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unirep.py
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"""
The trained 1900-dimensional mLSTM babbler.
"""
import tensorflow as tf
import numpy as np
import pandas as pd
import sys
sys.path.append('../')
from data_utils import aa_seq_to_int, int_to_aa, bucketbatchpad
import os
# Helpers
def tf_get_shape(tensor):
static_shape = tensor.shape.as_list()
dynamic_shape = tf.unstack(tf.shape(tensor))
dims = [s[1] if s[0] is None else s[0]
for s in zip(static_shape, dynamic_shape)]
return dims
def sample_with_temp(logits, t):
"""
Takes temperature between 0 and 1 -> zero most conservative, 1 most liberal. Samples.
"""
t_adjusted = logits / t # broadcast temperature normalization
softed = tf.nn.softmax(t_adjusted)
# Make a categorical distribution from the softmax and sample
return tf.distributions.Categorical(probs=softed).sample()
def initialize_uninitialized(sess):
"""
from https://stackoverflow.com/questions/35164529/in-tensorflow-is-there-any-way-to-just-initialize-uninitialised-variables
"""
global_vars = tf.global_variables()
is_not_initialized = sess.run([tf.is_variable_initialized(var) for var in global_vars])
not_initialized_vars = [v for (v, f) in zip(global_vars, is_not_initialized) if not f]
if len(not_initialized_vars):
sess.run(tf.variables_initializer(not_initialized_vars))
# Setup to initialize from the correctly named model files.
class mLSTMCell1900(tf.nn.rnn_cell.RNNCell):
def __init__(self,
num_units,
model_path="./",
wn=True,
scope='mlstm',
var_device='cpu:0',
):
# Really not sure if I should reuse here
super(mLSTMCell1900, self).__init__()
self._num_units = num_units
self._model_path = model_path
self._wn = wn
self._scope = scope
self._var_device = var_device
@property
def state_size(self):
# The state is a tuple of c and h
return (self._num_units, self._num_units)
@property
def output_size(self):
# The output is h
return (self._num_units)
def zero_state(self, batch_size, dtype):
c = tf.zeros([batch_size, self._num_units], dtype=dtype)
h = tf.zeros([batch_size, self._num_units], dtype=dtype)
return (c, h)
def call(self, inputs, state):
# Inputs will be a [batch_size, input_dim] tensor.
# Eg, input_dim for a 10-D embedding is 10
nin = inputs.get_shape()[1].value
# Unpack the state tuple
c_prev, h_prev = state
with tf.variable_scope(self._scope):
wx_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_wx:0.npy"))
wh_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_wh:0.npy"))
wmx_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_wmx:0.npy"))
wmh_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_wmh:0.npy"))
b_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_b:0.npy"))
gx_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_gx:0.npy"))
gh_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_gh:0.npy"))
gmx_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_gmx:0.npy"))
gmh_init = np.load(os.path.join(self._model_path, "rnn_mlstm_mlstm_gmh:0.npy"))
wx = tf.get_variable(
"wx", initializer=wx_init)
wh = tf.get_variable(
"wh", initializer=wh_init)
wmx = tf.get_variable(
"wmx", initializer=wmx_init)
wmh = tf.get_variable(
"wmh", initializer=wmh_init)
b = tf.get_variable(
"b", initializer=b_init)
if self._wn:
gx = tf.get_variable(
