def main():
sg.omp_set_num_threads(4)
lasso()
print "Finished lasso"
en()
print "Finished en"
group_lasso()
print "Finished group lasso"
lasso_heat()
print "Finished lasso-heat"
grp_heat()
print "Finished grp-heat"
## function is sufficiently smooth and then imposes a multivariate Gaussian with the
## covariance matrix
## \f$\mathbf{\Gamma}_{i,i} = 0.25^{\vert \mathbf{l} \vert_1 - d}\f$, where
## \f$ d \f$ corresponds to the dimension of the grid and
## \f$ \mathbf{\vert \mathbf{l} \vert_1} \f$ to the level sum of the ith grid point.
import requests as r
import numpy as np
import pandas as pd
import sklearn.preprocessing as pre
from sklearn.cross_validation import KFold
from scipy import stats
from zipfile import ZipFile
import io
import pysgpp as sg
sg.omp_set_num_threads(4)
## This function scales all predictors so that they are suitable for sparse grids.
def scale(df, scaler=None):
Y = df.ix[:,
-1] # save Y (don't need to transform it/useless for cat. data!)
X = df.values
if scaler:
X = scaler.transform(X)
else:
scaler = pre.MinMaxScaler()
X = scaler.fit_transform(X)
index = df.index
columns = df.columns
df = pd.DataFrame(data=X, index=index, columns=columns)
"""Example objective function from the title of my Master's thesis."""
def __init__(self):
super(ExampleFunction, self).__init__(2)
def eval(self, x):
"""Evaluates the function."""
return math.sin(8.0 * x[0]) + math.sin(7.0 * x[1])
def printLine():
print("----------------------------------------" + \
"----------------------------------------")
## We have to disable OpenMP within pysgpp since it interferes with SWIG's director feature.
pysgpp.omp_set_num_threads(1)
print("sgpp::optimization example program started.\n")
# increase verbosity of the output
pysgpp.OptPrinter.getInstance().setVerbosity(2)
## Here, we define some parameters: objective function, dimensionality,
## B-spline degree, maximal number of grid points, and adaptivity.
# objective function
f = ExampleFunction()
# dimension of domain
d = f.getNumberOfParameters()
# B-spline degree
p = 3
# maximal number of grid points
N = 30
#!/usr/bin/python
# Copyright (C) 2008-today The SG++ project
# This file is part of the SG++ project. For conditions of distribution and
# use, please see the copyright notice provided with SG++ or at
# sgpp.sparsegrids.org
## \page example_interactionExample_py Interaction Terms Aware Sparse Grids
##
## This example compares standard sparse grids with sparse grids that only contain
## a subset of all possible interaction terms.
## It uses the optical digits dataset as an example.
import numpy as np
import pysgpp as sg; sg.omp_set_num_threads(4)
import pandas as pd
import sklearn.preprocessing as pre
## This function scales all predictors so that they are suitable for sparse grids.
def scale(df, scaler=None):
Y = df.ix[:,-1] # save Y (don't need to transform it/useless for cat. data!)
X = df.values
if scaler:
X = scaler.transform(X)
else:
scaler = pre.MinMaxScaler()
X = scaler.fit_transform(X)
index = df.index
columns = df.columns
df = pd.DataFrame(data=X, index=index, columns=columns)
df.ix[:,-1] = Y
return scaler, df
def main(level, num, T, dataset, _log):
sg.omp_set_num_threads(4)
if 'optdigits' in dataset:
if 'sub' in dataset:
df_train = get_dataset('optdigits_sub_train')
df_test = get_dataset('optdigits_sub_test')
else:
df_train = get_dataset('optdigits_train')
df_test = get_dataset('optdigits_test')
X_train, y_train = get_xy(df_train)
X_test, y_test = get_xy(df_test)
else:
df = get_dataset(dataset)
train, test = split(df)
X_train, y_train = get_xy(train)
X_test, y_test = get_xy(test)
_log.debug("Read file.")
session = model.make_session()
_log.debug("Created SQL session.")
