def main(noeval, **args):
#args should be the info you need to specify the params
# for a given experiment, but only params should be used below
params = fill_params(**args)
utils.set_gpus(params["gpus"])
net = utils.create_network(**params)
if not noeval:
net.eval()
utils.log_tagged_modules(params["modules_used"], params["log_dir"],
params["log_tag"], params["chkpt_num"])
for dset in params["dsets"]:
print(dset)
fs = make_forward_scanner(dset, **params)
output = forward.forward(net,
fs,
params["scan_spec"],
activation=params["activation"])
save_output(output, dset, **params)
def main():
log.basicConfig(format = '[ %(levelname)s ] %(message)s',
level = log.INFO, stream = sys.stdout)
args = build_argparser().parse_args()
try:
model_wrapper = openvino_io_model_wrapper()
data_transformer = transformer()
io = io_adapter.get_io_adapter(args, model_wrapper, data_transformer)
iecore = utils.create_ie_core(args.extension, args.cldnn_config, args.device,
args.nthreads, None, args.dump, 'sync', log)
net = utils.create_network(iecore, args.model_xml, args.model_bin, log)
input_shapes = utils.get_input_shape(model_wrapper, net)
for layer in input_shapes:
log.info('Shape for input layer {0}: {1}'.format(layer, input_shapes[layer]))
utils.reshape_input(net, args.batch_size)
log.info('Prepare input data')
io.prepare_input(net, args.input)
log.info('Create executable network')
exec_net = utils.load_network(iecore, net, args.device, args.priority, 1)
log.info('Starting inference ({} iterations) on {}'.
format(args.number_iter, args.device))
result, time = infer_sync(exec_net, args.number_iter, io.get_slice_input)
average_time, latency, fps = process_result(time, args.batch_size, args.mininfer)
if not args.raw_output:
io.process_output(result, log)
result_output(average_time, fps, latency, log)
else:
raw_result_output(average_time, fps, latency)
del net
del exec_net
del iecore
except Exception as ex:
print('ERROR! : {0}'.format(str(ex)))
sys.exit(1)
def start_training(model_class, model_args, model_kwargs, chkpt_num, lr,
train_sets, val_sets, data_dir, **params):
#PyTorch Model
net = utils.create_network(model_class, model_args, model_kwargs)
monitor = utils.LearningMonitor()
#Loading model checkpoint (if applicable)
if chkpt_num != 0:
utils.load_chkpt(net, monitor, chkpt_num, params["model_dir"],
params["log_dir"])
#DataProvider Sampler
Sampler = params["sampler_class"]
train_sampler = utils.AsyncSampler(
Sampler(data_dir,
dsets=train_sets,
mode="train",
resize=params["resize"]))
val_sampler = utils.AsyncSampler(
Sampler(data_dir, dsets=val_sets, mode="val", resize=params["resize"]))
loss_fn = loss.BinomialCrossEntropyWithLogits()
optimizer = torch.optim.Adam(net.parameters(), lr=lr)
train.train(net,
loss_fn,
optimizer,
train_sampler,
val_sampler,
last_iter=chkpt_num,
monitor=monitor,
**params)
def main_fwd(noeval, **args):
#args should be the info you need to specify the params
# for a given experiment, but only params should be used below
params = fill_params_fwd(**args)
utils.set_gpus(params["gpus"])
net = utils.create_network(**params)
if not noeval:
net.eval()
utils.log_tagged_modules(params["modules_used"], params["log_dir"],
params["log_tag"], params["chkpt_num"])
#lightsheet mods - input folder contains list of our "big" patches
input_fld = os.path.join(params["data_dir"],
"input_patches") #set directory
output_fld = os.path.join(params["data_dir"],
"cnn_output") #set patches directory
if not os.path.exists(output_fld): os.mkdir(output_fld)
jobid = 0 #for demo only
#find files that need to be processed
fls = [os.path.join(input_fld, xx) for xx in os.listdir(input_fld)]
fls.sort()
#select the file to process for this batch job
if jobid > len(fls):
#essentially kill job if too high - doing this to hopefully help with karma score although might not make a difference
sys.stdout.write("\njobid {} > number of files {}\n".format(
jobid, len(fls)))
sys.stdout.flush()
else:
dset = fls[jobid]
start = time.time()
fs = make_forward_scanner(dset, **params)
sys.stdout.write("\striding by: {}".format(fs.stride))
sys.stdout.flush()
output = forward.forward(
net,
fs,
params["scan_spec"], #runs forward pass
activation=params["activation"])
save_output(output, dset, output_fld, jobid, params["output_tag"],
params["chkpt_num"]) #saves tif
fs._init() #clear out scanner
sys.stdout.write("\patch {}: {} min\n".format(
jobid + 1, round((time.time() - start) / 60, 1)))
sys.stdout.flush()
def main():
ontology = dag.DAG(config.go_fpath)
#gene_annotation = utils.get_annotation(config.annotation_fpath, config.filtered_annotation_fpath, ontology.get_root())
gene_annotation = utils.get_annotation(config.annotation_fpath, config.filtered_annotation_fpath, ontology.get_root())
