def add_percentiles_to_graph(x, percentile_list, fig_name):
for p in percentile_list:
# create percentile tensor
p_tensor = percentile(x, p)
# add tensors to a figure with name=enable_bn
figures.add_scalar(tensor=p_tensor, legend=str(p), fig_name=fig_name)
def normalized_sobel_edges(img,
subtract_median=True,
same_number_of_channels=True):
"""Applies the sobel filter to images and normalizes the result.
Args:
img: tensor of shape [B, H, W, C].
subtract_median: bool; if True it subtracts the median from every channel.
This makes constant backgrounds black.
same_number_of_channels: bool; returnd tensor has the same number of
channels as the input tensor if True.
Returns:
Tensor of shape [B, H, W, C] if same_number_of_channels
else [B, H, W, 2C].
"""
sobel_img = tf.image.sobel_edges(img)
if same_number_of_channels:
sobel_img = tf.reduce_sum(sobel_img, -1)
else:
n_channels = int(img.shape[-1])
sobel_img = tf.reshape(
sobel_img, sobel_img.shape[:-2].concatenate(2 * n_channels))
if subtract_median:
sobel_img = abs(sobel_img - contrib_distributions.percentile(
sobel_img, 50.0, axis=(1, 2), keep_dims=True))
smax = tf.reduce_max(sobel_img, (1, 2), keepdims=True)
smin = tf.reduce_min(sobel_img, (1, 2), keepdims=True)
sobel_img = (sobel_img - smin) / (smax - smin + 1e-8)
return sobel_img
def decode_and_resize(image_str_tensor):
"""Decodes an image string, resizes it, and performs custom equalization."""
image = tf.image.decode_image(image_str_tensor, channels=IMG_SIZE[2])
image = tf.reshape(image, IMG_SIZE)
# Shift bottom of color range to 0
image = image - tf.reduce_min(image, axis=(0, 1))
# Divide pixel intensity by some portion of max value
image = tf.cast(image, dtype=tf.float32)
image = tf.divide(image, percentile(image, PCT_CUTOFF))
return image
def stat_tensor(tensors):
out1 = K.mean(tensors, axis=(1, 2))
out2 = K.std(tensors, axis=(1, 2))
out3_5 = percentile(tensors, q=5., axis=(1, 2))
out3_15 = percentile(tensors, q=15., axis=(1, 2))
out3_35 = percentile(tensors, q=35., axis=(1, 2))
out3_50 = percentile(tensors, q=50., axis=(1, 2))
out3_65 = percentile(tensors, q=65., axis=(1, 2))
out3_85 = percentile(tensors, q=85., axis=(1, 2))
out3_95 = percentile(tensors, q=95., axis=(1, 2))
return K.concatenate(
[out1, out2,
out3_5, out3_15, out3_35, out3_50, out3_65, out3_85, out3_95],
axis=1
)
def sample_percentiles(predictor,
per=[10, 90],
interpolation='nearest',
name=None):
"""
Get the percentiles of the samples of a predictor.
Parameter
---------
predictor : Tensor
A tensor of samples, where the first dimension indexes the samples.
per : list
A list of the percentiles to calculate from the samples. These must be
in [0, 100].
interpolation : string
The type of interpolation method to use, see
tf.contrib.distributions.percentile for details.
name : str
name to give this operation
Returns
-------
percen: Tensor
A tensor whose first dimension indexes the percentiles, computed along
the first axis of the input.
"""
for p in per:
assert 0 <= p <= 100
pers = [
percentile(predictor, p, interpolation=interpolation, axis=0)
for p in per
]
percen = tf.stack(pers, name=name)
return percen
def peak_filter(input):
N, H, W, C = K.int_shape(input)
threshold = percentile(input, q=50, axis=(1,2))
threshold = K.reshape(threshold, [tf.shape(input)[0], 1, 1, C])
return threshold
def _percentile(x, interpolation):
return percentile(x, 50.0, interpolation=interpolation)
def do_clipped_factorization(
counts_df,
rank=3,
clip_percentile=99.9,
learning_rate=1.0,
minibatch_size=1024 * 32,
patience=5,
max_epochs=1000,
normalize_to_reads_per_million=True,
log_every_seconds=10,
):
"""
Attempt to detect and correct for clone and sample batch effects by
subtracting off a learned low-rank reconstruction of the counts matrix.
