healthcareio
/
data-maker
mirror of https://hiplab.mc.vanderbilt.edu/git/aou/data-maker.git
1
1
Fork 0
Code Issues Packages Projects Releases Wiki Activity

removing conditions, it blows up computational space

Browse Source
dev
Steve L. Nyemba 5 years ago
parent dab3ab7bf7
commit 4a25af6b13
3 changed files with 62 additions and 36 deletions
Show Stats Download Patch File Download Diff File

49
data/gan.py
Unescape View File

@ -72,7 +72,7 @@ class GNet :
elif 'label' in args and len(args['label']) == 1 : elif 'label' in args and len(args['label']) == 1 :
self.NUM_LABELS = args['label'].shape[0] self.NUM_LABELS = args['label'].shape[0]
else: else:
self.NUM_LABELS = 8 self.NUM_LABELS = None
# self.Z_DIM = 128 #self.X_SPACE_SIZE # self.Z_DIM = 128 #self.X_SPACE_SIZE
self.Z_DIM = 128 #-- used as rows down stream self.Z_DIM = 128 #-- used as rows down stream
self.G_STRUCTURE = [self.Z_DIM,self.Z_DIM] self.G_STRUCTURE = [self.Z_DIM,self.Z_DIM]
@ -180,13 +180,18 @@ class GNet :
shift = [0] if self.__class__.__name__.lower() == 'generator' else [1] #-- not sure what this is doing shift = [0] if self.__class__.__name__.lower() == 'generator' else [1] #-- not sure what this is doing
mean, var = tf.nn.moments(inputs, shift, keep_dims=True) mean, var = tf.nn.moments(inputs, shift, keep_dims=True)
shape = inputs.shape[1].value shape = inputs.shape[1].value
offset_m = self.get.variables(shape=[n_labels,shape], name='offset'+name, if labels is not None:
offset_m = self.get.variables(shape=[1,shape], name='offset'+name,
initializer=tf.zeros_initializer) initializer=tf.zeros_initializer)
scale_m = self.get.variables(shape=[n_labels,shape], name='scale'+name, scale_m = self.get.variables(shape=[n_labels,shape], name='scale'+name,
initializer=tf.ones_initializer) initializer=tf.ones_initializer)
offset = tf.nn.embedding_lookup(offset_m, labels) offset = tf.nn.embedding_lookup(offset_m, labels)
scale = tf.nn.embedding_lookup(scale_m, labels) scale = tf.nn.embedding_lookup(scale_m, labels)
else:
offset = None
scale = None
result = tf.nn.batch_normalization(inputs, mean, var,offset,scale, 1e-8) result = tf.nn.batch_normalization(inputs, mean, var,offset,scale, 1e-8)
return result return result
@ -248,7 +253,7 @@ class Generator (GNet):
x = args['inputs'] x = args['inputs']
tmp_dim = self.Z_DIM if 'dim' not in args else args['dim'] tmp_dim = self.Z_DIM if 'dim' not in args else args['dim']
label = args['label'] label = args['label']
print (self.NUM_LABELS)
with tf.compat.v1.variable_scope('G', reuse=tf.compat.v1.AUTO_REUSE , regularizer=l2_regularizer(0.00001)): with tf.compat.v1.variable_scope('G', reuse=tf.compat.v1.AUTO_REUSE , regularizer=l2_regularizer(0.00001)):
for i, dim in enumerate(self.G_STRUCTURE[:-1]): for i, dim in enumerate(self.G_STRUCTURE[:-1]):
kernel = self.get.variables(name='W_' + str(i), shape=[tmp_dim, dim]) kernel = self.get.variables(name='W_' + str(i), shape=[tmp_dim, dim])
@ -331,7 +336,7 @@ class Train (GNet):
self.generator = Generator(**args) self.generator = Generator(**args)
self.discriminator = Discriminator(**args) self.discriminator = Discriminator(**args)
self._REAL = args['real'] self._REAL = args['real']
self._LABEL= args['label'] self._LABEL= args['label'] if 'label' in args else None
self.column = args['column'] self.column = args['column']
# print ([" *** ",self.BATCHSIZE_PER_GPU]) # print ([" *** ",self.BATCHSIZE_PER_GPU])
@ -340,7 +345,7 @@ class Train (GNet):
self.logger.write( self.meta ) self.logger.write( self.meta )
self.log (real_shape=list(self._REAL.shape),label_shape = list(self._LABEL.shape),meta_data=self.meta) # self.log (real_shape=list(self._REAL.shape),label_shape = self._LABEL.shape,meta_data=self.meta)
def load_meta(self, column): def load_meta(self, column):
""" """
This function will delegate the calls to load meta data to it's dependents This function will delegate the calls to load meta data to it's dependents
@ -363,6 +368,9 @@ class Train (GNet):
stage = args['stage'] stage = args['stage']
real = args['real'] real = args['real']
label = args['label'] label = args['label']
if label is not None :
label = tf.cast(label, tf.int32) label = tf.cast(label, tf.int32)
# #
# @TODO: Ziqi needs to explain what's going on here # @TODO: Ziqi needs to explain what's going on here
@ -394,8 +402,13 @@ class Train (GNet):
This function seems to produce This function seems to produce
""" """
features_placeholder = tf.compat.v1.placeholder(shape=self._REAL.shape, dtype=tf.float32) features_placeholder = tf.compat.v1.placeholder(shape=self._REAL.shape, dtype=tf.float32)