"gx", initializer=gx_init)
gh = tf.get_variable(
"gh", initializer=gh_init)
gmx = tf.get_variable(
"gmx", initializer=gmx_init)
gmh = tf.get_variable(
"gmh", initializer=gmh_init)
if self._wn:
wx = tf.nn.l2_normalize(wx, dim=0) * gx
wh = tf.nn.l2_normalize(wh, dim=0) * gh
wmx = tf.nn.l2_normalize(wmx, dim=0) * gmx
wmh = tf.nn.l2_normalize(wmh, dim=0) * gmh
m = tf.matmul(inputs, wmx) * tf.matmul(h_prev, wmh)
z = tf.matmul(inputs, wx) + tf.matmul(m, wh) + b
i, f, o, u = tf.split(z, 4, 1)
i = tf.nn.sigmoid(i)
f = tf.nn.sigmoid(f)
o = tf.nn.sigmoid(o)
u = tf.tanh(u)
c = f * c_prev + i * u
h = o * tf.tanh(c)
return h, (c, h)
class mLSTMCell(tf.nn.rnn_cell.RNNCell):
def __init__(self,
num_units,
wx_init=tf.orthogonal_initializer(),
wh_init=tf.orthogonal_initializer(),
wmx_init=tf.orthogonal_initializer(),
wmh_init=tf.orthogonal_initializer(),
b_init=tf.orthogonal_initializer(),
gx_init=tf.ones_initializer(),
gh_init=tf.ones_initializer(),
gmx_init=tf.ones_initializer(),
gmh_init=tf.ones_initializer(),
wn=True,
scope='mlstm',
var_device='cpu:0',
):
# Really not sure if I should reuse here
super(mLSTMCell, self).__init__()
self._num_units = num_units
self._wn = wn
self._scope = scope
self._var_device = var_device
self._wx_init = wx_init
self._wh_init = wh_init
self._wmx_init = wmx_init
self._wmh_init = wmh_init
self._b_init = b_init
self._gx_init = gx_init
self._gh_init = gh_init
self._gmx_init = gmx_init
self._gmh_init = gmh_init
@property
def state_size(self):
# The state is a tuple of c and h
return (self._num_units, self._num_units)
@property
def output_size(self):
# The output is h
return (self._num_units)
def zero_state(self, batch_size, dtype):
c = tf.zeros([batch_size, self._num_units], dtype=dtype)
h = tf.zeros([batch_size, self._num_units], dtype=dtype)
return (c, h)
def call(self, inputs, state):
# Inputs will be a [batch_size, input_dim] tensor.
# Eg, input_dim for a 10-D embedding is 10
nin = inputs.get_shape()[1].value
# Unpack the state tuple
c_prev, h_prev = state
with tf.variable_scope(self._scope):
wx = tf.get_variable(
"wx", initializer=self._wx_init)
wh = tf.get_variable(
"wh", initializer=self._wh_init)
wmx = tf.get_variable(
"wmx", initializer=self._wmx_init)
wmh = tf.get_variable(
"wmh", initializer=self._wmh_init)
b = tf.get_variable(
"b", initializer=self._b_init)
if self._wn:
gx = tf.get_variable(
"gx", initializer=self._gx_init)
gh = tf.get_variable(
"gh", initializer=self._gh_init)
gmx = tf.get_variable(
"gmx", initializer=self._gmx_init)
gmh = tf.get_variable(
"gmh", initializer=self._gmh_init)
if self._wn:
wx = tf.nn.l2_normalize(wx, dim=0) * gx
wh = tf.nn.l2_normalize(wh, dim=0) * gh
wmx = tf.nn.l2_normalize(wmx, dim=0) * gmx
wmh = tf.nn.l2_normalize(wmh, dim=0) * gmh
m = tf.matmul(inputs, wmx) * tf.matmul(h_prev, wmh)
z = tf.matmul(inputs, wx) + tf.matmul(m, wh) + b
i, f, o, u = tf.split(z, 4, 1)
i = tf.nn.sigmoid(i)
f = tf.nn.sigmoid(f)
o = tf.nn.sigmoid(o)
u = tf.tanh(u)
c = f * c_prev + i * u
h = o * tf.tanh(c)
return h, (c, h)
class mLSTMCellStackNPY(tf.nn.rnn_cell.RNNCell):
def __init__(self,
num_units=256,
num_layers=4,
dropout=None,
res_connect=False,
wn=True,
scope='mlstm_stack',
var_device='cpu:0',
model_path="./"
):
# Really not sure if I should reuse here
super(mLSTMCellStackNPY, self).__init__()