print "Number of annotated genes:%d" % len(gene_annotation)
network = utils.create_network(config.network_fpath)
print "Number of nodes in network:%d" % network.number_of_nodes()
'''
def main(noeval, **args):
#args should be the info you need to specify the params
# for a given experiment, but only params should be used below
params = fill_params(**args)
utils.set_gpus(params["gpus"])
net = utils.create_network(**params)
if not noeval:
net.eval()
utils.log_tagged_modules(params["modules_used"], params["log_dir"],
params["log_tag"], params["chkpt_num"])
#lightsheet mods - input folder contains list of our "big" patches
input_fld = os.path.join(params["data_dir"],
"input_chnks") #set patches directory
sys.stdout.write("running inference on: \n{}\n".format(
os.path.basename(params["data_dir"])))
sys.stdout.flush()
output_fld = os.path.join(params["data_dir"],
"output_chnks") #set output directory
jobid = int(params["jobid"]) #set patch no. to run through cnn
#find files that need to be processed
fls = [os.path.join(input_fld, xx) for xx in os.listdir(input_fld)]
fls.sort()
#select the file to process for this array job
if jobid > len(fls) - 1:
sys.stdout.write("\njobid {} > number of files {}".format(
jobid, len(fls)))
sys.stdout.flush()
else:
start = time.time()
dset = fls[jobid]
fs = make_forward_scanner(dset, **params)
output = forward.forward(
net,
fs,
params["scan_spec"], #runs forward pass
activation=params["activation"])
save_output(output, dset, output_fld, **params) #saves tif
fs._init() #clear out scanner
sys.stdout.write("patch {}: {} min\n".format(
jobid + 1, round((time.time() - start) / 60, 1)))
sys.stdout.flush()
def generate():
""" Generate a piano midi file """
# Get all pitch names
notes = utils.get_nodes_duration_for_prediction(utils.seed_file)
normalized_input, network_input, _ = utils.prepare_sequences(notes)
model = utils.create_network(normalized_input)
# Load the weights to each node
model.load_weights(weights)
prediction_output = generate_notes(model, network_input)
create_midi(prediction_output)
def main():
in_args = get_train_args()
dataloaders, image_datasets = load_data(in_args)
model = create_network(in_args)
train_network(in_args, model, dataloaders)
save_checkpoint(model, in_args, image_datasets)
test_network(model, dataloaders, in_args)
return None
def start_training(model_class, model_args, model_kwargs, sampler_class,
sampler_spec, augmentor_constr, chkpt_num, lr, train_sets,
val_sets, data_dir, model_dir, log_dir, tb_train, tb_val,
**params):
#PyTorch Model
net = utils.create_network(model_class, model_args, model_kwargs)
train_writer = tensorboardX.SummaryWriter(tb_train)
val_writer = tensorboardX.SummaryWriter(tb_val)
monitor = utils.LearningMonitor()
#Loading model checkpoint (if applicable)
if chkpt_num != 0:
utils.load_chkpt(net, monitor, chkpt_num, model_dir, log_dir)
#DataProvider Stuff
train_aug = augmentor_constr(True)
train_sampler = utils.AsyncSampler(
sampler_class(data_dir,
sampler_spec,
vols=train_sets,
mode="train",
aug=train_aug))
val_aug = augmentor_constr(False)
val_sampler = utils.AsyncSampler(
sampler_class(data_dir,
sampler_spec,
vols=val_sets,
mode="val",
aug=val_aug))
loss_fn = loss.BinomialCrossEntropyWithLogits()
optimizer = torch.optim.Adam(net.parameters(), lr=lr)
train.train(net,
loss_fn,
optimizer,
train_sampler,
val_sampler,
train_writer=train_writer,
val_writer=val_writer,
last_iter=chkpt_num,
model_dir=model_dir,
log_dir=log_dir,
monitor=monitor,
**params)
def main(args):
video, video_writer, frame_count = init_video(args.video_file_path,
args.output_video_file_path)
net_id, runtime, input_binding_info, output_binding_info = create_network(
args.model_file_path, args.preferred_backends)
output_tensors = ann.make_output_tensors(output_binding_info)
labels, process_output, resize_factor = get_model_processing(
args.model_name, video, input_binding_info)
labels = dict_labels(
labels if args.label_path is None else args.label_path)
for _ in tqdm(frame_count, desc='Processing frames'):
frame_present, frame = video.read()
if not frame_present:
continue
input_tensors = preprocess(frame, input_binding_info)
inference_output = execute_network(input_tensors, output_tensors,
runtime, net_id)
detections = process_output(inference_output)
draw_bounding_boxes(frame, detections, resize_factor, labels)
video_writer.write(frame)
print('Finished processing frames')
video.release(), video_writer.release()
def main():
logging.basicConfig(filename='mfgo.log', level=logging.DEBUG)
ontology = dag.DAG(config.go_fpath)
#gene_annotation = utils.get_annotation(config.annotation_fpath, config.filtered_annotation_fpath, ontology.get_root().id)
gene_annotation = utils.get_slim_annotation(config.annotation_fpath, ontology.get_root().id)
