def statistics_quadratic_time_mmd (): from shogun.Features import RealFeatures from shogun.Features import MeanShiftRealDataGenerator from shogun.Kernel import GaussianKernel from shogun.Statistics import QuadraticTimeMMD from shogun.Statistics import BOOTSTRAP, MMD2_SPECTRUM, MMD2_GAMMA, BIASED, UNBIASED from shogun.Distance import EuclideanDistance from shogun.Mathematics import Statistics, IntVector # note that the quadratic time mmd has to store kernel matrices # which upper bounds the sample size n=500 dim=2 difference=0.5 # streaming data generator for mean shift distributions gen_p=MeanShiftRealDataGenerator(0, dim) gen_q=MeanShiftRealDataGenerator(difference, dim) # Stream examples and merge them in order to compute median on joint sample # alternative is to call a different constructor of QuadraticTimeMMD features=gen_p.get_streamed_features(n) features=features.create_merged_copy(gen_q.get_streamed_features(n)) # use data generator class to produce example data data=features.get_feature_matrix() print "dimension means of X", mean(data.T[0:n].T) print "dimension means of Y", mean(data.T[n:2*n+1].T) # compute median data distance in order to use for Gaussian kernel width # 0.5*median_distance normally (factor two in Gaussian kernel) # However, shoguns kernel width is different to usual parametrization # Therefore 0.5*2*median_distance^2 # Use a subset of data for that, only 200 elements. Median is stable # Use a permutation set to temporarily merge features in merged examples subset=IntVector.randperm_vec(features.get_num_vectors()) subset=subset[0:200] features.add_subset(subset) dist=EuclideanDistance(features, features) distances=dist.get_distance_matrix() features.remove_subset() median_distance=Statistics.matrix_median(distances, True) sigma=median_distance**2 print "median distance for Gaussian kernel:", sigma kernel=GaussianKernel(10,sigma) mmd=QuadraticTimeMMD(kernel,features, n) # perform test: compute p-value and test if null-hypothesis is rejected for # a test level of 0.05 using different methods to approximate # null-distribution statistic=mmd.compute_statistic() alpha=0.05 print "computing p-value using bootstrapping" mmd.set_null_approximation_method(BOOTSTRAP) # normally, at least 250 iterations should be done, but that takes long mmd.set_bootstrap_iterations(10) # bootstrapping allows usage of unbiased or biased statistic mmd.set_statistic_type(UNBIASED) p_value=mmd.compute_p_value(statistic) print "p_value:", p_value print "p_value <", alpha, ", i.e. test sais p!=q:", p_value<alpha # only can do this if SHOGUN was compiled with LAPACK so check if "sample_null_spectrum" in dir(QuadraticTimeMMD): print "computing p-value using spectrum method" mmd.set_null_approximation_method(MMD2_SPECTRUM) # normally, at least 250 iterations should be done, but that takes long mmd.set_num_samples_sepctrum(50) mmd.set_num_eigenvalues_spectrum(n-10) # spectrum method computes p-value for biased statistics only mmd.set_statistic_type(BIASED) p_value=mmd.compute_p_value(statistic) print "p_value:", p_value print "p_value <", alpha, ", i.e. test sais p!=q:", p_value<alpha print "computing p-value using gamma method" mmd.set_null_approximation_method(MMD2_GAMMA) # gamma method computes p-value for biased statistics only mmd.set_statistic_type(BIASED) p_value=mmd.compute_p_value(statistic) print "p_value:", p_value print "p_value <", alpha, ", i.e. test sais p!=q:", p_value<alpha # sample from null distribution (these may be plotted or whatsoever) # mean should be close to zero, variance stronly depends on data/kernel # bootstrapping, biased statistic print "sampling null distribution using bootstrapping" mmd.set_null_approximation_method(BOOTSTRAP) mmd.set_statistic_type(BIASED) mmd.set_bootstrap_iterations(10) null_samples=mmd.bootstrap_null() print "null mean:", mean(null_samples) print "null variance:", var(null_samples) # sample from null distribution (these may be plotted or whatsoever) # mean should be close to zero, variance stronly depends on data/kernel # spectrum, biased statistic print "sampling null distribution using spectrum method" mmd.set_null_approximation_method(MMD2_SPECTRUM) mmd.set_statistic_type(BIASED) # 200 samples using 100 eigenvalues null_samples=mmd.sample_null_spectrum(50,10) print "null mean:", mean(null_samples) print "null variance:", var(null_samples)
