def Logger(q):
import time
all_auc = []
registered_gpus = {}
logger = lib.logger.CSVLogger('results.csv', output_dir, [
'fold', 'seq_acc', 'gnn_nuc_acc', 'bilstm_nuc_acc', 'auc',
'original_seq_acc', 'original_gnn_nuc_acc', 'original_bilstm_nuc_acc',
'original_auc'
])
while True:
msg = q.get()
print(msg)
if type(msg) is str and msg == 'kill':
logger.close()
print('%s ROC AUC: %.3f\u00B1%.3f' %
(TRAIN_RBP_ID, np.mean(all_auc), np.std(all_auc)))
break
elif type(msg) is str and msg.startswith('worker'):
process_id = int(msg.split('_')[-1])
if process_id in registered_gpus:
print(process_id, 'found, returning',
registered_gpus[process_id])
q.put('master_%d_' % (process_id) +
registered_gpus[process_id])
else:
print(process_id, 'not found')
all_registered_devices = list(registered_gpus.values())
from collections import Counter
c1 = Counter(DEVICES)
c2 = Counter(all_registered_devices)
free_devices = list((c1 - c2).elements())
# free_devices = list(set(DEVICES).difference(set(all_registered_devices)))
if len(free_devices) > 0:
_device = np.random.choice(free_devices)
print('free device', _device)
q.put('master_%d_' % (process_id) + _device)
registered_gpus[process_id] = _device
else:
print('no free device!')
print(registered_gpus)
q.put('master_%d_/cpu:0' % (process_id))
elif type(msg) is dict:
logger.update_with_dict(msg)
all_auc.append(msg['original_auc'])
else:
q.put(msg)
time.sleep(np.random.rand() * 5)
# posterior decoding without RNA regularity
print('Test_recon_acc_no_reg',
ret_dict['recon_acc_noreg'] / ret_dict['total'] * 100)
print('Test_post_valid_no_reg',
ret_dict['post_valid_noreg'] / ret_dict['total'] * 100)
print('Test_post_fe_deviation_no_reg',
ret_dict['post_fe_deviation_noreg'] / ret_dict['post_valid_noreg'])
print(
'Test_post_fe_deviation_len_normed_no_reg',
ret_dict['post_fe_deviation_noreg_len_normed'] /
ret_dict['post_valid_noreg'])
# posterior decoding without RNA regularity and greedy
print('Test_recon_acc_no_reg_det',
ret_dict['recon_acc_noreg_det'] / ret_dict['total'] * 100 * 5)
print('Test_post_valid_no_reg_det',
ret_dict['post_valid_noreg_det'] / ret_dict['total'] * 100 * 5)
print(
'Test_post_fe_deviation_no_reg_det',
ret_dict['post_fe_deviation_noreg_det'] /
ret_dict['post_valid_noreg_det'])
print(
'Test_post_fe_deviation_len_normed_no_reg_det',
ret_dict['post_fe_deviation_noreg_det_len_normed'] /
ret_dict['post_valid_noreg_det'])
if mp_pool is not None:
mp_pool.close()
mp_pool.join()
logger.close()
def run_one_rbp(fold_idx, q):
fold_output = os.path.join(output_dir, 'fold%d' % (fold_idx))
os.makedirs(fold_output)
outfile = open(os.path.join(fold_output, str(os.getpid())) + ".out", "w")
sys.stdout = outfile
sys.stderr = outfile
import time
# todo: replace _identity with pid and let logger check if pid still alive
process_id = mp.current_process()._identity[0]
print('sending process id', mp.current_process()._identity[0])
q.put('worker_%d' % (process_id))
while True:
msg = q.get()
if type(msg) is str and msg.startswith('master'):
print('worker %d received' % (process_id), msg, str(int(msg.split('_')[1])))
if int(msg.split('_')[1]) == process_id:
device = msg.split('_')[-1]
print('Process', mp.current_process(), 'received', device)
break
q.put(msg)
time.sleep(np.random.rand() * 2)
print('training fold', fold_idx)
train_idx, test_idx = dataset['splits'][fold_idx]
model = JMRT(dataset['VOCAB_VEC'].shape[1], dataset['VOCAB_VEC'], device, **hp)
train_data = [dataset['seq'][train_idx], dataset['segment_size'][train_idx], dataset['raw_seq'][train_idx]]
model.fit(train_data, dataset['label'][train_idx], EPOCHS, BATCH_SIZE, fold_output, logging=True)
test_data = [dataset['seq'][test_idx], dataset['segment_size'][test_idx], dataset['raw_seq'][test_idx]]
