Example 1 with Env
use of water.exec.Env in project h2o-2 by h2oai.
the class Impute method serve.
@Override
protected Response serve() {
if (init())
return Inspect2.redirect(this, source._key.toString());
final int col_id = source.find(column);
final int[] _cols = group_by;
final Key mykey = Key.make();
try {
if (group_by == null) {
// just use "method" using the input "column"
double _replace_val = 0;
if (method == Method.mean) {
_replace_val = column.mean();
} else if (method == Method.median) {
QuantilesPage qp = new QuantilesPage();
qp.source_key = source;
qp.column = column;
qp.invoke();
_replace_val = qp.result;
} else if (method == Method.mode) {
String[] dom = column.domain();
long[][] levels = new long[1][];
levels[0] = new Vec.CollectDomain(column).doAll(new Frame(column)).domain();
long[][] counts = new ASTTable.Tabularize(levels).doAll(column)._counts;
long maxCounts = -1;
int mode = -1;
for (int i = 0; i < counts[0].length; ++i) {
if (counts[0][i] > maxCounts && !dom[i].equals("NA")) {
// check for "NA" in domain -- corner case from R
maxCounts = counts[0][i];
mode = i;
}
}
_replace_val = mode != -1 ? (double) mode : // could produce -1 if "NA" not in the domain -- that is we don't have the R corner case
(double) Arrays.asList(dom).indexOf("NA");
// OK to replace, since we're in the elif "mode" block
if (_replace_val == -1)
_replace_val = Double.NaN;
}
final double rv = _replace_val;
new MRTask2() {
@Override
public void map(Chunk[] cs) {
Chunk c = cs[col_id];
int rows = c.len();
for (int r = 0; r < rows; ++r) {
if (c.isNA0(r) || (c._vec.isEnum() && c._vec.domain()[(int) c.at0(r)].equals("NA"))) {
// leave as NA if replace value is NA
if (!Double.isNaN(rv))
c.set0(r, rv);
}
}
}
}.doAll(source);
} else {
// collect the groups HashMap and the frame from the ddply.
// create a vec of group IDs (each row is in some group)
// MRTask over the rows
water.exec.Exec2.exec(Key.make().toString() + " = anonymous <- function(x) \n{\n " + method + "(x[," + (col_id + 1) + "])\n}").remove_and_unlock();
Env env = water.exec.Exec2.exec(mykey.toString() + " = ddply(" + source._key.toString() + ", " + toAryString(_cols) + ", anonymous)");
final Frame grp_replacement = new Frame(env.peekAry());
env.remove_and_unlock();
Log.info("GROUP TASK NUM COLS: " + grp_replacement.numCols());
final GroupTask grp2val = new GroupTask(grp_replacement.numCols() - 1).doAll(grp_replacement);
new MRTask2() {
@Override
public void map(Chunk[] cs) {
Chunk c = cs[col_id];
int rows = cs[0].len();
for (int r = 0; r < rows; ++r) {
if (c.isNA0(r) || (c._vec.isEnum() && c._vec.domain()[(int) c.at0(r)].equals("NA"))) {
Group g = new Group(_cols.length);
g.fill(r, cs, _cols);
if (grp2val._grp2val.get(g) == null)
continue;
double rv = grp2val._grp2val.get(g);
c.set0(r, rv);
}
}
}
}.doAll(source);
}
return Inspect2.redirect(this, source._key.toString());
} catch (Throwable t) {
return Response.error(t);
} finally {
// Delete frames
UKV.remove(mykey);
}
}Example 2 with Env
use of water.exec.Env in project h2o-2 by h2oai.
the class DeepLearningProstateTest method runFraction.