self._model_path=model_path
self._num_units = num_units
self._num_layers = num_layers
self._dropout = dropout
self._res_connect = res_connect
self._wn = wn
self._scope = scope
self._var_device = var_device
bs = "rnn_mlstm_stack_mlstm_stack" # base scope see weight file names
join = lambda x: os.path.join(self._model_path, x)
layers = [mLSTMCell(
num_units=self._num_units,
wn=self._wn,
scope=self._scope + str(i),
var_device=self._var_device,
wx_init=np.load(join(bs + "{0}_mlstm_stack{1}_wx:0.npy".format(i,i))),
wh_init=np.load(join(bs + "{0}_mlstm_stack{1}_wh:0.npy".format(i,i))),
wmx_init=np.load(join(bs + "{0}_mlstm_stack{1}_wmx:0.npy".format(i,i))),
wmh_init=np.load(join(bs + "{0}_mlstm_stack{1}_wmh:0.npy".format(i,i))),
b_init=np.load(join(bs + "{0}_mlstm_stack{1}_b:0.npy".format(i,i))),
gx_init=np.load(join(bs + "{0}_mlstm_stack{1}_gx:0.npy".format(i,i))),
gh_init=np.load(join(bs + "{0}_mlstm_stack{1}_gh:0.npy".format(i,i))),
gmx_init=np.load(join(bs + "{0}_mlstm_stack{1}_gmx:0.npy".format(i,i))),
gmh_init=np.load(join(bs + "{0}_mlstm_stack{1}_gmh:0.npy".format(i,i)))
) for i in range(self._num_layers)]
if self._dropout:
layers = [
tf.contrib.rnn.DropoutWrapper(
layer, output_keep_prob=1-self._dropout) for layer in layers[:-1]] + layers[-1:]
self._layers = layers
@property
def state_size(self):
# The state is a tuple of c and h
return (
tuple(self._num_units for _ in range(self._num_layers)),
tuple(self._num_units for _ in range(self._num_layers))
)
@property
def output_size(self):
# The output is h
return (self._num_units)
def zero_state(self, batch_size, dtype):
c_stack = tuple(tf.zeros([batch_size, self._num_units], dtype=dtype) for _ in range(self._num_layers))
h_stack = tuple(tf.zeros([batch_size, self._num_units], dtype=dtype) for _ in range(self._num_layers))
return (c_stack, h_stack)
def call(self, inputs, state):
# Inputs will be a [batch_size, input_dim] tensor.
# Eg, input_dim for a 10-D embedding is 10
# Unpack the state tuple
c_prev, h_prev = state
new_outputs = []
new_cs = []
new_hs = []
for i, layer in enumerate(self._layers):
if i == 0:
h, (c,h_state) = layer(inputs, (c_prev[i],h_prev[i]))
else:
h, (c,h_state) = layer(new_outputs[-1], (c_prev[i],h_prev[i]))
new_outputs.append(h)
new_cs.append(c)
new_hs.append(h_state)
if self._res_connect:
# Make sure number of layers does not affect the scale of the output
scale_factor = tf.constant(1 / float(self._num_layers))
final_output = tf.scalar_mul(scale_factor,tf.add_n(new_outputs))
else:
final_output = new_outputs[-1]
return final_output, (tuple(new_cs), tuple(new_hs))
class babbler1900():
def __init__(self,
model_path="./pbab_weights",
batch_size=256
):
self._rnn_size = 1900
self._vocab_size = 26
self._embed_dim = 10
self._wn = True
self._shuffle_buffer = 10000
self._model_path = model_path
self._batch_size = batch_size
self._batch_size_placeholder = tf.placeholder(tf.int32, shape=[], name="batch_size")
self._minibatch_x_placeholder = tf.placeholder(
tf.int32, shape=[None, None], name="minibatch_x")
self._initial_state_placeholder = (
tf.placeholder(tf.float32, shape=[None, self._rnn_size]),
tf.placeholder(tf.float32, shape=[None, self._rnn_size])
)
self._minibatch_y_placeholder = tf.placeholder(
tf.int32, shape=[None, None], name="minibatch_y")