The return value is the clones x samples matrix of residuals after
correcting for batch effects, with a few additional rows and columns giving
the learned background effects.
Implements the factorization:
X = AB
where X is (clones x samples), A is (clones x rank), and B is
(rank x samples)
by minimizing the "clipped" loss:
||minimum(X - AB, percentile(X - AB, clip_percentile)||_2 + unclipped
The minimum is taken elementwise, and ||...||_2 is the Frobenius norm.
clip_percentile is a parameter giving the percentile to clip at. The
clipping makes the factorization robust to outliers, some of which are
likely phip-seq hits.
If the above is optimized without an `unclipped` term, a few phage clones
may have all of their residuals above the truncation threshold. Once this
happens they will likely stay stuck there since they do not contribute to
the gradient. The unclipped term fixes this by providing a small nudge
toward smaller errors without truncation.
Note that "beads-only" samples are not treated in any special way here.
The optimization is performed using stochastic gradient descent (SGD) on
tensorflow.
Parameters
----------
counts_df : pandas.DataFrame
Matrix of read counts (clones x samples)
rank : int
Rank of low-dimensional background effect matrices A and B
clip_percentile : float
Elements with reconstruction errors above this percentile do not
contribute to the gradient. Aim for a lower-bound on the fraction
of entries you expect NOT to be hits.
learning_rate : float
SGD optimizer learning rate
minibatch_size : int
Number of rows per SGD minibatch
patience : int
Number of epochs without improvement in training loss to tolerate before
stopping
max_epochs : int
Maximum number of epochs
normalize_to_reads_per_million : boolean
Before computing factorization, first divide each column by the total
number of reads for that sample and multiple by 1 million.
log_every_seconds : float
Seconds to wait before printing another optimization status update
Returns
-------
pandas.DataFrame : residuals after correcting for batch effects
In addition to the clones x samples residuals, rows and columns named
"_background_0", "_background_1", ... giving the learned background vectors
are also included.
"""
# Non-tf setup
if normalize_to_reads_per_million:
observed = (counts_df * 1e6 / counts_df.sum(0)).astype("float32")
else:
observed = counts_df.astype("float32")
(n, s) = observed.shape
if len(counts_df) < minibatch_size:
minibatch_size = len(counts_df)
# Placeholders
target = tf.placeholder(name="target", dtype="float32", shape=[None, s])
minibatch_indices = tf.placeholder(name="minibatch_indices", dtype="int32")
# Variables
a = tf.Variable(np.random.rand(n, rank), name="A", dtype="float32")
b = tf.Variable(np.random.rand(rank, s), name="B", dtype="float32")
clip_threshold = tf.Variable(observed.max().max())
# Derived quantities
reconstruction = tf.matmul(tf.gather(a, minibatch_indices), b)
differences = target - reconstruction
# unclipped_term is based only on the minimum unclipped error for each
# clone. The intuition is that we know for every clone at least one sample
# must be a non-hit (e.g. a beads only sample), and so should be well modeled
# by the background process.
unclipped_term = tf.reduce_min(tf.pow(differences, 2), axis=1)
loss = (
tf.reduce_mean(tf.pow(tf.minimum(differences, clip_threshold), 2)) +
tf.reduce_mean(unclipped_term) / s)
update_clip_value = clip_threshold.assign(
percentile(differences, clip_percentile))
# Training
train_step = tf.train.AdamOptimizer(
learning_rate=learning_rate).minimize(loss)
init = tf.global_variables_initializer()
best_cost_value = None
last_log_at = 0
with tf.Session() as session:
session.run(init)
all_indices = np.arange(observed.shape[0], dtype=int)
for i in range(max_epochs):
indices = np.array(list(range(observed.shape[0])))
np.random.shuffle(indices)
for minibatch_indices_value in np.array_split(
indices, int(len(indices) / minibatch_size)):
minibatch_indices_value = minibatch_indices_value[:
minibatch_size]
if len(minibatch_indices_value) == minibatch_size:
feed_dict = {
target: observed.values[minibatch_indices_value],
minibatch_indices: minibatch_indices_value,
}
session.run(train_step, feed_dict=feed_dict)
feed_dict = {target: observed, minibatch_indices: all_indices}
(clip_threshold_value,
cost_value) = session.run([update_clip_value, loss],
feed_dict=feed_dict)
# Update best epoch
if best_cost_value is None or cost_value < best_cost_value:
best_cost_value = cost_value
best_epoch = i
(best_a, best_b) = session.run([a, b], feed_dict=feed_dict)
# Log
if log_every_seconds and time.time(
) - last_log_at > log_every_seconds:
print("[Epoch %5d] %f, truncating at %f%s" % (
i,
cost_value,
clip_threshold_value,
" [new best]" if i == best_epoch else "",
))
# Stop criterion
if i - best_epoch > patience:
print("Early stopping at epoch %d." % i)
break
background_names = ["_background_%d" % i for i in range(rank)]
best_a = pd.DataFrame(best_a,
index=observed.index,
columns=background_names)
best_b = pd.DataFrame(best_b,
index=background_names,
columns=observed.columns)
results = observed - np.matmul(best_a, best_b)
for name in background_names:
results[name] = best_a[name]
results.loc[name] = best_b.loc[name]
return results
def _distribution(self, input_tensor):
"""
process * batch * actions
return batch * actions
"""
return tcd.percentile(input_tensor, self.flags.percentile, axis=0)
def train(with_gan=True, load_x=True, with_y=True, match_mask=False):
"""Train ring_net for a number of steps."""
