def test_smoothed(self):
import numpy as np
import parsimony.utils.consts as consts
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions.losses as losses
import parsimony.functions.penalties as penalties
import parsimony.functions.nesterov as nesterov
import parsimony.utils.start_vectors as start_vectors
import parsimony.datasets.simulate.l1_l2_tv as l1_l2_tv
start_vector = start_vectors.RandomStartVector(normalise=True)
np.random.seed(42)
n, p = 75, 100
penalty_start = 0
alpha = 0.9
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
beta = start_vector.get_vector(p)
beta[np.abs(beta) < 0.1] = 0.0
l = 0.618
k = 0.0
g = 0.0
mu_min = 0.001 # consts.TOLERANCE
A = np.eye(p)
A = [A, A, A]
snr = 100.0
X, y, beta_star = l1_l2_tv.load(l, k, g, beta, M, e, A, snr=snr)
function = CombinedFunction()
function.add_function(losses.LinearRegression(X, y,
# penalty_start=penalty_start,
mean=False))
A = nesterov.l1.A_from_variables(p, penalty_start=penalty_start)
function.add_penalty(nesterov.l1.L1(l, A=A, mu=mu_min,
penalty_start=penalty_start))
# function.add_prox(penalties.L1(l, penalty_start=penalty_start))
fista = proximal.FISTA(eps=mu_min, max_iter=20000)
beta = fista.run(function, beta)
assert np.linalg.norm(beta - beta_star) < 5e-2
def test_combo_overlapping_nonsmooth(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_gl as l1_l2_gl
import parsimony.utils.start_vectors as start_vectors
np.random.seed(42)
# Note that p must be even!
n, p = 25, 30
groups = [range(0, 2 * p / 3), range(p / 3, p)]
weights = [1.5, 0.5]
A = gl.A_from_groups(p, groups=groups, weights=weights)
l = 0.618
k = 1.0 - l
g = 2.718
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
X, y, beta_star = l1_l2_gl.load(l, k, g, beta, M, e, A, snr=snr)
eps = 1e-8
max_iter = 10000
beta_start = start_vector.get_vector(p)
mus = [5e-0, 5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_function(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(functions.penalties.L2Squared(l=k))
function.add_penalty(gl.GroupLassoOverlap(l=g, A=A, mu=mu,
penalty_start=0))
function.add_prox(functions.penalties.L1(l=l))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print berr
assert berr < 5e-3
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
# print abs(f_parsimony - f_star)
assert abs(f_parsimony - f_star) < 5e-6
def test_nonoverlapping_nonsmooth(self):
# Spams: http://spams-devel.gforge.inria.fr/doc-python/doc_spams.pdf
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_gl as l1_l2_gl
import parsimony.utils.start_vectors as start_vectors
np.random.seed(42)
# Note that p must be even!
n, p = 25, 20
groups = [range(0, p / 2), range(p / 2, p)]
# weights = [1.5, 0.5]
A = gl.A_from_groups(p, groups=groups) # , weights=weights)
l = 0.0
k = 0.0
g = 1.0
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
X, y, beta_star = l1_l2_gl.load(l, k, g, beta, M, e, A, snr=snr)
eps = 1e-8
max_iter = 8500
beta_start = start_vector.get_vector(p)
mus = [5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_function(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(gl.GroupLassoOverlap(l=g, A=A, mu=mu,
penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
try:
import spams
params = {"loss": "square",
"regul": "group-lasso-l2",
"groups": np.array([1] * (p / 2) + [2] * (p / 2),
dtype=np.int32),
"lambda1": g,
"max_it": max_iter,
"tol": eps,
"ista": False,
"numThreads": -1,
}
beta_spams, optim_info = \
spams.fistaFlat(Y=np.asfortranarray(y),
X=np.asfortranarray(X),
W0=np.asfortranarray(beta_start),
return_optim_info=True,
**params)
except ImportError:
beta_spams = np.asarray([[14.01111427],
[35.56508563],
[27.38245962],
[22.39716553],
[5.835744940],
[5.841502910],
[2.172209350],
[32.40227785],
[22.48364756],
[26.48822401],
[0.770391500],
[36.28288883],
[31.14118214],
[7.938279340],
[6.800713150],
[6.862914540],
[11.38161678],
[19.63087584],
[16.15855845],
[10.89356615]])
berr = np.linalg.norm(beta_parsimony - beta_spams)
# print berr
assert berr < 5e-2
f_parsimony = function.f(beta_parsimony)
f_spams = function.f(beta_spams)
ferr = abs(f_parsimony - f_spams)
# print ferr
assert ferr < 5e-6
def test_nonoverlapping_smooth(self):
# Spams: http://spams-devel.gforge.inria.fr/doc-python/doc_spams.pdf
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_glmu as l1_l2_glmu
import parsimony.utils.start_vectors as start_vectors
np.random.seed(42)