cost, acc, auc = model.evaluate(test_data, dataset['label'][test_idx], BATCH_SIZE, random_crop=False)
print('Evaluation (with masking) on modified held-out test set, acc: %s, auc: %.3f' % (acc, auc))
original_test_data = [original_dataset['seq'][test_idx], original_dataset['segment_size'][test_idx],
original_dataset['raw_seq'][test_idx]]
original_cost, original_acc, original_auc = model.evaluate(original_test_data, original_dataset['label'][test_idx],
BATCH_SIZE, random_crop=False)
print('Evaluation (with masking) on original held-out test set, acc: %s, auc: %.3f' % (original_acc, original_auc))
# get predictions
logger = lib.logger.CSVLogger('predictions.csv', fold_output,
['id', 'label', 'pred_neg', 'pred_pos'])
all_pos_preds = []
all_idx = []
for idx, (_id, _label, _pred) in enumerate(
zip(original_dataset['id'][test_idx], original_dataset['label'][test_idx],
model.predict(original_test_data, BATCH_SIZE))):
logger.update_with_dict({
'id': _id,
'label': np.max(_label),
'pred_neg': _pred[0],
'pred_pos': _pred[1],
})
if np.max(_label) == 1:
all_pos_preds.append(_pred[1])
all_idx.append(idx)
logger.close()
# plot some motifs
graph_dir = os.path.join(fold_output, 'integrated_gradients')
if not os.path.exists(graph_dir):
os.makedirs(graph_dir)
all_pos_preds = np.array(all_pos_preds)
all_idx = np.array(all_idx)
# top 10 strongly predicted examples, descending order
idx = all_idx[np.argsort(all_pos_preds)[::-1][:min(10, len(all_pos_preds))]]
model.integrated_gradients(model.indexing_iterable(original_test_data, idx),
original_dataset['label'][test_idx][idx],
original_dataset['id'][test_idx][idx], save_path=graph_dir)
# common ig plots
idx = []
for i, _id in enumerate(dataset['id'][test_idx]):
if _id in ig_ids:
idx.append(i)
common_graph_path = os.path.join(output_dir, 'common_integrated_gradients')
if not os.path.exists(common_graph_path):
os.makedirs(common_graph_path)
model.integrated_gradients(model.indexing_iterable(original_test_data, idx),
original_dataset['label'][test_idx][idx],
original_dataset['id'][test_idx][idx], save_path=common_graph_path)
model.delete()
reload(lib.plot)
reload(lib.logger)
q.put({
'fold': fold_idx,
'seq_acc': acc[0],
'nuc_acc': acc[1],
'auc': auc,
'original_seq_acc': original_acc[0],
'original_nuc_acc': original_acc[1],
'original_auc': original_auc
})
def fit(self, X, y, epochs, batch_size, output_dir, logging=False, epoch_to_start=0):
checkpoints_dir = os.path.join(output_dir, 'checkpoints/')
if not os.path.exists(checkpoints_dir):
os.makedirs(checkpoints_dir)
# split validation set
row_sum = np.array(list(map(lambda label: np.sum(label), y)))
pos_idx, neg_idx = np.where(row_sum > 0)[0], np.where(row_sum == 0)[0]
dev_idx = np.array(list(np.random.choice(pos_idx, int(len(pos_idx) * 0.1), False)) + \
list(np.random.choice(neg_idx, int(len(neg_idx) * 0.1), False)))
train_idx = np.delete(np.arange(len(y)), dev_idx)
dev_data = self.indexing_iterable(X, dev_idx)
dev_targets = y[dev_idx]
X = self.indexing_iterable(X, train_idx)
train_targets = y[train_idx]
best_dev_cost = np.inf
# best_dev_auc = 0.
lib.plot.set_output_dir(output_dir)
if logging:
logger = lib.logger.CSVLogger('run.csv', output_dir,
['epoch', 'cost', 'graph_cost', 'gnn_cost', 'bilstm_cost',
'seq_acc', 'gnn_acc', 'bilstm_acc', 'auc',
'dev_cost', 'dev_graph_cost', 'dev_gnn_cost', 'dev_bilstm_cost',
'dev_seq_acc', 'dev_gnn_acc', 'dev_bilstm_acc', 'dev_auc'])
train_generator = BackgroundGenerator(X, train_targets, batch_size, random_crop=False)
val_generator = BackgroundGenerator(dev_data, dev_targets, batch_size)
iters_per_epoch = train_generator.iters_per_epoch
for epoch in range(epoch_to_start, epochs):
prepro_time = 0.
