def __init__(self, args):
super(CNFVAE, self).__init__(args)
# CNF model
self.cnf = build_model_tabular(args, args.z_size)
if args.cuda:
self.cuda()
def visualize_evolution():
model = build_model_tabular(args, 1).to(device)
set_cnf_options(args, model)
checkpt = torch.load(os.path.join(args.save, 'checkpt.pth'))
model.load_state_dict(checkpt['state_dict'])
model.to(device)
viz_times = torch.linspace(0., args.time_length, args.ntimes)
errors = []
viz_times_np = viz_times[1:].detach().cpu().numpy()
xx = torch.linspace(-5, 5, args.num_particles).view(-1, 1)
xx_np = xx.detach().cpu().numpy()
xs, ys = np.meshgrid(xx, viz_times_np)
#xx,yy = np.meshgrid(args.num_particles, viz_times_np )
#all_evolutions = np.zeros((args.ntimes-1,args.num_particles))
all_evolutions = np.zeros((args.num_particles, args.ntimes - 1))
with torch.no_grad():
for i, t in enumerate(tqdm(viz_times[1:])):
model.eval()
set_cnf_options(args, model)
#xx = torch.linspace(-5, 5, args.num_particles).view(-1, 1)
#generated_p = model_density(xx, model)
generated_p = 0
for cnf in model.chain:
xx = xx.to(device)
z, delta_logp = cnf(xx,
torch.zeros_like(xx),
integration_times=torch.Tensor([0, t]))
generated_p = standard_normal_logprob(z) - delta_logp
generated_p = generated_p.detach()
#plt.plot(xx.view(-1).cpu().numpy(), generated_p.view(-1).exp().cpu().numpy(), label='Model')
cur_evolution = generated_p.view(-1).exp().cpu().numpy()
#all_evolutions[i]= np.array(cur_evolution)
all_evolutions[:, i] = np.array(cur_evolution)
#xx = np.array(xx.detach().cpu().numpy())
#yy = np.array(yy)
plt.figure(dpi=1200)
plt.clf()
all_evolutions = all_evolutions.astype('float32')
print(xs.shape)
print(ys.shape)
print(all_evolutions.shape)
#plt.pcolormesh(ys, xs, all_evolutions)
plt.pcolormesh(xs, ys, all_evolutions.transpose())
utils.makedirs(os.path.join(args.save, 'test_times', 'figs'))
plt.savefig(
os.path.join(args.save, 'test_times', 'figs',
'evolution.jpg'.format(i)))
plt.close()
def visualize_particle_flow():
model = build_model_tabular(args, 1).to(device)
set_cnf_options(args, model)
checkpt = torch.load(os.path.join(args.save, 'checkpt.pth'))
model.load_state_dict(checkpt['state_dict'])
model.to(device)
viz_times = torch.linspace(0., args.time_length, args.ntimes)
errors = []
xx = torch.linspace(-5, 5, args.num_particles).view(-1, 1)
zs = []
#zs.append(xx.view(-1).cpu().numpy())
with torch.no_grad():
for i, t in enumerate(tqdm(viz_times[1:])):
model.eval()
set_cnf_options(args, model)
#generated_p = model_density(xx, model)
generated_p = 0
for cnf in model.chain:
xx = xx.to(device)
z, delta_logp = cnf(xx,
torch.zeros_like(xx),
integration_times=torch.Tensor([0, t]))
generated_p = standard_normal_logprob(z) - delta_logp
zs.append(z.cpu().numpy())
#plt.plot(xx.view(-1).cpu().numpy(), generated_p.view(-1).exp().cpu().numpy(), label='Model')
#plt.savefig(os.path.join(args.save,'test_times', 'figs', '{:04d}.jpg'.format(i)))
#plt.close()
zs = np.array(zs).reshape(args.ntimes - 1, args.num_particles)
viz_t = viz_times[1:].numpy()
#print(zs)
plt.figure(dpi=1200)
plt.clf()
#plt.plot(viz_t , zs[:,0])
with sns.color_palette("Blues_d"):
plt.plot(viz_t, zs)
plt.xlabel("Test Time")
#plt.tight_layout()
utils.makedirs(os.path.join(args.save, 'test_times', 'figs'))
plt.savefig(
os.path.join(args.save, 'test_times', 'figs',
'particle_trajectory.jpg'.format(i)))
plt.close()
def gen_model(scale=10, fraction=0.5):
#build normalizing flow model from previous fit
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
args = pkl.load(open('args.pkl', 'rb'))
regularization_fns, regularization_coeffs = create_regularization_fns(args)
model = build_model_tabular(args, 5,
regularization_fns).to(device) #.cuda()
if args.spectral_norm: add_spectral_norm(model)