# Note that p must be even!
n, p = 25, 20
groups = [range(0, p / 2), range(p / 2, p)]
# weights = [1.5, 0.5]
A = gl.A_from_groups(p, groups=groups) # , weights=weights)
l = 0.0
k = 0.0
g = 0.9
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
mu_min = 5e-8
X, y, beta_star = l1_l2_glmu.load(l, k, g, beta, M, e, A,
mu=mu_min, snr=snr)
eps = 1e-8
max_iter = 18000
beta_start = start_vector.get_vector(p)
mus = [5e-0, 5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_function(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(gl.GroupLassoOverlap(l=g, A=A, mu=mu,
penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
try:
import spams
params = {"loss": "square",
"regul": "group-lasso-l2",
"groups": np.array([1] * (p / 2) + [2] * (p / 2),
dtype=np.int32),
"lambda1": g,
"max_it": max_iter,
"tol": eps,
"ista": False,
"numThreads": -1,
}
beta_spams, optim_info = \
spams.fistaFlat(Y=np.asfortranarray(y),
X=np.asfortranarray(X),
W0=np.asfortranarray(beta_start),
return_optim_info=True,
**params)
# print beta_spams
except ImportError:
beta_spams = np.asarray([[15.56784201],
[39.51679274],
[30.42583205],
[24.8816362],
[6.48671072],
[6.48350546],
[2.41477318],
[36.00285723],
[24.98522184],
[29.43128643],
[0.85520539],
[40.31463542],
[34.60084146],
[8.82322513],
[7.55741642],
[7.62364398],
[12.64594707],
[21.81113869],
[17.95400007],
[12.10507338]])
berr = np.linalg.norm(beta_parsimony - beta_spams)
# print berr
assert berr < 5e-3
f_parsimony = function.f(beta_parsimony)
f_spams = function.f(beta_spams)
ferr = abs(f_parsimony - f_spams)
# print ferr
assert ferr < 5e-6
def test_combo_smooth(self):
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.tv as tv
import parsimony.datasets.simulate.l1_l2_tvmu as l1_l2_tvmu
import parsimony.utils.start_vectors as start_vectors
np.random.seed(42)
px = 4
py = 4
pz = 4
shape = (pz, py, px)
n, p = 50, np.prod(shape)
l = 0.618
k = 1.0 - l
g = 1.1
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
A = tv.linear_operator_from_shape(shape)
mu_min = 5e-8
X, y, beta_star = l1_l2_tvmu.load(l=l, k=k, g=g, beta=beta, M=M, e=e,
A=A, mu=mu_min, snr=snr)
eps = 1e-8
max_iter = 5300
beta_start = start_vector.get_vector(p)
mus = [5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_function(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(tv.TotalVariation(l=g, A=A, mu=mu,
penalty_start=0))
function.add_penalty(functions.penalties.L2Squared(l=k))
function.add_prox(functions.penalties.L1(l=l))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print "berr:", berr
assert berr < 5e-3
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
ferr = abs(f_parsimony - f_star)
# print "ferr:", ferr
assert ferr < 5e-5
def test_combo_overlapping_nonsmooth(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_gl as l1_l2_gl
import parsimony.utils.weights as weights
np.random.seed(42)