training_time = 0.
for i in range(iters_per_epoch):
prepro_start = time.time()
_node_tensor, _mask_offset, all_adj_mat, _labels = train_generator.next()
feed_dict = {
self.node_input_ph: _node_tensor,
self.adj_mat_ph: all_adj_mat,
self.labels: _labels,
self.mask_offset: _mask_offset,
self.global_step: i + epoch * iters_per_epoch,
self.hf_iters_per_epoch: iters_per_epoch // 2,
self.is_training_ph: True,
}
prepro_end = time.time()
prepro_time += (prepro_end - prepro_start)
self.sess.run(self.train_op, feed_dict)
training_time += (time.time() - prepro_end)
print('preprocessing time: %.4f, training time: %.4f' % (prepro_time / (i + 1), training_time / (i + 1)))
train_cost, train_acc, train_auc = self.evaluate_with_generator(train_generator)
lib.plot.plot('train_cost', train_cost[0])
lib.plot.plot('train_graph_cost', train_cost[1])
lib.plot.plot('train_gnn_cost', train_cost[2])
lib.plot.plot('train_bilstm_cost', train_cost[3])
lib.plot.plot('train_seq_acc', train_acc[0])
lib.plot.plot('train_gnn_acc', train_acc[1])
lib.plot.plot('train_bilstm_acc', train_acc[2])
lib.plot.plot('train_auc', train_auc)
dev_cost, dev_acc, dev_auc = self.evaluate_with_generator(val_generator)
lib.plot.plot('dev_cost', dev_cost[0])
lib.plot.plot('dev_graph_cost', dev_cost[1])
lib.plot.plot('dev_gnn_cost', dev_cost[2])
lib.plot.plot('dev_bilstm_cost', dev_cost[3])
lib.plot.plot('dev_seq_acc', dev_acc[0])
lib.plot.plot('dev_gnn_acc', dev_acc[1])
lib.plot.plot('dev_bilstm_acc', dev_acc[2])
lib.plot.plot('dev_auc', dev_auc)
logger.update_with_dict({
'epoch': epoch, 'cost': train_cost[0], 'graph_cost': train_cost[1], 'gnn_cost': train_cost[2],
'bilstm_cost': train_cost[3], 'seq_acc': train_acc[0], 'gnn_acc': train_acc[1],
'bilstm_acc': train_acc[2], 'auc': train_auc,
'dev_cost': dev_cost[0], 'dev_graph_cost': dev_cost[1], 'dev_gnn_cost': dev_cost[2],
'dev_bilstm_cost': dev_cost[3], 'dev_seq_acc': dev_acc[0], 'dev_gnn_acc': dev_acc[1],
'dev_bilstm_acc': dev_acc[2], 'dev_auc': dev_auc,
})
lib.plot.flush()
lib.plot.tick()
if dev_cost[0] < best_dev_cost and epoch - epoch_to_start >= 10: # unstable loss in the beginning
best_dev_cost = dev_cost[0]
save_path = self.saver.save(self.sess, checkpoints_dir, global_step=epoch)
print('Validation sample cost improved. Saved to path %s\n' % (save_path), flush=True)
else:
print('\n', flush=True)
print('Loading best weights %s' % (save_path), flush=True)
self.saver.restore(self.sess, save_path)
if logging:
logger.close()
train_generator.kill.set()
val_generator.kill.set()
train_generator.next()
val_generator.next()
train_generator.join()
val_generator.join()
def fit(self,
X,
y,
epochs,
batch_size,
output_dir,
logging=False,
epoch_to_start=0,
random_crop=False):
checkpoints_dir = os.path.join(output_dir, 'checkpoints/')
if not os.path.exists(checkpoints_dir):
os.makedirs(checkpoints_dir)
# split validation set
row_sum = np.array(list(map(lambda label: np.sum(label), y)))
pos_idx, neg_idx = np.where(row_sum > 0)[0], np.where(row_sum == 0)[0]
dev_idx = np.array(list(np.random.choice(pos_idx, int(len(pos_idx) * 0.1), False)) + \
list(np.random.choice(neg_idx, int(len(neg_idx) * 0.1), False)))
train_idx = np.delete(np.arange(len(y)), dev_idx)
dev_data = self.indexing_iterable(X, dev_idx)
dev_targets = y[dev_idx]
X = self.indexing_iterable(X, train_idx)
train_targets = y[train_idx]
size_train = train_targets.shape[0]
iters_per_epoch = size_train // batch_size + (0 if size_train %
batch_size == 0 else 1)
best_dev_cost = np.inf
lib.plot.set_output_dir(output_dir)
if logging:
logger = lib.logger.CSVLogger('run.csv', output_dir, [
'epoch', 'cost', 'graph_cost', 'nuc_cost', 'seq_acc',
'nuc_acc', 'auc', 'dev_cost', 'dev_graph_cost', 'dev_nuc_cost',
'dev_seq_acc', 'dev_nuc_acc', 'dev_auc'
])
for epoch in range(epoch_to_start, epochs):
permute = np.random.permutation(size_train)
node_tensor, segment_length, raw_seq = self.indexing_iterable(
X, permute)
y = train_targets[permute]
if random_crop:
# augmentation
node_tensor, segment_length, y = \
self.random_crop(node_tensor, raw_seq, y)
prepro_time = 0.