with tf.Graph().as_default():
x_all = tf.placeholder(tf.float32, [None, FLAGS.seq_length, 512, 1])
if match_mask: with_gan = False
# possible dropout inside
keep_prob = tf.placeholder("float")
#x_dropout = tf.nn.dropout(x, keep_prob)
x_in = x_all[:, :FLAGS.seq_start, :, :]
# conv network
encoder_state = None
past_state = None
future_state = None
x_1, y_1, encoder_state, past_state, future_state = network_template(
x_in, encoder_state, past_state, future_state)
if not match_mask:
y = x_all[:, FLAGS.seq_start:, :, :]
x = x_all[:, :FLAGS.seq_start, :, :]
past_loss_l2 = tf.nn.l2_loss(x - x_1)
future_loss_l2 = tf.nn.l2_loss(y - y_1)
else:
x_mask = x_all > percentile(x_all, q=95.)
x_mask = tf.one_hot(tf.cast(x_mask, tf.int32), depth=2, axis=-1)
x_logit = tf.stack([x_1, 1. / x_1], axis=-1)
y_logit = tf.stack([y_1, 1. / y_1], axis=-1)
x_1 = tf.nn.softmax(logits=x_logit)
y_1 = tf.nn.softmax(logits=y_logit)
y = x_mask[:, FLAGS.seq_start:, :, :]
x = x_mask[:, :FLAGS.seq_start, :, :]
past_loss_l2 = tf.reduce_sum(
tf.nn.softmax_cross_entropy_with_logits(logits=x_logit,
labels=x))
future_loss_l2 = tf.reduce_sum(
tf.nn.softmax_cross_entropy_with_logits(logits=y_logit,
labels=y))
#import IPython; IPython.embed()
if with_gan:
img = x_all[:, FLAGS.seq_start:, :, :]
img_ = y_1
#import IPython; IPython.embed()
D, D_logits, D3 = discriminator(img, reuse=False)
#import IPython; IPython.embed()
D_, D_logits_, D3_ = discriminator(
y_1, reuse=True, fc_shape=D3.get_shape().as_list())
d_loss_real = tf.reduce_mean(
tf.nn.sigmoid_cross_entropy_with_logits(
logits=D_logits, labels=tf.ones_like(D)))
d_loss_fake = tf.reduce_mean(
tf.nn.sigmoid_cross_entropy_with_logits(
logits=D_logits_, labels=tf.zeros_like(D_)))
d_loss = d_loss_real + d_loss_fake
g_loss = tf.reduce_mean(
tf.nn.sigmoid_cross_entropy_with_logits(
logits=D_logits_, labels=tf.ones_like(D_)))
D3_loss = tf.nn.l2_loss(D3 - D3_)
t_vars = tf.trainable_variables()
d_vars = [var for var in t_vars if 'd_' in var.name]
g_vars = [var for var in t_vars if 'd_' not in var.name]
tf.summary.scalar('loss_g', g_loss)
tf.summary.scalar('loss_d', d_loss)
tf.summary.scalar('loss_feature', D3_loss)
loss = 0.05 * (past_loss_l2 +
future_loss_l2) + g_loss + D3_loss * 1.e-4
tf.summary.scalar('past_loss_l2', past_loss_l2)
tf.summary.scalar('future_loss_l2', future_loss_l2)
d_optim = tf.train.AdamOptimizer(FLAGS.lr).minimize(
d_loss, var_list=d_vars)
g_optim = tf.train.AdamOptimizer(FLAGS.lr).minimize(
loss, var_list=g_vars)
#import IPython; IPython.embed()
train_op = tf.group(d_optim, d_optim, g_optim)
else:
loss = past_loss_l2 + future_loss_l2
tf.summary.scalar('loss', loss)
# training
optimizer = tf.train.AdamOptimizer(FLAGS.lr)
gvs = optimizer.compute_gradients(loss)
# gradient clipping
capped_gvs = [(tf.clip_by_value(grad, -3., 3.), var)
for grad, var in gvs]
train_op = optimizer.apply_gradients(capped_gvs)
# List of all Variables
variables = tf.global_variables()
# Build a saver
saver = tf.train.Saver(tf.global_variables())
# Summary op
summary_op = tf.summary.merge_all()
