def svd_select(A, n, k=1, idxs=None, sps=False, **kwargs):
"""
Selection function which computes the CUR
indices using the SVD Decomposition
"""
if(idxs is None):
idxs = [] # indexA is initially empty.
else:
idxs = list(idxs)
Acopy = A.copy()
for nn in range(n):
if(len(idxs) <= n):
if(not sps):
(S, v, D) = np.linalg.svd(Acopy)
else:
(S, v, D) = svd(Acopy, k)
D = D[np.flip(np.argsort(v))]
pi = (D[:k]**2.0).sum(axis=0)
pi[idxs] = 0 # eliminate possibility of selecting same column twice
i = pi.argmax()
idxs.append(i)
v = Acopy[:, idxs[nn]] / \
np.sqrt(np.matmul(Acopy[:, idxs[nn]], Acopy[:, idxs[nn]]))
for i in range(Acopy.shape[1]):
Acopy[:, i] -= v * np.dot(v, Acopy[:, i])
return list(idxs)
def testMat():
S = np.zeros([5,6])
A=[[1,1,1,0,0],
[2,2,2,0,0],
[3,3,3,0,0],
[5,5,3,2,2],
[0,0,0,3,3],
[0,0,0,6,6]]
u,sigma,vt = la.svd(A)
print"-------------"
print(A)
print"-------------"
print(u)
print"-------------"
print(sigma)
print"-------------"
print(vt)
print"-------------"
i=0
while i < A.shape[0]:
tmp = 0;
j=0
while j < A.shape[1]:
k=0
tmp = 0;
while k < len(sigma):
tmp = tmp + u[i][k]*sigma[k]*vt[k][j]
k = k+1
j = j + 1
print tmp," ",
print ""
i=i+1
def spectral_partition(W,q,method = 'complete', metric = 'cosine'):
n,m = W.shape
K = Kmatrix(W)
if n == m:
try:
e,v = linalg.eigen(K, q)
except TypeError:
e,v = linalg.eigs(K, q)
else:
try:
u,e,v = linalg.svds(K, q)
except AttributeError:
u,e,v = linalg.svd(K, q)
v = np.concatenate((u, v.T), 0)
max_index = e.argmax()
v = np.delete(v,max_index,1)
Obs = np.real(v)
D = distance.pdist(Obs,metric = metric)
D = np.multiply(D >= 0, D)
Z = linkage(D, method = method, metric = metric)
cluster = fcluster(Z, q, criterion = 'maxclust')
cluster += - 1
cluster = {'spectral' : cluster}
return cluster
def simple_svd_reduced(A):
# try with full_matrices=False
U, s, Vh = linalg.svd(A, full_matrices=False, compute_uv=True)
S = np.diag(s)
print np.shape(U), np.shape(S), np.shape(Vh)
# check if SVD-resulting matrix is accurate enough
A_check = np.dot(np.dot(U, S), Vh)
print np.allclose(A, A_check)
return U, S, Vh
def dim_reduction(X, w, l, u = None, v_T = None): #print X if not u and not v_T: u, s, v_T = svd(X) print "done SVD" u_T = u[:, :w].transpose() print "done u_T" tmp = (u[:, :w].transpose()).dot(X) X = None print "dot V" X_reduce = (tmp).dot(v_T[:l, :].transpose()) tmp = None print "cool" return X_reduce, u, v_T
def GrowSparse(H, params, trans):
sys_dim = H.A.shape[0]
dim = sys_dim * params['loc_dim']
U = trans.A[len(trans.A) - 1]
Vh = trans.B[len(trans.B) - 1]
old_dim = U.shape[0]
H_Anew = kron(H.A, sigma_0)
H_Bnew = kron(sigma_0, H.B)
sz_Utrans = U.conj().T.dot(
kron(ids(old_dim // params['loc_dim'], dtype=np.float),
sigma_z).dot(U))
H_Adot = -params['J'] * kron(sz_Utrans, sigma_z)
sz_Vtrans = Vh.conj().dot(
kron(sigma_z, ids(old_dim // params['loc_dim'],
dtype=np.float)).dot(Vh.T))
H_dotB = -params['J'] * kron(sigma_z, sz_Vtrans)
H_dotdot = -params['J'] * kron(
kron(kron(ids(sys_dim, dtype=np.float), sigma_z), sigma_z),
ids(sys_dim, dtype=np.float))
H_dotdotA = -params['h'] * kron(ids(sys_dim, dtype=np.float), sigma_x)