network = utils.create_network(config.network_fpath)
print "Number of nodes in network: %d" % network.number_of_nodes()
# Remove individual nodes by getting the largest indepedent connected component
network = nx.connected_component_subgraphs(network)[0]
print "Number of nodes in network after removing individual genes: %d" % network.number_of_nodes()
print "Number of edges in network after removing individual genes:%d" % network.number_of_edges()
# Get annotated genes in the network
network_annotated_genes = {}
for node in network.nodes():
if node in gene_annotation:
network_annotated_genes[node] = gene_annotation[node]
print "Number of annotated genes in network:%d" % len(network_annotated_genes)
'''
# load pretrained model
model = models.__dict__[arch](pretrained=True)
# get pretrained model in_features number for the last layer
in_features, last_layer_name = utils.model_info(model)
# freeze pretrained model parameters
if hasattr(model, 'features'):
for param in model.features.parameters():
param.requires_grad = False
else: # resnet
for param in model.parameters():
param.requires_grad = False
# create network with custom classifier
model = utils.create_network(model, in_features, last_layer_name, hidden_units,
dropout)
print(model)
# set loss
criterion = nn.NLLLoss()
# set optimizer parameters
if hasattr(model, 'classifier'):
#optimizer = optim.Adam(model.classifier.parameters(), lr=learning_rate, weight_decay=weight_decay)
optimizer = optim.SGD(model.classifier.parameters(),
lr=learning_rate,
momentum=momentum,
weight_decay=weight_decay)
elif hasattr(model, 'fc'): # resnet
#optimizer = optim.Adam(model.fc.parameters(), lr=learning_rate, weight_decay=weight_decay)
def Trainer(opt):
# ----------------------------------------
# Initialize training parameters
# ----------------------------------------
# cudnn benchmark accelerates the network
cudnn.benchmark = opt.cudnn_benchmark
# Handle multiple GPUs
gpu_num = torch.cuda.device_count()
print("There are %d GPUs used" % gpu_num)
opt.batch_size *= gpu_num
opt.num_workers *= gpu_num
print("Batch size is changed to %d" % opt.batch_size)
print("Number of workers is changed to %d" % opt.num_workers)
# Create folders
save_folder = os.path.join('models', opt.type)
utils.check_path(save_folder)
# VGG16 network
net = utils.create_network(opt)
# To device
if opt.multi_gpu == True:
net = nn.DataParallel(net)
net = net.cuda()
else:
net = net.cuda()
# Loss functions
criterion = torch.nn.CrossEntropyLoss().cuda()
# Optimizers
optimizer = torch.optim.SGD(net.parameters(), lr = opt.lr, momentum = opt.momentum, weight_decay = opt.weight_decay)
# Learning rate decrease
def adjust_learning_rate(optimizer, epoch, opt):
"""Set the learning rate to the initial LR decayed by "lr_decrease_factor" every "lr_decrease_epoch" epochs"""
lr = opt.lr * (opt.lr_decrease_factor ** (epoch // opt.lr_decrease_epoch))
for param_group in optimizer.param_groups:
param_group['lr'] = lr
# Save the model if pre_train == True
def save_model(net, epoch, opt):
"""Save the model at "checkpoint_interval" and its multiple"""
modelname = '%s_%s_epoch%d_bs%d_no_norm.pth' % (opt.type, opt.task, epoch, opt.batch_size)
save_path = os.path.join(save_folder, modelname)
if opt.multi_gpu == True:
if epoch % opt.checkpoint_interval == 0:
torch.save(net.module.state_dict(), save_path)
else:
if epoch % opt.checkpoint_interval == 0:
torch.save(net.state_dict(), save_path)
print('The trained model is successfully saved at epoch %d' % epoch)
# ----------------------------------------
# Initialize training dataset
# ----------------------------------------
# Define the dataset
trainset = dataset.ImageNetTrainSet(opt)
print('The overall number of images equals to %d' % len(trainset))
# Define the dataloader
dataloader = DataLoader(trainset, batch_size = opt.batch_size, shuffle = True, num_workers = opt.num_workers, pin_memory = True)
# ----------------------------------------
# Training and Testing
# ----------------------------------------
# Initialize start time
prev_time = time.time()
# Training loop
for epoch in range(opt.epochs):
for batch_idx, (data, target) in enumerate(dataloader):
# Load data and put it to cuda
data = data.cuda()
target = target.cuda()
# Train one iteration
optimizer.zero_grad()
output = net(data)
loss = criterion(output, target)
loss.backward()
optimizer.step()
# Determine approximate time left
batches_done = epoch * len(dataloader) + batch_idx
batches_left = opt.epochs * len(dataloader) - batches_done
time_left = datetime.timedelta(seconds = batches_left * (time.time() - prev_time))
prev_time = time.time()
# Print log
print("\r[Epoch %d/%d] [Batch %d/%d] [Cross-Entropy Loss: %.5f] time_left: %s" %
((epoch + 1), opt.epochs, batch_idx, len(dataloader), loss.item(), time_left))
