hex.glm.GLM Maven / Gradle / Ivy
package hex.glm;
import hex.*;
import hex.deeplearning.DeepLearningModel.DeepLearningParameters.MissingValuesHandling;
import hex.glm.GLMModel.*;
import hex.optimization.ADMM.L1Solver;
import hex.optimization.L_BFGS;
import hex.glm.GLMModel.GLMParameters.Family;
import hex.glm.GLMModel.GLMParameters.Link;
import hex.glm.GLMModel.GLMParameters.Solver;
import hex.glm.GLMTask.*;
import hex.gram.Gram;
import hex.gram.Gram.Cholesky;
import hex.gram.Gram.NonSPDMatrixException;
import hex.optimization.ADMM;
import hex.optimization.ADMM.ProximalSolver;
import hex.optimization.L_BFGS.*;
import hex.optimization.OptimizationUtils.*;
import jsr166y.CountedCompleter;
import org.joda.time.format.DateTimeFormat;
import org.joda.time.format.DateTimeFormatter;
import water.*;
import water.exceptions.H2OModelBuilderIllegalArgumentException;
import water.fvec.*;
import water.parser.BufferedString;
import water.util.*;
import water.util.ArrayUtils;
import java.text.DecimalFormat;
import java.text.NumberFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
/**
* Created by tomasnykodym on 8/27/14.
*
* Generalized linear model implementation.
*/
public class GLM extends ModelBuilder {
protected boolean _cv; // flag signalling this is MB for one of the fold-models during cross-validation
static NumberFormat lambdaFormatter = new DecimalFormat(".##E0");
static NumberFormat devFormatter = new DecimalFormat(".##");
public static final int SCORING_INTERVAL_MSEC = 15000; // scoreAndUpdateModel every minute unless socre every iteration is set
public String _generatedWeights = null;
public GLM(boolean startup_once){super(new GLMParameters(),startup_once);}
public GLM(GLMModel.GLMParameters parms) {
super(parms);
init(false);
}
public GLM(GLMModel.GLMParameters parms,Key dest) {
super(parms,dest);
init(false);
}
private transient GLMDriver _driver;
public boolean isSupervised() {
return true;
}
@Override
public ModelCategory[] can_build() {
return new ModelCategory[]{
ModelCategory.Regression,
ModelCategory.Binomial,
};
}
@Override public boolean havePojo() { return true; }
@Override public boolean haveMojo() { return true; }
private double _lambdaCVEstimate = Double.NaN; // lambda cross-validation estimate
private boolean _doInit = true; // flag setting whether or not to run init
private double [] _xval_test_deviances;
private double [] _xval_test_sd;
/**
* GLM implementation of N-fold cross-validation.
* We need to compute the sequence of lambdas for the main model so the folds share the same lambdas.
* We also want to set the _cv flag so that the dependent jobs know they're being run withing CV (so e.g. they do not unlock the models in the end)
* @return Cross-validation Job
* (builds N+1 models, all have train+validation metrics, the main model has N-fold cross-validated validation metrics)
*/
@Override
public void computeCrossValidation() {
// init computes global list of lambdas
init(true);
_cv = true;
if (error_count() > 0)
throw H2OModelBuilderIllegalArgumentException.makeFromBuilder(GLM.this);
super.computeCrossValidation();
}
/**
* If run with lambda search, we need to take extra action performed after cross-val models are built.
* Each of the folds have been computed with ots own private validation datasetd and it performed early stopping based on it.
* => We need to:
* 1. compute cross-validated lambda estimate
* 2. set the lambda estimate too all n-folds models (might require extra model fitting if the particular model stopped too early!)
* 3. compute cross-validated scoring history (cross-validated deviance standard error per lambda)
* 4. unlock the n-folds models (they are changed here, so the unlocking happens here)
*/
@Override
public void cv_computeAndSetOptimalParameters(ModelBuilder[] cvModelBuilders) {
if(_parms._lambda_search) {
_xval_test_deviances = new double[_parms._lambda.length];
_xval_test_sd = new double [_parms._lambda.length];
double bestTestDev = Double.POSITIVE_INFINITY;
int lmin_max = 0;
for (int i = 0; i < cvModelBuilders.length; ++i) {
GLM g = (GLM) cvModelBuilders[i];
lmin_max = Math.max(lmin_max,g._model._output._best_lambda_idx);
}
int lidx = 0;
int bestId = 0;
int cnt = 0;
for (; lidx < lmin_max; ++lidx) {
double testDev = 0;
for (int i = 0; i < cvModelBuilders.length; ++i) {
GLM g = (GLM) cvModelBuilders[i];
double x = _parms._lambda[lidx];
if (g._model._output.getSubmodel(x) == null)
g._driver.computeSubmodel(lidx, x);
testDev += g._model._output.getSubmodel(x).devianceTest;
}
double testDevAvg = testDev / cvModelBuilders.length;
double testDevSE = 0;
// compute deviance standard error
for (int i = 0; i < cvModelBuilders.length; ++i) {
GLM g = (GLM) cvModelBuilders[i];
double x = _parms._lambda[lidx];
if (g._model._output.getSubmodel(x) == null)
g._driver.computeSubmodel(lidx, x); // stopped too early, need to FIT extra model
double diff = testDevAvg - (g._model._output.getSubmodel(x).devianceTest);
testDevSE += diff*diff;
}
_xval_test_sd[lidx] = Math.sqrt(testDevSE/((cvModelBuilders.length-1)*cvModelBuilders.length));
_xval_test_deviances[lidx] = testDevAvg;
if(testDevAvg < bestTestDev) {
bestTestDev = testDevAvg;
bestId = lidx;
}
// early stopping - no reason to move further if we're overfitting
if(testDevAvg > bestTestDev && ++cnt == 3) {
lmin_max = lidx;
break;
}
}
for (int i = 0; i < cvModelBuilders.length; ++i) {
GLM g = (GLM) cvModelBuilders[i];
if(g._toRemove != null)
for(Key k:g._toRemove)
Keyed.remove(k);
}
_parms._lambda = Arrays.copyOf(_parms._lambda,lmin_max+1);
_xval_test_deviances = Arrays.copyOf(_xval_test_deviances, lmin_max+1);
_xval_test_sd = Arrays.copyOf(_xval_test_sd, lmin_max+1);
for (int i = 0; i < cvModelBuilders.length; ++i) {
GLM g = (GLM) cvModelBuilders[i];
g._model._output.setSubmodelIdx(bestId);
g._model.update(_job);
}
double bestDev = _xval_test_deviances[bestId];
double bestDev1se = bestDev + _xval_test_sd[bestId];
int bestId1se = bestId;
while(bestId1se > 0 && _xval_test_deviances[bestId1se-1] <= bestDev1se)
--bestId1se;
_lambdaCVEstimate = _parms._lambda[bestId];
_model._output._lambda_1se = bestId1se;
_model._output._best_lambda_idx = bestId;
}
for (int i = 0; i < cvModelBuilders.length; ++i) {
GLM g = (GLM) cvModelBuilders[i];
g._model.unlock(_job);
}
_doInit = false;
_cv = false;
}
protected void checkMemoryFootPrint(DataInfo activeData) {
if (_parms._solver == Solver.IRLSM || _parms._solver == Solver.COORDINATE_DESCENT) {
int p = activeData.fullN();
HeartBeat hb = H2O.SELF._heartbeat;
long mem_usage = (long) (hb._cpus_allowed * (p * p + activeData.largestCat()) * 8/*doubles*/ * (1 + .5 * Math.log((double) _train.lastVec().nChunks()) / Math.log(2.))); //one gram per core
long max_mem = hb.get_free_mem();
if (mem_usage > max_mem) {
String msg = "Gram matrices (one per thread) won't fit in the driver node's memory ("
+ PrettyPrint.bytes(mem_usage) + " > " + PrettyPrint.bytes(max_mem)
+ ") - try reducing the number of columns and/or the number of categorical factors (or switch to the L-BFGS solver).";
error("_train", msg);
}
}
}
static class TooManyPredictorsException extends RuntimeException {}
DataInfo _dinfo;
private transient DataInfo _validDinfo;
// time per iteration in ms
private static class ScoringHistory {
private ArrayList _scoringIters = new ArrayList<>();
private ArrayList _scoringTimes = new ArrayList<>();
private ArrayList _likelihoods = new ArrayList<>();
private ArrayList _objectives = new ArrayList<>();
public synchronized void addIterationScore(int iter, double likelihood, double obj) {
if (_scoringIters.size() > 0 && _scoringIters.get(_scoringIters.size() - 1) == iter)
return; // do not record twice, happens for the last iteration, need to record scoring history in checkKKTs because of gaussian fam.
