def plot_count_sum_series(x, w, p, row_start, tit):
if len(w) != 3: # no statistics provided
return
expected, stdev_total, stdev_explained = w
count_sum_observed = np.sum(x, axis=0)
count_sum_expected = np.sum(expected, axis=0)
count_sum_stdev_total = np.sum(stdev_total, axis=0)
count_sum_stdev_explained = np.sum(stdev_explained, axis=0)
if p is not None:
p_sum = np.mean(p, axis=0)
for i, kws in enumerate(series_config):
ax = subplot(grid[row_start:row_start + 3,
(i * 3):(i * 3 + 3)])
ax, handles, indices = plot_series_statistics(
count_sum_observed,
count_sum_expected,
explained_stdev=count_sum_stdev_explained,
total_stdev=count_sum_stdev_total,
fontsize=8,
ax=ax,
legend_enable=False,
title=tit if i == 0 else None,
despine=True if p is None else False,
return_handles=True,
return_indices=True,
**kws)
if p is not None:
_show_zero_inflated_pi(p_sum, ax, handles, indices)
plt.legend(handles=handles,
loc='best',
markerscale=4,
fontsize=8)
def plot_countsum_series(original,
imputed,
p=None,
reduce_axis=0,
title=None,
ax=None):
"""
x: [n_samples, n_genes]
original count
w: tuple (expected, stdev_total, stdev_explained) [n_samples, n_genes]
the prediction
p: [n_samples, n_genes]
dropout probability
"""
if ax is None:
ax = visual.to_axis(ax)
reduce_axis = int(reduce_axis)
if isinstance(imputed, (tuple, list)): # no statistics provided
assert len(imputed) == 3
expected, stdev_total, stdev_explained = imputed
elif imputed.ndim == 3:
assert imputed.shape[0] == 3
expected, stdev_total, stdev_explained = imputed[0], imputed[
1], imputed[2]
else:
raise ValueError()
count_sum_observed = np.log1p(np.sum(original, axis=reduce_axis))
count_sum_expected = np.log1p(np.sum(expected, axis=reduce_axis))
count_sum_stdev_total = np.log1p(np.sum(stdev_total, axis=reduce_axis))
count_sum_stdev_explained = np.log1p(
np.sum(stdev_explained, axis=reduce_axis))
if p is not None:
p_sum = np.mean(p, axis=reduce_axis)
ax, handles, indices = plot_series_statistics(
count_sum_observed,
count_sum_expected,
explained_stdev=count_sum_stdev_explained,
total_stdev=count_sum_stdev_total,
fontsize=8,
ax=ax,
legend_enable=False,
title=title,
despine=True if p is None else False,
return_handles=True,
return_indices=True,
xscale='linear',
yscale='linear',
sort_by='expected')
if p is not None:
_show_zero_inflated_pi(p_sum, ax, handles, indices)
ax.legend(handles=handles, loc='best', markerscale=4, fontsize=8)
def plot_epoch(task):
if task is None:
curr_epoch = 0
else:
curr_epoch = task.curr_epoch
if not (curr_epoch < 5 or curr_epoch % 5 == 0):
return
rand = np.random.RandomState(seed=1234)
X, y = X_test, y_test
n_data = X.shape[0]
Z = f_z(X)
W, W_stdev_mcmc, W_stdev_analytic = f_w(X)
X_pca, W_pca_1 = fast_pca(X,
W,
n_components=2,
random_state=rand.randint(10e8))
W_pca_2 = fast_pca(W, n_components=2, random_state=rand.randint(10e8))
X_count_sum = np.sum(X, axis=tuple(range(1, X.ndim)))
W_count_sum = np.sum(W, axis=-1)
n_visual_samples = 8
nrow = 13 + n_visual_samples * 3
V.plot_figure(nrow=int(nrow * 1.8), ncol=18)
with V.plot_gridSpec(nrow=nrow + 3, ncol=6, hspace=0.8) as grid:
# plot the latent space
for i, (z, name) in enumerate(zip(Z, Z_names)):
if z.shape[1] > 2:
z = fast_pca(z,
n_components=2,
random_state=rand.randint(10e8))
ax = V.subplot(grid[:3, (i * 2):(i * 2 + 2)])
V.plot_scatter(x=z[:, 0],
y=z[:, 1],
color=y,
marker=y,
n_samples=4000,
ax=ax,
legend_enable=False,
legend_ncol=n_classes)
ax.set_title(name, fontsize=12)
# plot the reconstruction
for i, (x, name) in enumerate(
zip([X_pca, W_pca_1, W_pca_2], [
'Original data', 'Reconstruction',
'Reconstruction (separated PCA)'