# Learning rate decrease
adjust_learning_rate(optimizer, (epoch + 1), opt)
# Save the model
save_model(net, (epoch + 1), opt)
def Valer(opt):
# ----------------------------------------
# Initialize validation parameters
# ----------------------------------------
# VGG16 network
net = utils.create_network(opt)
net = net.eval()
# To device
if opt.multi_gpu == True:
net = nn.DataParallel(net)
net = net.cuda()
else:
net = net.cuda()
# ----------------------------------------
# Initialize validation dataset
# ----------------------------------------
# Define the dataset
valset = dataset.ImageNetValSet(opt)
overall_images = len(valset)
print('The overall number of images equals to %d' % overall_images)
# Define the dataloader
dataloader = DataLoader(valset, batch_size = opt.batch_size, shuffle = True, num_workers = opt.num_workers, pin_memory = True)
# ----------------------------------------
# Validation
# ----------------------------------------
# Initialize accuracy
overall_top1 = 0
overall_top5 = 0
# Validation loop
for batch_idx, (data, target) in enumerate(dataloader):
# Load data and put it to cuda
data = data.cuda()
target = target.cuda()
# Train one iteration
with torch.no_grad():
output = net(data)
# Get Top-5 accuracy
output = torch.softmax(output, 1)
maxk = max((1, 5))
_, pred = output.topk(maxk, 1, True, True)
pred_top5 = pred.cpu().numpy().squeeze()
# Compare the result and target label
if pred_top5[0] == target:
top1 = 1
else:
top1 = 0
top5 = 0
for i in range(len(pred_top5)):
if pred_top5[i] == target:
top5 = 1
overall_top1 = overall_top1 + top1
overall_top5 = overall_top5 + top5
# Print log
print("Batch %d: [Top-1: %d] [Top-5: %d]" % (batch_idx, top1, top5))
overall_top1 = overall_top1 / overall_images
overall_top5 = overall_top5 / overall_images
print('The accuracy of:', opt.finetune_path)
print("Overall: [Image numbers: %d] [Top-1 Acc: %.5f] [Top-5 Acc: %.5f]" % (overall_images, overall_top1, overall_top5))
parser.add_argument('data_dir', action='store')
parser.add_argument('--save-dir', action='store', default=os.getcwd())
parser.add_argument('--arch', action='store', default='vgg13')
parser.add_argument('--learning_rate',
action='store',
default=0.002,
type=float)
parser.add_argument('--gpu', action='store', default=True)
parser.add_argument('--hidden_units', action='store', default=512, type=int)
parser.add_argument('--epochs', action='store', default=5, type=int)
parser.add_argument('--checkpoint', action='store')
args = parser.parse_args()
print(args)
train_dataset, train_dataloader = utils.load_train_data(args.data_dir +
"/train/")
valid_dataset, valid_dataloader = utils.load_valid_data(args.data_dir +
"/valid/")
test_dataset, test_dataloader = utils.load_test_data(args.data_dir + "/test/")
model = utils.create_network(args.arch, args.hidden_units, True)
criterion = utils.create_criterion()
optimizer = utils.create_optimizer(model, args.learning_rate)
model = utils.train_model(model, criterion, optimizer, train_dataloader,
valid_dataloader, args.epochs, args.gpu)
utils.save_checkpoint(model, args.arch, args.hidden_units, train_dataset,
args.save_dir)
def train_network():
""" Train a Neural Network to generate music """
notes = utils.get_notes_duration()
network_input, _, network_output = utils.prepare_sequences(notes)
model = utils.create_network(network_input)
train(model, network_input, network_output)
import utils as ut
ut.create_network()
ut.translate("seed_genes", "sg_entrez")
ut.join_files("sg_entrez", "diamond", "intersection_list")
ut.top_ten("go_ora")
ut.top_ten("path_ora")
default=0.2)
parser.add_argument('--arch', dest="arch", action='store', default='vgg16')
parser.add_argument('--learning_rate', dest='lr', action='store', default=0.01)
parser.add_argument('--hidden_units',
dest='hidden_units',
action='store',
default=1024)
parser.add_argument('--epochs', dest='epochs', action='store', default=1)
parser.add_argument('--gpu', dest='gpu', action='store', default='gpu')
args = parser.parse_args()
data_dir = args.data_dir
save_dir = args.save_dir
dropout_prob = args.drop_prob
arch = args.arch
learning_rate = args.lr
hidden_units = args.hidden_units
gpu = args.gpu
epochs = args.epochs
trainloader, validloader, testloader = utils.data_load(data_dir)
model, criterion, optimizer = utils.create_network(arch, learning_rate,
hidden_units, dropout_prob)
model = utils.train_network(model, criterion, optimizer, trainloader,
validloader, epochs, gpu)
utils.save_checkpoint(model, data_dir, save_dir, arch, hidden_units,
dropout_prob, learning_rate, epochs)
def update_network_graph(scatterplot_input: dict, networkgraph_input: dict,
elements: list):
"""
Updates network graph after relevant input in either scatterplot or network graph.