_scoringIters.add(iter);
_scoringTimes.add(System.currentTimeMillis());
_likelihoods.add(likelihood);
_objectives.add(obj);
}
public synchronized TwoDimTable to2dTable() {
String[] cnames = new String[]{"timestamp", "duration", "iteration", "negative_log_likelihood", "objective"};
String[] ctypes = new String[]{"string", "string", "int", "double", "double"};
String[] cformats = new String[]{"%s", "%s", "%d", "%.5f", "%.5f"};
TwoDimTable res = new TwoDimTable("Scoring History", "", new String[_scoringIters.size()], cnames, ctypes, cformats, "");
int j = 0;
DateTimeFormatter fmt = DateTimeFormat.forPattern("yyyy-MM-dd HH:mm:ss");
for (int i = 0; i < _scoringIters.size(); ++i) {
int col = 0;
res.set(i, col++, fmt.print(_scoringTimes.get(i)));
res.set(i, col++, PrettyPrint.msecs(_scoringTimes.get(i) - _scoringTimes.get(0), true));
res.set(i, col++, _scoringIters.get(i));
res.set(i, col++, _likelihoods.get(i));
res.set(i, col++, _objectives.get(i));
}
return res;
}
}
private static class LambdaSearchScoringHistory {
ArrayList _scoringTimes = new ArrayList<>();
private ArrayList _lambdas = new ArrayList<>();
private ArrayList _lambdaIters = new ArrayList<>();
private ArrayList _lambdaPredictors = new ArrayList<>();
private ArrayList _lambdaDevTrain = new ArrayList<>();
private ArrayList _lambdaDevTest;
private ArrayList _lambdaDevXval;
private ArrayList _lambdaDevXvalSE;
public LambdaSearchScoringHistory(boolean hasTest, boolean hasXval) {
if(hasTest || true)_lambdaDevTest = new ArrayList<>();
if(hasXval){
_lambdaDevXval = new ArrayList<>();
_lambdaDevXvalSE = new ArrayList<>();
}
}
public synchronized void addLambdaScore(int iter, int predictors, double lambda, double devRatioTrain, double devRatioTest, double devRatioXval, double devRatoioXvalSE) {
_scoringTimes.add(System.currentTimeMillis());
_lambdaIters.add(iter);
_lambdas.add(lambda);
_lambdaPredictors.add(predictors);
_lambdaDevTrain.add(devRatioTrain);
if(_lambdaDevTest != null)_lambdaDevTest.add(devRatioTest);
if(_lambdaDevXval != null)_lambdaDevXval.add(devRatioXval);
if(_lambdaDevXvalSE != null)_lambdaDevXvalSE.add(devRatoioXvalSE);
}
public synchronized TwoDimTable to2dTable() {
String[] cnames = new String[]{"timestamp", "duration", "iteration", "lambda", "predictors", "deviance_train"};
if(_lambdaDevTest != null)
cnames = ArrayUtils.append(cnames,"deviance_test");
if(_lambdaDevXval != null)
cnames = ArrayUtils.append(cnames,new String[]{"deviance_xval","deviance_se"});
String[] ctypes = new String[]{"string", "string", "int", "string","int", "double"};
if(_lambdaDevTest != null)
ctypes = ArrayUtils.append(ctypes,"double");
if(_lambdaDevXval != null)
ctypes = ArrayUtils.append(ctypes, new String[]{"double","double"});
String[] cformats = new String[]{"%s", "%s", "%d","%s", "%d", "%.3f"};
if(_lambdaDevTest != null)
cformats = ArrayUtils.append(cformats,"%.3f");
if(_lambdaDevXval != null)
cformats = ArrayUtils.append(cformats,new String[]{"%.3f","%.3f"});
TwoDimTable res = new TwoDimTable("Scoring History", "", new String[_lambdaIters.size()], cnames, ctypes, cformats, "");
int j = 0;
DateTimeFormatter fmt = DateTimeFormat.forPattern("yyyy-MM-dd HH:mm:ss");
for (int i = 0; i < _lambdaIters.size(); ++i) {
int col = 0;
res.set(i, col++, fmt.print(_scoringTimes.get(i)));
res.set(i, col++, PrettyPrint.msecs(_scoringTimes.get(i) - _scoringTimes.get(0), true));
res.set(i, col++, _lambdaIters.get(i));
res.set(i, col++, lambdaFormatter.format(_lambdas.get(i)));
res.set(i, col++, _lambdaPredictors.get(i));
res.set(i, col++, _lambdaDevTrain.get(i));
if(_lambdaDevTest != null && _lambdaDevTest.size() > i)
res.set(i, col++, _lambdaDevTest.get(i));
if(_lambdaDevXval != null && _lambdaDevXval.size() > i) {
res.set(i, col++, _lambdaDevXval.get(i));
res.set(i, col++, _lambdaDevXvalSE.get(i));
}
}
return res;
}
}
private transient ScoringHistory _sc;
private transient LambdaSearchScoringHistory _lsc;
long _t0 = System.currentTimeMillis();
private transient double _iceptAdjust = 0;
private double _lmax;
private transient long _nobs;
private transient GLMModel _model;
@Override
public int nclasses() {
if (_parms._family == Family.multinomial)
return _nclass;
if (_parms._family == Family.binomial)
return 2;
return 1;
}
private transient double[] _nullBeta;
private double[] getNullBeta() {
if (_nullBeta == null) {
if (_parms._family == Family.multinomial) {
_nullBeta = MemoryManager.malloc8d((_dinfo.fullN() + 1) * nclasses());
int N = _dinfo.fullN() + 1;
if(_parms._intercept)
for (int i = 0; i < nclasses(); ++i)
_nullBeta[_dinfo.fullN() + i * N] = Math.log(_state._ymu[i]);
} else {
_nullBeta = MemoryManager.malloc8d(_dinfo.fullN() + 1);
if (_parms._intercept && !(_parms._family == Family.quasibinomial))
_nullBeta[_dinfo.fullN()] = new GLMModel.GLMWeightsFun(_parms).link(_state._ymu[0]);
else
_nullBeta[_dinfo.fullN()] = 0;
}
}
return _nullBeta;
}
protected boolean computePriorClassDistribution(){return _parms._family == Family.multinomial;}
@Override
public void init(boolean expensive) {
super.init(expensive);
hide("_balance_classes", "Not applicable since class balancing is not required for GLM.");
hide("_max_after_balance_size", "Not applicable since class balancing is not required for GLM.");
hide("_class_sampling_factors", "Not applicable since class balancing is not required for GLM.");
_parms.validate(this);
if(_response != null) {
if(!isClassifier() && _response.isCategorical())
error("_response", H2O.technote(2, "Regression requires numeric response, got categorical."));
switch (_parms._family) {
case binomial:
if (!_response.isBinary() && _nclass != 2)
error("_family", H2O.technote(2, "Binomial requires the response to be a 2-class categorical or a binary column (0/1)"));
break;
case multinomial:
if (_nclass <= 2)
error("_family", H2O.technote(2, "Multinomial requires a categorical response with at least 3 levels (for 2 class problem use family=binomial."));
break;
case poisson:
if (_nclass != 1) error("_family", "Poisson requires the response to be numeric.");
if (_response.min() < 0)
error("_family", "Poisson requires response >= 0");
if (!_response.isInt())
warn("_family", "Poisson expects non-negative integer response, got floats.");
break;
case gamma:
if (_nclass != 1) error("_distribution", H2O.technote(2, "Gamma requires the response to be numeric."));
if (_response.min() <= 0) error("_family", "Gamma requires positive respone");
break;
case tweedie:
if (_nclass != 1) error("_family", H2O.technote(2, "Tweedie requires the response to be numeric."));
break;
case quasibinomial:
if (_nclass != 1) error("_family", H2O.technote(2, "Quasi_binomial requires the response to be numeric."));
break;
case gaussian:
// if (_nclass != 1) error("_family", H2O.technote(2, "Gaussian requires the response to be numeric."));
break;
default:
error("_family", "Invalid distribution: " + _parms._distribution);
}
}
if (expensive) {
if (error_count() > 0) return;
if (_parms._alpha == null)
_parms._alpha = new double[]{_parms._solver == Solver.L_BFGS ? 0 : .5};
if (_parms._lambda_search &&_parms._nlambdas == -1)
_parms._nlambdas = _parms._alpha[0] == 0?30:100; // fewer lambdas needed for ridge
_lsc = new LambdaSearchScoringHistory(_parms._valid != null,_parms._nfolds > 1);
_sc = new ScoringHistory();
_train.bulkRollups(); // make sure we have all the rollups computed in parallel
_sc = new ScoringHistory();
_t0 = System.currentTimeMillis();
if (_parms._lambda_search || !_parms._intercept || _parms._lambda == null || _parms._lambda[0] > 0)
_parms._use_all_factor_levels = true;
if (_parms._link == Link.family_default)
_parms._link = _parms._family.defaultLink;
_dinfo = new DataInfo(_train.clone(), _valid, 1, _parms._use_all_factor_levels || _parms._lambda_search, _parms._standardize ? DataInfo.TransformType.STANDARDIZE : DataInfo.TransformType.NONE, DataInfo.TransformType.NONE, _parms._missing_values_handling == MissingValuesHandling.Skip, _parms._missing_values_handling == MissingValuesHandling.MeanImputation, false, hasWeightCol(), hasOffsetCol(), hasFoldCol(), _parms._interactions);
if (_parms._max_iterations == -1) { // fill in default max iterations
int numclasses = _parms._family == Family.multinomial?nclasses():1;
if (_parms._solver == Solver.L_BFGS) {
_parms._max_iterations = _parms._lambda_search ? _parms._nlambdas * 100 * numclasses : numclasses * Math.max(20, _dinfo.fullN() >> 2);
if(_parms._alpha[0] > 0)
_parms._max_iterations *= 10;
} else
_parms._max_iterations = _parms._lambda_search ? 10 * _parms._nlambdas : 50;
}
if (_valid != null)
_validDinfo = _dinfo.validDinfo(_valid);
_state = new ComputationState(_job, _parms, _dinfo, null, nclasses());
// skipping extra rows? (outside of weights == 0)GLMT
boolean skippingRows = (_parms._missing_values_handling == MissingValuesHandling.Skip && _train.hasNAs());
if (hasWeightCol() || skippingRows) { // need to re-compute means and sd
boolean setWeights = skippingRows;// && _parms._lambda_search && _parms._alpha[0] > 0;
if (setWeights) {
Vec wc = _weights == null ? _dinfo._adaptedFrame.anyVec().makeCon(1) : _weights.makeCopy();
_dinfo.setWeights(_generatedWeights = "__glm_gen_weights", wc);
}
YMUTask ymt = new YMUTask(_dinfo, _parms._family == Family.multinomial?nclasses():1, setWeights, skippingRows,true).doAll(_dinfo._adaptedFrame);
if (ymt.wsum() == 0)
throw new IllegalArgumentException("No rows left in the dataset after filtering out rows with missing values. Ignore columns with many NAs or impute your missing values prior to calling glm.");
Log.info(LogMsg("using " + ymt.nobs() + " nobs out of " + _dinfo._adaptedFrame.numRows() + " total"));
// if sparse data, need second pass to compute variance
_nobs = ymt.nobs();
if (_parms._obj_reg == -1)
_parms._obj_reg = 1.0 / ymt.wsum();
if(!_parms._stdOverride)
_dinfo.updateWeightedSigmaAndMean(ymt.predictorSDs(), ymt.predictorMeans());
if (_parms._family == Family.multinomial) {
_state._ymu = MemoryManager.malloc8d(_nclass);
for (int i = 0; i < _state._ymu.length; ++i)
_state._ymu[i] = _priorClassDist[i];
} else
_state._ymu = _parms._intercept?ymt._yMu:new double[]{_parms.linkInv(0)};
} else {
_nobs = _train.numRows();
if (_parms._obj_reg == -1)
_parms._obj_reg = 1.0 / _nobs;
if (_parms._family == Family.multinomial) {
_state._ymu = MemoryManager.malloc8d(_nclass);
for (int i = 0; i < _state._ymu.length; ++i)
_state._ymu[i] = _priorClassDist[i];
} else
_state._ymu = new double[]{_parms._intercept?_train.lastVec().mean():_parms.linkInv(0)};
}
BetaConstraint bc = (_parms._beta_constraints != null)?new BetaConstraint(_parms._beta_constraints.get()):new BetaConstraint();
if((bc.hasBounds() || bc.hasProximalPenalty()) && _parms._compute_p_values)
error("_compute_p_values","P-values can not be computed for constrained problems");
_state.setBC(bc);
if(hasOffsetCol() && _parms._intercept) { // fit intercept
GLMGradientSolver gslvr = new GLMGradientSolver(_job,_parms, _dinfo.filterExpandedColumns(new int[0]), 0, _state.activeBC());
double [] x = new L_BFGS().solve(gslvr,new double[]{-_offset.mean()}).coefs;
Log.info(LogMsg("fitted intercept = " + x[0]));
x[0] = _parms.linkInv(x[0]);
_state._ymu = x;
}
if (_parms._prior > 0)
_iceptAdjust = -Math.log(_state._ymu[0] * (1 - _parms._prior) / (_parms._prior * (1 - _state._ymu[0])));
ArrayList vecs = new ArrayList<>();
if(_weights != null) vecs.add(_weights);
if(_offset != null) vecs.add(_offset);
vecs.add(_response);
double [] beta = getNullBeta();
GLMGradientInfo ginfo = new GLMGradientSolver(_job,_parms, _dinfo, 0, _state.activeBC()).getGradient(beta);
_lmax = lmax(ginfo._gradient);
_state.setLambdaMax(_lmax);
_model = new GLMModel(_result, _parms, GLM.this, _state._ymu, _dinfo._adaptedFrame.lastVec().sigma(), _lmax, _nobs);
String[] warns = _model.adaptTestForTrain(_valid, true, true);
for (String s : warns) _job.warn(s);
if (_parms._lambda_min_ratio == -1) {
_parms._lambda_min_ratio = (_nobs >> 4) > _dinfo.fullN() ? 1e-4 : 1e-2;
if(_parms._alpha[0] == 0)
_parms._lambda_min_ratio *= 1e-2; // smalelr lambda min for ridge as we are starting quite high
}
_state.updateState(beta,ginfo);
if (_parms._lambda == null) { // no lambda given, we will base lambda as a fraction of lambda max
if (_parms._lambda_search) {
_parms._lambda = new double[_parms._nlambdas];
double dec = Math.pow(_parms._lambda_min_ratio, 1.0/(_parms._nlambdas - 1));
_parms._lambda[0] = _lmax;
double l = _lmax;
for (int i = 1; i < _parms._nlambdas; ++i)
_parms._lambda[i] = (l *= dec);
// todo set the null submodel
} else
_parms._lambda = new double[]{10 * _parms._lambda_min_ratio * _lmax};
}
if(!Double.isNaN(_lambdaCVEstimate)){
for(int i = 0; i < _parms._lambda.length; ++i)
if(_parms._lambda[i] < _lambdaCVEstimate){
_parms._lambda = Arrays.copyOf(_parms._lambda,i+1);
break;
}
_parms._lambda[_parms._lambda.length-1] = _lambdaCVEstimate;
}
if(_parms._objective_epsilon == -1) {
if(_parms._lambda_search)
_parms._objective_epsilon = 1e-4;
else // lower default objective epsilon for non-standardized problems (mostly to match classical tools)
_parms._objective_epsilon = _parms._lambda[0] == 0?1e-6:1e-4;
}
if(_parms._gradient_epsilon == -1) {
_parms._gradient_epsilon = _parms._lambda[0] == 0 ? 1e-6 : 1e-4;
if(_parms._lambda_search) _parms._gradient_epsilon *= 1e-2;
}
// clone2 so that I don't change instance which is in the DKV directly
// (clone2 also shallow clones _output)
_model.clone2().delete_and_lock(_job._key);
}
}
protected static final long WORK_TOTAL = 1000000;
transient Key [] _toRemove;
private Key[] removeLater(Key ...k){
_toRemove = _toRemove == null?k:ArrayUtils.append(_toRemove,k);
return k;
}
@Override protected GLMDriver trainModelImpl() { return _driver = new GLMDriver(); }
private final double lmax(double[] grad) {
return Math.max(ArrayUtils.maxValue(grad), -ArrayUtils.minValue(grad)) / Math.max(1e-2, _parms._alpha[0]);
}
private transient ComputationState _state;
/**
* Main loop of the glm algo.