grid_config = model.GridConfig(type=6, level=level, T=T)
adaptivity_config = model.AdaptivityConfig(num_refinements=0,
no_points=3,
treshold=0.0,
percent=0.0)
epsilon = np.sqrt(np.finfo(np.float).eps)
solver_type = sg.SLESolverType_CG
solver_config = model.SolverConfig(type=solver_type,
max_iterations=70,
epsilon=epsilon,
threshold=10e-5)
final_solver_config = model.SolverConfig(type=solver_type,
max_iterations=150,
epsilon=epsilon,
threshold=10e-6)
# solver_type = sg.SLESolverType_FISTA
# solver_config = model.SolverConfig(type=solver_type, max_iterations=200, epsilon=0.0, threshold=10e-5)
# final_solver_config = model.SolverConfig(type=solver_type, max_iterations=400, epsilon=0.0, threshold=10e-8)
regularization_type = sg.RegularizationType_Identity
#regularization_type = sg.RegularizationType_ElasticNet
regularization_config = model.RegularizationConfig(
type=regularization_type, l1_ratio=0.05, exponent_base=1.0)
experiment = model.Experiment(dataset=dataset)
session.add(grid_config)
session.add(adaptivity_config)
session.add(solver_config)
session.add(final_solver_config)
session.add(experiment)
_log.debug("Created configurations.")
interactions = None
#interactions = mnist_interactions(l2_distance, 2*np.sqrt(2), level)
grid_config.interactions = str(interactions)
if 'optdigits' in dataset:
estimator = SGClassificationLearner(grid_config, regularization_config,
solver_config, final_solver_config,
adaptivity_config, interactions)
else:
estimator = SGRegressionLearner(grid_config, regularization_config,
solver_config, final_solver_config,
adaptivity_config, interactions)
cv = get_cv(dataset, y_train)
experiment.cv = str(cv)
#lambda_grid = np.logspace(-6, -1, num=num)
lambda_grid = [0.1]
parameters = {'regularization_config__lambda_reg': lambda_grid}
grid_search = GridSearch(estimator, parameters, cv)
_log.info("Start learning.")
grid_search.fit(X_train, y_train)
_log.info("Finished learning.")
first = True
for score in sorted(grid_search.grid_scores_,
key=itemgetter(1),
reverse=True):
if 'optdigits' in dataset:
error_mult = 1
else:
error_mult = -1
validation_mse = error_mult * score.mean_validation_score
validation_std = np.std(np.abs(score.cv_validation_scores))
validation_grid_sizes = score.cv_grid_sizes
params = estimator.get_params()
params.update(score.parameters)
regularization_config = model.RegularizationConfig(
type=params['regularization_config__type'],
lambda_reg=params['regularization_config__lambda_reg'],
exponent_base=params['regularization_config__exponent_base'],
l1_ratio=params['regularization_config__l1_ratio'])
session.add(regularization_config)
result = model.Result(
validation_mse=validation_mse,
validation_std=validation_std,
grid_config=grid_config,
adaptivity_config=adaptivity_config,
solver_config=solver_config,
final_solver_config=final_solver_config,
regularization_config=regularization_config,
experiment=experiment,
validation_grid_points_mean=np.mean(validation_grid_sizes),
validation_grid_points_stdev=np.std(validation_grid_sizes))
# Retrain best learner and validate test set:
if first:
first = False
estimator.set_params(**params)
estimator.fit(X_train, y_train)
result.train_grid_points = estimator.get_grid_size()
result.train_mse = error_mult * estimator.score(X_train, y_train)
result.test_mse = error_mult * estimator.score(X_test, y_test)
if 'optdigits' not in dataset:
result.train_r2 = get_r_squared(estimator, X_train, y_train)
result.test_r2 = get_r_squared(estimator, X_test, y_test)
session.add(result)
_log.debug("Pushing to database.")
session.commit()
_log.info("Finished experiment.")
def main(level, num, num_init, T, dataset, _log):
sg.omp_set_num_threads(4)
if 'optdigits' in dataset:
df_train = get_dataset('optdigits_train')
df_test = get_dataset('optdigits_test')
X_train, y_train = get_xy(df_train)
X_test, y_test = get_xy(df_test)
else:
df = get_dataset(dataset)
train, test = split(df)
X_train, y_train = get_xy(train)
X_test, y_test = get_xy(test)
_log.debug("Read file.")