# Batch size dimensional placeholder which gives the
# Lengths of the input sequence batch. Used to index into
# The final_hidden output and select the stop codon -1
# final hidden for the graph operation.
self._seq_length_placeholder = tf.placeholder(
tf.int32, shape=[None], name="seq_len")
self._temp_placeholder = tf.placeholder(tf.float32, shape=[], name="temp")
rnn = mLSTMCell1900(self._rnn_size,
model_path=model_path,
wn=self._wn)
zero_state = rnn.zero_state(self._batch_size, tf.float32)
single_zero = rnn.zero_state(1, tf.float32)
mask = tf.sign(self._minibatch_y_placeholder) # 1 for nonpad, zero for pad
inverse_mask = 1 - mask # 0 for nonpad, 1 for pad
total_padded = tf.reduce_sum(inverse_mask)
pad_adjusted_targets = (self._minibatch_y_placeholder - 1) + inverse_mask
embed_matrix = tf.get_variable(
"embed_matrix", dtype=tf.float32, initializer=np.load(os.path.join(self._model_path, "embed_matrix:0.npy"))
)
embed_cell = tf.nn.embedding_lookup(embed_matrix, self._minibatch_x_placeholder)
self._output, self._final_state = tf.nn.dynamic_rnn(
rnn,
embed_cell,
initial_state=self._initial_state_placeholder,
swap_memory=True,
parallel_iterations=1
)
# If we are training a model on top of the rep model, we need to access
# the final_hidden rep from output. Recall we are padding these sequences
# to max length, so the -1 position will not necessarily be the right rep.
# to get the right rep, I will use the provided sequence length to index.
# Subtract one for the last place
indices = self._seq_length_placeholder - 1
self._top_final_hidden = tf.gather_nd(self._output, tf.stack([tf.range(tf_get_shape(self._output)[0], dtype=tf.int32), indices], axis=1))
# LEFTOFF self._output is a batch size, seq_len, num_hidden.
# I want to average along num_hidden, but I'll have to figure out how to mask out
# the dimensions along sequence_length which are longer than the given sequence.
flat = tf.reshape(self._output, [-1, self._rnn_size])
logits_flat = tf.contrib.layers.fully_connected(
flat, self._vocab_size - 1, activation_fn=None,
weights_initializer=tf.constant_initializer(np.load(os.path.join(self._model_path, "fully_connected_weights:0.npy"))),
biases_initializer=tf.constant_initializer(np.load(os.path.join(self._model_path, "fully_connected_biases:0.npy"))))
self._logits = tf.reshape(
logits_flat, [batch_size, tf_get_shape(self._minibatch_x_placeholder)[1], self._vocab_size - 1])
batch_losses = tf.contrib.seq2seq.sequence_loss(
self._logits,
tf.cast(pad_adjusted_targets, tf.int32),
tf.cast(mask, tf.float32),
average_across_batch=False
)
self._loss = tf.reduce_mean(batch_losses)
self._sample = sample_with_temp(self._logits, self._temp_placeholder)
with tf.Session() as sess:
self._zero_state = sess.run(zero_state)
self._single_zero = sess.run(single_zero)
def get_rep(self,seq):
"""
Input a valid amino acid sequence,
outputs a tuple of average hidden, final hidden, final cell representation arrays.
Unfortunately, this method accepts one sequence at a time and is as such quite
slow.