# Note that p must be even!
n, p = 25, 30
groups = [list(range(0, 2 * int(p / 3))), list(range(int(p / 3), p))]
group_weights = [1.5, 0.5]
A = gl.linear_operator_from_groups(p,
groups=groups,
weights=group_weights)
l = 0.618
k = 1.0 - l
g = 2.718
start_vector = weights.RandomUniformWeights(normalise=True)
beta = start_vector.get_weights(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
X, y, beta_star = l1_l2_gl.load(l, k, g, beta, M, e, A, snr=snr)
eps = 1e-8
max_iter = 10000
beta_start = start_vector.get_weights(p)
mus = [5e-0, 5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_loss(
functions.losses.LinearRegression(X, y, mean=False))
function.add_penalty(functions.penalties.L2Squared(l=k))
function.add_penalty(
gl.GroupLassoOverlap(l=g, A=A, mu=mu, penalty_start=0))
function.add_prox(functions.penalties.L1(l=l))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print berr
assert berr < 5e-3
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
# print abs(f_parsimony - f_star)
assert abs(f_parsimony - f_star) < 5e-6
def test_nonoverlapping_smooth(self):
# Spams: http://spams-devel.gforge.inria.fr/doc-python/doc_spams.pdf
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_glmu as l1_l2_glmu
import parsimony.utils.weights as weights
np.random.seed(42)
# Note that p must be even!
n, p = 25, 20
groups = [list(range(0, int(p / 2))), list(range(int(p / 2), p))]
# weights = [1.5, 0.5]
A = gl.linear_operator_from_groups(p,
groups=groups) # , weights=weights)
l = 0.0
k = 0.0
g = 0.9
start_vector = weights.RandomUniformWeights(normalise=True)
beta = start_vector.get_weights(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
mu_min = 5e-8
X, y, beta_star = l1_l2_glmu.load(l,
k,
g,
beta,
M,
e,
A,
mu=mu_min,
snr=snr)
eps = 1e-8
max_iter = 18000
beta_start = start_vector.get_weights(p)
mus = [5e-0, 5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_loss(
functions.losses.LinearRegression(X, y, mean=False))
function.add_penalty(
gl.GroupLassoOverlap(l=g, A=A, mu=mu, penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
try:
import spams
params = {
"loss":
"square",
"regul":
"group-lasso-l2",
"groups":
np.array([1] * (int(p / 2)) + [2] * (int(p / 2)),
dtype=np.int32),
"lambda1":
g,
"max_it":
max_iter,
"tol":
eps,
"ista":
False,
"numThreads":
-1,
}
beta_spams, optim_info = \
spams.fistaFlat(Y=np.asfortranarray(y),
X=np.asfortranarray(X),
W0=np.asfortranarray(beta_start),
return_optim_info=True,
**params)
# print beta_spams
except ImportError:
# beta_spams = np.asarray([[15.56784201],
# [39.51679274],
# [30.42583205],
# [24.8816362],
# [6.48671072],
# [6.48350546],
# [2.41477318],
# [36.00285723],
# [24.98522184],
# [29.43128643],
# [0.85520539],
# [40.31463542],
# [34.60084146],
# [8.82322513],
# [7.55741642],
# [7.62364398],
# [12.64594707],
# [21.81113869],
# [17.95400007],
# [12.10507338]])
beta_spams = np.asarray([[-11.93855944], [42.889350930],
[22.076438880], [9.3869208300],
[-32.73310431], [-32.73509107],
[-42.05298794], [34.844819990],
[9.6210946300], [19.799892400],
[-45.62041548], [44.716039010],
[31.634706630], [-27.37416567],
[-30.27711859], [-30.12673231],
[-18.62803747], [2.3561952400],
[-6.476922020], [-19.86630857]])
berr = np.linalg.norm(beta_parsimony - beta_spams)
# print berr
assert berr < 5e-3
f_parsimony = function.f(beta_parsimony)
f_spams = function.f(beta_spams)
ferr = abs(f_parsimony - f_spams)
# print ferr
assert ferr < 5e-6
def test_overlapping_smooth(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_glmu as l1_l2_glmu
import parsimony.utils.weights as weights
np.random.seed(314)