training_time = 0.
for i in range(iters_per_epoch):
prepro_start = time.time()
_node_tensor, _segment, _labels \
= node_tensor[i * batch_size: (i + 1) * batch_size], \
segment_length[i * batch_size: (i + 1) * batch_size], \
y[i * batch_size: (i + 1) * batch_size]
_max_len = max(_segment)
_labels = np.array([
np.pad(label, [_max_len - len(label), 0], mode='constant')
for label in _labels
])
feed_dict = {
self.node_input_ph: np.concatenate(_node_tensor, axis=0),
self.labels: _labels,
self.max_len: _max_len,
self.segment_length: _segment,
self.global_step: i,
self.hf_iters_per_epoch: iters_per_epoch // 2,
self.is_training_ph: True
}
prepro_end = time.time()
prepro_time += (prepro_end - prepro_start)
self.sess.run(self.train_op, feed_dict)
training_time += (time.time() - prepro_end)
print('preprocessing time: %.4f, training time: %.4f' %
(prepro_time / (i + 1), training_time / (i + 1)))
train_cost, train_acc, train_auc = self.evaluate(
X, train_targets, batch_size)
lib.plot.plot('train_cost', train_cost[0])
lib.plot.plot('train_graph_cost', train_cost[1])
lib.plot.plot('train_nuc_cost', train_cost[2])
lib.plot.plot('train_seq_acc', train_acc[0])
lib.plot.plot('train_nuc_acc', train_acc[1])
lib.plot.plot('train_auc', train_auc)
dev_cost, dev_acc, dev_auc = self.evaluate(dev_data, dev_targets,
batch_size)
lib.plot.plot('dev_cost', dev_cost[0])
lib.plot.plot('dev_graph_cost', dev_cost[1])
lib.plot.plot('dev_nuc_cost', dev_cost[2])
lib.plot.plot('dev_seq_acc', dev_acc[0])
lib.plot.plot('dev_nuc_acc', dev_acc[1])
lib.plot.plot('dev_auc', dev_auc)
logger.update_with_dict({
'epoch': epoch,
'cost': train_cost[0],
'graph_cost': train_cost[1],
'nuc_cost': train_cost[2],
'seq_acc': train_acc[0],
'nuc_acc': train_acc[1],
'auc': train_auc,
'dev_cost': dev_cost[0],
'dev_graph_cost': dev_cost[1],
'dev_nuc_cost': dev_cost[2],
'dev_seq_acc': dev_acc[0],
'dev_nuc_acc': dev_acc[1],
'dev_auc': dev_auc,
})
lib.plot.flush()
lib.plot.tick()
if dev_cost[
0] < best_dev_cost and epoch - epoch_to_start >= 10: # unstable loss in the beginning
best_dev_cost = dev_cost[0]
save_path = self.saver.save(self.sess,
checkpoints_dir,
global_step=epoch)
print('Validation sample cost improved. Saved to path %s\n' %
(save_path),
flush=True)
else:
print('\n', flush=True)
print('Loading best weights %s' % (save_path), flush=True)
self.saver.restore(self.sess, save_path)
if logging:
logger.close()