public void runFraction(float fraction) {
long seed = 0xDECAF;
Random rng = new Random(seed);
String[] datasets = new String[2];
int[][] responses = new int[datasets.length][];
//CAPSULE (binomial), AGE (regression), GLEASON (multi-class)
datasets[0] = "smalldata/./logreg/prostate.csv";
//CAPSULE (binomial), AGE (regression), GLEASON (multi-class)
responses[0] = new int[] { 1, 2, 8 };
//Iris-type (multi-class)
datasets[1] = "smalldata/iris/iris.csv";
//Iris-type (multi-class)
responses[1] = new int[] { 4 };
int testcount = 0;
int count = 0;
for (int i = 0; i < datasets.length; ++i) {
String dataset = datasets[i];
Key file = NFSFileVec.make(find_test_file(dataset));
Frame frame = ParseDataset2.parse(Key.make(), new Key[] { file });
Key vfile = NFSFileVec.make(find_test_file(dataset));
Frame vframe = ParseDataset2.parse(Key.make(), new Key[] { vfile });
try {
for (boolean replicate : new boolean[] { true, false }) {
for (boolean load_balance : new boolean[] { true, false }) {
for (boolean shuffle : new boolean[] { true, false }) {
for (boolean balance_classes : new boolean[] { true, false }) {
for (int resp : responses[i]) {
for (DeepLearning.ClassSamplingMethod csm : new DeepLearning.ClassSamplingMethod[] { DeepLearning.ClassSamplingMethod.Stratified, DeepLearning.ClassSamplingMethod.Uniform }) {
for (int scoretraining : new int[] { 200, 20, 0 }) {
for (int scorevalidation : new int[] { 200, 20, 0 }) {
for (int vf : new int[] { //no validation
0, //same as source
1, //different validation frame
-1 }) {
for (int n_folds : new int[] { 0, 2 }) {
if (n_folds != 0 && vf != 0)
continue;
for (boolean keep_cv_splits : new boolean[] { false }) {
//otherwise it leaks
for (boolean override_with_best_model : new boolean[] { false, true }) {
for (int train_samples_per_iteration : new int[] { //auto-tune
-2, //N epochs per iteration
-1, //1 epoch per iteration
0, // <1 epoch per iteration
rng.nextInt(200), //>1 epoch per iteration
500 }) {
DeepLearningModel model1 = null, model2 = null;
Key dest = null, dest_tmp = null;
count++;
if (fraction < rng.nextFloat())
continue;
try {
Log.info("**************************)");
Log.info("Starting test #" + count);
Log.info("**************************)");
final double epochs = 7 + rng.nextDouble() + rng.nextInt(4);
final int[] hidden = new int[] { 1 + rng.nextInt(4), 1 + rng.nextInt(6) };
//no validation
Frame valid = null;
if (//use the same frame for validation
vf == 1)
//use the same frame for validation
valid = frame;
else //different validation frame (here: from the same file)
if (vf == -1)
valid = vframe;
// build the model, with all kinds of shuffling/rebalancing/sampling
dest_tmp = Key.make("first");
{
Log.info("Using seed: " + seed);
DeepLearning p = new DeepLearning();
p.checkpoint = null;
p.destination_key = dest_tmp;
p.source = frame;
p.response = frame.vecs()[resp];
p.validation = valid;
p.hidden = hidden;
if (i == 0 && resp == 2)
p.classification = false;
// p.best_model_key = best_model_key;
p.override_with_best_model = override_with_best_model;
p.epochs = epochs;
p.n_folds = n_folds;
p.keep_cross_validation_splits = keep_cv_splits;
p.seed = seed;
p.train_samples_per_iteration = train_samples_per_iteration;
p.force_load_balance = load_balance;
p.replicate_training_data = replicate;
p.shuffle_training_data = shuffle;
p.score_training_samples = scoretraining;
p.score_validation_samples = scorevalidation;
p.classification_stop = -1;
p.regression_stop = -1;
p.balance_classes = balance_classes;
p.quiet_mode = true;
p.score_validation_sampling = csm;
try {
p.invoke();
} catch (Throwable t) {
t.printStackTrace();
throw new RuntimeException(t);
} finally {
p.delete();
}
model1 = UKV.get(dest_tmp);
assert (((p.train_samples_per_iteration <= 0 || p.train_samples_per_iteration >= frame.numRows()) && model1.epoch_counter > epochs) || Math.abs(model1.epoch_counter - epochs) / epochs < 0.20);
if (n_folds != 0) // test HTML of cv models
{
for (Key k : model1.get_params().xval_models) {
DeepLearningModel cv_model = UKV.get(k);
StringBuilder sb = new StringBuilder();
cv_model.generateHTML("cv", sb);
cv_model.delete_best_model();
cv_model.delete();
}
}
}
// Do some more training via checkpoint restart
// For n_folds, continue without n_folds (not yet implemented) - from now on, model2 will have n_folds=0...