# Note that p must be even!
n, p = 25, 30
groups = [list(range(0, 2 * int(p / 3))), list(range(int(p / 3), p))]
group_weights = [1.5, 0.5]
A = gl.linear_operator_from_groups(p, groups=groups,
weights=group_weights)
l = 0.0
k = 0.0
g = 0.9
start_vector = weights.RandomUniformWeights(normalise=True)
beta = start_vector.get_weights(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
mu_min = 5e-8
X, y, beta_star = l1_l2_glmu.load(l, k, g, beta, M, e, A,
mu=mu_min, snr=snr)
eps = 1e-8
max_iter = 15000
beta_start = start_vector.get_weights(p)
mus = [5e-0, 5e-2, 5e-4, 5e-6, 5e-8]
fista = FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_loss(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(gl.GroupLassoOverlap(l=g, A=A, mu=mu,
penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print berr
assert berr < 5e-2
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
# print(abs(f_parsimony - f_star))
assert abs(f_parsimony - f_star) < 5e-6
def test_smoothed_l1tv(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.penalties as penalties
import parsimony.functions.nesterov.tv as tv
import parsimony.functions.nesterov.l1tv as l1tv
import parsimony.utils.start_vectors as start_vectors
import parsimony.datasets.simulate as simulate
np.random.seed(42)
px = 10
py = 1
pz = 1
shape = (pz, py, px)
n, p = 5, np.prod(shape)
l = 0.618
k = 0.01
g = 1.1
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
mu = 5e-3
A = tv.linear_operator_from_shape(shape)
# X, y, beta_star = l1_l2_tvmu.load(l=l, k=k, g=g, beta=beta, M=M, e=e,
# A=A, mu=mu, snr=snr)
funs = [simulate.grad.L1(l),
simulate.grad.L2Squared(k),
simulate.grad.TotalVariation(g, A)]
lr = simulate.LinearRegressionData(funs, M, e, snr=snr,
intercept=False)
X, y, beta_star = lr.load(beta)
eps = 1e-8
max_iter = 810
alg = proximal.FISTA(eps=eps, max_iter=max_iter)
function = CombinedFunction()
function.add_loss(functions.losses.LinearRegression(X, y, mean=False))
function.add_penalty(penalties.L2Squared(l=k))
A = l1tv.linear_operator_from_shape(shape, p)
function.add_prox(l1tv.L1TV(l, g, A=A, mu=mu, penalty_start=0))
# A = tv.linear_operator_from_shape(shape)
# function.add_penalty(tv.TotalVariation(l=g, A=A, mu=mu,
# penalty_start=0))
# function.add_prox(penalties.L1(l=l))
beta_start = start_vector.get_vector(p)
beta = alg.run(function, beta_start)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 5e-1
assert_less(berr, 5e-1, "The found regression vector is not correct.")
f_parsimony = function.f(beta)
f_star = function.f(beta_star)
ferr = abs(f_parsimony - f_star)
# print "ferr:", ferr
# assert ferr < 5e-3
assert_less(ferr, 5e-3, "The found regression vector is not correct.")