set_cnf_options(args, model)
model.load_state_dict(torch.load('model_10000.pt'))
#if torch.cuda.is_available():
# model = init_flow_model(
# num_inputs=5,
# num_cond_inputs=None).cuda() #len(cond_cols)).cuda()
#else:
# model = init_flow_model(
# num_inputs=5,
# num_cond_inputs=None) #len(cond_cols)).cuda()
#num_layers = 5
#base_dist = StandardNormal(shape=(5,))
#transforms = []
#for _ in range(num_layers):
# transforms.append(ReversePermutation(features=5))
# transforms.append(MaskedAffineAutoregressiveTransform(features=5,
# hidden_features=4))
#transform = CompositeTransform(transforms)
#model = Flow(transform, base_dist).to(device)
#model.cpu()
#filename = 'checkpoint11434epochs_cycle.pth'
#filename = f'gauss_scale{scale}_frac{fraction}/checkpoint200000epochs_cycle_gauss.pth'
#filename = 'gauss_scale10_frac0.25/checkpoint100000epochs_cycle_gauss.pth'
#filename = 'checkpoint_epoch{}.pth'.format(95000)
#data = torch.load(filename, map_location=device)
#breakpoint()
#model.load_state_dict(data['model'])
#if torch.cuda.is_available():
# data = torch.load(filename)
# model.load_state_dict(data['model'])
# model.cuda();
#else:
# data = torch.load(filename, map_location=torch.device('cpu'))
# model.load_state_dict(data['model'])
return model
def get_ckpt_model_and_data(args):
# Load checkpoint.
checkpt = torch.load(args.checkpt, map_location=lambda storage, loc: storage)
ckpt_args = checkpt['args']
state_dict = checkpt['state_dict']
# Construct model and restore checkpoint.
regularization_fns, regularization_coeffs = create_regularization_fns(ckpt_args)
model = build_model_tabular(ckpt_args, 2, regularization_fns).to(device)
if ckpt_args.spectral_norm: add_spectral_norm(model)
set_cnf_options(ckpt_args, model)
model.load_state_dict(state_dict)
model.to(device)
print(model)
print("Number of trainable parameters: {}".format(count_parameters(model)))
# Load samples from dataset
data_samples = toy_data.inf_train_gen(ckpt_args.data, batch_size=2000)
return model, data_samples
def compute_loss(args, model, batch_size=args.batch_size):
x = toy_data.inf_train_gen(args.data, batch_size=batch_size)
x = torch.from_numpy(x).type(torch.float32).to(device)
zero = torch.zeros(x.shape[0], 1).to(x)
z, change = model(x, zero)
logpx = standard_normal_logprob(z).sum(1, keepdim=True) - change
loss = -torch.mean(logpx)
return loss
if __name__ == '__main__':
regularization_fns, regularization_coeffs = create_regularization_fns(args)
model = build_model_tabular(args, 2, regularization_fns).to(device)
if args.spectral_norm: add_spectral_norm(model)
set_cnf_options(args, model)
logger.info(model)
logger.info("Number of trainable parameters: {}".format(count_parameters(model)))
optimizer = optim.Adam(model.parameters(), lr=args.lr, weight_decay=args.weight_decay)
time_meter = utils.RunningAverageMeter(0.93)
loss_meter = utils.RunningAverageMeter(0.93)
nfef_meter = utils.RunningAverageMeter(0.93)
nfeb_meter = utils.RunningAverageMeter(0.93)
tt_meter = utils.RunningAverageMeter(0.93)
end = time.time()
if __name__ == '__main__':
device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")
cvt = lambda x: x.type(torch.float32).to(device, non_blocking=True)
logger.info('Using {} GPUs.'.format(torch.cuda.device_count()))
data = load_data(args.data)
data.trn.x = torch.from_numpy(data.trn.x)
data.val.x = torch.from_numpy(data.val.x)
data.tst.x = torch.from_numpy(data.tst.x)
args.dims = '-'.join([str(args.hdim_factor * data.n_dims)] * args.nhidden)
regularization_fns, regularization_coeffs = create_regularization_fns(args)
model = build_model_tabular(args, data.n_dims,
regularization_fns).to(device)
set_cnf_options(args, model)
for k in model.state_dict().keys():
logger.info(k)
if args.resume is not None:
checkpt = torch.load(args.resume)