"""
with tf.Session() as sess:
initialize_uninitialized(sess)
# Strip any whitespace and convert to integers with the correct coding
int_seq = aa_seq_to_int(seq.strip())[:-1]
# Final state is a cell_state, hidden_state tuple. Output is
# all hidden states
final_state_, hs = sess.run(
[self._final_state, self._output], feed_dict={
self._batch_size_placeholder: 1,
self._minibatch_x_placeholder: [int_seq],
self._initial_state_placeholder: self._zero_state}
)
final_cell, final_hidden = final_state_
# Drop the batch dimension so it is just seq len by
# representation size
final_cell = final_cell[0]
final_hidden = final_hidden[0]
hs = hs[0]
avg_hidden = np.mean(hs, axis=0)
return avg_hidden, final_hidden, final_cell
def get_babble(self, seed, length=250, temp=1):
"""
Return a babble at temperature temp (on (0,1] with 1 being the noisiest)
starting with seed and continuing to length length.
Unfortunately, this method accepts one sequence at a time and is as such quite
slow.
"""
with tf.Session() as sess:
initialize_uninitialized(sess)
int_seed = aa_seq_to_int(seed.strip())[:-1]
# No need for padding because this is a single element
seed_samples, final_state_ = sess.run(
[self._sample, self._final_state],
feed_dict={
self._minibatch_x_placeholder: [int_seed],
self._initial_state_placeholder: self._zero_state,
self._batch_size_placeholder: 1,
self._temp_placeholder: temp
}
)
# Just the actual character prediction
pred_int = seed_samples[0, -1] + 1
seed = seed + int_to_aa[pred_int]
for i in range(length - len(seed)):
pred_int, final_state_ = sess.run(
[self._sample, self._final_state],
feed_dict={
self._minibatch_x_placeholder: [[pred_int]],
self._initial_state_placeholder: final_state_,
self._batch_size_placeholder: 1,
self._temp_placeholder: temp
}
)
pred_int = pred_int[0, 0] + 1
seed = seed + int_to_aa[pred_int]
return seed
def get_rep_ops(self):
"""
Return tensorflow operations for the final_hidden state and placeholder.
POSTPONED: Implement avg. hidden
"""
return self._top_final_hidden, self._minibatch_x_placeholder, self._batch_size_placeholder, self._seq_length_placeholder, self._initial_state_placeholder
def get_babbler_ops(self):
"""
Return tensorflow operations for
the logits, masked loss, minibatch_x placeholder, minibatch y placeholder, batch_size placeholder, initial_state placeholder
Use if you plan on using babbler1900 as an initialization for another babbler,
eg for fine tuning the babbler to babble a differenct distribution.
"""
return self._logits, self._loss, self._minibatch_x_placeholder, self._minibatch_y_placeholder, self._batch_size_placeholder, self._initial_state_placeholder
def dump_weights(self,sess,dir_name="./1900_weights"):
"""
Saves the weights of the model in dir_name in the format required
for loading in this module. Must be called within a tf.Session
For which the weights are already initialized.
"""
vs = tf.trainable_variables()
for v in vs:
name = v.name
value = sess.run(v)
print(name)
print(value)
np.save(os.path.join(dir_name,name.replace('/', '_') + ".npy"), np.array(value))
def format_seq(self,seq,stop=False):
"""
Takes an amino acid sequence, returns a list of integers in the codex of the babbler.
Here, the default is to strip the stop symbol (stop=False) which would have
otherwise been added to the end of the sequence. If you are trying to generate
a rep, do not include the stop. It is probably best to ignore the stop if you are
co-tuning the babbler and a top model as well.
"""
if stop:
int_seq = aa_seq_to_int(seq.strip())
else:
int_seq = aa_seq_to_int(seq.strip())[:-1]
return int_seq
def bucket_batch_pad(self,filepath, upper=2000, lower=50, interval=10):
"""
Read sequences from a filepath, batch them into buckets of similar lengths, and
pad out to the longest sequence.