])):
ax = V.subplot(grid[3:6, (i * 2):(i * 2 + 2)])
V.plot_scatter(x=x[:, 0],
y=x[:, 1],
color=y,
marker=y,
n_samples=4000,
ax=ax,
legend_enable=i == 1,
legend_ncol=n_classes,
title=name)
# plot the reconstruction count sum
for i, (x, count_sum, name) in enumerate(
zip([X_pca, W_pca_1], [X_count_sum, W_count_sum], [
'Original data (Count-sum)', 'Reconstruction (Count-sum)'
])):
ax = V.subplot(grid[6:10, (i * 3):(i * 3 + 3)])
V.plot_scatter(x=x[:, 0],
y=x[:, 1],
val=count_sum,
n_samples=2000,
marker=y,
ax=ax,
size=8,
legend_enable=i == 0,
legend_ncol=n_classes,
title=name,
colorbar=True,
fontsize=10)
# plot the count-sum series
count_sum_observed = np.sum(X, axis=0).ravel()
count_sum_expected = np.sum(W, axis=0)
count_sum_stdev_explained = np.sum(W_stdev_mcmc, axis=0)
count_sum_stdev_total = np.sum(W_stdev_analytic, axis=0)
for i, kws in enumerate([
dict(xscale='linear', yscale='linear', sort_by=None),
dict(xscale='linear', yscale='linear', sort_by='expected'),
dict(xscale='log', yscale='log', sort_by='expected')
]):
ax = V.subplot(grid[10:10 + 3, (i * 2):(i * 2 + 2)])
V.plot_series_statistics(count_sum_observed,
count_sum_expected,
explained_stdev=count_sum_stdev_explained,
total_stdev=count_sum_stdev_total,
fontsize=8,
title="Count-sum" if i == 0 else None,
**kws)
# plot the mean and variances
curr_grid_index = 13
ids = rand.permutation(n_data)
ids = ids[:n_visual_samples]
for i in ids:
observed, expected, stdev_explained, stdev_total = \
X[i], W[i], W_stdev_mcmc[i], W_stdev_analytic[i]
observed = observed.ravel()
for j, kws in enumerate([
dict(xscale='linear', yscale='linear', sort_by=None),
dict(xscale='linear', yscale='linear', sort_by='expected'),
dict(xscale='log', yscale='log', sort_by='expected')
]):
ax = V.subplot(grid[curr_grid_index:curr_grid_index + 3,
(j * 2):(j * 2 + 2)])
V.plot_series_statistics(observed,
expected,
explained_stdev=stdev_explained,
total_stdev=stdev_total,
fontsize=8,
title="Test Sample #%d" %
i if j == 0 else None,
**kws)
curr_grid_index += 3
V.plot_save(os.path.join(FIGURE_PATH, 'latent_%d.png' % curr_epoch),
dpi=200,
log=True)
exit()
def plot_monitoring_epoch(X, X_drop, y, Z, Z_drop, W_outputs, W_drop_outputs,
pi, pi_drop, row_name, dropout_percentage,
curr_epoch, ds_name, labels, save_dir):
# Order of W_outputs: [W, W_stdev_total, W_stdev_explained]
from matplotlib import pyplot as plt
if y.ndim == 2:
y = np.argmax(y, axis=-1)
y = np.array([labels[i] for i in y])
dropout_percentage_text = '%g%%' % (dropout_percentage * 100)
Z_pca = fast_pca(Z, n_components=2, random_state=5218)
Z_pca_drop = fast_pca(Z_drop, n_components=2, random_state=5218)
if W_outputs is not None:
X_pca, X_pca_drop, W_pca, W_pca_drop = fast_pca(X,
X_drop,
W_outputs[0],
W_drop_outputs[0],
n_components=2,
random_state=5218)
# ====== downsampling ====== #
rand = np.random.RandomState(seed=5218)
n_test_samples = len(y)
ids = np.arange(n_test_samples, dtype='int32')
if n_test_samples > 8000:
ids = rand.choice(ids, size=8000, replace=False)
# ====== scatter configuration ====== #
config = dict(size=6, labels=None)
y = y[ids]
X = X[ids]
X_drop = X_drop[ids]
Z_pca = Z_pca[ids]
X_pca = X_pca[ids]
W_pca = W_pca[ids]
W_outputs = [w[ids] for w in W_outputs]
W_drop_outputs = [w[ids] for w in W_drop_outputs]
Z_pca_drop = Z_pca_drop[ids]
X_pca_drop = X_pca_drop[ids]
W_pca_drop = W_pca_drop[ids]
if pi is not None:
pi = pi[ids]
pi_drop = pi_drop[ids]
# ====== plotting NO reconstruction ====== #
if W_outputs is None:
plot_figure(nrow=8, ncol=20)
fast_scatter(x=Z_pca,
y=y,
title="[PCA] Test data latent space",
enable_legend=True,
ax=(1, 2, 1),