H_dotdotB = -params['h'] * kron(sigma_x, ids(sys_dim, dtype=np.float))
H_super = kron(H_Anew,ids(dim,dtype=np.float)) + \
kron(ids(dim,dtype=np.float),H_Bnew) + \
kron(H_Adot,ids(dim,dtype=np.float)) + \
kron(ids(dim,dtype=np.float),H_dotB) + \
H_dotdot + \
kron(H_dotdotA,ids(dim,dtype=np.float)) + \
kron(ids(dim,dtype=np.float),H_dotdotB)
eigval, psi = eigsh(H_super, k=1, tol=1.e-8, which='SA')
energy.append(eigval.tolist()[0])
# Since we have A <-> B symmetry, we may reshape psi here instead of
# looking at tr_A |psi><psi|
rho_dim = int(np.sqrt(psi.shape[0]))
if (np.abs(rho_dim - np.sqrt(psi.shape[0])) > 1e-10): # Check int sqrt
print('Error: Density matrix dimension not int')
quit()
psi_ij = np.reshape(psi, (rho_dim, rho_dim), order='C')
psi_ijs = sparse.coo_matrix(psi_ij)
num_SV = min(params['maxM'], dim - 1)
U, s, Vh = svd(psi_ijs, k=num_SV)
if sys_dim >= params['maxM']:
U = U[:, 0:params['maxM']]
Vh = Vh[0:params['maxM'], :]
trans.A.append(U)
trans.B.append(Vh)
H_Amod = H_Anew + H_Adot + H_dotdotA
H_Bmod = H_Bnew + H_dotB + H_dotdotB
H_new = Ham(U.conj().T.dot(H_Amod.dot(U)), Vh.conj().dot(H_Bmod.dot(Vh.T)))
return H_new
def simple_svd(A):
# try with full_matrices = True
U, s, Vh = linalg.svd(A, full_matrices=True, compute_uv=True)
M, N = np.shape(A)
S = np.zeros((M, N), dtype=complex)
S[:N, :N] = np.diag(s)
A_check = np.dot(np.dot(U, S), Vh)
# check if SVD-resulting matrix is accurate enough
for i in range(0, M):
for j in range(0, N):
try:
abs(A[i, j] - A_check[i, j]) < 1.0e-14
except ValueError:
print "Oops! A and A_check are not accurately close to each other."
return U, S, Vh
def filter_sparse(g1, n_c = 5,
max_edges = -1,
last_component = False):
'''
Filter a sparse version of the network by PCA.
g1: The input network graph.
n_c: The number of principal components to compute
max_edges: The maximum number of edges to keep. -1 => keep all.
last_component: Keep only the final principal component
'''
import scipy.sparse.linalg as las
import scipy.sparse.lil as ll
import scipy.sparse as ssp
adj = ssp.csr_matrix(nx.to_scipy_sparse_matrix(g1))
nodes = g1.nodes()
U,s, Vh = svd = las.svd(adj, n_c)
U[less(abs(U), .001)] = 0
Vh[less(abs(Vh), .001)] = 0
if last_component:
s_last = s; s_last[1:] *= 0
filtered = ll.lil_matrix(U)*ll.lil_matrix(diag(s_last)) *ll.lil_matrix(Vh)
else:
filtered = ll.lil_matrix(U)*ll.lil_matrix(diag(s)) *ll.lil_matrix(Vh)
if max_edges != -1:
filtered.data[argsort(abs(filtered.data))[:-1 * max_edges]] = 0
filtered.eliminate_zeros()
g = nx.DiGraph()
g.add_nodes_from(nodes)
g.add_weighted_edges_from([(nodes[nz[0]],nodes[nz[1]],nz[2])
for nz in zip(*ssp.find(filtered))])
return g
def whiten_with_filled_zeros(data, k):
judgement_columns = data.columns[2:]
raw_data = data[judgement_columns]
# need to interpolate missing judgements:
# we'll fill them in w/ the avg of all other ratings
matrix = raw_data.fillna(0).as_matrix()
#matrix = raw_data.as_matrix()
U, S, V = svd(matrix, k)
# actual whitening
S[k:] = 0
# multiply stuff back out
W = np.dot(U, np.dot(np.diag(S), V))
