inv_infmatrixWithOut;
vector<double> betasWithOut;
vector<vector<double> > inWithout;
inWithout = cov;
inWithout.push_back(ones);
inv_infmatrixWithOut = vecops::getDblVec(inWithout.size() , inWithout.size());
int retry = 0;
double startVal = 0; // value to start betas with.
while(retry < 3){
try{
betasWithOut = without.newtonRaphson(inWithout, phenotype, inv_infmatrixWithOut, startVal);
break;
}catch(NewtonRaphsonFailureEx){
handleException(stats, startVal, retry, "Unable to compute reduced model: Newton-Raphson setup failure.");
}catch(NewtonRaphsonIterationEx){
handleException(stats, startVal, retry, "Unable to compute reduced model: max iterations hit.");
}catch(SingularMatrixEx){
handleException(stats, startVal, retry, "Unable to compute reduced model: information matrix was singular.");
}catch(ConditionNumberEx err){
LogisticRegression lr;
int separableVariable = lr.dataIsSeparable(inWithout, phenotype);
string message;
if (separableVariable < 0){
// Error: poor conditioning.
stringstream ss;
ss << "Unable to compute reduced model: Poor conditioning in information matrix. ";
ss << "Condition number (1-norm) is " << err.conditionNumber;
message = ss.str();
}else{
stringstream ss;
ss << "Unable to compute reduced model: Separable data matrix.";
ss << "Condition number (1-norm) is " << err.conditionNumber;
message = ss.str();
}
handleException(stats, startVal, retry, message);
if (retry >= 3) return stats;
}catch(ADTException e){
// This one is generic.
string message = "Unable to compute reduced model: Newton-Raphson error.";
handleException(stats, startVal, retry, message);
if (retry >= 3) return stats;
}catch(alglib::ap_error err){
stringstream ss;
ss << "Unable to compute reduced model due to linalg exception: " << err.msg;
handleException(stats, startVal, retry, ss.str());
if (retry >= 3) return stats;
}
}
/*
* Run with the haplotypes:
*/
vector<vector<double> > inv_infmatrixWith, inWith;
vector<double> betasWith;
inWith = inWithout;
for (unsigned int i=0; i < haps.size()-1; i++){ // NOTE: Don't push the very last haplotype.
inWith.push_back(haps.at(i));
}
inv_infmatrixWith = vecops::getDblVec(inWith.size() , inWith.size());
retry = 0;
startVal = 0; // value to start betas with.
while(retry < 3){
try{
betasWith = with.newtonRaphson(inWith, phenotype, inv_infmatrixWith, startVal);
break;
}catch(NewtonRaphsonFailureEx){
handleException(stats, startVal, retry, "Unable to compute full model: Newton-Raphson setup failure.");
}catch(NewtonRaphsonIterationEx){
handleException(stats, startVal, retry, "Unable to compute full model: max iterations hit.");
}catch(SingularMatrixEx){
handleException(stats, startVal, retry, "Unable to compute full model: information matrix was singular.");
}catch(ConditionNumberEx err){
LogisticRegression lr;
int separableVariable = lr.dataIsSeparable(inWith, phenotype);
stringstream ss;
if (separableVariable < 0){
// Error: poor conditioning.