# Backwards compatibility with an older version of the code.
# TODO: remove upon release.
filtered_state_dict = {}
for k, v in checkpt['state_dict'].items():
if 'diffeq.diffeq' not in k:
filtered_state_dict[k.replace('module.', '')] = v
model.load_state_dict(filtered_state_dict)
if __name__ == '__main__':
# only a single block of diffeq is supported now
assert args.num_blocks == 1
centers = DEFAULT_CENTERS.to(device)
dim = centers.shape[1]
convection = lambda x: -gaussian_mixture_score(x, centers)
writer = SummaryWriter('out/wgf/gaussian')
regularization_fns, regularization_coeffs = create_regularization_fns(args)
regularization_fns = None
model = build_model_tabular(args=args,
dims=dim,
convection=convection,
regularization_fns=regularization_fns,
exp_decay=args.exp_decay).to(device)
model_validate_dvp = build_model_compare_DVP(
args=args,
convection=convection,
mollifier=IsometricGaussianMollifier(args.mollifier_sigma_square),
diffeq=model.chain[0].odefunc.diffeq).to(device)
if args.spectral_norm: add_spectral_norm(model)
set_cnf_options(args, model)
logger.info(model)
logger.info("Number of trainable parameters: {}".format(
count_parameters(model)))
cvt = lambda x: x.type(torch.float32).to(device, non_blocking=True)
# logger.info('Using {} GPUs.'.format(torch.cuda.device_count()))
data = load_data(args.data)
data.trn.x = torch.from_numpy(data.trn.x)
data.val.x = torch.from_numpy(data.val.x)
data.tst.x = torch.from_numpy(data.tst.x)
args.dims = '-'.join([str(args.hdim_factor * data.n_dims)] * args.nhidden)
regularization_fns, regularization_coeffs = create_regularization_fns(args)
model, cnfs = build_model_tabular(
args,
data.n_dims,
regularization_fns,
return_intermediate_points=args.return_inter_points)
model = model.to(device)
set_cnf_options(args, model)
# for k in model.state_dict().keys():
# logger.info(k)
if args.resume is not None:
checkpt = torch.load(args.resume)
# Backwards compatibility with an older version of the code.
# TODO: remove upon release.
filtered_state_dict = {}
for k, v in checkpt['state_dict'].items():
def train():
model = build_model_tabular(args, 1).to(device)
set_cnf_options(args, model)
logger.info(model)
logger.info("Number of trainable parameters: {}".format(
count_parameters(model)))
optimizer = optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
time_meter = utils.RunningAverageMeter(0.93)
loss_meter = utils.RunningAverageMeter(0.93)
nfef_meter = utils.RunningAverageMeter(0.93)
nfeb_meter = utils.RunningAverageMeter(0.93)
tt_meter = utils.RunningAverageMeter(0.93)
end = time.time()
best_loss = float('inf')
model.train()
for itr in range(1, args.niters + 1):
optimizer.zero_grad()
loss = compute_loss(args, model)
loss_meter.update(loss.item())
total_time = count_total_time(model)
nfe_forward = count_nfe(model)
loss.backward()
optimizer.step()
nfe_total = count_nfe(model)
nfe_backward = nfe_total - nfe_forward
nfef_meter.update(nfe_forward)
nfeb_meter.update(nfe_backward)
time_meter.update(time.time() - end)
tt_meter.update(total_time)
log_message = (
'Iter {:04d} | Time {:.4f}({:.4f}) | Loss {:.6f}({:.6f}) | NFE Forward {:.0f}({:.1f})'
' | NFE Backward {:.0f}({:.1f}) | CNF Time {:.4f}({:.4f})'.format(