dest = Key.make("restart");
DeepLearning p = new DeepLearning();
//this actually *requires* frame to also still be in UKV (because of DataInfo...)
final DeepLearningModel tmp_model = UKV.get(dest_tmp);
//HEX-1817
Assert.assertTrue(tmp_model.get_params().state == Job.JobState.DONE);
Assert.assertTrue(tmp_model.model_info().get_processed_total() >= frame.numRows() * epochs);
assert (tmp_model != null);
p.checkpoint = dest_tmp;
p.destination_key = dest;
p.n_folds = 0;
p.source = frame;
p.validation = valid;
p.response = frame.vecs()[resp];
if (i == 0 && resp == 2)
p.classification = false;
p.override_with_best_model = override_with_best_model;
p.epochs = epochs;
p.seed = seed;
p.train_samples_per_iteration = train_samples_per_iteration;
try {
p.invoke();
} catch (Throwable t) {
t.printStackTrace();
throw new RuntimeException(t);
} finally {
p.delete();
}
// score and check result (on full data)
//this actually *requires* frame to also still be in UKV (because of DataInfo...)
model2 = UKV.get(dest);
//HEX-1817
Assert.assertTrue(model2.get_params().state == Job.JobState.DONE);
// test HTML
{
StringBuilder sb = new StringBuilder();
model2.generateHTML("test", sb);
}
// score and check result of the best_model
if (model2.actual_best_model_key != null) {
final DeepLearningModel best_model = UKV.get(model2.actual_best_model_key);
//HEX-1817
Assert.assertTrue(best_model.get_params().state == Job.JobState.DONE);
// test HTML
{
StringBuilder sb = new StringBuilder();
best_model.generateHTML("test", sb);
}
if (override_with_best_model) {
Assert.assertEquals(best_model.error(), model2.error(), 0);
}
}
if (valid == null)
valid = frame;
double threshold = 0;
if (model2.isClassifier()) {
Frame pred = null, pred2 = null;
try {
pred = model2.score(valid);
StringBuilder sb = new StringBuilder();
AUC auc = new AUC();
double error = 0;
// binary
if (model2.nclasses() == 2) {
auc.actual = valid;
assert (resp == 1);
auc.vactual = valid.vecs()[resp];
auc.predict = pred;
auc.vpredict = pred.vecs()[2];
auc.invoke();
auc.toASCII(sb);
AUCData aucd = auc.data();
threshold = aucd.threshold();
error = aucd.err();
Log.info(sb);
// check that auc.cm() is the right CM
Assert.assertEquals(new ConfusionMatrix(aucd.cm()).err(), error, 1e-15);
// check that calcError() is consistent as well (for CM=null, AUC!=null)
Assert.assertEquals(model2.calcError(valid, auc.vactual, pred, pred, "training", false, 0, null, auc, null), error, 1e-15);
}
// Compute CM
double CMerrorOrig;
{
sb = new StringBuilder();
water.api.ConfusionMatrix CM = new water.api.ConfusionMatrix();
CM.actual = valid;
CM.vactual = valid.vecs()[resp];
CM.predict = pred;
CM.vpredict = pred.vecs()[0];
CM.invoke();
sb.append("\n");
sb.append("Threshold: " + "default\n");
CM.toASCII(sb);
Log.info(sb);
CMerrorOrig = new ConfusionMatrix(CM.cm).err();