def statistics_linear_time_mmd (): from shogun.Features import RealFeatures from shogun.Features import MeanShiftRealDataGenerator from shogun.Kernel import GaussianKernel from shogun.Statistics import LinearTimeMMD from shogun.Statistics import BOOTSTRAP, MMD1_GAUSSIAN from shogun.Distance import EuclideanDistance from shogun.Mathematics import Statistics, Math # note that the linear time statistic is designed for much larger datasets n=10000 dim=2 difference=0.5 # streaming data generator for mean shift distributions gen_p=MeanShiftRealDataGenerator(0, dim) gen_q=MeanShiftRealDataGenerator(difference, dim) # compute median data distance in order to use for Gaussian kernel width # 0.5*median_distance normally (factor two in Gaussian kernel) # However, shoguns kernel width is different to usual parametrization # Therefore 0.5*2*median_distance^2 # Use a subset of data for that, only 200 elements. Median is stable # Stream examples and merge them in order to compute median on joint sample features=gen_p.get_streamed_features(100) features=features.create_merged_copy(gen_q.get_streamed_features(100)) # compute all pairwise distances dist=EuclideanDistance(features, features) distances=dist.get_distance_matrix() # compute median and determine kernel width (using shogun) median_distance=Statistics.matrix_median(distances, True) sigma=median_distance**2 print "median distance for Gaussian kernel:", sigma kernel=GaussianKernel(10,sigma) # mmd instance using streaming features, blocksize of 10000 mmd=LinearTimeMMD(kernel, gen_p, gen_q, n, 10000) # perform test: compute p-value and test if null-hypothesis is rejected for # a test level of 0.05 statistic=mmd.compute_statistic() print "test statistic:", statistic # do the same thing using two different way to approximate null-dstribution # bootstrapping and gaussian approximation (ony for really large samples) alpha=0.05 print "computing p-value using bootstrapping" mmd.set_null_approximation_method(BOOTSTRAP) mmd.set_bootstrap_iterations(50) # normally, far more iterations are needed p_value=mmd.compute_p_value(statistic) print "p_value:", p_value print "p_value <", alpha, ", i.e. test sais p!=q:", p_value<alpha print "computing p-value using gaussian approximation" mmd.set_null_approximation_method(MMD1_GAUSSIAN) p_value=mmd.compute_p_value(statistic) print "p_value:", p_value print "p_value <", alpha, ", i.e. test sais p!=q:", p_value<alpha # sample from null distribution (these may be plotted or whatsoever) # mean should be close to zero, variance stronly depends on data/kernel mmd.set_null_approximation_method(BOOTSTRAP) mmd.set_bootstrap_iterations(10) # normally, far more iterations are needed null_samples=mmd.bootstrap_null() print "null mean:", mean(null_samples) print "null variance:", var(null_samples)
def statistics_linear_time_mmd():
from shogun.Features import RealFeatures
from shogun.Features import MeanShiftRealDataGenerator
from shogun.Kernel import GaussianKernel
from shogun.Statistics import LinearTimeMMD
from shogun.Statistics import BOOTSTRAP, MMD1_GAUSSIAN
from shogun.Distance import EuclideanDistance
from shogun.Mathematics import Statistics, Math
# note that the linear time statistic is designed for much larger datasets
n = 10000
dim = 2
difference = 0.5
# streaming data generator for mean shift distributions
gen_p = MeanShiftRealDataGenerator(0, dim)
gen_q = MeanShiftRealDataGenerator(difference, dim)
# compute median data distance in order to use for Gaussian kernel width
# 0.5*median_distance normally (factor two in Gaussian kernel)
# However, shoguns kernel width is different to usual parametrization
# Therefore 0.5*2*median_distance^2
# Use a subset of data for that, only 200 elements. Median is stable
# Stream examples and merge them in order to compute median on joint sample
features = gen_p.get_streamed_features(100)