*/
public final class GLMDriver extends Driver implements ProgressMonitor {
private long _workPerIteration;
private transient double[][] _vcov;
private void doCleanup() {
try {
if(_parms._lambda_search && _parms._is_cv_model)
Scope.untrack(removeLater(_dinfo.getWeightsVec()._key));
if(!_cv && _model!=null)
_model.unlock(_job);
} catch(Throwable t){
// nada
}
}
private transient Cholesky _chol;
private transient L1Solver _lslvr;
private double [] solveGram(Solver s, GLMIterationTask t) {
int [] zeros = t._gram.findZeroCols();
if(zeros.length > 0) {
t._gram.dropCols(zeros);
t._xy = ArrayUtils.removeIds(t._xy, zeros);
if(t._beta != null)
t._beta = ArrayUtils.removeIds(t._beta, zeros);
_state.removeCols(zeros);
}
t._gram.mul(_parms._obj_reg);
ArrayUtils.mult(t._xy, _parms._obj_reg);
return (s == Solver.COORDINATE_DESCENT)?COD_solve(t,_state._alpha,_state.lambda()):ADMM_solve(t._gram, t._xy);
}
private double[] ADMM_solve(Gram gram, double [] xy) {
if(_parms._remove_collinear_columns || _parms._compute_p_values) {
if(!_parms._intercept) throw H2O.unimpl();
ArrayList ignoredCols = new ArrayList<>();
Cholesky chol = ((_state._iter == 0)?gram.qrCholesky(ignoredCols, _parms._standardize):gram.cholesky(null));
if(!ignoredCols.isEmpty() && !_parms._remove_collinear_columns) {
int [] collinear_cols = new int[ignoredCols.size()];
for(int i = 0; i < collinear_cols.length; ++i)
collinear_cols[i] = ignoredCols.get(i);
throw new Gram.CollinearColumnsException("Found collinear columns in the dataset. P-values can not be computed with collinear columns in the dataset. Set remove_collinear_columns flag to true to remove collinear columns automatically. Found collinear columns " + Arrays.toString(ArrayUtils.select(_dinfo.coefNames(),collinear_cols)));
}
if(!chol.isSPD()) throw new NonSPDMatrixException();
_chol = chol;
if(!ignoredCols.isEmpty()) { // got some redundant cols
int [] collinear_cols = new int[ignoredCols.size()];
for(int i = 0; i < collinear_cols.length; ++i)
collinear_cols[i] = ignoredCols.get(i);
String [] collinear_col_names = ArrayUtils.select(_state.activeData().coefNames(),collinear_cols);
// need to drop the cols from everywhere
_model.addWarning("Removed collinear columns " + Arrays.toString(collinear_col_names));
Log.warn("Removed collinear columns " + Arrays.toString(collinear_col_names));
_state.removeCols(collinear_cols);
gram.dropCols(collinear_cols);
xy = ArrayUtils.removeIds(xy,collinear_cols);
}
xy = xy.clone();
chol.solve(xy);
} else {
gram = gram.deep_clone();
xy = xy.clone();
GramSolver slvr = new GramSolver(gram.clone(), xy.clone(), _parms._intercept, _state.l2pen(),_state.l1pen(), _state.activeBC()._betaGiven, _state.activeBC()._rho, _state.activeBC()._betaLB, _state.activeBC()._betaUB);
_chol = slvr._chol;
if(_state.l1pen() == 0 && !_state.activeBC().hasBounds()) {
slvr.solve(xy);
} else {
xy = MemoryManager.malloc8d(xy.length);
if(_state._u == null && _parms._family != Family.multinomial) _state._u = MemoryManager.malloc8d(_state.activeData().fullN()+1);
(_lslvr = new ADMM.L1Solver(1e-4, 10000, _state._u)).solve(slvr, xy, _state.l1pen(), _parms._intercept, _state.activeBC()._betaLB, _state.activeBC()._betaUB);
}
}
return xy;
}
private void fitIRLSM_multinomial(Solver s){
assert _dinfo._responses == 3:"IRLSM for multinomial needs extra information encoded in additional reponses, expected 3 response vecs, got " + _dinfo._responses;
double [] beta = _state.betaMultinomial();
do {
beta = beta.clone();
for (int c = 0; c < _nclass; ++c) {
boolean onlyIcpt = _state.activeDataMultinomial(c).fullN() == 0;
_state.setActiveClass(c);
LineSearchSolver ls = (_state.l1pen() == 0)
? new MoreThuente(_state.gslvrMultinomial(c), _state.betaMultinomial(c,beta), _state.ginfoMultinomial(c))
: new SimpleBacktrackingLS(_state.gslvrMultinomial(c), _state.betaMultinomial(c,beta), _state.l1pen());
GLMWeightsFun glmw = new GLMWeightsFun(_parms);
long t1 = System.currentTimeMillis();
new GLMMultinomialUpdate(_state.activeDataMultinomial(), _job._key, beta, c).doAll(_state.activeDataMultinomial()._adaptedFrame);
long t2 = System.currentTimeMillis();
GLMIterationTask t = new GLMTask.GLMIterationTask(_job._key, _state.activeDataMultinomial(c), glmw, ls.getX(), c).doAll(_state.activeDataMultinomial(c)._adaptedFrame);
long t3 = System.currentTimeMillis();
double[] betaCnd = solveGram(s,t);
long t4 = System.currentTimeMillis();
if (!onlyIcpt && !ls.evaluate(ArrayUtils.subtract(betaCnd, ls.getX(), betaCnd))) {
Log.info(LogMsg("Ls failed " + ls));
continue;
}
long t5 = System.currentTimeMillis();
_state.setBetaMultinomial(c, beta,ls.getX());
// update multinomial
Log.info(LogMsg("computed in " + (t2 - t1) + "+" + (t3 - t2) + "+" + (t4 - t3) + "+" + (t5 - t4) + "=" + (t5 - t1) + "ms, step = " + ls.step() + ((_lslvr != null) ? ", l1solver " + _lslvr : "")));
}
_state.setActiveClass(-1);
} while(progress(beta,_state.gslvr().getGradient(beta)));
}
private void fitLSM(Solver s){
GLMIterationTask t = new GLMTask.GLMIterationTask(_job._key, _state.activeData(), new GLMWeightsFun(_parms), null).doAll(_state.activeData()._adaptedFrame);
double [] beta = solveGram(s,t);
// compute mse
double [] x = t._gram.mul(beta);
for(int i = 0; i < x.length; ++i)
x[i] = (x[i] - 2*t._xy[i]);
double l = .5*(ArrayUtils.innerProduct(x,beta)/_parms._obj_reg + t._yy );
_state.updateState(beta, l);
}
private void fitIRLSM(Solver s) {
GLMWeightsFun glmw = new GLMWeightsFun(_parms);
double [] betaCnd = _state.beta();
LineSearchSolver ls = null;
boolean firstIter = true;
try {
while (true) {
long t1 = System.currentTimeMillis();
GLMIterationTask t = new GLMTask.GLMIterationTask(_job._key, _state.activeData(), glmw, betaCnd).doAll(_state.activeData()._adaptedFrame);
long t2 = System.currentTimeMillis();
if (!_state._lsNeeded && (Double.isNaN(t._likelihood) || _state.objective(t._beta, t._likelihood) > _state.objective() + _parms._objective_epsilon)) {
_state._lsNeeded = true;
} else {
if (!firstIter && !_state._lsNeeded && !progress(t._beta, t._likelihood))
return;
betaCnd = solveGram(s,t);
}
firstIter = false;
long t3 = System.currentTimeMillis();
if(_state._lsNeeded) {
if(ls == null)
ls = (_state.l1pen() == 0 && !_state.activeBC().hasBounds())
? new MoreThuente(_state.gslvr(),_state.beta(), _state.ginfo())
: new SimpleBacktrackingLS(_state.gslvr(),_state.beta().clone(), _state.l1pen(), _state.ginfo());
if (!ls.evaluate(ArrayUtils.subtract(betaCnd, ls.getX(), betaCnd))) {
Log.info(LogMsg("Ls failed " + ls));
return;
}
betaCnd = ls.getX();
if(!progress(betaCnd,ls.ginfo()))
return;
long t4 = System.currentTimeMillis();
Log.info(LogMsg("computed in " + (t2 - t1) + "+" + (t3 - t2) + "+" + (t4 - t3) + "=" + (t4 - t1) + "ms, step = " + ls.step() + ((_lslvr != null) ? ", l1solver " + _lslvr : "")));
} else
Log.info(LogMsg("computed in " + (t2 - t1) + "+" + (t3 - t2) + "=" + (t3 - t1) + "ms, step = " + 1 + ((_lslvr != null) ? ", l1solver " + _lslvr : "")));
}
} catch(NonSPDMatrixException e) {
Log.warn(LogMsg("Got Non SPD matrix, stopped."));
}
}
private void fitLBFGS() {
double [] beta = _state.beta();
final double l1pen = _state.l1pen();
GLMGradientSolver gslvr = _state.gslvr();
GLMWeightsFun glmw = new GLMWeightsFun(_parms);
if (beta == null && _parms._family == Family.multinomial) {
beta = MemoryManager.malloc8d((_state.activeData().fullN() + 1) * _nclass);
int P = _state.activeData().fullN() + 1;
if(_parms._intercept)
for (int i = 0; i < _nclass; ++i)
beta[i * P + P - 1] = glmw.link(_state._ymu[i]);
}
if (beta == null) {
beta = MemoryManager.malloc8d(_state.activeData().fullN() + 1);
if (_parms._intercept)
beta[beta.length - 1] = glmw.link(_state._ymu[0]);
}
L_BFGS lbfgs = new L_BFGS().setObjEps(_parms._objective_epsilon).setGradEps(_parms._gradient_epsilon).setMaxIter(_parms._max_iterations);
assert beta.length == _state.ginfo()._gradient.length;
int P = _dinfo.fullN();
if (l1pen > 0 || _state.activeBC().hasBounds()) {
double[] nullBeta = MemoryManager.malloc8d(beta.length); // compute ginfo at null beta to get estimate for rho
if (_dinfo._intercept) {
if (_parms._family == Family.multinomial) {
for (int c = 0; c < _nclass; c++)
nullBeta[(c + 1) * (P + 1) - 1] = glmw.link(_state._ymu[c]);
} else
nullBeta[nullBeta.length - 1] = glmw.link(_state._ymu[0]);
}
GradientInfo ginfo = gslvr.getGradient(nullBeta);
double[] direction = ArrayUtils.mult(ginfo._gradient.clone(), -1);
double t = 1;
if (l1pen > 0) {
MoreThuente mt = new MoreThuente(gslvr,nullBeta);
mt.evaluate(direction);
t = mt.step();
}
double[] rho = MemoryManager.malloc8d(beta.length);
double r = _state.activeBC().hasBounds()?1:.1;
BetaConstraint bc = _state.activeBC();
// compute rhos
for (int i = 0; i < rho.length - 1; ++i)
rho[i] = r * ADMM.L1Solver.estimateRho(nullBeta[i] + t * direction[i], l1pen, bc._betaLB == null ? Double.NEGATIVE_INFINITY : bc._betaLB[i], bc._betaUB == null ? Double.POSITIVE_INFINITY : bc._betaUB[i]);
for (int ii = P; ii < rho.length; ii += P + 1)
rho[ii] = r * ADMM.L1Solver.estimateRho(nullBeta[ii] + t * direction[ii], 0, bc._betaLB == null ? Double.NEGATIVE_INFINITY : bc._betaLB[ii], bc._betaUB == null ? Double.POSITIVE_INFINITY : bc._betaUB[ii]);