}
// confirm that orig CM was made with threshold 0.5
// put pred2 into UKV, and allow access
pred2 = new Frame(Key.make("pred2"), pred.names(), pred.vecs());
pred2.delete_and_lock(null);
pred2.unlock(null);
if (model2.nclasses() == 2) {
// make labels with 0.5 threshold for binary classifier
Env ev = Exec2.exec("pred2[,1]=pred2[,3]>=" + 0.5);
try {
pred2 = ev.popAry();
String skey = ev.key();
ev.subRef(pred2, skey);
} finally {
if (ev != null)
ev.remove_and_unlock();
}
water.api.ConfusionMatrix CM = new water.api.ConfusionMatrix();
CM.actual = valid;
CM.vactual = valid.vecs()[1];
CM.predict = pred2;
CM.vpredict = pred2.vecs()[0];
CM.invoke();
sb = new StringBuilder();
sb.append("\n");
sb.append("Threshold: " + 0.5 + "\n");
CM.toASCII(sb);
Log.info(sb);
double threshErr = new ConfusionMatrix(CM.cm).err();
Assert.assertEquals(threshErr, CMerrorOrig, 1e-15);
// make labels with AUC-given threshold for best F1
ev = Exec2.exec("pred2[,1]=pred2[,3]>=" + threshold);
try {
pred2 = ev.popAry();
String skey = ev.key();
ev.subRef(pred2, skey);
} finally {
if (ev != null)
ev.remove_and_unlock();
}
CM = new water.api.ConfusionMatrix();
CM.actual = valid;
CM.vactual = valid.vecs()[1];
CM.predict = pred2;
CM.vpredict = pred2.vecs()[0];
CM.invoke();
sb = new StringBuilder();
sb.append("\n");
sb.append("Threshold: ").append(threshold).append("\n");
CM.toASCII(sb);
Log.info(sb);
double threshErr2 = new ConfusionMatrix(CM.cm).err();
Assert.assertEquals(threshErr2, error, 1e-15);
}
} finally {
if (pred != null)
pred.delete();
if (pred2 != null)
pred2.delete();
}
}
//classifier
Log.info("Parameters combination " + count + ": PASS");
testcount++;
} catch (Throwable t) {
t.printStackTrace();
throw new RuntimeException(t);
} finally {
if (model1 != null) {
model1.delete_xval_models();
model1.delete_best_model();
model1.delete();
}
if (model2 != null) {
model2.delete_xval_models();
model2.delete_best_model();
model2.delete();
}
}
}
}
}
}
}
}
}
}
}
}
}
}
}
} finally {
frame.delete();
vframe.delete();
}
}
Log.info("\n\n=============================================");
Log.info("Tested " + testcount + " out of " + count + " parameter combinations.");
Log.info("=============================================");
}
Also used :
Frame(water.fvec.Frame)
AUCData(water.api.AUCData)
DeepLearning(hex.deeplearning.DeepLearning)
Env(water.exec.Env)
AUC(water.api.AUC)
Random(java.util.Random)
water(water)
DeepLearningModel(hex.deeplearning.DeepLearningModel)
Aggregations
Env (water.exec.Env)2
Frame (water.fvec.Frame)2
DeepLearning (hex.deeplearning.DeepLearning)1
DeepLearningModel (hex.deeplearning.DeepLearningModel)1
Random (java.util.Random)1
water (water)1
AUC (water.api.AUC)1
AUCData (water.api.AUCData)1
Group (water.exec.ASTddply.Group)1
Chunk (water.fvec.Chunk)1
Vec (water.fvec.Vec)1