ss << "Unable to compute reduced model: Poor conditioning in information matrix. ";
ss << "Condition number (1-norm) is " << err.conditionNumber;
}else{
ss << "Unable to compute reduced model: Separable data matrix.";
ss << "Condition number (1-norm) is " << err.conditionNumber;
}
string message = ss.str();
handleException(stats, startVal, retry, message);
if (retry >= 3) return stats;
}catch(ADTException e){
string message = "Unable to compute full model: Newton-Raphson error.";
handleException(stats, startVal, retry, message);
if (retry >= 3) return stats;
}catch(alglib::ap_error err){
stringstream ss;
ss << "Unable to compute full model due to linalg exception: " << err.msg;
handleException(stats, startVal, retry,ss.str());
if (retry >= 3) return stats;
}
}
double likeRatio = with.likelihoodRatio(betasWithOut, inWithout, betasWith, inWith, phenotype);
try{
stats.pvalue = Statistics::chi2prob(likeRatio, betasWith.size() - betasWithOut.size());
stats.testStat = likeRatio;
stats.degFreedom = betasWith.size() - betasWithOut.size();
}catch(...){
stringstream ss;
ss << "Zaykin's method: unable to compute chi square: " << likeRatio << " " << betasWith.size() - betasWithOut.size() << endl;
Logger::Instance()->writeLine(ss.str());
stats.fillDefault();
return stats;
}
return stats;
}
int main()
{
LogisticRegression lr;
lr.Test();
return 0;
}
bool train( CommandLineParser &parser ){
infoLog << "Training regression model..." << endl;
string trainDatasetFilename = "";
string modelFilename = "";
float learningRate = 0;
float minChange = 0;
unsigned int maxEpoch = 0;
unsigned int batchSize = 0;
//Get the filename
if( !parser.get("filename",trainDatasetFilename) ){
errorLog << "Failed to parse filename from command line! You can set the filename using the -f." << endl;
printHelp();
return false;
}
//Get the parameters from the parser
parser.get("model-filename",modelFilename);
parser.get( "learning-rate", learningRate );
parser.get( "min-change", minChange );
parser.get( "max-epoch", maxEpoch );
parser.get( "batch-size", batchSize );
infoLog << "settings: learning-rate: " << learningRate << " min-change: " << minChange << " max-epoch: " << maxEpoch << " batch-size: " << batchSize << endl;
//Load the training data to train the model
RegressionData trainingData;
//Try and parse the input and target dimensions
unsigned int numInputDimensions = 0;
unsigned int numTargetDimensions = 0;
if( parser.get("num-inputs",numInputDimensions) && parser.get("num-targets",numTargetDimensions) ){
infoLog << "num input dimensions: " << numInputDimensions << " num target dimensions: " << numTargetDimensions << endl;
trainingData.setInputAndTargetDimensions( numInputDimensions, numTargetDimensions );
}
if( (numInputDimensions == 0 || numTargetDimensions == 0) && Util::stringEndsWith( trainDatasetFilename, ".csv" ) ){
errorLog << "Failed to parse num input dimensions and num target dimensions from input arguments. You must supply the input and target dimensions if the data format is CSV!" << endl;
printHelp();
return false;
}
infoLog << "- Loading Training Data..." << endl;
if( !trainingData.load( trainDatasetFilename ) ){
errorLog << "Failed to load training data!\n";
return false;
}
const unsigned int N = trainingData.getNumInputDimensions();
const unsigned int T = trainingData.getNumTargetDimensions();
infoLog << "- Num training samples: " << trainingData.getNumSamples() << endl;
infoLog << "- Num input dimensions: " << N << endl;
infoLog << "- Num target dimensions: " << T << endl;
//Create a new regression instance
LogisticRegression regression;
regression.setMaxNumEpochs( maxEpoch );
regression.setMinChange( minChange );
regression.setUseValidationSet( true );
regression.setValidationSetSize( 20 );
regression.setRandomiseTrainingOrder( true );
regression.enableScaling( true );
//Create a new pipeline that will hold the regression algorithm
GestureRecognitionPipeline pipeline;
//Add a multidimensional regression instance and set the regression algorithm to Linear Regression
pipeline.setRegressifier( MultidimensionalRegression( regression, true ) );
infoLog << "- Training model...\n";
//Train the classifier
if( !pipeline.train( trainingData ) ){
errorLog << "Failed to train model!" << endl;
return false;
}
infoLog << "- Model trained!" << endl;
infoLog << "- Saving model to: " << modelFilename << endl;
//Save the pipeline
if( pipeline.save( modelFilename ) ){
infoLog << "- Model saved." << endl;
}else warningLog << "Failed to save model to file: " << modelFilename << endl;
infoLog << "- TrainingTime: " << pipeline.getTrainingTime() << endl;
return true;
}