features = features.create_merged_copy(gen_q.get_streamed_features(100))
# compute all pairwise distances
dist = EuclideanDistance(features, features)
distances = dist.get_distance_matrix()
# compute median and determine kernel width (using shogun)
median_distance = Statistics.matrix_median(distances, True)
sigma = median_distance**2
print "median distance for Gaussian kernel:", sigma
kernel = GaussianKernel(10, sigma)
# mmd instance using streaming features, blocksize of 10000
mmd = LinearTimeMMD(kernel, gen_p, gen_q, n, 10000)
# perform test: compute p-value and test if null-hypothesis is rejected for
# a test level of 0.05
statistic = mmd.compute_statistic()
print "test statistic:", statistic
# do the same thing using two different way to approximate null-dstribution
# bootstrapping and gaussian approximation (ony for really large samples)
alpha = 0.05
print "computing p-value using bootstrapping"
mmd.set_null_approximation_method(BOOTSTRAP)
mmd.set_bootstrap_iterations(
50) # normally, far more iterations are needed
p_value = mmd.compute_p_value(statistic)
print "p_value:", p_value
print "p_value <", alpha, ", i.e. test sais p!=q:", p_value < alpha
print "computing p-value using gaussian approximation"
mmd.set_null_approximation_method(MMD1_GAUSSIAN)
p_value = mmd.compute_p_value(statistic)
print "p_value:", p_value
print "p_value <", alpha, ", i.e. test sais p!=q:", p_value < alpha
# sample from null distribution (these may be plotted or whatsoever)
# mean should be close to zero, variance stronly depends on data/kernel
mmd.set_null_approximation_method(BOOTSTRAP)
mmd.set_bootstrap_iterations(
10) # normally, far more iterations are needed
null_samples = mmd.bootstrap_null()
print "null mean:", mean(null_samples)
print "null variance:", var(null_samples)
# for nice plotting that fits into our shogun tutorial import latex_plot_inits # parameters, change to get different results m = 100 dim = 2 # setting the difference of the first dimension smaller makes a harder test difference = 0.5 # number of samples taken from null and alternative distribution num_null_samples = 500 # streaming data generator for mean shift distributions gen_p = MeanShiftRealDataGenerator(0, dim) gen_q = MeanShiftRealDataGenerator(difference, dim) # compute median data distance in order to use for Gaussian kernel width # 0.5*median_distance normally (factor two in Gaussian kernel) # However, shoguns kernel width is different to usual parametrization # Therefore 0.5*2*median_distance^2 # Use a subset of data for that, only 200 elements. Median is stable # Stream examples and merge them in order to compute median on joint sample features = gen_p.get_streamed_features(100) features = features.create_merged_copy(gen_q.get_streamed_features(100)) # compute all pairwise distances dist = EuclideanDistance(features, features) distances = dist.get_distance_matrix()
# for nice plotting that fits into our shogun tutorial import latex_plot_inits # parameters, change to get different results m=100 dim=2 # setting the difference of the first dimension smaller makes a harder test difference=0.5 # number of samples taken from null and alternative distribution num_null_samples=500 # streaming data generator for mean shift distributions gen_p=MeanShiftRealDataGenerator(0, dim) gen_q=MeanShiftRealDataGenerator(difference, dim) # compute median data distance in order to use for Gaussian kernel width # 0.5*median_distance normally (factor two in Gaussian kernel) # However, shoguns kernel width is different to usual parametrization # Therefore 0.5*2*median_distance^2 # Use a subset of data for that, only 200 elements. Median is stable # Stream examples and merge them in order to compute median on joint sample features=gen_p.get_streamed_features(100) features=features.create_merged_copy(gen_q.get_streamed_features(100)) # compute all pairwise distances dist=EuclideanDistance(features, features) distances=dist.get_distance_matrix()