final double[] objvals = new double[2];
objvals[1] = Double.POSITIVE_INFINITY;
double reltol = L1Solver.DEFAULT_RELTOL;
double abstol = L1Solver.DEFAULT_ABSTOL;
double ADMM_gradEps = 1e-3;
ProximalGradientSolver innerSolver = new ProximalGradientSolver(gslvr, beta, rho, _parms._objective_epsilon * 1e-1, _parms._gradient_epsilon, _state.ginfo(), this);
// new ProgressMonitor() {
// @Override
// public boolean progress(double[] betaDiff, GradientInfo ginfo) {
// return ++_state._iter < _parms._max_iterations;
// }
// });
ADMM.L1Solver l1Solver = new ADMM.L1Solver(ADMM_gradEps, 250, reltol, abstol, _state._u);
l1Solver._pm = this;
l1Solver.solve(innerSolver, beta, l1pen, true, _state.activeBC()._betaLB, _state.activeBC()._betaUB);
_state._u = l1Solver._u;
_state.updateState(beta,gslvr.getGradient(beta));
} else {
if(!_parms._lambda_search && _state._iter == 0)
updateProgress(false);
Result r = lbfgs.solve(gslvr, beta, _state.ginfo(), new ProgressMonitor() {
@Override
public boolean progress(double[] beta, GradientInfo ginfo) {
if(_state._iter < 4 || ((_state._iter & 3) == 0))
Log.info(LogMsg("LBFGS, gradient norm = " + ArrayUtils.linfnorm(ginfo._gradient, false)));
return GLMDriver.this.progress(beta,ginfo);
}
});
Log.info(LogMsg(r.toString()));
_state.updateState(r.coefs,(GLMGradientInfo)r.ginfo);
}
}
private void fitCOD() {
double [] beta = _state.beta();
int p = _state.activeData().fullN()+ 1;
double wsum,wsumu; // intercept denum
double [] denums;
boolean skipFirstLevel = !_state.activeData()._useAllFactorLevels;
double [] betaold = beta.clone();
double objold = _state.objective();
int iter2=0; // total cd iters
// get reweighted least squares vectors
Vec[] newVecs = _state.activeData()._adaptedFrame.anyVec().makeZeros(3);
Vec w = newVecs[0]; // fixed before each CD loop
Vec z = newVecs[1]; // fixed before each CD loop
Vec zTilda = newVecs[2]; // will be updated at every variable within CD loop
long startTimeTotalNaive = System.currentTimeMillis();
// generate new IRLS iteration
while (iter2++ < 30) {
Frame fr = new Frame(_state.activeData()._adaptedFrame);
fr.add("w", w); // fr has all data
fr.add("z", z);
fr.add("zTilda", zTilda);
GLMGenerateWeightsTask gt = new GLMGenerateWeightsTask(_job._key, _state.activeData(), _parms, beta).doAll(fr);
double objVal = objVal(gt._likelihood, gt._betaw, _state.lambda());
denums = gt.denums;
wsum = gt.wsum;
wsumu = gt.wsumu;
int iter1 = 0;
// coordinate descent loop
while (iter1++ < 100) {
Frame fr2 = new Frame();
fr2.add("w", w);
fr2.add("z", z);
fr2.add("zTilda", zTilda); // original x%*%beta if first iteration
for(int i=0; i < _state.activeData()._cats; i++) {
Frame fr3 = new Frame(fr2);
int level_num = _state.activeData()._catOffsets[i+1]-_state.activeData()._catOffsets[i];
int prev_level_num = 0;
fr3.add("xj", _state.activeData()._adaptedFrame.vec(i));
boolean intercept = (i == 0); // prev var is intercept
if(!intercept) {
prev_level_num = _state.activeData()._catOffsets[i]-_state.activeData()._catOffsets[i-1];
fr3.add("xjm1", _state.activeData()._adaptedFrame.vec(i-1)); // add previous categorical variable
}
int start_old = _state.activeData()._catOffsets[i];
GLMCoordinateDescentTaskSeqNaive stupdate;
if(intercept)
stupdate = new GLMCoordinateDescentTaskSeqNaive(intercept, false, 4 , Arrays.copyOfRange(betaold, start_old, start_old+level_num),
new double [] {beta[p-1]}, _state.activeData()._catLvls[i], null, null, null, null, null, skipFirstLevel).doAll(fr3);
else
stupdate = new GLMCoordinateDescentTaskSeqNaive(intercept, false, 1 , Arrays.copyOfRange(betaold, start_old,start_old+level_num),
Arrays.copyOfRange(beta, _state.activeData()._catOffsets[i-1], _state.activeData()._catOffsets[i]) , _state.activeData()._catLvls[i] ,
_state.activeData()._catLvls[i-1], null, null, null, null, skipFirstLevel ).doAll(fr3);
for(int j=0; j < level_num; ++j)
beta[_state.activeData()._catOffsets[i]+j] = ADMM.shrinkage(stupdate._temp[j] / wsumu, _state.lambda() * _parms._alpha[0])
/ (denums[_state.activeData()._catOffsets[i]+j] / wsumu + _state.lambda() * (1 - _parms._alpha[0]));
}
int cat_num = 2; // if intercept, or not intercept but not first numeric, then both are numeric .
for (int i = 0; i < _state.activeData()._nums; ++i) {
GLMCoordinateDescentTaskSeqNaive stupdate;
Frame fr3 = new Frame(fr2);
fr3.add("xj", _state.activeData()._adaptedFrame.vec(i+_state.activeData()._cats)); // add current variable col
boolean intercept = (i == 0 && _state.activeData().numStart() == 0); // if true then all numeric case and doing beta_1
double [] meannew=null, meanold=null, varnew=null, varold=null;
if(i > 0 || intercept) {// previous var is a numeric var
cat_num = 3;
if(!intercept)
fr3.add("xjm1", _state.activeData()._adaptedFrame.vec(i - 1 + _state.activeData()._cats)); // add previous one if not doing a beta_1 update, ow just pass it the intercept term
if( _state.activeData()._normMul!=null ) {
varold = new double[]{_state.activeData()._normMul[i]};
meanold = new double[]{_state.activeData()._normSub[i]};
if (i!= 0){
varnew = new double []{ _state.activeData()._normMul[i-1]};
meannew = new double [] { _state.activeData()._normSub[i-1]};
}
}
stupdate = new GLMCoordinateDescentTaskSeqNaive(intercept, false, cat_num , new double [] { betaold[_state.activeData().numStart()+ i]},
new double []{ beta[ (_state.activeData().numStart()+i-1+p)%p ]}, null, null,
varold, meanold, varnew, meannew, skipFirstLevel ).doAll(fr3);
beta[i+_state.activeData().numStart()] = ADMM.shrinkage(stupdate._temp[0] / wsumu, _state.lambda() * _parms._alpha[0])
/ (denums[i+_state.activeData().numStart()] / wsumu + _state.lambda() * (1 - _parms._alpha[0]));
}
else if (i == 0 && !intercept){ // previous one is the last categorical variable
int prev_level_num = _state.activeData().numStart()-_state.activeData()._catOffsets[_state.activeData()._cats-1];
fr3.add("xjm1", _state.activeData()._adaptedFrame.vec(_state.activeData()._cats-1)); // add previous categorical variable
if( _state.activeData()._normMul!=null){
varold = new double []{ _state.activeData()._normMul[i]};
meanold = new double [] { _state.activeData()._normSub[i]};
}
stupdate = new GLMCoordinateDescentTaskSeqNaive(intercept, false, cat_num , new double [] {betaold[ _state.activeData().numStart()]},
Arrays.copyOfRange(beta,_state.activeData()._catOffsets[_state.activeData()._cats-1],_state.activeData().numStart() ), null, _state.activeData()._catLvls[_state.activeData()._cats-1],
varold, meanold, null, null, skipFirstLevel ).doAll(fr3);
beta[_state.activeData().numStart()] = ADMM.shrinkage(stupdate._temp[0] / wsumu, _state.lambda() * _parms._alpha[0])
/ (denums[_state.activeData().numStart()] / wsumu + _state.lambda() * (1 - _parms._alpha[0]));
}
}
if(_state.activeData()._nums + _state.activeData()._cats > 0) {
// intercept update: preceded by a categorical or numeric variable
Frame fr3 = new Frame(fr2);
fr3.add("xjm1", _state.activeData()._adaptedFrame.vec(_state.activeData()._cats + _state.activeData()._nums - 1)); // add last variable updated in cycle to the frame
GLMCoordinateDescentTaskSeqNaive iupdate;
if (_state.activeData()._adaptedFrame.vec(_state.activeData()._cats + _state.activeData()._nums - 1).isCategorical()) { // only categorical vars
cat_num = 2;
iupdate = new GLMCoordinateDescentTaskSeqNaive(false, true, cat_num, new double[]{betaold[betaold.length - 1]},
Arrays.copyOfRange(beta, _state.activeData()._catOffsets[_state.activeData()._cats - 1], _state.activeData()._catOffsets[_state.activeData()._cats]),
null, _state.activeData()._catLvls[_state.activeData()._cats - 1], null, null, null, null, skipFirstLevel).doAll(fr3);
} else { // last variable is numeric
cat_num = 3;
double[] meannew = null, varnew = null;
if (_state.activeData()._normMul != null) {
varnew = new double[]{_state.activeData()._normMul[_state.activeData()._normMul.length - 1]};
meannew = new double[]{_state.activeData()._normSub[_state.activeData()._normSub.length - 1]};
}
iupdate = new GLMCoordinateDescentTaskSeqNaive(false, true, cat_num,
new double[]{betaold[betaold.length - 1]}, new double[]{beta[beta.length - 2]}, null, null,
null, null, varnew, meannew, skipFirstLevel).doAll(fr3);
}
if (_parms._intercept)
beta[beta.length - 1] = iupdate._temp[0] / wsum;
}
double maxdiff = ArrayUtils.linfnorm(ArrayUtils.subtract(beta, betaold), false); // false to keep the intercept
System.arraycopy(beta, 0, betaold, 0, beta.length);
if (maxdiff < _parms._beta_epsilon)
break;
}
double percdiff = Math.abs((objold - objVal)/objold);
if (percdiff < _parms._objective_epsilon & iter2 >1 )
break;
objold=objVal;
System.out.println("iter1 = " + iter1);
}
System.out.println("iter2 = " + iter2);
long endTimeTotalNaive = System.currentTimeMillis();
long durationTotalNaive = (endTimeTotalNaive - startTimeTotalNaive)/1000;
System.out.println("Time to run Naive Coordinate Descent " + durationTotalNaive);
_state._iter = iter2;
for (Vec v : newVecs) v.remove();
_state.updateState(beta,objold);
}