labels_placeholder = tf.compat.v1.placeholder(shape=self._LABEL.shape, dtype=tf.float32) LABEL_SHAPE = [None,None] if self._LABEL is None else self._LABEL.shape
labels_placeholder = tf.compat.v1.placeholder(shape=LABEL_SHAPE, dtype=tf.float32)
if self._LABEL is not None :
dataset = tf.data.Dataset.from_tensor_slices((features_placeholder, labels_placeholder)) dataset = tf.data.Dataset.from_tensor_slices((features_placeholder, labels_placeholder))
else :
dataset = tf.data.Dataset.from_tensor_slices(features_placeholder)
# labels_placeholder = None
dataset = dataset.repeat(10000) dataset = dataset.repeat(10000)
dataset = dataset.batch(batch_size=3000) dataset = dataset.batch(batch_size=3000)
dataset = dataset.prefetch(1) dataset = dataset.prefetch(1)
@ -413,7 +426,10 @@ class Train (GNet):
for i in range(self.NUM_GPUS): for i in range(self.NUM_GPUS):
with tf.device('/gpu:%d' % i): with tf.device('/gpu:%d' % i):
with tf.name_scope('%s_%d' % ('TOWER', i)) as scope: with tf.name_scope('%s_%d' % ('TOWER', i)) as scope:
if self._LABEL is not None :
(real, label) = iterator.get_next() (real, label) = iterator.get_next()
else:
real = iterator.get_next()
loss, w = self.loss(scope=scope, stage=stage, real=self._REAL, label=self._LABEL) loss, w = self.loss(scope=scope, stage=stage, real=self._REAL, label=self._LABEL)
#tf.get_variable_scope().reuse_variables() #tf.get_variable_scope().reuse_variables()
tf.compat.v1.get_variable_scope().reuse_variables() tf.compat.v1.get_variable_scope().reuse_variables()
@ -450,10 +466,11 @@ class Train (GNet):
#with tf.Session(config=tf.ConfigProto(allow_soft_placement=True, log_device_placement=False)) as sess: #with tf.Session(config=tf.ConfigProto(allow_soft_placement=True, log_device_placement=False)) as sess:
with tf.compat.v1.Session(config=tf.compat.v1.ConfigProto(allow_soft_placement=True, log_device_placement=False)) as sess: with tf.compat.v1.Session(config=tf.compat.v1.ConfigProto(allow_soft_placement=True, log_device_placement=False)) as sess:
sess.run(init) sess.run(init)
sess.run(iterator_d.initializer, sess.run(iterator_d.initializer,
feed_dict={features_placeholder_d: REAL, labels_placeholder_d: LABEL}) feed_dict={features_placeholder_d: REAL})
sess.run(iterator_g.initializer, sess.run(iterator_g.initializer,
feed_dict={features_placeholder_g: REAL, labels_placeholder_g: LABEL}) feed_dict={features_placeholder_g: REAL})
for epoch in range(1, self.MAX_EPOCHS + 1): for epoch in range(1, self.MAX_EPOCHS + 1):
start_time = time.time() start_time = time.time()
@ -511,9 +528,11 @@ class Predict(GNet):
tf.compat.v1.reset_default_graph() tf.compat.v1.reset_default_graph()
z = tf.random.normal(shape=[self.BATCHSIZE_PER_GPU, self.Z_DIM]) z = tf.random.normal(shape=[self.BATCHSIZE_PER_GPU, self.Z_DIM])
y = tf.compat.v1.placeholder(shape=[self.BATCHSIZE_PER_GPU, self.NUM_LABELS], dtype=tf.int32) y = tf.compat.v1.placeholder(shape=[self.BATCHSIZE_PER_GPU, self.NUM_LABELS], dtype=tf.int32)
if self._LABEL is not None :
ma = [[i] for i in np.arange(self.NUM_LABELS - 2)] ma = [[i] for i in np.arange(self.NUM_LABELS - 2)]
label = y[:, 1] * len(ma) + tf.squeeze(tf.matmul(y[:, 2:], tf.constant(ma, dtype=tf.int32))) label = y[:, 1] * len(ma) + tf.squeeze(tf.matmul(y[:, 2:], tf.constant(ma, dtype=tf.int32)))
else:
label = None
fake = self.generator.network(inputs=z, label=label) fake = self.generator.network(inputs=z, label=label)
init = tf.compat.v1.global_variables_initializer() init = tf.compat.v1.global_variables_initializer()
saver = tf.compat.v1.train.Saver() saver = tf.compat.v1.train.Saver()
@ -524,13 +543,19 @@ class Predict(GNet):
# sess.run(init) # sess.run(init)
saver.restore(sess, model_dir) saver.restore(sess, model_dir)
if self._LABEL is not None :
labels = np.zeros((self.ROW_COUNT,self.NUM_LABELS) ) labels = np.zeros((self.ROW_COUNT,self.NUM_LABELS) )
labels= demo
else:
labels = None
found = [] found = []
labels= demo
for i in np.arange(CANDIDATE_COUNT) :
for i in np.arange(CANDIDATE_COUNT) :
if labels :
f = sess.run(fake,feed_dict={y:labels}) f = sess.run(fake,feed_dict={y:labels})
else:
f = sess.run(fake)
# #
# if we are dealing with numeric values only we can perform a simple marginal sum against the indexes # if we are dealing with numeric values only we can perform a simple marginal sum against the indexes
# The code below will insure we have some acceptable cardinal relationships between id and synthetic values # The code below will insure we have some acceptable cardinal relationships between id and synthetic values

