ds_test = tf.data.Dataset.from_tensor_slices((idx_test, y_label[idx_test]))
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: ((tf.gather(tf.constant(D['seq_5p'], dtype=tf.int32), x),
tf.gather(tf.constant(D['seq_3p'], dtype=tf.int32), x),
tf.gather(tf.constant(D['seq_ref'], dtype=tf.int32), x),
tf.gather(tf.constant(D['seq_alt'], dtype=tf.int32), x),
tf.gather(tf.constant(D['strand_emb'], dtype=tf.float32), x),
tf.gather(tf.constant(D['cds_emb'], dtype=tf.float32), x)
),
y,
))
sequence_encoder = InstanceModels.VariantSequence(6, 4, 2, [64, 64, 64, 64], fusion_dimension=128, use_frame=True)
mil = RaggedModels.MIL(instance_encoders=[], sample_encoders=[sequence_encoder.model], output_dim=y_label.shape[-1], output_type='other', mil_hidden=[128, 128, 64, 32], mode='none')
losses = [Losses.CrossEntropy()]
mil.model.compile(loss=losses,
metrics=[Metrics.Accuracy(), Metrics.CrossEntropy()],
weighted_metrics=[Metrics.Accuracy(), Metrics.CrossEntropy()],
optimizer=tf.keras.optimizers.Adam(learning_rate=0.001,
))
callbacks = [tf.keras.callbacks.EarlyStopping(monitor='val_weighted_CE', min_delta=0.001, patience=10, mode='min', restore_best_weights=True)]
mil.model.fit(ds_train, steps_per_epoch=50,
validation_data=ds_valid,
epochs=10000,
callbacks=callbacks,
)
cwd / 'figures' / 'tmb' / 'tcga' / 'VICC_01_R2' / 'results' /
'run_position.pkl', 'rb')),
pickle.load(
open(
cwd / 'figures' / 'tmb' / 'tcga' / 'VICC_01_R2' / 'results' /
'run_sequence.pkl', 'rb'))
]
results = {}
for encoder, loaders, weights, name in zip(encoders, loaders, all_weights,
['naive', 'position', 'sequence']):
mil = RaggedModels.MIL(instance_encoders=[encoder.model],
output_dim=1,
pooling='sum',
mil_hidden=(64, 32, 16),
output_type='quantiles',
regularization=0)
mil.model.compile(loss=losses,
metrics=metrics,
optimizer=tf.keras.optimizers.Adam(learning_rate=0.001))
##test eval
test_idx = []
predictions = []
for index, (idx_train, idx_test) in enumerate(
StratifiedKFold(n_splits=8, random_state=0,
shuffle=True).split(y_strat, y_strat)):
mil.model.set_weights(weights[index])
ds_test = tf.data.Dataset.from_tensor_slices(
ds_test = tf.data.Dataset.from_tensor_slices((idx_test, y_label[idx_test]))
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: (
(five_p_loader(x, ragged_output=True), three_p_loader(x,
ragged_output=True),
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), y))
histories = []
evaluations = []
weights = []
for i in range(3):
tile_encoder = InstanceModels.VariantSequence(6, 4, 2, [16, 16, 8, 8])
# mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model], output_dim=1, pooling='both', output_type='regression', pooled_layers=[32, ])
mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model],
output_dim=1,
pooling='dynamic',
output_type='regression')
losses = ['mse']
mil.model.compile(loss=losses,
metrics=['mse'],
optimizer=tf.keras.optimizers.Adam(
learning_rate=0.001, ))
callbacks = [
tf.keras.callbacks.EarlyStopping(monitor='val_mse',
min_delta=0.001,
patience=20,
mode='min',
restore_best_weights=True)
]
history = mil.model.fit(ds_train,
steps_per_epoch=10,
x, ragged_output=True), ref_loader(x, ragged_output=True),
alt_loader(x, ragged_output=True), strand_loader(x, ragged_output=True),
tf.gather(tf.constant(types), x)), y))
histories = []
evaluations = []
weights = []
for i in range(3):
sequence_encoder = InstanceModels.VariantSequence(6, 4, 2, [16, 16, 8, 8])
sample_encoder = SampleModels.Type(shape=(), dim=len(np.unique(types)))
# mil = RaggedModels.MIL(instance_encoders=[sequence_encoder.model], sample_encoders=[sample_encoder.model], sample_layers=[64, ], output_dim=1, pooling='both', output_type='other', pooled_layers=[32, ])
mil = RaggedModels.MIL(instance_encoders=[sequence_encoder.model],
sample_encoders=[sample_encoder.model],
fusion='before',
output_dim=1,
pooling='both',
output_type='other',
pooled_layers=[
32,
])
losses = ['mse']
mil.model.compile(loss=losses,
metrics=['mse'],
optimizer=tf.keras.optimizers.Adam(
learning_rate=0.001, ))
callbacks = [
tf.keras.callbacks.EarlyStopping(monitor='val_mse',
min_delta=0.001,
patience=20,
mode='min',
restore_best_weights=True)
ds_test = tf.data.Dataset.from_tensor_slices((idx_test, y_label[idx_test]))
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: (
(five_p_loader(x, ragged_output=True), three_p_loader(x,
