def test(n=10):
"""
the model to be optimized here is a quadratic form
f(x) = 1/2 (Ax-a)^2, the gradient is A'(Ax-a). Find parameters x given data A, a
"""
a = np.random.randn(n)
x = np.abs(np.random.randn(n)*3)
A = np.random.randn(n,n)
A = np.dot(A.T, A)
A = np.eye(n) + A
print 'Eigenvalues: ', np.linalg.eigvals(A)
args = (A, a) # parameters of the model to optimize: plug in PCA data here.
lam = .1 # this is a sparseness parameter?!
m = 8 #would increase this to the dimension of problem to
maxit = 300
obj = Obj(f, args) # creating an instantiation of
# to call qn.owLBFGS need to package the function to optimize in an object.
q = qn.owlbfgs(obj, n, lam=lam * np.ones((n)),
debug=True, maxit=maxit, m=m, pos=True) # orthant wise LBFGS, dimensions, lambdas, iterations...
ret = q.run(x) # q is a c function, no idea what this does
b = np.dot(np.linalg.inv(A), a) # true minimumu
print 'True min: ', f(b, np.zeros_like(x), (A, a))
print 'True argmin: ', b
print 'Initial value: ', x
print 'My solution: ', ret
print 'Error: ', np.linalg.norm(ret-b)
def sparseqn_batch(phi,
X,
lam=1.,
maxit=25,
positive=False,
Sin=None,
debug=False,
delta=0.01,
past=6,
mask=None):
"""
phi - basis
X - array of batches
maxit - maximum quasi-newton steps
positive - positive only coefficients
Sin - warm start for coefficients
debug - print debug info
delta - sufficient decrease condition
past
mask - an array of dims of coefficients used
to mask derivative
Sin is not modified
"""
C, N, P = phi.shape
npats = X.shape[0]
T = X.shape[2]
alen = T + P - 1
# instantiate objective class
obj = Objective(phi, X, mask)
# warm start values
if Sin is not None:
A = Sin.copy()
else:
A = np.zeros((npats, N, alen))
lam = lam * np.ones(N * alen)
# don't regularized coefficients that are masked out
if mask is not None: lam *= mask.flatten()
q = qn.owlbfgs(obj,
N * alen,
lam=lam,
debug=debug,
maxit=maxit,
delta=delta,
past=past,
pos=positive)
for i in range(npats):
q.clear()
A[i] = q.run(A[i].flatten()).reshape(A[i].shape)
obj.indx += 1
return A
def sparseqn_batch(self, phi, X, lam=1., maxit=25,
positive=False, Sin=None, debug=True,
delta=0.01, past=6, mask=None):
"""Use quasinewton method to infer coefficients.
Parameters
----------
phi : 3d array
Basis
X : 2d array
Patch
lam : float
L1 penalty
maxit : int
Maximum number of quasi-newton iterations
positive : bool
If True, only allow positive coefficients
Sin : 2d array
Starting value for coefficients; if None, zeros are used.
debug : bool
Print debugging information
delta : int
?????
past : int
?????
mask : 2d array
An array of dims of coefficients used to mask derivative.
Returns
-------
2d array
Coefficients for this dataset and this basis.
"""
C, N, P = phi.shape
npats = X.shape[0]
T = X.shape[-1]
alen = T + P - 1
A = Sin if Sin else np.zeros((N,alen))
lam = lam * np.ones(N*alen)
# don't regularized coefficients that are masked out
if mask is not None: lam *= mask.flatten()
# instantiate objective class
obj = Owlbfgs.Objective(phi, X, mask)
q = qn.owlbfgs(obj, N*alen, lam=lam,
debug=debug, maxit=maxit, delta=delta,
past=past, pos=positive)
A = q.run(A.flatten()).reshape(N, alen)
return A
def sparseqn_batch(phi, X, lam=1., maxit=25,
positive=False, Sin=None, debug=False,
delta=0.01, past=6, mask=None):
"""
phi - basis
X - array of batches
maxit - maximum quasi-newton steps
positive - positive only coefficients
Sin - warm start for coefficients
debug - print debug info
delta - sufficient decrease condition
past
mask - an array of dims of coefficients used
to mask derivative
Sin is not modified
"""
C, N, P = phi.shape
npats = X.shape[0]
T = X.shape[2]
alen = T + P - 1
# instantiate objective class
obj = Objective(phi, X, mask)
# warm start values
if Sin is not None:
A = Sin.copy()
else:
A = np.zeros((npats, N, alen))
lam = lam * np.ones(N*alen)
# don't regularized coefficients that are masked out
if mask is not None: lam *= mask.flatten()
q = qn.owlbfgs(obj, N*alen, lam=lam,
debug=debug, maxit=maxit, delta=delta,
past=past, pos=positive)
for i in range(npats):
q.clear()
A[i] = q.run(A[i].flatten()).reshape(A[i].shape)
obj.indx += 1
return A
def test(n):
display = True if n == 2 else False
a = np.random.randn(n)
x = np.abs(np.random.randn(n) * 3)
A = np.random.randn(n, n)
A = np.dot(A.T, A)
A = np.eye(n) + A
A = power(n, 2)
# A = np.eye(n)
print "Eigenvalues: ", np.linalg.eigvals(A)
args = (A, a)
lam = 0.02
m = 8
maxit = 300
obj = Obj(f, args)
# q = qn.l1_penalty(obj, lam=lam * np.ones((n)))
q = qn.owlbfgs(obj, n, lam=lam * np.ones((n)), debug=False, maxit=maxit, m=m, pos=False)
# q = qn.owlbfgs(f, n, args=args, lam=lam * np.ones((n)), debug=True, maxit=maxit, m=m, stype='wolfe')
x2 = x.copy()
x3 = x.copy()
tic = now()
ret = q.run(x2)
T1 = now() - tic
# (ret, allvec) = q.run(x)
b = np.dot(np.linalg.inv(A), a)
print "True min: ", f(b, np.zeros_like(x), (A, a))
print "True argmin: ", b
print "Initial value: ", x
print "My solution: ", ret
print "Error: ", np.linalg.norm(ret - b)
if False:
print "BFGS:"
res = fmin_bfgs(f2, x, fprime=df2, args=args, full_output=1, retall=1)
print res[0]
print "Error: ", np.linalg.norm(res[0] - b)
# print 'Hessian: ', np.linalg.inv(res[3])
logfile = os.path.join(os.path.expanduser("~"), "sn", "py", "spikes", "qn", "test.h5")
# tic = now()
# res2 = lbfgs.bfgsl1(f3, x3, lam = lam, args=args, debug=False, log=None)
# t2 = now() - tic
# print 'bfgsl1: ', t1, f4(res2, A, a, lam)[0], res2
# print 'qn: ', t2, f4(ret, A, a, lam)[0], ret
# bounds = ((0, None),) * n
# tic = now()
# x, _, _ = fmin_l_bfgs_b(f4, x3,args=(A,a,lam), bounds=bounds, maxfun=maxit)
# t3 = now() - tic
# print 'lbfgsb: ', t3, f4(x, A, a, lam)[0], x
# if n < 10:
# print 'A.T A: ', np.dot(A.T, A)
# B = q.unroll()
# print 'B^-1: ', np.linalg.inv(B)
# h5 = h5py.File(logfile, 'r')
# allvec5 = h5['x'][:]
# h5.close()
if False and display:
plot_path(allvec, args, 1, f)
# plot_path(allvec2, args, 2, f)
input = raw_input()