itr, time_meter.val, time_meter.avg, loss_meter.val,
loss_meter.avg, nfef_meter.val, nfef_meter.avg, nfeb_meter.val,
nfeb_meter.avg, tt_meter.val, tt_meter.avg))
logger.info(log_message)
if itr % args.val_freq == 0 or itr == args.niters:
with torch.no_grad():
model.eval()
test_loss = compute_loss(args,
model,
batch_size=args.test_batch_size)
test_nfe = count_nfe(model)
log_message = '[TEST] Iter {:04d} | Test Loss {:.6f} | NFE {:.0f}'.format(
itr, test_loss, test_nfe)
logger.info(log_message)
if test_loss.item() < best_loss:
best_loss = test_loss.item()
utils.makedirs(args.save)
torch.save(
{
'args': args,
'state_dict': model.state_dict(),
}, os.path.join(args.save, 'checkpt.pth'))
model.train()
if itr % args.viz_freq == 0:
with torch.no_grad():
model.eval()
xx = torch.linspace(-10, 10, 10000).view(-1, 1)
true_p = data_density(xx)
plt.plot(xx.view(-1).cpu().numpy(),
true_p.view(-1).exp().cpu().numpy(),
label='True')
true_p = model_density(xx, model)
plt.plot(xx.view(-1).cpu().numpy(),
true_p.view(-1).exp().cpu().numpy(),
label='Model')
utils.makedirs(os.path.join(args.save, 'figs'))
plt.savefig(
os.path.join(args.save, 'figs', '{:06d}.jpg'.format(itr)))
plt.close()
model.train()
end = time.time()
logger.info('Training has finished.')
def density_fn(x, logpx=None):
if logpx is not None:
return model(x, logpx, reverse=False)
else:
return model(x, reverse=False)
return sample_fn, density_fn
if __name__ == '__main__':
if args.discrete:
model = construct_discrete_model().to(device)
model.load_state_dict(torch.load(args.checkpt)['state_dict'])
else:
model = build_model_tabular(args, 2).to(device)
sd = torch.load(args.checkpt)['state_dict']
fixed_sd = {}
for k, v in sd.items():
fixed_sd[k.replace('odefunc.odefunc', 'odefunc')] = v
model.load_state_dict(fixed_sd)
print(model)
print("Number of trainable parameters: {}".format(count_parameters(model)))
model.eval()
p_samples = toy_data.inf_train_gen(args.data, batch_size=800**2)
with torch.no_grad():
sample_fn, density_fn = get_transforms(model)
# transform to z
z, delta_logp = model(x, zero)
# compute log q(z)
logpz = standard_normal_logprob(z).sum(1, keepdim=True)
logpx = logpz - delta_logp
loss = -torch.mean(logpx)
return loss
if __name__ == '__main__':
regularization_fns, regularization_coeffs = create_regularization_fns(args)
input_dim = 2 if args.data != 'HDline' else 16
model = build_model_tabular(args, input_dim, regularization_fns).to(device)
if args.spectral_norm: add_spectral_norm(model)
set_cnf_options(args, model)
logger.info(model)
logger.info("Number of trainable parameters: {}".format(
count_parameters(model)))
optimizer = optim.Adam(model.parameters(),
lr=args.lr,
weight_decay=args.weight_decay)
time_meter = utils.RunningAverageMeter(0.93)
loss_meter = utils.RunningAverageMeter(0.93)
nfef_meter = utils.RunningAverageMeter(0.93)
nfeb_meter = utils.RunningAverageMeter(0.93)
def main(args):
# logger
print(args.no_display_loss)
utils.makedirs(args.save)
logger = utils.get_logger(
logpath=os.path.join(args.save, "logs"),
filepath=os.path.abspath(__file__),
displaying=~args.no_display_loss,
)
if args.layer_type == "blend":
logger.info("!! Setting time_scale from None to 1.0 for Blend layers.")