Upper, lower and interval define how the buckets are created.
Any sequence shorter than lower will be grouped together, as with any greater
than upper. Interval defines the "walls" of all the other buckets.
WARNING: Define large intervals for small datasets because the default behavior
is to repeat the same sequence to fill a batch. If there is only one sequence
within a bucket, it will be repeated batch_size -1 times to fill the batch.
"""
self._bucket_upper = upper
self._bucket_lower = lower
self._bucket_interval = interval
self._bucket = [self._bucket_lower + (i * self._bucket_interval) for i in range(int(self._bucket_upper / self._bucket_interval))]
self._bucket_batch = bucketbatchpad(
batch_size=self._batch_size,
pad_shape=([None]),
window_size=self._batch_size,
bounds=self._bucket,
path_to_data=filepath,
shuffle_buffer=self._shuffle_buffer,
repeat=None
).make_one_shot_iterator().get_next()
return self._bucket_batch
def split_to_tuple(self, seq_batch):
"""
NOTICE THAT BY DEFAULT THIS STRIPS THE LAST CHARACTER.
IF USING IN COMBINATION WITH format_seq then set stop=True there.
Return a list of batch, target tuples.
The input (array-like) should
look like
1. . . . . . . . sequence_length
.
.
.
batch_size
"""
q = None
num_steps = seq_batch.shape[1]
# Minibatches should start at zero index and go to -1
# Don't even try to get what is happenning here its a brainfuck and
# probably inefficient
xypairs = [
(seq_batch[:, :-1][:, idx:idx + num_steps], seq_batch[:, idx + 1:idx + num_steps + 1]) for idx in np.arange(len(seq_batch[0]))[0:-1:num_steps]
]
if q:
for e in xypairs:
q.put(e)
else:
return xypairs[0]
def is_valid_seq(self, seq, max_len=2000):
"""
True if seq is valid for the babbler, False otherwise.
"""
l = len(seq)
valid_aas = "MRHKDESTNQCUGPAVIFYWLO"
if (l < max_len) and set(seq) <= set(valid_aas):
return True
else:
return False
class babbler256(babbler1900):
"""
Tested get_rep and get_rep_ops, assumed rest was unaffected by subclassing.
"""
def __init__(self,
model_path="./256_weights/",
batch_size=256
):
self._rnn_size = 256
self._vocab_size = 26
self._embed_dim = 10
self._num_layers = 4
self._wn = True
self._shuffle_buffer = 10000
self._model_path = model_path
self._batch_size = batch_size
self._batch_size_placeholder = tf.placeholder(tf.int32, shape=[], name="batch_size")
self._minibatch_x_placeholder = tf.placeholder(
tf.int32, shape=[None, None], name="minibatch_x")
self._initial_state_placeholder = (
tuple(tf.placeholder(tf.float32, shape=[None, self._rnn_size]) for _ in range(self._num_layers)),
tuple(tf.placeholder(tf.float32, shape=[None, self._rnn_size]) for _ in range(self._num_layers))
)
self._minibatch_y_placeholder = tf.placeholder(
tf.int32, shape=[None, None], name="minibatch_y")