session = model.make_session()
_log.debug("Created SQL session.")
grid_config = model.GridConfig(type=6, level=level, T=T)
adaptivity_config = model.AdaptivityConfig(num_refinements=0, no_points=0, treshold=0.0, percent=0.0)
epsilon = np.sqrt(np.finfo(np.float).eps)
solver_type = sg.SLESolverType_CG
solver_config = model.SolverConfig(type=solver_type, max_iterations=70, epsilon=epsilon, threshold=10e-5)
final_solver_config = model.SolverConfig(type=solver_type, max_iterations=250, epsilon=epsilon, threshold=10e-6)
# solver_type = sg.SLESolverType_FISTA
# solver_config = model.SolverConfig(type=solver_type, max_iterations=200, epsilon=0.0, threshold=10e-5)
# final_solver_config = model.SolverConfig(type=solver_type, max_iterations=400, epsilon=0.0, threshold=10e-6)
regularization_type = sg.RegularizationType_Identity
regularization_config = model.RegularizationConfig(type=regularization_type, l1_ratio=1.0, exponent_base=1.0)
experiment = model.Experiment(dataset=dataset)
_log.debug("Created configurations.")
interactions = [[0,1]] + [[i] for i in range(0,11)]
#interactions = None
grid_config.interactions = str(interactions)
estimator = SGRegressionLearner(grid_config, regularization_config, solver_config,
final_solver_config, adaptivity_config, interactions)
cv = get_cv(dataset, X_train)
experiment.cv = str(cv)
params = [Hyp_param('regularization_config__lambda_reg', 0.0, 0.3)]
#Hyp_param('regularization_config__exponent_base', 3.0, 7.0)]
bayes_search = BayesOptReg(estimator, cv, X_train, y_train,
params, num, n_init_samples=num_init)
_log.info("Start learning.")
validation_score, best_params, cv_grid_sizes = bayes_search.optimize()
_log.info("Finished learning.")
_log.info("Best CV-MSE was {}. With params {}".format(validation_score, best_params))
validation_mse = validation_score
validation_grid_sizes = cv_grid_sizes
#Retrain estimator with best parameters
params = estimator.get_params()
params.update(best_params)
estimator.set_params(**params)
estimator.fit(X_train, y_train)
result = model.Result(validation_mse=validation_mse,
grid_config=grid_config,
adaptivity_config=adaptivity_config,
solver_config=solver_config,
final_solver_config=final_solver_config,
regularization_config=regularization_config,
experiment=experiment,
validation_grid_points_mean=np.mean(validation_grid_sizes),
validation_grid_points_stdev=np.std(validation_grid_sizes))
result.train_grid_points = estimator.get_grid_size()
result.train_mse = -estimator.score(X_train, y_train)
result.train_r2 = get_r_squared(estimator, X_train, y_train)
result.test_mse = -estimator.score(X_test, y_test)
result.test_r2 = get_r_squared(estimator, X_test, y_test)
regularization_config = model.RegularizationConfig(
type=params['regularization_config__type'],
lambda_reg=params['regularization_config__lambda_reg'],
exponent_base=params['regularization_config__exponent_base'])
session.add(grid_config)
session.add(adaptivity_config)
session.add(solver_config)
session.add(final_solver_config)
session.add(experiment)
session.add(regularization_config)
session.add(result)
_log.debug("Pushing to database.")
session.commit()
_log.info("Finished experiment.")
super(ExampleFunction, self).__init__(2)
def eval(self, x):
"""Evaluates the function."""
return math.sin(8.0 * x[0]) + math.sin(7.0 * x[1])
def printLine():
print "----------------------------------------" + \
"----------------------------------------"
# disable multi-threading
pysgpp.omp_set_num_threads(1)
# increase output verbosity
pysgpp.OptPrinter.getInstance().setVerbosity(2)
print "SGPP::optimization example program started.\n"
# objective function
f = ExampleFunction()
# dimension of domain
d = f.getNumberOfParameters()
# B-spline degree
p = 3
# maximal number of grid points
N = 30
# adaptivity of grid generation
gamma = 0.95