**config)
fast_scatter(x=Z_pca_drop,
y=y,
title="[PCA][Dropped:%s] Test data latent space" %
dropout_percentage_text,
ax=(1, 2, 2),
**config)
# ====== plotting WITH reconstruction ====== #
else:
plot_figure(nrow=16, ncol=20)
# original test data WITHOUT dropout
fast_scatter(x=X_pca,
y=y,
title="[PCA][Test Data] Original",
ax=(2, 3, 1),
**config)
fast_scatter(x=W_pca,
y=y,
title="Reconstructed",
ax=(2, 3, 2),
**config)
fast_scatter(x=Z_pca,
y=y,
title="Latent space",
ax=(2, 3, 3),
**config)
# original test data WITH dropout
fast_scatter(x=X_pca_drop,
y=y,
title="[PCA][Dropped:%s][Test Data] Original" %
dropout_percentage_text,
ax=(2, 3, 4),
**config)
fast_scatter(x=W_pca_drop,
y=y,
title="Reconstructed",
ax=(2, 3, 5),
enable_legend=True,
**config)
fast_scatter(x=Z_pca_drop,
y=y,
title="Latent space",
ax=(2, 3, 6),
**config)
plot_save(os.path.join(save_dir, 'latent_epoch%d.png') % curr_epoch,
dpi=180,
clear_all=True,
log=True)
# ====== plot count-sum ====== #
if W_outputs is not None:
X_countsum = _clip_count_sum(np.sum(X, axis=-1))
W_countsum = _clip_count_sum(np.sum(W_outputs[0], axis=-1))
X_drop_countsum = _clip_count_sum(np.sum(X_drop, axis=-1))
W_drop_countsum = _clip_count_sum(np.sum(W_drop_outputs[0], axis=-1))
series_config = [
dict(xscale='linear', yscale='linear', sort_by=None),
dict(xscale='linear', yscale='linear', sort_by='expected')
]
if pi is not None:
pi_sum = np.mean(pi, axis=-1)
pi_drop_sum = np.mean(pi_drop, axis=-1)
# plot the reconstruction count sum
plot_figure(nrow=3 * 5 + 8, ncol=18)
with plot_gridSpec(nrow=3 * (2 if pi is None else 3) + 4 * 3 + 1,
ncol=6,
wspace=1.0,
hspace=0.8) as grid:
kws = dict(colorbar=True,
fontsize=10,
size=10,
marker=y,
n_samples=1200)
# without dropout
ax = subplot(grid[:3, 0:3])
plot_scatter(x=X_pca,
val=X_countsum,
ax=ax,
legend_enable=False,
title='Original data (Count-sum)',
**kws)
ax = subplot(grid[:3, 3:6])
plot_scatter(x=W_pca,
val=W_countsum,
ax=ax,
legend_enable=False,
title='Reconstruction (Count-sum)',
**kws)
# with dropout
ax = subplot(grid[3:6, 0:3])
plot_scatter(x=X_pca_drop,
val=X_drop_countsum,
ax=ax,
legend_enable=True if pi is None else False,
legend_ncol=len(labels),
title='[Dropped:%s]Original data (Count-sum)' %
dropout_percentage_text,
**kws)
ax = subplot(grid[3:6, 3:6])
plot_scatter(x=W_pca_drop,
val=W_drop_countsum,
ax=ax,
legend_enable=False,
title='[Dropped:%s]Reconstruction (Count-sum)' %
dropout_percentage_text,
**kws)
row_start = 6
# zero-inflated pi
if pi is not None:
ax = subplot(grid[6:9, 0:3])
plot_scatter(x=X_pca,
val=pi_sum,
ax=ax,
legend_enable=True,
legend_ncol=len(labels),
title='Zero-inflated probabilities',
**kws)
ax = subplot(grid[6:9, 3:6])
plot_scatter(x=X_pca,
val=pi_drop_sum,
ax=ax,
legend_enable=False,
title='[Dropped:%s]Zero-inflated probabilities' %
dropout_percentage_text,
**kws)
row_start += 3
# plot the count-sum series
def plot_count_sum_series(x, w, p, row_start, tit):
if len(w) != 3: # no statistics provided
return
expected, stdev_total, stdev_explained = w
count_sum_observed = np.sum(x, axis=0)
count_sum_expected = np.sum(expected, axis=0)
count_sum_stdev_total = np.sum(stdev_total, axis=0)
count_sum_stdev_explained = np.sum(stdev_explained, axis=0)
if p is not None:
p_sum = np.mean(p, axis=0)
for i, kws in enumerate(series_config):
ax = subplot(grid[row_start:row_start + 3,
(i * 3):(i * 3 + 3)])
ax, handles, indices = plot_series_statistics(
count_sum_observed,
count_sum_expected,
explained_stdev=count_sum_stdev_explained,
total_stdev=count_sum_stdev_total,
fontsize=8,
ax=ax,
legend_enable=False,
title=tit if i == 0 else None,