# Batch size dimensional placeholder which gives the
# Lengths of the input sequence batch. Used to index into
# The final_hidden output and select the stop codon -1
# final hidden for the graph operation.
self._seq_length_placeholder = tf.placeholder(
tf.int32, shape=[None], name="seq_len")
self._temp_placeholder = tf.placeholder(tf.float32, shape=[], name="temp")
rnn = mLSTMCellStackNPY(num_units=self._rnn_size,
num_layers=self._num_layers,
model_path=model_path,
wn=self._wn)
zero_state = rnn.zero_state(self._batch_size, tf.float32)
single_zero = rnn.zero_state(1, tf.float32)
mask = tf.sign(self._minibatch_y_placeholder) # 1 for nonpad, zero for pad
inverse_mask = 1 - mask # 0 for nonpad, 1 for pad
total_padded = tf.reduce_sum(inverse_mask)
pad_adjusted_targets = (self._minibatch_y_placeholder - 1) + inverse_mask
embed_matrix = tf.get_variable(
"embed_matrix", dtype=tf.float32, initializer=np.load(os.path.join(self._model_path, "embed_matrix:0.npy"))
)
embed_cell = tf.nn.embedding_lookup(embed_matrix, self._minibatch_x_placeholder)
self._output, self._final_state = tf.nn.dynamic_rnn(
rnn,
embed_cell,
initial_state=self._initial_state_placeholder,
swap_memory=True,
parallel_iterations=1
)
# If we are training a model on top of the rep model, we need to access
# the final_hidden rep from output. Recall we are padding these sequences
# to max length, so the -1 position will not necessarily be the right rep.
# to get the right rep, I will use the provided sequence length to index.
# Subtract one for the last place
indices = self._seq_length_placeholder - 1
self._top_final_hidden = tf.gather_nd(self._output, tf.stack([tf.range(tf_get_shape(self._output)[0], dtype=tf.int32), indices], axis=1))
# LEFTOFF self._output is a batch size, seq_len, num_hidden.
# I want to average along num_hidden, but I'll have to figure out how to mask out
# the dimensions along sequence_length which are longer than the given sequence.
flat = tf.reshape(self._output, [-1, self._rnn_size])
logits_flat = tf.contrib.layers.fully_connected(
flat, self._vocab_size - 1, activation_fn=None,
weights_initializer=tf.constant_initializer(np.load(os.path.join(self._model_path, "fully_connected_weights:0.npy"))),
biases_initializer=tf.constant_initializer(np.load(os.path.join(self._model_path, "fully_connected_biases:0.npy"))))
self._logits = tf.reshape(
logits_flat, [batch_size, tf_get_shape(self._minibatch_x_placeholder)[1], self._vocab_size - 1])
batch_losses = tf.contrib.seq2seq.sequence_loss(
self._logits,
tf.cast(pad_adjusted_targets, tf.int32),
tf.cast(mask, tf.float32),
average_across_batch=False
)
self._loss = tf.reduce_mean(batch_losses)
self._sample = sample_with_temp(self._logits, self._temp_placeholder)
with tf.Session() as sess:
self._zero_state = sess.run(zero_state)
self._single_zero = sess.run(single_zero)
def get_rep(self,seq):
"""
get_rep needs to be minorly adjusted to accomadate the different state size of the
stack.
Input a valid amino acid sequence,
outputs a tuple of average hidden, final hidden, final cell representation arrays.
Unfortunately, this method accepts one sequence at a time and is as such quite
slow.
"""
with tf.Session() as sess:
initialize_uninitialized(sess)
# Strip any whitespace and convert to integers with the correct coding
int_seq = aa_seq_to_int(seq.strip())[:-1]
# Final state is a cell_state, hidden_state tuple. Output is
# all hidden states
final_state_, hs = sess.run(
[self._final_state, self._output], feed_dict={
self._batch_size_placeholder: 1,
self._minibatch_x_placeholder: [int_seq],
self._initial_state_placeholder: self._zero_state}
)
final_cell, final_hidden = final_state_
# Because this is a deep model, each of final hidden and final cell is tuple of num_layers
final_cell = final_cell[-1]
final_hidden = final_hidden[-1]
hs = hs[0]
avg_hidden = np.mean(hs, axis=0)
return avg_hidden, final_hidden[0], final_cell[0]
class babbler64(babbler256):
"""
Tested get_rep and dump weights. Assumed rest unaffected by subclassing.