def test_nonsmooth(self):
import numpy as np
import parsimony.utils.consts as consts
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions.losses as losses
import parsimony.functions.penalties as penalties
import parsimony.functions.nesterov as nesterov
import parsimony.utils.start_vectors as start_vectors
import parsimony.datasets.simulate.l1_l2_tv as l1_l2_tv
start_vector = start_vectors.RandomStartVector(normalise=True)
np.random.seed(42)
n, p = 75, 100
alpha = 0.9
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
beta_start = start_vector.get_vector(p)
beta_start[np.abs(beta_start) < 0.1] = 0.0
l = 0.618
k = 0.0
g = 0.0
A = np.eye(p)
A = [A, A, A]
snr = 100.0
X, y, beta_star = l1_l2_tv.load(l, k, g, beta_start, M, e, A, snr=snr)
beta = beta_start
for mu in [5e-2, 5e-3, 5e-4, 5e-5]:
function = CombinedFunction()
function.add_function(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(p, penalty_start=0)
function.add_penalty(nesterov.l1.L1(l, A=A, mu=mu,
penalty_start=0))
fista = proximal.FISTA(eps=consts.TOLERANCE, max_iter=910)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
assert berr < 5e-2
# Test proximal operator
beta = beta_start
function = CombinedFunction()
function.add_function(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(p, penalty_start=0)
# function.add_penalty(nesterov.l1.L1(l, A=A, mu=mu_min,
# penalty_start=penalty_start))
function.add_prox(nesterov.l1.L1(l, A=A, mu=5e-5, penalty_start=0))
fista = proximal.FISTA(eps=consts.TOLERANCE, max_iter=800)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
assert berr < 5e-0
def test_smoothed_l1tv(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.penalties as penalties
import parsimony.functions.nesterov.tv as tv
import parsimony.functions.nesterov.l1tv as l1tv
import parsimony.datasets.simulate.l1_l2_tvmu as l1_l2_tvmu
import parsimony.utils.start_vectors as start_vectors
import parsimony.datasets.simulate as simulate
np.random.seed(42)
px = 10
py = 1
pz = 1
shape = (pz, py, px)
n, p = 5, np.prod(shape)
l = 0.618
k = 0.01
g = 1.1
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
mu = 5e-3
A = tv.linear_operator_from_shape(shape)
# X, y, beta_star = l1_l2_tvmu.load(l=l, k=k, g=g, beta=beta, M=M, e=e,
# A=A, mu=mu, snr=snr)
funs = [
simulate.grad.L1(l),
simulate.grad.L2Squared(k),
simulate.grad.TotalVariation(g, A)
]
lr = simulate.LinearRegressionData(funs,
M,
e,
snr=snr,
intercept=False)
X, y, beta_star = lr.load(beta)
eps = 1e-8
max_iter = 810
alg = proximal.FISTA(eps=eps, max_iter=max_iter)
function = CombinedFunction()
function.add_function(
functions.losses.LinearRegression(X, y, mean=False))
function.add_penalty(penalties.L2Squared(l=k))
A = l1tv.linear_operator_from_shape(shape, p)
function.add_prox(l1tv.L1TV(l, g, A=A, mu=mu, penalty_start=0))
# A = tv.linear_operator_from_shape(shape)
# function.add_penalty(tv.TotalVariation(l=g, A=A, mu=mu,
# penalty_start=0))
# function.add_prox(penalties.L1(l=l))
beta_start = start_vector.get_vector(p)
beta = alg.run(function, beta_start)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
assert berr < 5e-1
f_parsimony = function.f(beta)
f_star = function.f(beta_star)
ferr = abs(f_parsimony - f_star)
# print "ferr:", ferr
assert ferr < 5e-3
def test_smoothed(self):
import numpy as np
import scipy.sparse
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions.losses as losses
import parsimony.functions.nesterov as nesterov
import parsimony.utils.weights as weights
import parsimony.datasets.simulate.l1_l2_tv as l1_l2_tv
start_vector = weights.RandomUniformWeights(normalise=True)
np.random.seed(42)
n, p = 75, 100
penalty_start = 0
alpha = 0.9
V = np.random.randn(p, p)
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.dot(V.T, V)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
beta = start_vector.get_weights(p)
beta[np.abs(beta) < 0.1] = 0.0
l = 0.618
k = 0.0
g = 0.0
mu_min = 0.001 # consts.TOLERANCE
A = scipy.sparse.eye(p)
# A = np.eye(p)
A = [A, A, A]
snr = 100.0
X, y, beta_star = l1_l2_tv.load(l, k, g, beta, M, e, A, snr=snr)
function = CombinedFunction()
function.add_loss(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(p,
penalty_start=penalty_start)
function.add_penalty(nesterov.l1.L1(l, A=A, mu=mu_min,
penalty_start=penalty_start))
# function.add_prox(penalties.L1(l, penalty_start=penalty_start))
fista = proximal.FISTA(eps=mu_min, max_iter=23500)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 5
assert_less(berr, 5.0, "The found regression vector is not correct.")