ragged_output=True),
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), y))
histories = []
evaluations = []
weights = []
for i in range(3):
tile_encoder = InstanceModels.VariantSequence(6, 4, 2, [16, 16, 8, 8])
mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model],
output_dim=2,
pooling='dynamic')
# mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model], output_dim=2, pooling='both', pooled_layers=[32, ])
losses = [tf.keras.losses.CategoricalCrossentropy(from_logits=True)]
mil.model.compile(
loss=losses,
metrics=[
'accuracy',
tf.keras.metrics.CategoricalCrossentropy(from_logits=True)
],
optimizer=tf.keras.optimizers.Adam(learning_rate=0.001, ))
callbacks = [
tf.keras.callbacks.EarlyStopping(
monitor='val_categorical_crossentropy',
min_delta=0.00001,
patience=20,
tf.gather(tf.constant(y_weights, dtype=tf.float32), x)
))
ds_valid = tf.data.Dataset.from_tensor_slices((idx_valid, y_label[idx_valid]))
ds_valid = ds_valid.batch(len(idx_valid), drop_remainder=False)
ds_valid = ds_valid.map(lambda x, y: ((pos_loader(x, ragged_output=True),
bin_loader(x, ragged_output=True),
chr_loader(x, ragged_output=True),
),
y,
tf.gather(tf.constant(y_weights, dtype=tf.float32), x)
))
while True:
position_encoder = InstanceModels.VariantPositionBin(24, 100)
mil = RaggedModels.MIL(instance_encoders=[position_encoder.model], output_dim=2, pooling='sum', mil_hidden=(64, 32, 16, 8), output_type='anlulogits')
mil.model.compile(loss=losses,
metrics=[Metrics.CrossEntropy(), Metrics.Accuracy()],
weighted_metrics=[Metrics.CrossEntropy(), Metrics.Accuracy()],
optimizer=tf.keras.optimizers.Adam(learning_rate=0.005,
clipvalue=10000))
mil.model.fit(ds_train,
steps_per_epoch=20,
validation_data=ds_valid,
epochs=10000,
callbacks=callbacks)
eval = mil.model.evaluate(ds_valid)
if eval[2] >= .985:
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), y))
ds_test = tf.data.Dataset.from_tensor_slices((idx_test, y_label[idx_test]))
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: (
(five_p_loader(x, ragged_output=True), three_p_loader(x,
ragged_output=True),
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), y))
tile_encoder = InstanceModels.VariantSequence(6, 4, 2, [16, 16, 8, 8])
# mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model], output_dim=2, pooling='dynamic')
mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model],
output_dim=2,
pooling='both',
pooled_layers=[
32,
])
attentions = []
evaluations, histories, weights = pickle.load(
open(
cwd / 'figures' / 'controls' / 'samples' / 'sim_data' /
'classification' / 'experiment_4' / 'sample_model_attention_both.pkl',
'rb'))
for i in range(3):
mil.model.set_weights(weights[i])
temp = mil.attention_model.predict(ds_test)
attentions.append(mil.attention_model.predict(ds_test).to_list())
with open(
cwd / 'figures' / 'controls' / 'samples' / 'sim_data' /
losses = [Losses.QuantileLoss()]
metrics = [Metrics.QuantileLoss()]
pass_encoder = InstanceModels.PassThrough(shape=(1, ))
type_encoder = SampleModels.Type(shape=(), dim=max(y_strat) + 1)
weights = pickle.load(
open(
cwd / 'figures' / 'tmb' / 'tcga' / 'MDA_409' / 'results' /
'run_naive_sample_tcga.pkl', 'rb'))
mil = RaggedModels.MIL(
sample_encoders=[pass_encoder.model, type_encoder.model],
output_dim=1,
mil_hidden=(64, 32, 16),
output_type='quantiles',
regularization=0,
mode='none')
##test eval
test_idx = []
predictions = []
for index, (idx_train, idx_test) in enumerate(
StratifiedKFold(n_splits=8, random_state=0,
shuffle=True).split(y_strat, y_strat)):
mil.model.set_weights(weights[index])
ds_test = tf.data.Dataset.from_tensor_slices((idx_test, y_label[idx_test]))
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
y_weights = np.array([1 / class_counts[_] for _ in y_strat])
y_weights /= np.sum(y_weights)
weights = []
callbacks = [
tf.keras.callbacks.EarlyStopping(monitor='val_CE',
min_delta=0.0001,
patience=50,
mode='min',
restore_best_weights=True)
]
losses = [Losses.CrossEntropy(from_logits=False)]
sequence_encoder = InstanceModels.VariantSequence(20, 4, 2, [8, 8, 8, 8])
mil = RaggedModels.MIL(instance_encoders=[sequence_encoder.model],
output_dim=2,
pooling='sum',
mil_hidden=(64, 64, 32, 16),
output_type='classification_probability')
mil.model.compile(
loss=losses,
metrics=[Metrics.CrossEntropy(from_logits=False),
Metrics.Accuracy()],
