def test_reclasso(n=5, m=5, mu0=.5, mu1=.8, thresh=1e-4, verbose=True):
"""
test the reclasso algorithm using random data
"""
# sample a problem
X = np.random.randn(n+1, m)
y = np.random.randn(n+1, 1)
# solve both problems using an interior point method
theta0 = algo.interior_point(X[:-1, :], y[:-1], mu0)
theta1 = algo.interior_point(X, y, mu1)
# prepare warm-start solution for the homotopy
theta0, nz0, K0, truesol0 = algo.fix_sol(X[:-1, :], y[:-1], mu0, theta0, thresh=thresh)
theta1, nz1, K1, truesol1 = algo.fix_sol(X, y, mu1, theta1, thresh=thresh)
if not truesol0 or not truesol1: raise NameError, "bad threshold for interior point solution"
# solve the problem using reclasso
theta_nz, nz, K, nbr1, nbr2 = reclasso(X, y, mu0, mu1, theta0[nz0], nz0, K0, verbose=verbose, showpath=False)
theta = np.zeros((m, 1))
theta[nz] = theta_nz
# check the result is the same as with the interior point method
error = np.sum((theta1 - theta)**2)/np.sum(theta1**2)
assert_almost_equals(error, 0)
def compare_algos(n=250, m=100, d=25, N=10, mu=.1, sigma=0.01, verbose=True, showfig=False, simuname='test'):
"""
batch experiment
compare performance of reclasso, lars, and coordinate descent with warm start
"""
if not showfig:
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from matplotlib.patches import Polygon
# sample observations
thetaopt = np.zeros((m, 1))
thetaopt[:d] = 1.
# regularization parameter schedule
lam = mu * np.arange(1, n+1)
# create arrays to store the results
br1 = np.empty((n-1, N)) # nb of transition points in the first step
br2 = np.empty((n-1, N)) # nb of transition points in the second step
brlars = np.empty((n-1, N)) # nb of transition points in lars
err_hamming = np.empty((n-1, N)) # hamming distance between the current solution and hte optimal solution
err_l2 = np.empty((n-1, N)) # l2 distance between the current solution and hte optimal solution
t_h = np.empty((n-1, N)) # timing for the homorotpy
t_lars = np.empty((n-1, N)) # timing for lars
t_cd = np.empty((n-m/2, N)) # timing for coordinate descent + warm-start
for j in range(N):
# sample data
X = np.random.randn(n, m)
y = np.dot(X, thetaopt) + sigma*np.sqrt(d)*np.random.randn(n,1)
# get first solution
theta_nz, nz, K = algo.one_observation(X[0,:], y[0], lam[0])
theta = np.zeros((m, 1))
theta[nz] = theta_nz
for i in range(1, n):
if verbose: print '\nsimulation %d, observation %d'%(j, i)
# solve using coordinate descent + warm-start
if i >= (m/2):
t0_cd = now()
theta_cd, niter_cd = algo.coordinate_descent(X[:i+1, :], y[:i+1], lam[i], theta=theta.copy())
t_cd[i-m/2, j] = now() - t0_cd
# solve recursive lasso
t0_h = now()
theta_nz, nz, K, nbr1, nbr2 = reclasso(X[:i+1, :], y[:i+1], lam[i-1], lam[i], theta_nz, nz, K, verbose=verbose)
t_h[i-1, j] = now() - t0_h
br1[i-1, j] = nbr1
br2[i-1, j] = nbr2
# update current solution using the homotopy solution
theta = np.zeros((m, 1))
theta[nz] = theta_nz
# solve using lars
t0_lars = now()
thetalars_nz, nzlars, Klars, nbrlars = algo.lars(X[:i+1, :], y[:i+1], lam[i], verbose=verbose)
t_lars[i-1, j] = now() - t0_lars
brlars[i-1, j] = nbrlars
thetalars = np.zeros((m, 1))
thetalars[nzlars] = thetalars_nz
# look at the error terms
err_l2[i-1, j] = np.sqrt(((theta - thetaopt)**2).sum()) / np.sqrt((thetaopt**2).sum())
err_hamming[i-1, j] = len(np.where((abs(thetaopt) > 0) != (abs(theta) > 0))[0])
if i >= (m/2):
# verify that the solution from coordinate descent is correct
error = np.sqrt(((theta_cd - theta)**2).sum()) / np.sqrt((theta**2).sum())
if error > 1e-3: print '\ncoordinate descent has not converged'
# verify the result
if verbose:
print '\ncompute solution using interior point method'
thetaip = algo.interior_point(X, y, lam[-1])
thetaip, nzip, Kip, truesol = algo.fix_sol(X, y, lam[-1], thetaip)
print '\ntheta (ip) =',
print thetaip.T
print '\ntheta (homotopy), error = ', np.sqrt(((theta - thetaip)**2).sum()) / np.sqrt((thetaip**2).sum())
print theta.T
print '\ntheta (lars), error = ', np.sqrt(((thetalars - thetaip)**2).sum()) / np.sqrt((thetaip**2).sum())
print thetalars.T
fig1 = plt.figure(1)
plt.clf()
ax = plt.subplot(111)
brmean = (br1+br2).mean(axis=1)
brstd = (br1+br2).std(axis=1)
brlarsmean = (brlars).mean(axis=1)
brlarsstd = (brlars).std(axis=1)
iters = np.arange(1, n)
p1 = plt.plot(iters, brmean)
p2 = plt.plot(iters, brlarsmean)
verts1 = zip(iters, brmean+brstd) + zip(iters[::-1], brmean[::-1] - brstd[::-1])
verts2 = zip(iters, brlarsmean+brlarsstd) + zip(iters[::-1], brlarsmean[::-1] - brlarsstd[::-1])
plt.legend((p1[0], p2[0]), ('Reclasso', 'Lars'), loc='upper right')
poly1 = Polygon(verts1, facecolor=(.5,.5,1), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly1)
poly2 = Polygon(verts2, facecolor=(.5,1,.5), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly2)
plt.xlim(1, n-1)
plt.xlabel('Iteration', fontsize=16)
plt.ylabel('Number of transition points', fontsize=16)
if showfig: plt.show()
fig1.savefig(simuname+'_transitionpoints.pdf')
fig2 = plt.figure(2)
plt.clf()
ax = plt.subplot(111)
hammean = err_hamming.mean(axis=1)
hamstd = err_hamming.std(axis=1)
p = plt.plot(iters, hammean)
verts = zip(iters, hammean+hamstd) + zip(iters[::-1], hammean[::-1] - hamstd[::-1])
poly = Polygon(verts, facecolor=(.5,.5,1), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly)
plt.xlim(1, n-1)
plt.xlabel('Iteration', fontsize=16)
plt.ylabel('Hamming distance', fontsize=16)
if showfig: plt.show()
fig2.savefig(simuname+'_hammingdistance.pdf')
fig3 = plt.figure(3)
plt.clf()
ax = plt.subplot(111)
l2mean = err_l2.mean(axis=1)
l2std = err_l2.std(axis=1)
p = plt.plot(iters, l2mean)
verts = zip(iters, l2mean+l2std) + zip(iters[::-1], l2mean[::-1] - l2std[::-1])
poly = Polygon(verts, facecolor=(.5,.5,1), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly)
plt.xlim(1, n-1)
plt.xlabel('Iteration', fontsize=16)
plt.ylabel('Relative MSE', fontsize=16)
if showfig: plt.show()
fig3.savefig(simuname+'_relativel2.pdf')
fig4 = plt.figure(4)
plt.clf()
iters_cd = np.arange(m/2, n)
ax = plt.subplot(111)
t_hmean = t_h.mean(axis=1)
t_hstd = t_h.std(axis=1)
t_larsmean = t_lars.mean(axis=1)
t_larsstd = t_lars.std(axis=1)
t_cdmean = t_cd.mean(axis=1)
t_cdstd = t_cd.std(axis=1)
p_h = plt.plot(iters, t_hmean)
p_lars = plt.plot(iters, t_larsmean)
p_cd = plt.plot(iters_cd, t_cdmean)
plt.legend((p_h[0], p_lars[0], p_cd[0]), ('Reclasso', 'Lars', 'CD'), loc='best')
verts_h = zip(iters, t_hmean+t_hstd) + zip(iters[::-1], t_hmean[::-1] - t_hstd[::-1])
verts_lars = zip(iters, t_larsmean+t_larsstd) + zip(iters[::-1], t_larsmean[::-1] - t_larsstd[::-1])
verts_cd = zip(iters_cd, t_cdmean+t_cdstd) + zip(iters_cd[::-1], t_cdmean[::-1] - t_cdstd[::-1])
poly_h = Polygon(verts_h, facecolor=(.5,.5,1), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly_h)
poly_lars = Polygon(verts_lars, facecolor=(.5,1,.5), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly_lars)
poly_cd = Polygon(verts_cd, facecolor=(1,.5,.5), edgecolor='w', alpha=.4, lw=0.)
ax.add_patch(poly_cd)
plt.xlim(1, n-1)
ymax = 1.2 * max((t_larsmean+t_larsstd).max(), (t_hmean+t_hstd).max())
plt.ylim(0, ymax)
plt.xlabel('Iteration', fontsize=16)
plt.ylabel('Time', fontsize=16)
if showfig: plt.show()
fig4.savefig(simuname+'_timinginfo.pdf')