private void fitModel() {
Solver solver = (_parms._solver == Solver.AUTO) ? defaultSolver() : _parms._solver;
switch (solver) {
case COORDINATE_DESCENT: // fall through to IRLSM
case IRLSM:
if(_parms._family == Family.multinomial)
fitIRLSM_multinomial(solver);
else if(_parms._family == Family.gaussian && _parms._link == Link.identity)
fitLSM(solver);
else
fitIRLSM(solver);
break;
case L_BFGS:
fitLBFGS();
break;
case COORDINATE_DESCENT_NAIVE:
fitCOD();
break;
default:
throw H2O.unimpl();
}
if(_parms._compute_p_values) { // compute p-values
double se = 1;
boolean seEst = false;
double [] beta = _state.beta();
if(_parms._family != Family.binomial && _parms._family != Family.poisson) {
seEst = true;
ComputeSETsk ct = new ComputeSETsk(null, _state.activeData(), _job._key, beta, _parms).doAll(_state.activeData()._adaptedFrame);
se = ct._sumsqe / (_nobs - 1 - _state.activeData().fullN());
}
double [] zvalues = MemoryManager.malloc8d(_state.activeData().fullN()+1);
Cholesky chol = _chol;
if(_parms._standardize){ // compute non-standardized t(X)%*%W%*%X
DataInfo activeData = _state.activeData();
double [] beta_nostd = activeData.denormalizeBeta(beta);
DataInfo.TransformType transform = activeData._predictor_transform;
activeData.setPredictorTransform(DataInfo.TransformType.NONE);
Gram g = new GLMIterationTask(_job._key,activeData,new GLMWeightsFun(_parms),beta_nostd).doAll(activeData._adaptedFrame)._gram;
activeData.setPredictorTransform(transform); // just in case, restore the trasnform
g.mul(_parms._obj_reg);
chol = g.cholesky(null);
beta = beta_nostd;
}
double [][] inv = chol.getInv();
ArrayUtils.mult(inv,_parms._obj_reg*se);
_vcov = inv;
for(int i = 0; i < zvalues.length; ++i)
zvalues[i] = beta[i]/Math.sqrt(inv[i][i]);
_model.setZValues(expandVec(zvalues,_state.activeData()._activeCols,_dinfo.fullN()+1,Double.NaN),se, seEst);
}
}
private long _lastScore = System.currentTimeMillis();
private long timeSinceLastScoring(){return System.currentTimeMillis() - _lastScore;}
private void scoreAndUpdateModel(){
// compute full validation on train and test
Log.info(LogMsg("Scoring after " + timeSinceLastScoring() + "ms"));
long t1 = System.currentTimeMillis();
Frame train = DKV.getGet(_parms._train);
_model.score(train).delete();
ModelMetrics mtrain = ModelMetrics.getFromDKV(_model, train); // updated by model.scoreAndUpdateModel
_model._output._training_metrics = mtrain;
long t2 = System.currentTimeMillis();
Log.info(LogMsg("Training metrics computed in " + (t2-t1) + "ms"));
Log.info(LogMsg(mtrain.toString()));
if(_valid != null) {
Frame valid = DKV.getGet(_parms._valid);
_model.score(valid).delete();
_model._output._validation_metrics = ModelMetrics.getFromDKV(_model, valid); //updated by model.scoreAndUpdateModel
}
_model._output._scoring_history = _parms._lambda_search?_lsc.to2dTable():_sc.to2dTable();
_model.update(_job._key);
_model.generateSummary(_parms._train,_state._iter);
_lastScore = System.currentTimeMillis();
long scoringTime = System.currentTimeMillis() - t1;
_scoringInterval = Math.max(_scoringInterval,20*scoringTime); // at most 5% overhead for scoring
}
protected Submodel computeSubmodel(int i,double lambda) {
Submodel sm;
if(lambda >= _lmax)
_model.addSubmodel(sm = new Submodel(lambda,getNullBeta(),_state._iter,_nullDevTrain,_nullDevTest));
else {
_model.addSubmodel(sm = new Submodel(lambda, _state.beta(),_state._iter,-1,-1));
_state.setLambda(lambda);
checkMemoryFootPrint(_state.activeData());
do {
if (_parms._family == Family.multinomial)
for (int c = 0; c < _nclass; ++c)
Log.info(LogMsg("Class " + c + " got " + _state.activeDataMultinomial(c).fullN() + " active columns out of " + _state._dinfo.fullN() + " total"));
else
Log.info(LogMsg("Got " + _state.activeData().fullN() + " active columns out of " + _state._dinfo.fullN() + " total"));
fitModel();
} while (!_state.checkKKTs());
Log.info(LogMsg("solution has " + ArrayUtils.countNonzeros(_state.beta()) + " nonzeros"));
if (_parms._lambda_search) { // need train and test deviance, only "the best" submodel will be fully scored
double trainDev = _state.deviance() / _nobs;
double testDev = Double.NaN;
if (_validDinfo != null) {
testDev = _parms._family == Family.multinomial
? new GLMResDevTaskMultinomial(_job._key, _validDinfo, _dinfo.denormalizeBeta(_state.beta()), _nclass).doAll(_validDinfo._adaptedFrame).avgDev()
: new GLMResDevTask(_job._key, _validDinfo, _parms, _dinfo.denormalizeBeta(_state.beta())).doAll(_validDinfo._adaptedFrame).avgDev();
}
Log.info(LogMsg("train deviance = " + trainDev + ", test deviance = " + testDev));
double xvalDev = _xval_test_deviances == null ? -1 : _xval_test_deviances[i];
double xvalDevSE = _xval_test_sd == null ? -1 : _xval_test_sd[i];
_lsc.addLambdaScore(_state._iter, ArrayUtils.countNonzeros(_state.beta()), _state.lambda(), trainDev, testDev, xvalDev, xvalDevSE);
_model.updateSubmodel(sm = new Submodel(_state.lambda(), _state.beta(), _state._iter, trainDev, testDev));
} else // model is gonna be scored subsequently anyways
_model.updateSubmodel(sm = new Submodel(lambda, _state.beta(), _state._iter, -1, -1));
}
_model.update(_job);
return sm;
}
private transient double _nullDevTrain = Double.NaN;
private transient double _nullDevTest = Double.NaN;
@Override
public void computeImpl() {
if(_doInit)
init(true);
if (error_count() > 0)
throw H2OModelBuilderIllegalArgumentException.makeFromBuilder(GLM.this);
if(_parms._lambda_search) {
_nullDevTrain = _parms._family == Family.multinomial
?new GLMResDevTaskMultinomial(_job._key,_state._dinfo,getNullBeta(), _nclass).doAll(_state._dinfo._adaptedFrame).avgDev()
:new GLMResDevTask(_job._key, _state._dinfo, _parms, getNullBeta()).doAll(_state._dinfo._adaptedFrame).avgDev();
if(_validDinfo != null)
_nullDevTest = _parms._family == Family.multinomial
?new GLMResDevTaskMultinomial(_job._key,_validDinfo,getNullBeta(), _nclass).doAll(_validDinfo._adaptedFrame).avgDev()
:new GLMResDevTask(_job._key, _validDinfo, _parms, getNullBeta()).doAll(_validDinfo._adaptedFrame).avgDev();
_workPerIteration = WORK_TOTAL/_parms._nlambdas;
} else
_workPerIteration = 1 + (WORK_TOTAL/_parms._max_iterations);
if(_parms._family == Family.multinomial && _parms._solver != Solver.L_BFGS ) {
double [] nb = getNullBeta();
double maxRow = ArrayUtils.maxValue(nb);
double sumExp = 0;
int P = _dinfo.fullN();
int N = _dinfo.fullN()+1;
for(int i = 1; i < _nclass; ++i)
sumExp += Math.exp(nb[i*N + P] - maxRow);
Vec [] vecs = _dinfo._adaptedFrame.anyVec().makeDoubles(2, new double[]{sumExp,maxRow});
if(_parms._lambda_search && _parms._is_cv_model) {
Scope.untrack(vecs[0]._key, vecs[1]._key);
removeLater(vecs[0]._key,vecs[1]._key);
}
_dinfo.addResponse(new String[]{"__glm_sumExp", "__glm_maxRow"}, vecs);
}
double oldDevTrain = _nullDevTrain;
double oldDevTest = _nullDevTest;
double [] devHistoryTrain = new double[5];
double [] devHistoryTest = new double[5];
if(!_parms._lambda_search)
updateProgress(false);
// lambda search loop
for (int i = 0; i < _parms._lambda.length; ++i) { // lambda search
if(_parms._max_iterations != -1 && _state._iter >= _parms._max_iterations)
break;
Submodel sm = computeSubmodel(i,_parms._lambda[i]);
double trainDev = sm.devianceTrain;
double testDev = sm.devianceTest;
devHistoryTest[i % devHistoryTest.length] = (oldDevTest - testDev)/oldDevTest;
oldDevTest = testDev;
devHistoryTrain[i % devHistoryTrain.length] = (oldDevTrain - trainDev)/oldDevTrain;
oldDevTrain = trainDev;
if(_parms._lambda[i] < _lmax && Double.isNaN(_lambdaCVEstimate) /** if we have cv lambda estimate we should use it, can not stop before reaching it */) {
if (_parms._early_stopping && _state._iter >= devHistoryTrain.length) {
double s = ArrayUtils.maxValue(devHistoryTrain);
if (s < 1e-4) {
Log.info(LogMsg("converged at lambda[" + i + "] = " + _parms._lambda[i] + ", improvement on train = " + s));
break; // started overfitting
}
if (_validDinfo != null && _parms._nfolds <= 1) { // check for early stopping on test but only if not doing xval
s = ArrayUtils.maxValue(devHistoryTest);
if (s < 0) {
Log.info(LogMsg("converged at lambda[" + i + "] = " + _parms._lambda[i] + ", improvement on test = " + s));
break; // started overfitting
}
}
}
}
if(_parms._lambda_search && (_parms._score_each_iteration || timeSinceLastScoring() > _scoringInterval)) {
_model._output.setSubmodelIdx(_model._output._best_lambda_idx = i);
scoreAndUpdateModel(); // update partial results
}
_job.update(_workPerIteration,"iter=" + _state._iter + " lmb=" + lambdaFormatter.format(_state.lambda()) + "deviance trn/tst= " + devFormatter.format(trainDev) + "/" + devFormatter.format(testDev) + " P=" + ArrayUtils.countNonzeros(_state.beta()));
}
if(_state._iter >= _parms._max_iterations)
_job.warn("Reached maximum number of iterations " + _parms._max_iterations + "!");
if(_parms._nfolds > 1 && !Double.isNaN(_lambdaCVEstimate))
_model._output.setSubmodel(_lambdaCVEstimate);
else
_model._output.pickBestModel();
scoreAndUpdateModel();
if(_vcov != null) {
_model.setVcov(_vcov);
_model.update(_job._key);
}
if(!(_parms)._lambda_search && _state._iter < _parms._max_iterations){