despine=True if p is None else False,
return_handles=True,
return_indices=True,
**kws)
if p is not None:
_show_zero_inflated_pi(p_sum, ax, handles, indices)
plt.legend(handles=handles,
loc='best',
markerscale=4,
fontsize=8)
# add one row extra padding
row_start += 1
plot_count_sum_series(x=X,
w=W_outputs,
p=pi,
row_start=row_start,
tit="Count-sum X_original - W_original")
row_start += 1
plot_count_sum_series(
x=X_drop,
w=W_drop_outputs,
p=pi_drop,
row_start=row_start + 3,
tit="[Dropped:%s]Count-sum X_drop - W_dropout" %
dropout_percentage_text)
row_start += 1
plot_count_sum_series(
x=X,
w=W_drop_outputs,
p=pi_drop,
row_start=row_start + 6,
tit="[Dropped:%s]Count-sum X_original - W_dropout" %
dropout_percentage_text)
plot_save(os.path.join(save_dir, 'countsum_epoch%d.png') % curr_epoch,
dpi=180,
clear_all=True,
log=True)
# ====== plot series of samples ====== #
if W_outputs is not None and len(W_outputs) == 3:
# NOTe: turn off pi here
pi = None
n_visual_samples = 8
plot_figure(nrow=3 * n_visual_samples + 8, ncol=25)
col_width = 5
with plot_gridSpec(nrow=3 * n_visual_samples,
ncol=4 * col_width,
wspace=5.0,
hspace=1.0) as grid:
curr_grid_index = 0
for i in rand.permutation(len(X))[:n_visual_samples]:
observed = X[i]
expected, stdev_explained, stdev_total = [
w[i] for w in W_outputs
]
expected_drop, stdev_explained_drop, stdev_total_drop = [
w[i] for w in W_drop_outputs
]
if pi is not None:
p_zi = pi[i]
p_zi_drop = pi_drop[i]
# compare to W_original
for j, kws in enumerate(series_config):
ax = subplot(grid[curr_grid_index:curr_grid_index + 3,
(j * col_width):(j * col_width +
col_width)])
ax, handles, indices = plot_series_statistics(
observed,
expected,
explained_stdev=stdev_explained,
total_stdev=stdev_total,
fontsize=8,
legend_enable=False,
despine=True if pi is None else False,
title=("'%s' X_original - W_original" %
row_name[i]) if j == 0 else None,
return_handles=True,
return_indices=True,
**kws)
if pi is not None:
_show_zero_inflated_pi(p_zi, ax, handles, indices)
plt.legend(handles=handles,
loc='best',
markerscale=4,
fontsize=8)
# compare to W_dropout
for j, kws in enumerate(series_config):
col_start = col_width * 2
ax = subplot(
grid[curr_grid_index:curr_grid_index + 3,
(col_start +
j * col_width):(col_start + j * col_width +
col_width)])
ax, handles, indices = plot_series_statistics(
observed,
expected_drop,
explained_stdev=stdev_explained_drop,
total_stdev=stdev_total_drop,
fontsize=8,
legend_enable=False,
despine=True if pi is None else False,
title=("[Dropped:%s]'%s' X_original - W_dropout" %
(dropout_percentage_text, row_name[i]))
if j == 0 else None,
return_handles=True,
return_indices=True,
**kws)
if pi is not None:
_show_zero_inflated_pi(p_zi_drop, ax, handles, indices)
plt.legend(handles=handles,
loc='best',
markerscale=4,
fontsize=8)
curr_grid_index += 3
plot_save(os.path.join(save_dir, 'samples_epoch%d.png') % curr_epoch,
dpi=180,
clear_all=True,
log=True)
# ====== special case for mnist ====== #
if 'mnist' in ds_name and W_outputs is not None:
plot_figure(nrow=3, ncol=18)
n_images = 32
ids = rand.choice(np.arange(X.shape[0], dtype='int32'),
size=n_images,
replace=False)
meta_data = [("Org", X[ids]), ("Rec", W_outputs[0][ids]),
("OrgDropout", X_drop[ids]),
("RecDropout", W_drop_outputs[0][ids])]
count = 1
for name, data in meta_data:
for i in range(n_images):
x = data[i].reshape(28, 28)
plt.subplot(4, n_images, count)
show_image(x)
if i == 0:
plt.ylabel(name, fontsize=8)
count += 1
plt.subplots_adjust(wspace=0.05, hspace=0.05)
plot_save(os.path.join(save_dir, 'image_epoch%d.png') % curr_epoch,
dpi=180,
clear_all=True,
log=True)