7
data/maker/__init__.py
Unescape View File

@ -25,7 +25,7 @@ def train (**args) :
""" """
column = args['column'] if (isinstance(args['column'],list)) else [args['column']] column = args['column'] if (isinstance(args['column'],list)) else [args['column']]
column_id = args['id'] # column_id = args['id']
df = args['data'] if not isinstance(args['data'],str) else pd.read_csv(args['data']) df = args['data'] if not isinstance(args['data'],str) else pd.read_csv(args['data'])
df.columns = [name.lower() for name in df.columns] df.columns = [name.lower() for name in df.columns]
@ -35,7 +35,8 @@ def train (**args) :
# #
handler = Binary() handler = Binary()
# args['label'] = pd.get_dummies(df[column_id]).astype(np.float32).values # args['label'] = pd.get_dummies(df[column_id]).astype(np.float32).values
args['label'] = handler.Export(df[[column_id]]) # args['label'] = handler.Export(df[[column_id]])
# args['label'] = np.ones(df.shape[0]).reshape(df.shape[0],1)
for col in column : for col in column :
# args['real'] = pd.get_dummies(df[col]).astype(np.float32).values # args['real'] = pd.get_dummies(df[col]).astype(np.float32).values
args['real'] = handler.Export(df[[col]]) args['real'] = handler.Export(df[[col]])
@ -83,7 +84,7 @@ def generate(**args):
# #
# args['label'] = pd.get_dummies(df[column_id]).astype(np.float32).values # args['label'] = pd.get_dummies(df[column_id]).astype(np.float32).values
bwrangler = Binary() bwrangler = Binary()
args['label'] = bwrangler.Export(df[[column_id]]) # args['label'] = bwrangler.Export(df[[column_id]])
_df = df.copy() _df = df.copy()
for col in column : for col in column :
args['context'] = col args['context'] = col

2
setup.py
Unescape View File

@ -7,7 +7,7 @@ def read(fname):
args = {"name":"data-maker","version":"1.1.0","author":"Vanderbilt University Medical Center","author_email":"steve.l.nyemba@vanderbilt.edu","license":"MIT", args = {"name":"data-maker","version":"1.1.0","author":"Vanderbilt University Medical Center","author_email":"steve.l.nyemba@vanderbilt.edu","license":"MIT",
"packages":find_packages(),"keywords":["healthcare","data","transport","protocol"]} "packages":find_packages(),"keywords":["healthcare","data","transport","protocol"]}
args["install_requires"] = ['data-transport@git+https://dev.the-phi.com/git/steve/data-transport.git','tensorflow==1.15','pandas','pandas-gbq','pymongo'] args["install_requires"] = ['data-transport@git+https://dev.the-phi.com/git/steve/data-transport.git','tensorflow==1.15','pandas','pandas-gbq','pymongo']
args['url'] = 'https://hiplab.mc.vanderbilt.edu/aou/data-maker.git' args['url'] = 'https://hiplab.mc.vanderbilt.edu/git/aou/data-maker.git'
if sys.version_info[0] == 2 : if sys.version_info[0] == 2 :
args['use_2to3'] = False args['use_2to3'] = False

Write Preview
Loading…
Cancel
Save