def plot_dist(X, clusters, distargs=None):
Y = range(distargs['K'])
X_hist = numpy.array(utils.bincount(X, Y))
X_hist = X_hist / float(len(X))
K = len(clusters)
pdf = numpy.zeros((K, distargs['K']))
denom = log(float(len(X)))
a = clusters[0].alpha
pylab.bar(Y, X_hist, color="black", alpha=1, edgecolor="none")
W = [log(clusters[k].N) - denom for k in range(K)]
for k in range(K):
w = W[k]
N = clusters[k].N
ww = clusters[k].w
for n in range(len(Y)):
y = Y[n]
pdf[k, n] = numpy.exp(
w + cc_multinomial.calc_predictive_logp(y, N, ww, a))
pylab.bar(Y, pdf[k, :], color="white", edgecolor="none", alpha=.5)
pylab.bar(Y,
numpy.sum(pdf, axis=0),
color='none',
edgecolor="red",
linewidth=1)
# pylab.ylim([0,1.0])
pylab.title('multinomial')
def plot_dist(X, clusters, distargs=None):
Y = range(distargs['K'])
X_hist = numpy.array(utils.bincount(X,Y))
X_hist = X_hist/float(len(X))
K = len(clusters)
pdf = numpy.zeros((K,distargs['K']))
denom = log(float(len(X)))
a = clusters[0].alpha
pylab.bar(Y, X_hist, color="black", alpha=1, edgecolor="none")
W = [log(clusters[k].N) - denom for k in range(K)]
for k in range(K):
w = W[k]
N = clusters[k].N
ww = clusters[k].w
for n in range(len(Y)):
y = Y[n]
pdf[k, n] = numpy.exp(w + cc_multinomial.calc_predictive_logp(y, N, ww, a))
pylab.bar(Y, pdf[k,:], color="white", edgecolor="none", alpha=.5)
pylab.bar(Y, numpy.sum(pdf,axis=0), color='none', edgecolor="red", linewidth=1)
# pylab.ylim([0,1.0])
pylab.title('multinomial')
def plot_dist(X, clusters, distargs=None):
colors = [
"red", "blue", "green", "yellow", "orange", "purple", "brown",
"black"
]
x_min = min(X)
x_max = max(X)
Y = range(int(x_max) + 1)
nn = len(Y)
K = len(clusters)
pdf = numpy.zeros((K, nn))
denom = log(float(len(X)))
a = clusters[0].a
b = clusters[0].b
nbins = min([len(Y), 50])
toplt = numpy.array(utils.bincount(X, Y)) / float(len(X))
pylab.bar(Y, toplt, color="gray", edgecolor="none")
W = [log(clusters[k].N) - denom for k in range(K)]
for k in range(K):
w = W[k]
N = clusters[k].N
sum_x = clusters[k].sum_x
sum_log_fact_x = clusters[k].sum_log_fact_x
for n in range(nn):
y = Y[n]
pdf[k, n] = numpy.exp(w + cc_poisson.calc_predictive_logp(
y, N, sum_x, sum_log_fact_x, a, b))
if k >= 8:
color = "white"
alpha = .3
else:
color = colors[k]
alpha = .7
pylab.bar(Y, pdf[k, :], color=color, edgecolor='none', alpha=alpha)
pylab.bar(Y,
numpy.sum(pdf, axis=0),
color='none',
edgecolor='black',
linewidth=3)
# print integral for debugging (should never be greater that 1)
# print utils.line_quad(Y, numpy.sum(pdf,axis=0))
pylab.xlim([0, x_max + 1])
pylab.title('poisson')
def plot_dist(X, clusters, distargs=None):
colors = ["red", "blue", "green", "yellow", "orange", "purple", "brown", "black"]
x_min = min(X)
x_max = max(X)
Y = range(int(x_max)+1)
nn = len(Y)
K = len(clusters)
pdf = numpy.zeros((K,nn))
denom = log(float(len(X)))
a = clusters[0].a
b = clusters[0].b
nbins = min([len(Y), 50])
toplt = numpy.array(utils.bincount(X,Y))/float(len(X))
pylab.bar(Y, toplt, color="gray", edgecolor="none")
W = [log(clusters[k].N) - denom for k in range(K)]
for k in range(K):
w = W[k]
N = clusters[k].N
sum_x = clusters[k].sum_x
sum_log_fact_x = clusters[k].sum_log_fact_x
for n in range(nn):
y = Y[n]
pdf[k, n] = numpy.exp(w + cc_poisson.calc_predictive_logp(y, N, sum_x,
sum_log_fact_x, a, b))
if k >= 8:
color = "white"
alpha=.3
else:
color = colors[k]
alpha=.7
pylab.bar(Y, pdf[k,:], color=color, edgecolor='none', alpha=alpha)
pylab.bar(Y, numpy.sum(pdf,axis=0), color='none', edgecolor='black', linewidth=3)
# print integral for debugging (should never be greater that 1)
# print utils.line_quad(Y, numpy.sum(pdf,axis=0))
pylab.xlim([0, x_max+1])
pylab.title('poisson')
def __init__(self, dims, alpha=None, Z=None, n_grid=30):
"""
Constructor
input arguments:
-- dims: a list of cc_dim objects
optional arguments:
-- alpha: crp concentration parameter. If none, is selected from grid.