# Test proximal operator
function = CombinedFunction()
function.add_loss(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(p,
penalty_start=penalty_start)
function.add_prox(nesterov.l1.L1(l, A=A, mu=mu_min,
penalty_start=penalty_start))
fista = proximal.FISTA(eps=mu_min, max_iter=20000)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 0.1
assert_less(berr, 0.1, "The found regression vector is not correct.")
def test_overlapping_smooth(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_glmu as l1_l2_glmu
import parsimony.utils.start_vectors as start_vectors
np.random.seed(314)
# Note that p must be even!
n, p = 25, 30
groups = [list(range(0, 2 * int(p / 3))), list(range(int(p / 3), p))]
weights = [1.5, 0.5]
A = gl.linear_operator_from_groups(p, groups=groups, weights=weights)
l = 0.0
k = 0.0
g = 0.9
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
mu_min = 5e-8
X, y, beta_star = l1_l2_glmu.load(l,
k,
g,
beta,
M,
e,
A,
mu=mu_min,
snr=snr)
eps = 1e-8
max_iter = 15000
beta_start = start_vector.get_vector(p)
mus = [5e-0, 5e-2, 5e-4, 5e-6, 5e-8]
fista = FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_function(
functions.losses.LinearRegression(X, y, mean=False))
function.add_penalty(
gl.GroupLassoOverlap(l=g, A=A, mu=mu, penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print berr
assert berr < 5e-2
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
# print abs(f_parsimony - f_star)
assert abs(f_parsimony - f_star) < 5e-7
def test_nonoverlapping_nonsmooth(self):
# Spams: http://spams-devel.gforge.inria.fr/doc-python/doc_spams.pdf
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions as functions
import parsimony.functions.nesterov.gl as gl
import parsimony.datasets.simulate.l1_l2_gl as l1_l2_gl
import parsimony.utils.start_vectors as start_vectors
np.random.seed(42)
# Note that p must be even!
n, p = 25, 20
groups = [list(range(0, int(p / 2))), list(range(int(p / 2), p))]
# weights = [1.5, 0.5]
A = gl.linear_operator_from_groups(p,
groups=groups) # , weights=weights)
l = 0.0
k = 0.0
g = 1.0
start_vector = start_vectors.RandomStartVector(normalise=True)
beta = start_vector.get_vector(p)
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
X, y, beta_star = l1_l2_gl.load(l, k, g, beta, M, e, A, snr=snr)
eps = 1e-8
max_iter = 8500
beta_start = start_vector.get_vector(p)
mus = [5e-2, 5e-4, 5e-6, 5e-8]
fista = proximal.FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
# function = functions.LinearRegressionL1L2GL(X, y, l, k, g,
# A=A, mu=mu,
# penalty_start=0)
function = CombinedFunction()
function.add_function(
functions.losses.LinearRegression(X, y, mean=False))
function.add_penalty(
gl.GroupLassoOverlap(l=g, A=A, mu=mu, penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
try:
import spams
params = {
"loss":
"square",
"regul":
"group-lasso-l2",
"groups":
np.array([1] * (int(p / 2)) + [2] * (int(p / 2)),
dtype=np.int32),
"lambda1":
g,
"max_it":
max_iter,
"tol":
eps,
"ista":
False,
"numThreads":
-1,
}
beta_spams, optim_info = \
spams.fistaFlat(Y=np.asfortranarray(y),
X=np.asfortranarray(X),
W0=np.asfortranarray(beta_start),
return_optim_info=True,
**params)
except ImportError:
beta_spams = np.asarray(
[[14.01111427], [35.56508563], [27.38245962], [22.39716553],
[5.835744940], [5.841502910], [2.172209350], [32.40227785],
[22.48364756], [26.48822401], [0.770391500], [36.28288883],
[31.14118214], [7.938279340], [6.800713150], [6.862914540],
[11.38161678], [19.63087584], [16.15855845], [10.89356615]])
berr = np.linalg.norm(beta_parsimony - beta_spams)
# print berr
assert berr < 5e-2
f_parsimony = function.f(beta_parsimony)
f_spams = function.f(beta_spams)
ferr = abs(f_parsimony - f_spams)
# print ferr
assert ferr < 5e-6
def test_smoothed(self):
import numpy as np
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions.losses as losses
import parsimony.functions.nesterov as nesterov
import parsimony.utils.start_vectors as start_vectors
import parsimony.datasets.simulate.l1_l2_tv as l1_l2_tv
start_vector = start_vectors.RandomStartVector(normalise=True)
np.random.seed(42)
n, p = 75, 100
penalty_start = 0
alpha = 0.9
V = np.random.randn(p, p)
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.dot(V.T, V)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
beta = start_vector.get_vector(p)
beta[np.abs(beta) < 0.1] = 0.0
l = 0.618
k = 0.0
g = 0.0
mu_min = 0.001 # consts.TOLERANCE
A = np.eye(p)
A = [A, A, A]
snr = 100.0
X, y, beta_star = l1_l2_tv.load(l, k, g, beta, M, e, A, snr=snr)
function = CombinedFunction()
function.add_loss(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(
p, penalty_start=penalty_start)
function.add_penalty(
nesterov.l1.L1(l, A=A, mu=mu_min, penalty_start=penalty_start))
# function.add_prox(penalties.L1(l, penalty_start=penalty_start))
fista = proximal.FISTA(eps=mu_min, max_iter=23500)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 5
assert_less(berr, 5.0, "The found regression vector is not correct.")