"""
def __init__(self,
model_path="./64_weights/",
batch_size=256
):
self._rnn_size = 64
self._vocab_size = 26
self._embed_dim = 10
self._num_layers = 4
self._wn = True
self._shuffle_buffer = 10000
self._model_path = model_path
self._batch_size = batch_size
self._batch_size_placeholder = tf.placeholder(tf.int32, shape=[], name="batch_size")
self._minibatch_x_placeholder = tf.placeholder(
tf.int32, shape=[None, None], name="minibatch_x")
self._initial_state_placeholder = (
tuple(tf.placeholder(tf.float32, shape=[None, self._rnn_size]) for _ in range(self._num_layers)),
tuple(tf.placeholder(tf.float32, shape=[None, self._rnn_size]) for _ in range(self._num_layers))
)
self._minibatch_y_placeholder = tf.placeholder(
tf.int32, shape=[None, None], name="minibatch_y")
# Batch size dimensional placeholder which gives the
# Lengths of the input sequence batch. Used to index into
# The final_hidden output and select the stop codon -1
# final hidden for the graph operation.
self._seq_length_placeholder = tf.placeholder(
tf.int32, shape=[None], name="seq_len")
self._temp_placeholder = tf.placeholder(tf.float32, shape=[], name="temp")
rnn = mLSTMCellStackNPY(num_units=self._rnn_size,
num_layers=self._num_layers,
model_path=model_path,
wn=self._wn)
zero_state = rnn.zero_state(self._batch_size, tf.float32)
single_zero = rnn.zero_state(1, tf.float32)
mask = tf.sign(self._minibatch_y_placeholder) # 1 for nonpad, zero for pad
inverse_mask = 1 - mask # 0 for nonpad, 1 for pad
total_padded = tf.reduce_sum(inverse_mask)
pad_adjusted_targets = (self._minibatch_y_placeholder - 1) + inverse_mask
embed_matrix = tf.get_variable(
"embed_matrix", dtype=tf.float32, initializer=np.load(os.path.join(self._model_path, "embed_matrix:0.npy"))
)
embed_cell = tf.nn.embedding_lookup(embed_matrix, self._minibatch_x_placeholder)
self._output, self._final_state = tf.nn.dynamic_rnn(
rnn,
embed_cell,
initial_state=self._initial_state_placeholder,
swap_memory=True,
parallel_iterations=1
)
# If we are training a model on top of the rep model, we need to access
# the final_hidden rep from output. Recall we are padding these sequences
# to max length, so the -1 position will not necessarily be the right rep.
# to get the right rep, I will use the provided sequence length to index.
# Subtract one for the last place
indices = self._seq_length_placeholder - 1
self._top_final_hidden = tf.gather_nd(self._output, tf.stack([tf.range(tf_get_shape(self._output)[0], dtype=tf.int32), indices], axis=1))
# LEFTOFF self._output is a batch size, seq_len, num_hidden.
# I want to average along num_hidden, but I'll have to figure out how to mask out
# the dimensions along sequence_length which are longer than the given sequence.
flat = tf.reshape(self._output, [-1, self._rnn_size])
logits_flat = tf.contrib.layers.fully_connected(
flat, self._vocab_size - 1, activation_fn=None,
weights_initializer=tf.constant_initializer(np.load(os.path.join(self._model_path, "fully_connected_weights:0.npy"))),
biases_initializer=tf.constant_initializer(np.load(os.path.join(self._model_path, "fully_connected_biases:0.npy"))))
self._logits = tf.reshape(
logits_flat, [batch_size, tf_get_shape(self._minibatch_x_placeholder)[1], self._vocab_size - 1])
batch_losses = tf.contrib.seq2seq.sequence_loss(
self._logits,
tf.cast(pad_adjusted_targets, tf.int32),
tf.cast(mask, tf.float32),
average_across_batch=False
)
self._loss = tf.reduce_mean(batch_losses)
self._sample = sample_with_temp(self._logits, self._temp_placeholder)
with tf.Session() as sess:
self._zero_state = sess.run(zero_state)
self._single_zero = sess.run(single_zero)