_job.update(_workPerIteration*(_parms._max_iterations - _state._iter));
}
if(_iceptAdjust != 0) { // apply the intercept adjust according to prior probability
assert _parms._intercept;
double [] b = _model._output._global_beta;
b[b.length-1] += _iceptAdjust;
for(Submodel sm:_model._output._submodels)
sm.beta[sm.beta.length-1] += _iceptAdjust;
_model.update(_job._key);
}
doCleanup();
}
@Override public boolean onExceptionalCompletion(Throwable t, CountedCompleter caller){
doCleanup();
return true;
}
@Override public boolean progress(double [] beta, GradientInfo ginfo) {
_state._iter++;
if(ginfo instanceof ProximalGradientInfo) {
ginfo = ((ProximalGradientInfo) ginfo)._origGinfo;
GLMGradientInfo gginfo = (GLMGradientInfo) ginfo;
_state.updateState(beta, gginfo);
if (!_parms._lambda_search)
updateProgress(false);
return !timeout() && !_job.stop_requested() && _state._iter < _parms._max_iterations;
} else {
GLMGradientInfo gginfo = (GLMGradientInfo) ginfo;
if(gginfo._gradient == null)
_state.updateState(beta,gginfo._likelihood);
else
_state.updateState(beta, gginfo);
if (!_parms._lambda_search)
updateProgress(true);
boolean converged = _state.converged();
if (converged) Log.info(LogMsg(_state.convergenceMsg));
return !timeout() && !_job.stop_requested() && !converged && _state._iter < _parms._max_iterations;
}
}
public boolean progress(double [] beta, double likelihood) {
_state._iter++;
_state.updateState(beta,likelihood);
if(!_parms._lambda_search)
updateProgress(true);
boolean converged = _state.converged();
if(converged) Log.info(LogMsg(_state.convergenceMsg));
return !_job.stop_requested() && !converged && _state._iter < _parms._max_iterations ;
}
private transient long _scoringInterval = SCORING_INTERVAL_MSEC;
// update user visible progress
protected void updateProgress(boolean canScore){
assert !_parms._lambda_search;
_sc.addIterationScore(_state._iter, _state.likelihood(), _state.objective());
_job.update(_workPerIteration,_state.toString());
if(canScore && (_parms._score_each_iteration || timeSinceLastScoring() > _scoringInterval)) {
_model.update(_state.expandBeta(_state.beta()), -1, -1, _state._iter);
scoreAndUpdateModel();
}
}
}
private Solver defaultSolver() {
Solver s = Solver.IRLSM;
int max_active = 0;
if(_parms._family == Family.multinomial )
for(int c = 0; c < _nclass; ++c)
max_active = Math.max(_state.activeDataMultinomial(c).fullN(),max_active);
else max_active = _state.activeData().fullN();
if(max_active >= 5000) // cutoff has to be somewhere
s = Solver.L_BFGS;
else if(_parms._lambda_search) { // lambda search prefers coordinate descent
// l1 lambda search is better with coordinate descent!
s = Solver.COORDINATE_DESCENT;
} else if(_state.activeBC().hasBounds() && !_state.activeBC().hasProximalPenalty()) {
s = Solver.COORDINATE_DESCENT;
} else if(_parms._family == Family.multinomial && _parms._alpha[0] == 0)
s = Solver.L_BFGS; // multinomial does better with lbfgs
else
Log.info(LogMsg("picked solver " + s));
if(s != Solver.L_BFGS && _parms._max_active_predictors == -1)
_parms._max_active_predictors = 5000;
_parms._solver = s;
return s;
}
double objVal(double likelihood, double[] beta, double lambda) {
double alpha = _parms._alpha[0];
double proximalPen = 0;
BetaConstraint bc = _state.activeBC();
if (_state.activeBC()._betaGiven != null && bc._rho != null) {
for (int i = 0; i < bc._betaGiven.length; ++i) {
double diff = beta[i] - bc._betaGiven[i];
proximalPen += diff * diff * bc._rho[i];
}
}
return (likelihood * _parms._obj_reg
+ .5 * proximalPen
+ lambda * (alpha * ArrayUtils.l1norm(beta, _parms._intercept)
+ (1 - alpha) * .5 * ArrayUtils.l2norm2(beta, _parms._intercept)));
}
private String LogMsg(String msg) {return "GLM[dest=" + dest() + ", " + _state + "] " + msg;}
private static final double[] expandVec(double[] beta, final int[] activeCols, int fullN) {
return expandVec(beta, activeCols, fullN, 0);
}
private static final double[] expandVec(double[] beta, final int[] activeCols, int fullN, double filler) {
assert beta != null;
if (activeCols == null) return beta;
double[] res = MemoryManager.malloc8d(fullN);
Arrays.fill(res, filler);
int i = 0;
for (int c : activeCols)
res[c] = beta[i++];
res[res.length - 1] = beta[beta.length - 1];
return res;
}
private static double [] doUpdateCD(double [] grads, double [] ary, double diff , int variable_min, int variable_max) {
for (int i = 0; i < variable_min; i++)
grads[i] += diff * ary[i];
for (int i = variable_max; i < grads.length; i++)
grads[i] += diff * ary[i];
return grads;
}
private static double [] doSparseUpdateCD(double [] grads, double [] ary, int[] ids, double diff , int variable_min, int variable_max) {
for(int i = 0; i < ids.length; ++i)
grads[ids[i]] += diff * ary[i];
return grads;
}
public double [] COD_solve(GLMIterationTask gt, double alpha, double lambda) {
double wsumInv = 1.0/(gt.wsum*_parms._obj_reg);
double l1pen = lambda * alpha;
double l2pen = lambda*(1-alpha);
double [][] xx = gt._gram.getXX();
double [] diagInv = MemoryManager.malloc8d(xx.length);
for(int i = 0; i < diagInv.length; ++i)
diagInv[i] = 1.0/(xx[i][i] + l2pen);
int [][] nzs = new int[_state.activeData().numStart()][];
if(nzs.length > 1000) {
final int [] nzs_ary = new int[xx.length];
for (int i = 0; i < nzs.length; ++i) {
double[] x = xx[i].clone();
int k = 0;
for (int j = 0; j < x.length; ++j) {
if (i != j && x[j] != 0) {
x[k] = x[j];
nzs_ary[k++] = j;
}
}
if (k < (nzs_ary.length >> 3)) {
nzs[i] = Arrays.copyOf(nzs_ary, k);
xx[i] = Arrays.copyOf(x,k);
}
}
}
double [] grads = new double [gt._xy.length];
double [] beta = _state.beta().clone();
for(int i = 0; i < grads.length; ++i) {
double ip = 0;
if(i < nzs.length && nzs[i] != null) {
int [] ids = nzs[i];
double [] x = xx[i];
for(int j = 0; j < nzs[i].length; ++j)
ip += x[j]*beta[ids[j]];
grads[i] = gt._xy[i] - ip;
} else {
grads[i] = gt._xy[i] - ArrayUtils.innerProduct(xx[i], beta) + xx[i][i] * beta[i];
}
}
int iter1 = 0;
int P = gt._xy.length - 1;
final BetaConstraint bc = _state.activeBC();
DataInfo activeData = _state.activeData();
// CD loop
while (iter1++ < 1000 /*Math.max(P,500)*/) {
double bdiffPos = 0;
double bdiffNeg = 0;
for (int i = 0; i < activeData._cats; ++i) {
for(int j = activeData._catOffsets[i]; j < activeData._catOffsets[i+1]; ++j) { // can do in parallel
double b = bc.applyBounds(ADMM.shrinkage(grads[j], l1pen) * diagInv[j],j);
double bd = beta[j] - b;
bdiffPos = bd > bdiffPos?bd:bdiffPos;
bdiffNeg = bd < bdiffNeg?bd:bdiffNeg;
if(nzs[j] == null)
doUpdateCD(grads, xx[j], bd, activeData._catOffsets[i], activeData._catOffsets[i + 1]);
else
doSparseUpdateCD(grads, xx[j], nzs[j], bd, activeData._catOffsets[i], activeData._catOffsets[i + 1]);
beta[j] = b;
}
}
int numStart = activeData.numStart();
for (int i = numStart; i < P; ++i) {
double b = bc.applyBounds(ADMM.shrinkage(grads[i], l1pen) * diagInv[i],i);
double bd = beta[i] - b;
bdiffPos = bd > bdiffPos?bd:bdiffPos;
bdiffNeg = bd < bdiffNeg?bd:bdiffNeg;
doUpdateCD(grads, xx[i], bd, i,i+1);
beta[i] = b;
}
// intercept
if(_parms._intercept) {
double b = bc.applyBounds(grads[P] * wsumInv,P);
double bd = beta[P] - b;
doUpdateCD(grads, xx[P], bd, P, P + 1);
bdiffPos = bd > bdiffPos ? bd : bdiffPos;
bdiffNeg = bd < bdiffNeg ? bd : bdiffNeg;
beta[P] = b;
}
if (-1e-4 < bdiffNeg && bdiffPos < 1e-4)
break;
}
return beta;
}
/**
* Created by tomasnykodym on 3/30/15.
*/
public static final class GramSolver implements ProximalSolver {
private final Gram _gram;
private Cholesky _chol;
private final double[] _xy;
final double _lambda;
double[] _rho;
boolean _addedL2;
double _betaEps;
private static double boundedX(double x, double lb, double ub) {
if (x < lb) x = lb;
if (x > ub) x = ub;
return x;
}
public GramSolver(Gram gram, double[] xy, double lmax, double betaEps, boolean intercept) {
_gram = gram;
_lambda = 0;
_betaEps = betaEps;
_xy = xy;
double[] rhos = MemoryManager.malloc8d(xy.length);
computeCholesky(gram, rhos, lmax * 1e-8,intercept);
_addedL2 = rhos[0] != 0;
_rho = _addedL2 ? rhos : null;
}
// solve non-penalized problem
public void solve(double[] result) {
System.arraycopy(_xy, 0, result, 0, _xy.length);
_chol.solve(result);
double gerr = Double.POSITIVE_INFINITY;
if (_addedL2) { // had to add l2-pen to turn the gram to be SPD
double[] oldRes = MemoryManager.arrayCopyOf(result, result.length);
for (int i = 0; i < 1000; ++i) {
solve(oldRes, result);
double[] g = gradient(result)._gradient;
gerr = Math.max(-ArrayUtils.minValue(g), ArrayUtils.maxValue(g));
if (gerr < 1e-4) return;
System.arraycopy(result, 0, oldRes, 0, result.length);
}
Log.warn("Gram solver did not converge, gerr = " + gerr);
}
}
public GramSolver(Gram gram, double[] xy, boolean intercept, double l2pen, double l1pen, double[] beta_given, double[] proxPen, double[] lb, double[] ub) {
if (ub != null && lb != null)
for (int i = 0; i < ub.length; ++i) {
assert ub[i] >= lb[i] : i + ": ub < lb, ub = " + Arrays.toString(ub) + ", lb = " + Arrays.toString(lb);
}
_lambda = l2pen;
_gram = gram;
// Try to pick optimal rho constant here used in ADMM solver.