-- Z: starting partiton of rows to categories. If nonde, is intialized
from CRP(alpha)
-- n_grid: number of grid points in the hyperparameter grids
"""
N = dims[0].N
self.N = N
# generate alpha
self.alpha_grid = utils.log_linspace(1.0/self.N, self.N, n_grid)
if alpha is None:
alpha = random.choice(self.alpha_grid)
else:
assert alpha > 0.0
if Z is None:
Z, Nk, K = utils.crp_gen(N, alpha)
else:
assert len(Z) == dims[0].X.shape[0]
Nk = utils.bincount(Z)
K = len(Nk)
assert sum(Nk) == N
assert K == len(Nk)
self.dims = dict()
for dim in dims:
dim.reassign(Z)
self.dims[dim.index] = dim
self.alpha = alpha
self.Z = numpy.array(Z)
self.K = K
self.Nk = Nk
def __init__(self, dims, alpha=None, Z=None, n_grid=30):
"""
Constructor
input arguments:
-- dims: a list of cc_dim objects
optional arguments:
-- alpha: crp concentration parameter. If none, is selected from grid.
-- Z: starting partiton of rows to categories. If nonde, is intialized
from CRP(alpha)
-- n_grid: number of grid points in the hyperparameter grids
"""
N = dims[0].N
self.N = N
# generate alpha
self.alpha_grid = utils.log_linspace(1.0 / self.N, self.N, n_grid)
if alpha is None:
alpha = random.choice(self.alpha_grid)
else:
assert alpha > 0.0
if Z is None:
Z, Nk, K = utils.crp_gen(N, alpha)
else:
assert len(Z) == dims[0].X.shape[0]
Nk = utils.bincount(Z)
K = len(Nk)
assert sum(Nk) == N
assert K == len(Nk)
self.dims = dict()
for dim in dims:
dim.reassign(Z)
self.dims[dim.index] = dim
self.alpha = alpha
self.Z = numpy.array(Z)
self.K = K
self.Nk = Nk
def __init__(self, X, cctypes, distargs, n_grid=30, Zv=None, Zrcv=None, hypers=None, seed=None):
"""
cc_state constructor
input arguments:
-- X: a list of numpy data columns.
-- cctypes: a list of strings where each entry is the data type for
each column.
-- distargs: a list of distargs appropriate for each type in cctype.
For details on distrags see the documentation for each data type.
optional arguments:
-- n_grid: number of bins for hyperparameter grids. Default = 30.
-- Zv: The assignment of columns to views. If not specified, a
partition is generated randomly
-- Zrcv: The assignment of rows to clusters for each view
-- ct_kernel: which column transition kenerl to use. Default = 0 (Gibbs)
-- seed: seed the random number generator. Default = system time.
example:
>>> import numpy
>>> n_rows = 100
>>> X = [numpy.random.normal(n_rows), numpy.random.normal(n_rows)]
>>> State = cc_state(X, ['normal', 'normal'], [None, None])
"""
if seed is not None:
random.seed(seed)
numpy.random.seed(seed)
self.n_rows = len(X[0])
self.n_cols = len(X)
self.n_grid = n_grid
# construct the dims
self.dims = []
for col in range(self.n_cols):
Y = X[col]
cctype = cctypes[col]
if _is_uncollapsed[cctype]:
dim = cc_dim_uc(Y, _cctype_class[cctype], col, n_grid=n_grid, distargs=distargs[col])
else:
dim = cc_dim(Y, _cctype_class[cctype], col, n_grid=n_grid, distargs=distargs[col])
self.dims.append(dim)
# set the hyperparameters in the dims
if hypers is not None:
for d in range(self.n_cols):
self.dims[d].set_hypers(hypers[d])
# initialize CRP alpha
self.alpha_grid = utils.log_linspace(1.0/self.n_cols, self.n_cols, self.n_grid)
self.alpha = random.choice(self.alpha_grid)
assert len(self.dims) == self.n_cols
if Zrcv is not None:
assert Zv is not None
assert len(Zv) == self.n_cols
assert len(Zrcv) == max(Zv)+1
assert len(Zrcv[0]) == self.n_rows
# construct the view partition
if Zv is None:
Zv, Nv, V = utils.crp_gen(self.n_cols, self.alpha)
else:
Nv = utils.bincount(Zv)
V = len(Nv)
# construct views
self.views = []
for view in range(V):
indices = [i for i in range(self.n_cols) if Zv[i] == view]
dims_view = []
for index in indices:
dims_view.append(self.dims[index])
if Zrcv is None:
self.views.append(cc_view(dims_view, n_grid=n_grid))
else:
self.views.append(cc_view(dims_view, Z=numpy.array(Zrcv[view]), n_grid=n_grid))
self.Zv = numpy.array(Zv)
self.Nv = Nv
self.V = V