:param scatterplot_input:
:param networkgraph_input:
:param elements:
"""
fc: pd.DataFrame = filtered_courses
if scatterplot_input is not None:
global last_guid
guid: str = str(scatterplot_input["points"][0]["customdata"])
if last_guid != guid:
last_guid = guid
local_network: tuple = None
# Show courses for chosen Tadira technique.
if guid.startswith("TT"):
local_network = utils.create_network(
fc[(fc.index.isin(tadirah_techniques.loc[[guid
]].course_id))],
tadirah_objects.head(0), tadirah_techniques.loc[[guid]],
tadirah_objects_counts, tadirah_techniques_counts,
embedding)
# Show courses for chosen Tadira object.
elif guid.startswith("TO"):
local_network = utils.create_network(
fc[(fc.index.isin(tadirah_objects.loc[[guid]].course_id))],
tadirah_objects.loc[[guid]], tadirah_techniques.head(0),
tadirah_objects_counts, tadirah_techniques_counts,
embedding)
else:
local_network = utils.create_network(
fc.loc[[int(guid)]], tadirah_objects, tadirah_techniques,
tadirah_objects_counts, tadirah_techniques_counts,
embedding)
return local_network[0].tolist() + local_network[1].tolist()
if networkgraph_input is not None:
global node_extensions
if networkgraph_input["id"] not in node_extensions:
related_wiki = find_related_wiki(networkgraph_input, elements)
node_extensions[networkgraph_input["id"]] = set()
for wiki in related_wiki:
uuid_wiki: str = str(uuid.uuid1())
node_id: str = 'W{}'.format(uuid_wiki)
elements.extend([
{
'data': {
'id': node_id,
'label': wiki
}
},
{
'data': {
'target': node_id,
'source': networkgraph_input["id"],
'weight': 0.5,
# Assign anonymous ID to edge.
'id': str(uuid.uuid1())
}
}
])
node_extensions[networkgraph_input["id"]].add(node_id)
elif networkgraph_input["id"] in node_extensions:
# Collapse node.
utils.collapse_node_in_network_graph(elements,
networkgraph_input["id"],
node_extensions, False)
return elements
else:
return []
def simulate(conn, output_dir, fname_peaks, fname_lfps_prefix, dt, n_runs, total_time, temperature, with_v1_l4, with_v1_l6, with_trn, input, con_input_lgn,
n_e_lgn, n_i_lgn, n_e_l6, n_i_l6, n_e_l4, n_i_l4, n_trn,
threshold, delay, delay_distbtn_e_l6_lgn, delay_e_l4_e_lgn, delay_e_lgn_i_l4, delay_e_lgn_e_l4, delay_e_lgn_e_l6,
delay_e_lgn_trn, delay_e_l4_trn, delay_distbtn_e_l6_trn, delay_e_lgn_i_l6,
lgn_params, l4_params, l6_params, trn_params, w_e_lgn_trn, w_trn_e_lgn, w_e_l6_trn, w_e_l4_e_l6,
w_e_lgn_e_l4, w_e_l4_e_lgn, w_e_l6_e_lgn, w_e_lgn_e_l6, w_e_lgn_i_l6, w_e_lgn_i_l4, w_e_l4_trn,
connect_e_lgn_e_l4, connect_e_lgn_i_l4, connect_e_l4_e_lgn, connect_e_lgn_i_l6, connect_e_lgn_e_l6, connect_e_l6_e_lgn, connect_e_l4_trn, connect_e_l6_trn,
connect_e_lgn_trn, connect_trn_e_lgn, connect_e_l4_e_l6):
start = np.empty(shape=0)
bf_plot = np.empty(shape=0)
af_plot = np.empty(shape=0)
end = np.empty(shape=0)
h.celsius = temperature
print "* * * Simulating %d runs * * *" % n_runs
h.tstop = total_time
for n_sim in range(n_runs):
print "#%d: Constructing circuits..." % (n_sim + 1)
start = np.append(start, timer())
# creating LGN network
i_lgn, i_lgn_rec = create_network(n_i_lgn)
e_lgn, e_lgn_rec = create_network(n_e_lgn)
# create connections in LGN
e_lgn_e_lgn_syn = e_net_connect(e_lgn, e_lgn, threshold, delay, lgn_params['w_e_lgn_e_lgn'], 1)
i_lgn_i_lgn_syn = i_net_connect(i_lgn, i_lgn, threshold, delay, lgn_params['w_i_lgn_i_lgn'], 1)
i_lgn_e_lgn_syn = i_net_connect(i_lgn, e_lgn, threshold, lgn_params['delay_i_e'], lgn_params['w_i_lgn_e_lgn'], 1)
e_lgn_i_lgn_syn = e_net_connect(e_lgn, i_lgn, threshold, lgn_params['delay_e_i'], lgn_params['w_e_lgn_i_lgn'], 1) # weight should be set to zero
e_l4, e_l4_rec = create_network(n_e_l4)
i_l4, i_l4_rec = create_network(n_i_l4)
if with_v1_l4:
# create connections in V1 L4
e_l4_e_l4_sin = e_net_connect(e_l4, e_l4, threshold, delay, l4_params['w_e_l4_e_l4'], l4_params['p_e_e'])
i_l4_i_l4_sin = i_net_connect(i_l4, i_l4, threshold, delay, l4_params['w_i_l4_i_l4'], l4_params['p_i_i'])
e_l4_i_l4_sin = e_net_connect(e_l4, i_l4, threshold, delay, l4_params['w_e_l4_i_l4'], l4_params['p_e_i'])
i_l4_e_l4_sin = i_net_connect(i_l4, e_l4, threshold, delay, l4_params['w_i_l4_e_l4'], l4_params['p_i_e'])
# extrinsic connections
# Population 1) 15 LGN E cells connect to 15 V1 L4 E cells
# Population 2) 5 LGN E cells connect to 5 V1 L4 I cells
#
# Population 1 and population 2 are different
#
# Hirsch et al., 1998
if connect_e_lgn_e_l4:
# connections from Glutamatergic neurons of network LGN to network V1 L4
e_lgn_e_l4_syn = partial_e_net_connect(e_lgn, e_l4, 2./4, 1, 2./4, 1, threshold, delay_e_lgn_e_l4, w_e_lgn_e_l4)
# e_lgn_e_l4_syn = topographically_e_connect(e_lgn, e_l4, 0, 1, threshold, delay_e_lgn_e_l4, w_e_lgn_e_l4)
if connect_e_l4_e_lgn:
# TODO: feedback connections are only of 3/4 of neurons?
# connections from Glutamatergic neurons of network 2 (V1) to network 1 (LGN)
e_l4_e_lgn_syn = partial_e_net_connect(e_l4, e_lgn, 1./4, 1, 1./4, 1, threshold, delay_e_l4_e_lgn, w_e_l4_e_lgn)
if connect_e_lgn_i_l4:
# connections from Glutamatergic neurons of network (LGN) to network V1 L4
e_lgn_i_l4_syn = partial_e_net_connect(e_lgn, i_l4, 0, 2./4, 0, 2./4, threshold, delay_e_lgn_i_l4, w_e_lgn_i_l4)
# e_lgn_i_l4_syn = topographically_e_connect(e_lgn, i_l4, 0, 1./4, threshold, delay_e_lgn_i_l4, w_e_lgn_i_l4)
i_l6, i_l6_rec = create_network_L6(n_i_l6)
e_l6, e_l6_rec = create_network_L6(n_e_l6)
if with_v1_l6:
# create connections in V1 L6
e_l6_e_l6_sin = e_net_connect(e_l6, e_l6, threshold, delay, l6_params['w_e_l6_e_l6'], l6_params['p_e_e'])
i_l6_i_l6_sin = i_net_connect(i_l6, i_l6, threshold, delay, l6_params['w_i_l6_i_l6'], l6_params['p_i_i'])
e_l6_i_l6_syn = e_net_connect(e_l6, i_l6, threshold, delay, l6_params['w_e_l6_i_l6'], l6_params['p_e_i'])
i_l6_e_l6_syn = i_net_connect(i_l6, e_l6, threshold, delay, l6_params['w_i_l6_e_l6'], l6_params['p_i_e'])
# connections from V1 input (L4) layer to L6
if connect_e_l4_e_l6:
e_l4_e_l6_sin = e_net_connect(e_l4, e_l6, threshold, 1, w_e_l4_e_l6, 1)
# ALL-to-ALL connections of feedback
if connect_e_l6_e_lgn:
e_l6_e_lgn_sin = e_ct_net_connect_delay_dist(e_l6, e_lgn, threshold, delay_distbtn_e_l6_lgn, w_e_l6_e_lgn)
# TODO: Connectivity as Hirsch
if connect_e_lgn_e_l6:
e_lgn_e_l6_syn = e_net_connect(e_lgn, e_l6, threshold, delay_e_lgn_e_l6, w_e_lgn_e_l6, 1)
# TODO: Connectivity as Hirsch
if connect_e_lgn_i_l6:
e_lgn_i_l6_syn = e_net_connect(e_lgn, i_l6, threshold, delay_e_lgn_i_l6, w_e_lgn_i_l6, 1)
# create trn neurons (inhibitory only)
trn, trn_rec = create_network(n_trn)
if with_trn:
trn_trn_syn = i_net_connect(trn, trn, threshold, trn_params['delay_i_i'], trn_params['w_trn_trn'],
trn_params['p_i_i'])
# connections from Glutamatergic neurons of network V1 L4 to trn
if with_v1_l4 and connect_e_l4_trn:
e_l4_trn_syn = e_net_connect(e_l4, trn, threshold, delay_e_l4_trn, w_e_l4_trn, 1)
if with_v1_l6 and connect_e_l6_trn:
e_l6_trn_syn = e_net_connect_delay_dist(e_l6, trn, threshold, delay_distbtn_e_l6_trn, w_e_l6_trn, 1)
if connect_e_lgn_trn:
# connections from Glutamatergic neurons of LGN to TRN
# ALL-to-ALL
e_lgn_trn_syn = e_net_connect(e_lgn, trn, threshold, delay_e_lgn_trn, w_e_lgn_trn, 1)
# # topographic
# topographically_connect(e_lgn, trn, 0, 1, threshold, delay_e_lgn_trn, w_e_lgn_trn)
if connect_trn_e_lgn:
# ALL-to-ALL
trn_e_lgn_sin = i_net_connect(trn, e_lgn, threshold, delay, w_trn_e_lgn, 1)
# generate inputs to LGN
netStim = list()
i_stims = list()
e_stims = list()
stim_rec = h.Vector()
for stim_i in range(0, input['nstims']):
netStim.append(h.NetStimPois(input['position']))
netStim[stim_i].start = 0
netStim[stim_i].mean = input['stimrate'] # 100 = 10 Hz, 10 = 100 Hz, 1 = 1000Hz, 5 = 200 Hz, 6 = 150 Hz
netStim[stim_i].number = 0
if stim_i < n_i_lgn:
i_stims.append(h.NetCon(netStim[stim_i], i_lgn[stim_i].synE, con_input_lgn['gaba_threshold'],
con_input_lgn['gaba_delay'], con_input_lgn['gaba_weight']))
if stim_i < n_e_lgn:
e_stims.append(h.NetCon(netStim[stim_i], e_lgn[stim_i].synE, con_input_lgn['glut_threshold'],
con_input_lgn['glut_delay'], con_input_lgn['glut_weight']))
e_stims[0].record(stim_rec) # measure poisson input #0 to LGN Excitatory Cell #0
timeaxis = h.Vector()
timeaxis.record(h._ref_t)
print "#%d: Running simulation..." % (n_sim + 1)
h.run()
bf_plot = np.append(bf_plot, timer())
mean_lgn, mean_trn, mean_v1_l4, mean_v1_l6 = plot_all(conn, output_dir, fname_peaks, n_sim, dt, timeaxis, stim_rec, with_v1_l4, with_v1_l6, with_trn,
e_lgn_rec, i_lgn_rec, trn_rec, e_l4_rec, i_l4_rec, e_l6_rec, i_l6_rec,
n_e_lgn, n_i_lgn, n_trn, n_e_l4, n_i_l4, n_e_l6, n_i_l6)
af_plot = np.append(af_plot, timer())
ofname = fname_lfps_prefix + str(n_sim) + ".txt"