optimizer=tf.keras.optimizers.Adam(learning_rate=0.001, clipvalue=10000))
initial_weights = mil.model.get_weights()
##stratified K fold for test
for idx_train, idx_test in StratifiedKFold(n_splits=9,
random_state=0,
shuffle=True).split(
y_strat, y_strat):
##due to the y_strat levels not being constant this idx_train/idx_valid split is not deterministic
ds_test = tf.data.Dataset.from_tensor_slices((idx_test, y_label[idx_test]))
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: (
(five_p_loader(x, ragged_output=True), three_p_loader(x,
ragged_output=True),
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), y))
histories = []
evaluations = []
weights = []
for i in range(3):
tile_encoder = InstanceModels.VariantSequence(6, 4, 2, [16, 16, 8, 8])
# mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model], output_dim=2, pooling='both', pooled_layers=[32, ])
mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model],
output_dim=2,
pooling='sum',
mode='none')
losses = [tf.keras.losses.CategoricalCrossentropy(from_logits=True)]
mil.model.compile(
loss=losses,
metrics=[
'accuracy',
tf.keras.metrics.CategoricalCrossentropy(from_logits=True)
],
optimizer=tf.keras.optimizers.Adam(learning_rate=0.001, ))
callbacks = [
tf.keras.callbacks.EarlyStopping(
monitor='val_categorical_crossentropy',
min_delta=0.00001,
patience=20,
mode='min',
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: (
(five_p_loader(x, ragged_output=True), three_p_loader(x,
ragged_output=True),
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), ))
from model.Sample_MIL import InstanceModels, RaggedModels
evaluations, histories, weights = pickle.load(
open(
cwd / 'figures' / 'controls' / 'samples' / 'sim_data' / 'regression' /
'experiment_1' / 'sample_model_mean.pkl', 'rb'))
predictions = []
attentions = []
for i in range(3):
tile_encoder = InstanceModels.VariantSequence(6, 4, 2, [16, 16, 8, 8])
# mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model], output_dim=1, pooling='both', output_type='regression', pooled_layers=[32, ])
mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model],
output_dim=1,
pooling='mean',
output_type='regression',
mode='none')
mil.model.set_weights(weights[i])
predictions.append(mil.model.predict(ds_test))
# attentions.append(mil.attention_model.predict(ds_test).to_list())
#
with open(
cwd / 'figures' / 'controls' / 'samples' / 'sim_data' / 'regression' /
'experiment_1' / 'sample_model_mean_predictions.pkl', 'wb') as f:
pickle.dump([idx_test, predictions], f)
tf.gather(tf.constant(D['pos_bin'], dtype=tf.float32), x),
tf.gather(tf.constant(D['chr'], dtype=tf.int32), x),
),
y,
))
ds_train = iter(ds_train).get_next()
ds_valid_batch = iter(ds_valid).get_next()
losses = [Losses.CrossEntropy()]
while True:
position_encoder = InstanceModels.VariantPositionBin(24, 100)
mil = RaggedModels.MIL(instance_encoders=[],
sample_encoders=[position_encoder.model],
output_dim=y_label.shape[-1],
output_type='anlulogits',
mil_hidden=[32, 16],
mode='none')
mil.model.compile(loss=losses,
metrics=[Metrics.CrossEntropy(),
Metrics.Accuracy()],
optimizer=tf.keras.optimizers.Adam(
learning_rate=0.01, ))
mil.model.fit(x=ds_train[0],
y=ds_train[1],
batch_size=len(idx_train) // 4,
epochs=1000000,
validation_data=ds_valid_batch,
shuffle=True,
callbacks=callbacks)
ds_test = ds_test.batch(len(idx_test), drop_remainder=False)
ds_test = ds_test.map(lambda x, y: (
(five_p_loader(x, ragged_output=True),
three_p_loader(x, ragged_output=True),
ref_loader(x, ragged_output=True), alt_loader(x, ragged_output=True),
strand_loader(x, ragged_output=True)), y))
X = False
while X == False:
print(index)
try:
tile_encoder = InstanceModels.VariantSequence(
6, 4, 2, [16, 16, 8, 8])
# mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model], output_dim=1, pooling='both', output_type='other', pooled_layers=[32, 128, 64])
mil = RaggedModels.MIL(instance_encoders=[tile_encoder.model],
output_dim=1,
pooling='dynamic',
output_type='other',
pooled_layers=[128, 64])
losses = [Losses.CoxPH()]
mil.model.compile(loss=losses,
metrics=[Losses.CoxPH()],
optimizer=tf.keras.optimizers.Adam(
learning_rate=0.001, ))
callbacks = [
tf.keras.callbacks.EarlyStopping(monitor='val_coxph',
min_delta=0.0001,
patience=20,
mode='min',
restore_best_weights=True)
]
history = mil.model.fit(ds_train,