# Build an initialization operation to run below.
init = tf.global_variables_initializer()
# Start running operations on the Graph.
sess = tf.Session()
# init if this is the very time training
sess.run(init)
if FLAGS.resume:
latest = tf.train.latest_checkpoint(FLAGS.train_dir)
if not latest:
print("No checkpoint to continue from in", FLAGS.train_dir)
sys.exit(1)
print("resume", latest)
saver.restore(sess, latest)
else:
print("init network from scratch")
# Summary op
graph_def = sess.graph.as_graph_def(add_shapes=True)
summary_writer = tf.summary.FileWriter(FLAGS.train_dir,
graph_def=graph_def)
if not with_y:
files = find_files(FLAGS.train_data_index)
else:
files = find_pairs(FLAGS.train_data_index)
sample_dir = FLAGS.train_dir + '/samples/'
if not os.path.exists(sample_dir):
os.makedirs(sample_dir)
for step in range(FLAGS.max_step):
dat = load_batch(FLAGS.batch_size,
files,
step,
with_y=with_y,
normalize=FLAGS.norm_input)
dat = random_flip(dat)
t = time.time()
errG, errD = sess.run([g_loss, d_loss],
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
if errG > 0.6 and errD > 0.6:
_, loss_r = sess.run([train_op, loss],
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
else:
i = 0
while errG > 0.6:
_ = sess.run(g_optim,
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
i += 1
if i > 2: break
else:
errG = sess.run(g_loss,
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
print('G', i, errG)
i = 0
while errD > 0.6:
# only update discriminator if loss are within given bounds
_ = sess.run(d_optim,
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
i += 1
if i > 2: break
else:
errD = sess.run(d_loss,
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
print('D', i, errD)
loss_r = sess.run(loss,
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
#_, loss_r = sess.run([train_op, loss],feed_dict={x:dat, keep_prob:FLAGS.keep_prob})
elapsed = time.time() - t
if step % 1000 == 0 and step != 0:
summary_str = sess.run(summary_op,
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
summary_writer.add_summary(summary_str, step)
print("time per batch is " + str(elapsed))
print(step)
print(loss_r)
assert not np.isnan(loss_r), 'Model diverged with loss = NaN'
if step % 4000 == 0:
checkpoint_path = os.path.join(FLAGS.train_dir, 'model.ckpt')
saver.save(sess, checkpoint_path, global_step=step)
print("saved to " + FLAGS.train_dir)
print("now saving sample!")
im_x, im_y = sess.run([x_1, y_1],
feed_dict={
x_all: dat,
keep_prob: FLAGS.keep_prob
})
if match_mask:
im_x = im_x[..., 1]
im_y = im_y[..., 1]
_plot_samples(dat[:, :FLAGS.seq_start, :, :].squeeze(),
sample_dir + 'step_{}_past_t.png'.format(step))
_plot_samples(im_x.squeeze(),
sample_dir + 'step_{}_past.png'.format(step))
_plot_samples(dat[:, FLAGS.seq_start:, :, :].squeeze(),
sample_dir + 'step_{}_future_t.png'.format(step))
_plot_samples(im_y.squeeze(),
sample_dir + 'step_{}_future.png'.format(step))
def summary_percentiles(x, percents):
for p in percents:
name = "percentile_" + str(p)
tf.summary.scalar(name, percentile(x, p))