# Test proximal operator
function = CombinedFunction()
function.add_loss(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(
p, penalty_start=penalty_start)
function.add_prox(
nesterov.l1.L1(l, A=A, mu=mu_min, penalty_start=penalty_start))
fista = proximal.FISTA(eps=mu_min, max_iter=20000)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 0.1
assert_less(berr, 0.1, "The found regression vector is not correct.")
def test_smooth_2D_l1(self):
from parsimony.functions import CombinedFunction
import parsimony.functions as functions
import parsimony.functions.nesterov.grouptv as grouptv
import parsimony.datasets.simulate.l1_l2_grouptvmu as l1_l2_grouptvmu
import parsimony.utils.weights as weights
np.random.seed(1337)
n, p = 10, 18
shape = (1, 3, 6)
l = 0.618
k = 0.0
g = 1.618
start_vector = weights.ZerosWeights()
beta = start_vector.get_weights(p)
rects = [[(0, 1), (0, 3)], [(1, 2), (3, 6)]]
beta = np.reshape(beta, shape[1:])
beta[0:2, 0:4] = 1.0
beta[1:3, 3:6] = 2.0
beta[1, 3] = 1.5
beta = np.reshape(beta, (p, 1))
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
A = grouptv.linear_operator_from_rects(rects, shape)
mu_min = 5e-8
X, y, beta_star = l1_l2_grouptvmu.load(l=l, k=k, g=g, beta=beta,
M=M, e=e, A=A, mu=mu_min,
snr=snr)
eps = 1e-5
max_iter = 10000
beta_start = start_vector.get_weights(p)
mus = [5e-2, 5e-4, 5e-6, 5e-8]
fista = FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
function = CombinedFunction()
function.add_loss(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(grouptv.GroupTotalVariation(l=g,
A=A, mu=mu,
penalty_start=0))
function.add_prox(functions.penalties.L1(l=l, penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print "berr:", berr
assert berr < 5e-2
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
ferr = abs(f_parsimony - f_star)
# print "ferr:", ferr
assert ferr < 5e-5
def test_smooth_1D_l2(self):
from parsimony.functions import CombinedFunction
import parsimony.functions as functions
import parsimony.functions.nesterov.grouptv as grouptv
import parsimony.datasets.simulate.l1_l2_grouptvmu as l1_l2_grouptvmu
import parsimony.utils.weights as weights
np.random.seed(1337)
n, p = 10, 15
shape = (1, 1, p)
l = 0.0
k = 0.1 # Must have some regularisation for all variables.