n = len(timeaxis)
indx = np.arange(0, n+1, 40) # store one in every 40 values
lfp_lgn = np.array(mean_lgn)
lfp_trn = np.array(mean_trn)
lfp_l4 = np.array(mean_v1_l4)
lfp_l6 = np.array(mean_v1_l6)
time = np.array(timeaxis)
np.savetxt(ofname, (lfp_lgn[indx], lfp_trn[indx], lfp_l4[indx], lfp_l6[indx], time[indx]))
end = np.append(end, timer())
print "Progress: %d runs simulated %d runs missing" % (n_sim + 1, n_runs - n_sim - 1)
print_time_stats(start, bf_plot, af_plot, end)
variables_dict = load_from_json(predictors, response, verbose=True)
# Split the data into training and test sets
xtrain, xtest, ytrain, ytest, ytrain_hot, ytest_hot = create_model_data(
variables_dict, predictors, response, model_type='Both')
# Iterate through regression and classification models
for model_type in ['Regression', 'Classification']:
print('Beginning {} Model for {} Predictions'.format(
model_type, response))
print('Setting up TensorBoard')
# Create the model structure, define the cost optimization functions
x = tf.placeholder(tf.float32, [None, len(predictors)], name='x')
if model_type == 'Classification':
y = tf.placeholder(tf.float32, [None, 2], name='y')
output_layer = create_network(x, hidden_layers, num_classes=2)
cost = tf.reduce_mean(
tf.nn.softmax_cross_entropy_with_logits(labels=y,
logits=output_layer))
else:
y = tf.placeholder(tf.float32, name='y')
output_layer = tf.transpose(
create_network(x, hidden_layers, num_classes=1))
cost = tf.reduce_mean(tf.square(output_layer - y))
optimizer = tf.train.AdamOptimizer(learning_rate).minimize(cost)
# Train the model
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
print('Starting Model Training')
for epoch in range(num_epochs):
running_loss += loss.item()
else:
validation_loss, validation_accuracy = test_network(
model, validation_loader, device)
print(
f"Epoch {epoch+1}/{epochs}.. "
f"Train loss: {running_loss/len(train_loader):.3f}.. "
f"Validation loss: {validation_loss/len(validation_loader):.3f}.. "
f"Validation accuracy: {validation_accuracy/len(validation_loader):.3f}"
)
running_loss = 0
return model, optimizer
train_data, validation_data = create_data(data_dir)
train_loader, validation_loader = create_loaders(train_data, validation_data)
print('Data is loaded from {}'.format(data_dir))
model, criterion, optimizer = create_network(arch, device, learning_rate,
dropout, hidden_units)
print('Starting to train network')
model, optimizer = train_network(model, device, optimizer, train_loader,
validation_loader, epochs)
print('Network training finished')
if save_dir != None:
save_checkpoint(save_dir, model, arch, train_data, learning_rate, dropout,
hidden_units)
print('Checkpoint is saved to {}'.format(save_dir))
nterms = gene_annotation[node]
sim = compute_gene_sim_total(nterms, terms)
#sim = compute_gene_sim_max(nterms, terms)
non_sim_avg += sim
non_sim_avg /= count
print "%s, %f, %f" % (gene, sim_avg, non_sim_avg)
if __name__ == "__main__":
dag = DAG(config.go_fpath)
gene_annotation = utils.get_annotation(config.annotation_fpath, config.filtered_annotation_fpath, dag.get_root().id)
term_ic = utils.calculate_ic(gene_annotation, dag, config.ic_fpath)
network = utils.create_network(config.network_fpath)
# Remove unannotated gene from network
for node in network.nodes():
if not node in gene_annotation:
network.remove_node(node)
# Remove individual nodes by get the largest indepedent connected component
network = nx.connected_component_subgraphs(network)[0]
sim_cache = utils.read_sim(config.simcache_fpath)
#compute_term_in_neighbour_ratio()
#compute_avg_term_num()
compute_avg_sim()
predictors, variables_dict[current_response], random_state=33)
print('Finished Splitting Data')
# Parameters
learning_rate = 0.01
training_epochs = 10
# Network Parameters
hidden_layer_nodes = [100, 100, 100]
# tf Graph input
x = tf.placeholder("float", [None, len(xtrain[0])], name='x')
y = tf.placeholder("float", [None])