//
// Rho defines the strength of proximal-penalty and also the strentg of L1 penalty aplpied in each step.
// Picking good rho constant is tricky and greatly influences the speed of convergence and precision with which we are able to solve the problem.
//
// Intuitively, we want the proximal l2-penalty ~ l1 penalty (l1 pen = lambda/rho, where lambda is the l1 penalty applied to the problem)
// Here we compute the rho for each coordinate by using equation for computing coefficient for single coordinate and then making the two penalties equal.
//
int ii = intercept ? 1 : 0;
int icptCol = gram.fullN()-1;
double[] rhos = MemoryManager.malloc8d(xy.length);
double min = Double.POSITIVE_INFINITY;
for (int i = 0; i < xy.length - ii; ++i) {
double d = xy[i];
d = d >= 0 ? d : -d;
if (d < min && d != 0) min = d;
}
double ybar = xy[icptCol];
for (int i = 0; i < rhos.length - ii; ++i) {
double y = xy[i];
if (y == 0) y = min;
double xbar = gram.get(icptCol, i);
double x = ((y - ybar * xbar) / ((gram.get(i, i) - xbar * xbar) + l2pen));///gram.get(i,i);
rhos[i] = ADMM.L1Solver.estimateRho(x, l1pen, lb == null ? Double.NEGATIVE_INFINITY : lb[i], ub == null ? Double.POSITIVE_INFINITY : ub[i]);
}
// do the intercept separate as l1pen does not apply to it
if (intercept && (lb != null && !Double.isInfinite(lb[icptCol]) || ub != null && !Double.isInfinite(ub[icptCol]))) {
int icpt = xy.length - 1;
rhos[icpt] = 1;//(xy[icpt] >= 0 ? xy[icpt] : -xy[icpt]);
}
if (l2pen > 0)
gram.addDiag(l2pen);
if (proxPen != null && beta_given != null) {
gram.addDiag(proxPen);
xy = xy.clone();
for (int i = 0; i < xy.length; ++i)
xy[i] += proxPen[i] * beta_given[i];
}
_xy = xy;
_rho = rhos;
computeCholesky(gram, rhos, 1e-5,intercept);
}
private void computeCholesky(Gram gram, double[] rhos, double rhoAdd, boolean intercept) {
gram.addDiag(rhos);
if(!intercept) {
gram.dropIntercept();
rhos = Arrays.copyOf(rhos,rhos.length-1);
_xy[_xy.length-1] = 0;
}
_chol = gram.cholesky(null, true, null);
if (!_chol.isSPD()) { // make sure rho is big enough
gram.addDiag(ArrayUtils.mult(rhos, -1));
gram.addDiag(rhoAdd,!intercept);
Log.info("Got NonSPD matrix with original rho, re-computing with rho = " + (_rho[0]+rhoAdd));
_chol = gram.cholesky(null, true, null);
int cnt = 0;
double rhoAddSum = rhoAdd;
while (!_chol.isSPD() && cnt++ < 5) {
gram.addDiag(rhoAdd,!intercept);
rhoAddSum += rhoAdd;
Log.warn("Still NonSPD matrix, re-computing with rho = " + (rhos[0] + rhoAddSum));
_chol = gram.cholesky(null, true, null);
}
if (!_chol.isSPD())
throw new NonSPDMatrixException();
}
gram.addDiag(ArrayUtils.mult(rhos, -1));
ArrayUtils.mult(rhos, -1);
}
@Override
public double[] rho() {
return _rho;
}
@Override
public boolean solve(double[] beta_given, double[] result) {
if (beta_given != null)
for (int i = 0; i < _xy.length; ++i)
result[i] = _xy[i] + _rho[i] * beta_given[i];
else
System.arraycopy(_xy, 0, result, 0, _xy.length);
_chol.solve(result);
return true;
}
@Override
public boolean hasGradient() {
return false;
}
@Override
public GradientInfo gradient(double[] beta) {
double[] grad = _gram.mul(beta);
for (int i = 0; i < _xy.length; ++i)
grad[i] -= _xy[i];
return new GradientInfo(Double.NaN,grad); // todo compute the objective
}
@Override
public int iter() {
return 0;
}
}
public static class ProximalGradientInfo extends GradientInfo {
final GradientInfo _origGinfo;
public ProximalGradientInfo(GradientInfo origGinfo, double objVal, double[] gradient) {
super(objVal, gradient);
_origGinfo = origGinfo;
}
}
/**
* Simple wrapper around ginfo computation, adding proximal penalty
*/
public static class ProximalGradientSolver implements GradientSolver, ProximalSolver {
final GradientSolver _solver;
double[] _betaGiven;
double[] _beta;
private ProximalGradientInfo _ginfo;
private final ProgressMonitor _pm;
final double[] _rho;
private final double _objEps;
private final double _gradEps;
public ProximalGradientSolver(GradientSolver s, double[] betaStart, double[] rho, double objEps, double gradEps, GradientInfo ginfo,ProgressMonitor pm) {
super();
_solver = s;
_rho = rho;
_objEps = objEps;
_gradEps = gradEps;
_pm = pm;
_beta = betaStart;
_betaGiven = MemoryManager.malloc8d(betaStart.length);
// _ginfo = new ProximalGradientInfo(ginfo,ginfo._objVal,ginfo._gradient);
}
public static double proximal_gradient(double[] grad, double obj, double[] beta, double[] beta_given, double[] rho) {
for (int i = 0; i < beta.length; ++i) {
double diff = (beta[i] - beta_given[i]);
double pen = rho[i] * diff;
if(grad != null)
grad[i] += pen;
obj += .5 * pen * diff;
}
return obj;
}
private ProximalGradientInfo computeProxGrad(GradientInfo ginfo, double [] beta) {
assert !(ginfo instanceof ProximalGradientInfo);
double[] gradient = ginfo._gradient.clone();
double obj = proximal_gradient(gradient, ginfo._objVal, beta, _betaGiven, _rho);
return new ProximalGradientInfo(ginfo, obj, gradient);
}
@Override
public ProximalGradientInfo getGradient(double[] beta) {
return computeProxGrad(_solver.getGradient(beta),beta);
}
@Override
public GradientInfo getObjective(double[] beta) {
GradientInfo ginfo = _solver.getObjective(beta);
double obj = proximal_gradient(null, ginfo._objVal, beta, _betaGiven, _rho);
return new ProximalGradientInfo(ginfo,obj,null);
}
@Override
public double[] rho() {
return _rho;
}
private int _iter;
@Override
public boolean solve(double[] beta_given, double[] beta) {
GradientInfo origGinfo = (_ginfo == null || !Arrays.equals(_beta,beta))
?_solver.getGradient(beta)
:_ginfo._origGinfo;
System.arraycopy(beta_given,0,_betaGiven,0,beta_given.length);
L_BFGS.Result r = new L_BFGS().setObjEps(_objEps).setGradEps(_gradEps).solve(this, beta, _ginfo = computeProxGrad(origGinfo,beta), _pm);
System.arraycopy(r.coefs,0,beta,0,r.coefs.length);
_beta = r.coefs;
_iter += r.iter;
_ginfo = (ProximalGradientInfo) r.ginfo;
return r.converged;
}
@Override
public boolean hasGradient() {
return true;
}
@Override
public GradientInfo gradient(double[] beta) {
return getGradient(beta)._origGinfo;
}
@Override
public int iter() {
return _iter;
}
}
public static class GLMGradientInfo extends GradientInfo {
final double _likelihood;
public GLMGradientInfo(double likelihood, double objVal, double[] grad) {
super(objVal, grad);
_likelihood = likelihood;
}
public String toString(){
return "GLM grad info: likelihood = " + _likelihood + super.toString();
}
}
/**
* Gradient and line search computation for L_BFGS and also L_BFGS solver wrapper (for ADMM)
*/
public static final class GLMGradientSolver implements GradientSolver {
final GLMParameters _parms;
final DataInfo _dinfo;
final BetaConstraint _bc;
final double _l2pen; // l2 penalty
double[][] _betaMultinomial;
final Job _job;
public GLMGradientSolver(Job job, GLMParameters glmp, DataInfo dinfo, double l2pen, BetaConstraint bc) {
_job = job;
_bc = bc;
_parms = glmp;
_dinfo = dinfo;
_l2pen = l2pen;
}
@Override
public GLMGradientInfo getGradient(double[] beta) {
if (_parms._family == Family.multinomial) {
if (_betaMultinomial == null) {
int nclasses = beta.length / (_dinfo.fullN() + 1);
assert beta.length % (_dinfo.fullN() + 1) == 0:"beta len = " + beta.length + ", fullN +1 == " + (_dinfo.fullN()+1);
_betaMultinomial = new double[nclasses][];
for (int i = 0; i < nclasses; ++i)
_betaMultinomial[i] = MemoryManager.malloc8d(_dinfo.fullN() + 1);
}
int off = 0;
for (int i = 0; i < _betaMultinomial.length; ++i) {
System.arraycopy(beta, off, _betaMultinomial[i], 0, _betaMultinomial[i].length);
off += _betaMultinomial[i].length;
}
GLMMultinomialGradientTask gt = new GLMMultinomialGradientTask(_job,_dinfo, _l2pen, _betaMultinomial, _parms._obj_reg).doAll(_dinfo._adaptedFrame);
double l2pen = 0;
for (double[] b : _betaMultinomial)
l2pen += ArrayUtils.l2norm2(b, _dinfo._intercept);
double [] grad = gt.gradient();
if(!_parms._intercept){
for(int i = _dinfo.fullN(); i < beta.length; i += _dinfo.fullN()+1)
grad[i] = 0;
}
return new GLMGradientInfo(gt._likelihood, gt._likelihood * _parms._obj_reg + .5 * _l2pen * l2pen, grad);
} else {
assert beta.length == _dinfo.fullN() + 1;
assert _parms._intercept || (beta[beta.length-1] == 0);
GLMGradientTask gt;
if(_parms._family == Family.binomial && _parms._link == Link.logit)
gt = new GLMBinomialGradientTask(_job == null?null:_job._key,_dinfo,_parms,_l2pen, beta).doAll(_dinfo._adaptedFrame);
else if(_parms._family == Family.gaussian && _parms._link == Link.identity)
gt = new GLMGaussianGradientTask(_job == null?null:_job._key,_dinfo,_parms,_l2pen, beta).doAll(_dinfo._adaptedFrame);
else if(_parms._family == Family.poisson && _parms._link == Link.log)
gt = new GLMPoissonGradientTask(_job == null?null:_job._key,_dinfo,_parms,_l2pen, beta).doAll(_dinfo._adaptedFrame);
else if(_parms._family == Family.quasibinomial)
gt = new GLMQuasiBinomialGradientTask(_job == null?null:_job._key,_dinfo,_parms,_l2pen, beta).doAll(_dinfo._adaptedFrame);
else
gt = new GLMGenericGradientTask(_job == null?null:_job._key, _dinfo, _parms, _l2pen, beta).doAll(_dinfo._adaptedFrame);
double [] gradient = gt._gradient;