args.time_scale = 1.0
logger.info(args)
device = torch.device(
"cuda:" + str(args.gpu) if torch.cuda.is_available() else "cpu"
)
if args.use_cpu:
device = torch.device("cpu")
args.data = dataset.SCData.factory(args.dataset, args.max_dim)
args.timepoints = args.data.get_unique_times()
# Use maximum timepoint to establish integration_times
# as some timepoints may be left out for validation etc.
args.int_tps = (np.arange(max(args.timepoints) + 1) + 1.0) * args.time_scale
regularization_fns, regularization_coeffs = create_regularization_fns(args)
model = build_model_tabular(args, args.data.get_shape()[0], regularization_fns).to(
device
)
if args.use_growth:
if args.leaveout_timepoint == -1:
growth_model_path = (
"../data/externel/growth_model_v2.ckpt"
)
elif args.leaveout_timepoint in [1, 2, 3]:
assert args.max_dim == 5
growth_model_path = (
"../data/growth/model_%d"
% args.leaveout_timepoint
)
else:
print("WARNING: Cannot use growth with this timepoint")
growth_model = torch.load(growth_model_path, map_location=device)
if args.spectral_norm:
add_spectral_norm(model)
set_cnf_options(args, model)
if args.test:
state_dict = torch.load(args.save + "/checkpt.pth", map_location=device)
model.load_state_dict(state_dict["state_dict"])
# if "growth_state_dict" not in state_dict:
# print("error growth model note in save")
# growth_model = None
# else:
# checkpt = torch.load(args.save + "/checkpt.pth", map_location=device)
# growth_model.load_state_dict(checkpt["growth_state_dict"])
# TODO can we load the arguments from the save?
# eval_utils.generate_samples(
# device, args, model, growth_model, timepoint=args.leaveout_timepoint
# )
# with torch.no_grad():
# evaluate(device, args, model, growth_model)
# exit()
else:
logger.info(model)
n_param = count_parameters(model)
logger.info("Number of trainable parameters: {}".format(n_param))
train(
device,
args,
model,
growth_model,
regularization_coeffs,
regularization_fns,
logger,
)
if args.data.data.shape[1] == 2:
plot_output(device, args, model)
def main(args):
device = torch.device(
"cuda:" + str(args.gpu) if torch.cuda.is_available() else "cpu")
if args.use_cpu:
device = torch.device("cpu")
data = dataset.SCData.factory(args.dataset, args)
args.timepoints = data.get_unique_times()
# Use maximum timepoint to establish integration_times
# as some timepoints may be left out for validation etc.
args.int_tps = (np.arange(max(args.timepoints) + 1) +
1.0) * args.time_scale
regularization_fns, regularization_coeffs = create_regularization_fns(args)
model = build_model_tabular(args,
data.get_shape()[0],
regularization_fns).to(device)
if args.use_growth:
growth_model_path = data.get_growth_net_path()
#growth_model_path = "/home/atong/TrajectoryNet/data/externel/growth_model_v2.ckpt"
growth_model = torch.load(growth_model_path, map_location=device)
if args.spectral_norm:
add_spectral_norm(model)
set_cnf_options(args, model)
state_dict = torch.load(args.save + "/checkpt.pth", map_location=device)
model.load_state_dict(state_dict["state_dict"])
#plot_output(device, args, model, data)
#exit()
# get_trajectory_samples(device, model, data)
args.data = data
args.timepoints = args.data.get_unique_times()
args.int_tps = (np.arange(max(args.timepoints) + 1) +
1.0) * args.time_scale
print('integrating backwards')
#end_time_data = data.data_dict[args.embedding_name]
end_time_data = data.get_data()[args.data.get_times() == np.max(
args.data.get_times())]
#np.random.permutation(end_time_data)
#rand_idx = np.random.randint(end_time_data.shape[0], size=5000)
#end_time_data = end_time_data[rand_idx,:]
integrate_backwards(end_time_data,
model,
args.save,
ntimes=100,
device=device)
exit()
losses_list = []
#for factor in np.linspace(0.05, 0.95, 19):
#for factor in np.linspace(0.91, 0.99, 9):
if args.dataset == 'CHAFFER': # Do timepoint adjustment
print('adjusting_timepoints')
lt = args.leaveout_timepoint
if lt == 1:
factor = 0.6799872494335812
factor = 0.95
elif lt == 2:
factor = 0.2905983814032348
factor = 0.01
else:
raise RuntimeError('Unknown timepoint %d' %
args.leaveout_timepoint)
args.int_tps[lt] = (
1 - factor) * args.int_tps[lt - 1] + factor * args.int_tps[lt + 1]
losses = eval_utils.evaluate_kantorovich_v2(device, args, model)
losses_list.append(losses)
print(np.array(losses_list))
np.save(os.path.join(args.save, 'emd_list'), np.array(losses_list))