# Construct model
pred = tf.transpose(create_network(x, hidden_layer_nodes, num_classes=1))
# Define loss and optimizer
cost = tf.reduce_mean(tf.square(pred - y))
optimizer = tf.train.AdamOptimizer(learning_rate=learning_rate).minimize(cost)
# Launch the graph
with tf.Session() as sess:
sess.run(tf.global_variables_initializer())
# Training cycle
for epoch in range(training_epochs):
# Run optimization op (backprop) and cost op (to get loss value)
sess.run([optimizer, cost, pred], feed_dict={x: xtrain, y: ytrain})
print('Completed Epoch {} of {}'.format(epoch + 1, training_epochs))
xtrain, xtest, ytrain, ytest = train_test_split(predictors, variables_dict[response], random_state=33)
print('Finished Splitting Data')
ytrain = np.where(np.array(ytrain) >= 0, 1, 0)
ytest = np.where(np.array(ytest) >= 0, 1, 0)
ytrain_hot = np.zeros((len(ytrain), 2))
ytrain_hot[np.arange(len(ytrain)), ytrain] = 1
ytest_hot = np.zeros((len(ytest), 2))
ytest_hot[np.arange(len(ytest)), ytest] = 1
x = tf.placeholder(tf.float32, [None, len(predictor_names)], name='x')
y = tf.placeholder(tf.float32, [None, 2])
output_layer = create_network(x, [33, 33, 33], num_classes=2)
cross_entropy = tf.reduce_mean(tf.nn.softmax_cross_entropy_with_logits(labels=y, logits=output_layer))
train_step = tf.train.AdamOptimizer(.01).minimize(cross_entropy)
sess = tf.InteractiveSession()
tf.global_variables_initializer().run()
print('Starting Model Training')
num_epochs = 33
for epoch in range(num_epochs):
sess.run(train_step, feed_dict={x: xtrain, y: ytrain_hot})
print('Completed Epoch {} of {}'.format(epoch + 1, num_epochs))
correct_prediction = tf.equal(tf.argmax(output_layer, 1), tf.argmax(y, 1))
def create():
""" Create a set of Openstack resources.
If the required resources do not exist, new one will be created.
"""
if not conn.network.find_network(my_network_name):
netw = utils.create_network(conn, my_network_name)
else:
netw = conn.network.find_network(my_network_name)
print("Network {} exists already.".format(my_network_name))
if not conn.network.find_subnet(my_subnet_name):
subn = utils.create_subnet(conn, netw, my_subnet_name, my_cidr)
else:
subn = conn.network.find_subnet(my_subnet_name)
print("Subnet {} exists already.".format(my_subnet_name))
if not conn.network.find_router(my_router_name):
rout = utils.create_router(conn, my_router_name, public_net)
utils.add_router_interface(conn, rout, subn)
else:
rout = conn.network.find_router(my_router_name)
print("Router {} exists already.".format(my_router_name))
""" Check whether the provided resources exist. If they do not exist
prompt message will show and servers creating will not continue.
Otherwise servers will be created.
"""
if not (image and flavour and keypair and security_group):
print(
"Please make sure the provided image {}, flavour {}, keypair {} or security_group {} exists already.".format(
IMAGE, FLAVOUR, KEYPAIR, SECURITYGROUP
)
)
else:
# Create server one by one
for server in server_list:
n_serv = conn.compute.find_server(server)
if not n_serv:
print("------------ Creating server {}... --------".format(server))
n_serv = conn.compute.create_server(
name=server,
image_id=image.id,
flavor_id=flavour.id,
networks=[{"uuid": conn.network.find_network(my_network_name).id}],
key_name=keypair.name,
security_groups=[{"sgid": security_group.id}],
)
conn.compute.wait_for_server(n_serv, wait=180)
print("Server {} is created successfully".format(n_serv))
else:
print("Server {} exists already".format(server))
# Checking, creating and attaching floating ip to web server
if not conn.get_server(name_or_id=server_list[0])["interface_ip"]:
print(
"-------- Creating and attaching floating ip to server {} --------".format(
server_list[0]
)
)
conn.compute.wait_for_server(n_serv)
conn.create_floating_ip(
network=PUBLICNET, server=conn.compute.find_server(server_list[0])
)
else:
print("Floating ip is attached to server {} already".format(server_list[0]))