double likelihood = gt._likelihood;
if (!_parms._intercept) // no intercept, null the ginfo
gradient[gradient.length - 1] = 0;
double obj = likelihood * _parms._obj_reg + .5 * _l2pen * ArrayUtils.l2norm2(beta, true);
if (_bc != null && _bc._betaGiven != null && _bc._rho != null)
obj = ProximalGradientSolver.proximal_gradient(gradient, obj, beta, _bc._betaGiven, _bc._rho);
return new GLMGradientInfo(likelihood, obj, gradient);
}
}
@Override
public GradientInfo getObjective(double[] beta) {
double l = new GLMResDevTask(_job._key,_dinfo,_parms,beta).doAll(_dinfo._adaptedFrame)._likelihood;
return new GLMGradientInfo(l,l*_parms._obj_reg + .5*_l2pen*ArrayUtils.l2norm2(beta,true),null);
}
}
protected static double sparseOffset(double[] beta, DataInfo dinfo) {
double etaOffset = 0;
if (dinfo._normMul != null && dinfo._normSub != null && beta != null) {
int ns = dinfo.numStart();
for (int i = 0; i < dinfo._nums; ++i)
etaOffset -= beta[i + ns] * dinfo._normSub[i] * dinfo._normMul[i];
}
return etaOffset;
}
public final class BetaConstraint extends Iced {
double[] _betaStart;
double[] _betaGiven;
double[] _rho;
double[] _betaLB;
double[] _betaUB;
public BetaConstraint() {
if (_parms._non_negative) setNonNegative();
}
public void setNonNegative() {
if (_betaLB == null) {
_betaLB = MemoryManager.malloc8d(_dinfo.fullN() + 1);
_betaLB[_dinfo.fullN()] = Double.NEGATIVE_INFINITY;
} else for (int i = 0; i < _betaLB.length - 1; ++i)
_betaLB[i] = Math.max(0, _betaLB[i]);
if (_betaUB == null) {
_betaUB = MemoryManager.malloc8d(_dinfo.fullN() + 1);
Arrays.fill(_betaUB, Double.POSITIVE_INFINITY);
}
}
public double applyBounds(double d, int i) {
if(_betaLB != null && d < _betaLB[i])
return _betaLB[i];
if(_betaUB != null && d > _betaUB[i])
return _betaUB[i];
return d;
}
public BetaConstraint(Frame beta_constraints) {
Vec v = beta_constraints.vec("names");
String[] dom;
int[] map;
if (v.isString()) {
dom = new String[(int) v.length()];
map = new int[dom.length];
BufferedString tmpStr = new BufferedString();
for (int i = 0; i < dom.length; ++i) {
dom[i] = v.atStr(tmpStr, i).toString();
map[i] = i;
}
// check for dups
String[] sortedDom = dom.clone();
Arrays.sort(sortedDom);
for (int i = 1; i < sortedDom.length; ++i)
if (sortedDom[i - 1].equals(sortedDom[i]))
throw new IllegalArgumentException("Illegal beta constraints file, got duplicate constraint for predictor '" + sortedDom[i - 1] + "'!");
} else if (v.isCategorical()) {
dom = v.domain();
map = FrameUtils.asInts(v);
// check for dups
int[] sortedMap = MemoryManager.arrayCopyOf(map, map.length);
Arrays.sort(sortedMap);
for (int i = 1; i < sortedMap.length; ++i)
if (sortedMap[i - 1] == sortedMap[i])
throw new IllegalArgumentException("Illegal beta constraints file, got duplicate constraint for predictor '" + dom[sortedMap[i - 1]] + "'!");
} else
throw new IllegalArgumentException("Illegal beta constraints file, names column expected to contain column names (strings)");
// for now only categoricals allowed here
String[] names = ArrayUtils.append(_dinfo.coefNames(), "Intercept");
if (!Arrays.deepEquals(dom, names)) { // need mapping
HashMap m = new HashMap();
for (int i = 0; i < names.length; ++i)
m.put(names[i], i);
int[] newMap = MemoryManager.malloc4(dom.length);
for (int i = 0; i < map.length; ++i) {
if (_removedCols.contains(dom[map[i]])) {
newMap[i] = -1;
continue;
}
Integer I = m.get(dom[map[i]]);
if (I == null) {
throw new IllegalArgumentException("Unrecognized coefficient name in beta-constraint file, unknown name '" + dom[map[i]] + "'");
}
newMap[i] = I;
}
map = newMap;
}
final int numoff = _dinfo.numStart();
String[] valid_col_names = new String[]{"names", "beta_given", "beta_start", "lower_bounds", "upper_bounds", "rho", "mean", "std_dev"};
Arrays.sort(valid_col_names);
for (String s : beta_constraints.names())
if (Arrays.binarySearch(valid_col_names, s) < 0)
error("beta_constraints", "Unknown column name '" + s + "'");
if ((v = beta_constraints.vec("beta_start")) != null) {
_betaStart = MemoryManager.malloc8d(_dinfo.fullN() + (_dinfo._intercept ? 1 : 0));
for (int i = 0; i < (int) v.length(); ++i)
if (map[i] != -1)
_betaStart[map[i]] = v.at(i);
}
if ((v = beta_constraints.vec("beta_given")) != null) {
_betaGiven = MemoryManager.malloc8d(_dinfo.fullN() + (_dinfo._intercept ? 1 : 0));
for (int i = 0; i < (int) v.length(); ++i)
if (map[i] != -1)
_betaGiven[map[i]] = v.at(i);
}
if ((v = beta_constraints.vec("upper_bounds")) != null) {
_betaUB = MemoryManager.malloc8d(_dinfo.fullN() + (_dinfo._intercept ? 1 : 0));
Arrays.fill(_betaUB, Double.POSITIVE_INFINITY);
for (int i = 0; i < (int) v.length(); ++i)
if (map[i] != -1)
_betaUB[map[i]] = v.at(i);
}
if ((v = beta_constraints.vec("lower_bounds")) != null) {
_betaLB = MemoryManager.malloc8d(_dinfo.fullN() + (_dinfo._intercept ? 1 : 0));
Arrays.fill(_betaLB, Double.NEGATIVE_INFINITY);
for (int i = 0; i < (int) v.length(); ++i)
if (map[i] != -1)
_betaLB[map[i]] = v.at(i);
}
if ((v = beta_constraints.vec("rho")) != null) {
_rho = MemoryManager.malloc8d(_dinfo.fullN() + (_dinfo._intercept ? 1 : 0));
for (int i = 0; i < (int) v.length(); ++i)
if (map[i] != -1)
_rho[map[i]] = v.at(i);
}
// mean override (for data standardization)
if ((v = beta_constraints.vec("mean")) != null) {
_parms._stdOverride = true;
for (int i = 0; i < v.length(); ++i) {
if (!v.isNA(i) && map[i] != -1) {
int idx = map == null ? i : map[i];
if (idx > _dinfo.numStart() && idx < _dinfo.fullN()) {
_dinfo._normSub[idx - _dinfo.numStart()] = v.at(i);
} else {
// categorical or Intercept, will be ignored
}
}
}
}
// standard deviation override (for data standardization)
if ((v = beta_constraints.vec("std_dev")) != null) {
_parms._stdOverride = true;
for (int i = 0; i < v.length(); ++i) {
if (!v.isNA(i) && map[i] != -1) {
int idx = map == null ? i : map[i];
if (idx > _dinfo.numStart() && idx < _dinfo.fullN()) {
_dinfo._normMul[idx - _dinfo.numStart()] = 1.0 / v.at(i);
} else {
// categorical or Intercept, will be ignored
}
}
}
}
if (_dinfo._normMul != null) {
double normG = 0, normS = 0, normLB = 0, normUB = 0;
for (int i = numoff; i < _dinfo.fullN(); ++i) {
double s = _dinfo._normSub[i - numoff];
double d = 1.0 / _dinfo._normMul[i - numoff];
if (_betaUB != null && !Double.isInfinite(_betaUB[i])) {
normUB *= s;
_betaUB[i] *= d;
}
if (_betaLB != null && !Double.isInfinite(_betaUB[i])) {
normLB *= s;
_betaLB[i] *= d;
}
if (_betaGiven != null) {
normG += _betaGiven[i] * s;
_betaGiven[i] *= d;
}
if (_betaStart != null) {
normS += _betaStart[i] * s;
_betaStart[i] *= d;
}
}
if (_dinfo._intercept) {
int n = _dinfo.fullN();
if (_betaGiven != null)
_betaGiven[n] += normG;
if (_betaStart != null)
_betaStart[n] += normS;
if (_betaLB != null)
_betaLB[n] += normLB;
if (_betaUB != null)
_betaUB[n] += normUB;
}
}
if (_betaStart == null && _betaGiven != null)
_betaStart = _betaGiven.clone();
if (_betaStart != null) {
if (_betaLB != null || _betaUB != null) {
for (int i = 0; i < _betaStart.length; ++i) {
if (_betaLB != null && _betaLB[i] > _betaStart[i])
_betaStart[i] = _betaLB[i];
if (_betaUB != null && _betaUB[i] < _betaStart[i])
_betaStart[i] = _betaUB[i];
}
}
}
if (_parms._non_negative) setNonNegative();
check();
}
public String toString() {
double[][] ary = new double[_betaGiven.length][3];
for (int i = 0; i < _betaGiven.length; ++i) {
ary[i][0] = _betaGiven[i];
ary[i][1] = _betaLB[i];
ary[i][2] = _betaUB[i];
}
return ArrayUtils.pprint(ary);
}
public boolean hasBounds() {
if (_betaLB != null)
for (double d : _betaLB)
if (!Double.isInfinite(d)) return true;
if (_betaUB != null)
for (double d : _betaUB)
if (!Double.isInfinite(d)) return true;
return false;
}
public boolean hasProximalPenalty() {
return _betaGiven != null && _rho != null && ArrayUtils.countNonzeros(_rho) > 0;
}
public void adjustGradient(double[] beta, double[] grad) {
if (_betaGiven != null && _rho != null) {
for (int i = 0; i < _betaGiven.length; ++i) {
double diff = beta[i] - _betaGiven[i];
grad[i] += _rho[i] * diff;
}
}
}
double proxPen(double[] beta) {
double res = 0;
if (_betaGiven != null && _rho != null) {
for (int i = 0; i < _betaGiven.length; ++i) {
double diff = beta[i] - _betaGiven[i];
res += _rho[i] * diff * diff;
}
res *= .5;
}
return res;
}
public void check() {
if (_betaLB != null && _betaUB != null)
for (int i = 0; i < _betaLB.length; ++i)
if (!(_betaLB[i] <= _betaUB[i]))
throw new IllegalArgumentException("lower bounds must be <= upper bounds, " + _betaLB[i] + " !<= " + _betaUB[i]);
}
public BetaConstraint filterExpandedColumns(int[] activeCols) {
BetaConstraint res = new BetaConstraint();
if (_betaLB != null)
res._betaLB = ArrayUtils.select(_betaLB, activeCols);
if (_betaUB != null)
res._betaUB = ArrayUtils.select(_betaUB, activeCols);
if (_betaGiven != null)
res._betaGiven = ArrayUtils.select(_betaGiven, activeCols);
if (_rho != null)
res._rho = ArrayUtils.select(_rho, activeCols);
if (_betaStart != null)
res._betaStart = ArrayUtils.select(_betaStart, activeCols);
return res;
}
}
}
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