# we should renull the values?
whitened_data = data.copy()
for i, j in enumerate(judgement_columns):
whitened_data[j] = W[:, i]
#nulls = data[j].isnull()
#whitened_data[j][nulls] = float("nan")
return whitened_data
def whiten_with_filled_zeros(data, k):
judgement_columns = data.columns[2:]
raw_data = data[judgement_columns]
# need to interpolate missing judgements:
# we'll fill them in w/ the avg of all other ratings
matrix = raw_data.fillna(0).as_matrix()
#matrix = raw_data.as_matrix()
U, S, V = svd(matrix, k)
# actual whitening
S[k:] = 0
# multiply stuff back out
W = np.dot(U, np.dot(np.diag(S), V))
# we should renull the values?
whitened_data = data.copy()
for i, j in enumerate(judgement_columns):
whitened_data[j] = W[:,i]
#nulls = data[j].isnull()
#whitened_data[j][nulls] = float("nan")
return whitened_data
def CUR(mat, numr, numc, nrows, ncols):
A_T = np.transpose(mat)
A = sp.csr_matrix(mat)
A_T = sp.csr_matrix(A_T)
rows = np.zeros(nrows, dtype=float)
r = []
rowsprob = np.zeros(nrows, dtype=float)
total = 0
tempr = sp.coo_matrix(A)
#calculating the probability of each row being selected
for i, j, v in zip(tempr.row, tempr.col, tempr.data):
rowsprob[i] = rowsprob[i] + v * v
total = total + v * v
rowsprob = rowsprob / total
#calculating the cumulative probabilities
cumrowsprob = np.zeros(nrows, dtype=float)
cumrowsprob[0] = rowsprob[0]
for i in range(1, rowsprob.size):
cumrowsprob[i] = cumrowsprob[i - 1] + rowsprob[i]
#generating random rows and building r matrix
for i in range(0, numr):
rand = random.random()
entry = np.searchsorted(cumrowsprob, rand)
rows[entry] = rows[entry] + 1
#handling duplicates by multiplying duplicate rows with square root of number of duplications and removing duplicates
selectedrows = []
rows = np.sqrt(rows)
for i in range(0, nrows):
if rows[i] > 0:
r.append((A[i].toarray() / ((numr * rowsprob[i])**0.5)) * rows[i])
selectedrows.append(i)
cols = np.zeros(ncols, dtype=float)
c = []
colsprob = np.zeros(ncols, dtype=float)
total = 0
tempc = sp.coo_matrix(A_T)
#calculating the probability of each column being selected
for i, j, v in zip(tempc.row, tempc.col, tempc.data):
colsprob[i] = colsprob[i] + v * v
total = total + v * v
colsprob = colsprob / total
#calculating the cumulative probabilities
cumcolsprob = np.zeros(ncols, dtype=float)
cumcolsprob[0] = colsprob[0]
for i in range(1, colsprob.size):
cumcolsprob[i] = cumcolsprob[i - 1] + colsprob[i]
#generating random cols and building r matrix
for i in range(0, numc):
rand = random.random()
entry = np.searchsorted(cumcolsprob, rand)
cols[entry] = cols[entry] + 1
#handling duplicates by multiplying duplicate columns with square root of number of duplications and removing duplicates
selectedcols = []
cols = np.sqrt(cols)
for i in range(0, ncols):
if cols[i] > 0:
c.append(
(A_T[i].toarray() / ((numc * colsprob[i])**0.5)) * cols[i])
selectedcols.append(i)
c = np.vstack(c)
r = np.vstack(r)
#finding the intersection of c and r = w
w = np.zeros(shape=(len(selectedrows), len(selectedcols)))
for i in range(0, len(selectedrows)):
for j in range(0, len(selectedcols)):
w[i][j] = mat[selectedrows[i]][selectedcols[j]]
c = sp.csr_matrix(c)
c = c.transpose()
r = sp.csr_matrix(r)
#computing the SVD decomposition of the w matrix
x, z, y_T = linalg.svd(w)
z = linalg.diagsvd(z, x.shape[1], y_T.shape[0])
y = np.transpose(y_T)
#computing the u matrix
zplus = linalg.pinv(np.matrix(z))
zplussquare = zplus * zplus
u = np.matmul(y, np.matmul(zplussquare, np.transpose(x)))
#computing the reconstructed matrix and error
reconstructedmatrix = c * (u * r)
errormatrix = sp.csr_matrix(A - reconstructedmatrix)
reconstructionerror = norm(errormatrix)
return (c, u, r, reconstructionerror)
def calc(self): # calculate the svd
self.U, self.S, self.Vt = svd(self.A)
def dim_reduction(X, w, l, u = None, v_T = None): if not u and not v_T: u, s, v_T = svd(X) X_reduce = ((u[:, :w].transpose()).dot(X)).dot(v_T[:l, :].transpose()) return X_reduce, u, v_T