g = 0.9
start_vector = weights.RandomUniformWeights(normalise=True)
beta = start_vector.get_weights(p)
rects = [[(0, 5)], [(4, 10)], [(13, 15)]]
# 0 [ 5 ] 0
# 1 [ 5 ] 0
# 2 [ 5 ] 0
# 3 [ 5 ] 0
# 4 [ 4 ] 0 / 1
beta[:5, :] = 5.0 # 5 [ 3 ] 1
beta[4, :] = 4.0 # 6 [ 3 ] 1
beta[5:10, :] = 3.0 # 7 [ 3 ] 1
beta[13:15, :] = 7.0 # 8 [ 3 ] 1
# 9 [ 3 ] 1
# 0 [ x ] -
# 1 [ x ] -
# 2 [ x ] -
# 3 [ 7 ] 2
# 4 [ 7 ] 2
alpha = 1.0
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.random.randn(p, p)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
snr = 100.0
A = grouptv.linear_operator_from_rects(rects, shape)
mu_min = 5e-8
X, y, beta_star = l1_l2_grouptvmu.load(l=l, k=k, g=g, beta=beta,
M=M, e=e, A=A, mu=mu_min,
snr=snr)
eps = 1e-5
max_iter = 12000
beta_start = start_vector.get_weights(p)
mus = [5e-2, 5e-4, 5e-6, 5e-8]
fista = FISTA(eps=eps, max_iter=max_iter / len(mus))
beta_parsimony = beta_start
for mu in mus:
function = CombinedFunction()
function.add_loss(functions.losses.LinearRegression(X, y,
mean=False))
function.add_penalty(grouptv.GroupTotalVariation(l=g,
A=A, mu=mu,
penalty_start=0))
function.add_penalty(functions.penalties.L2Squared(l=k,
penalty_start=0))
beta_parsimony = fista.run(function, beta_parsimony)
berr = np.linalg.norm(beta_parsimony - beta_star)
# print "berr:", berr
assert berr < 5e-2
f_parsimony = function.f(beta_parsimony)
f_star = function.f(beta_star)
ferr = abs(f_parsimony - f_star)
# print "ferr:", ferr
assert ferr < 5e-5
def test_nonsmooth(self):
import numpy as np
import parsimony.utils.consts as consts
from parsimony.functions import CombinedFunction
import parsimony.algorithms.proximal as proximal
import parsimony.functions.losses as losses
import parsimony.functions.nesterov as nesterov
import parsimony.utils.start_vectors as start_vectors
import parsimony.datasets.simulate.l1_l2_tv as l1_l2_tv
start_vector = start_vectors.RandomStartVector(normalise=True)
np.random.seed(42)
n, p = 75, 100
alpha = 0.9
V = np.random.randn(p, p)
Sigma = alpha * np.eye(p, p) \
+ (1.0 - alpha) * np.dot(V.T, V)
mean = np.zeros(p)
M = np.random.multivariate_normal(mean, Sigma, n)
e = np.random.randn(n, 1)
beta_start = start_vector.get_vector(p)
beta_start[np.abs(beta_start) < 0.1] = 0.0
l = 0.618
k = 0.0
g = 0.0
A = np.eye(p)
A = [A, A, A]
snr = 100.0
X, y, beta_star = l1_l2_tv.load(l, k, g, beta_start, M, e, A, snr=snr)
beta = beta_start
for mu in [5e-2, 5e-3, 5e-4, 5e-5]:
function = CombinedFunction()
function.add_loss(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(p, penalty_start=0)
function.add_penalty(nesterov.l1.L1(l, A=A, mu=mu,
penalty_start=0))
fista = proximal.FISTA(eps=consts.TOLERANCE, max_iter=2300)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 5e-2
assert_less(berr, 5e-2, "The found regression vector is not correct.")
# Test proximal operator
beta = beta_start
function = CombinedFunction()
function.add_loss(losses.LinearRegression(X, y, mean=False))
A = nesterov.l1.linear_operator_from_variables(p, penalty_start=0)
# function.add_penalty(nesterov.l1.L1(l, A=A, mu=mu_min,
# penalty_start=penalty_start))
function.add_prox(nesterov.l1.L1(l, A=A, mu=5e-5, penalty_start=0))
fista = proximal.FISTA(eps=consts.TOLERANCE, max_iter=2000)
beta = fista.run(function, beta)
berr = np.linalg.norm(beta - beta_star)
# print "berr:", berr
# assert berr < 5e-0
assert_less(berr, 5e-0, "The found regression vector is not correct.")