def main(hparams):
if not isinstance(hparams, dict):
hparams = vars(hparams)
# print hparams to console
_print_hparams(hparams)
# start at random times (so test tube creates separate folders)
np.random.seed(random.randint(0, 1000))
time.sleep(np.random.uniform(1))
# create test-tube experiment
hparams, sess_ids, exp = create_tt_experiment(hparams)
if hparams is None:
print('Experiment exists! Aborting fit')
return
# build data generator
data_generator = build_data_generator(hparams, sess_ids)
# ####################
# ### CREATE MODEL ###
# ####################
# get all latents in list
n_datasets = len(data_generator)
print('collecting observations from data generator...', end='')
data_key = 'ae_latents'
if hparams['model_class'].find('labels') > -1:
data_key = 'labels'
latents, trial_idxs = get_latent_arrays_by_dtype(
data_generator, sess_idxs=list(range(n_datasets)), data_key=data_key)
obs_dim = latents['train'][0].shape[1]
hparams['total_train_length'] = np.sum([l.shape[0] for l in latents['train']])
# get separated by dataset as well
latents_sess = {d: None for d in range(n_datasets)}
trial_idxs_sess = {d: None for d in range(n_datasets)}
for d in range(n_datasets):
latents_sess[d], trial_idxs_sess[d] = get_latent_arrays_by_dtype(
data_generator, sess_idxs=d, data_key=data_key)
print('done')
if hparams['model_class'] == 'arhmm' or hparams['model_class'] == 'hmm':
hparams['ae_model_path'] = os.path.join(
os.path.dirname(data_generator.datasets[0].paths['ae_latents']))
hparams['ae_model_latents_file'] = data_generator.datasets[0].paths['ae_latents']
# collect model constructor inputs
if hparams['noise_type'] == 'gaussian':
if hparams['n_arhmm_lags'] > 0:
if hparams['model_class'][:5] != 'arhmm': # 'arhmm' or 'arhmm-labels'
raise ValueError('Must specify model_class as arhmm when using AR lags')
obs_type = 'ar'
else:
if hparams['model_class'][:3] != 'hmm': # 'hmm' or 'hmm-labels'
raise ValueError('Must specify model_class as hmm when using 0 AR lags')
obs_type = 'gaussian'
elif hparams['noise_type'] == 'studentst':
if hparams['n_arhmm_lags'] > 0:
if hparams['model_class'][:5] != 'arhmm': # 'arhmm' or 'arhmm-labels'
raise ValueError('Must specify model_class as arhmm when using AR lags')
obs_type = 'robust_ar'
else:
if hparams['model_class'][:3] != 'hmm': # 'hmm' or 'hmm-labels'
raise ValueError('Must specify model_class as hmm when using 0 AR lags')
obs_type = 'studentst'
else:
raise ValueError('%s is not a valid noise type' % hparams['noise_type'])
if hparams['n_arhmm_lags'] > 0:
obs_kwargs = {'lags': hparams['n_arhmm_lags']}
obs_init_kwargs = {'localize': True}
else:
obs_kwargs = None
obs_init_kwargs = {}
if hparams['kappa'] == 0:
transitions = 'stationary'
transition_kwargs = None
else:
transitions = 'sticky'
transition_kwargs = {'kappa': hparams['kappa']}
print('constructing model...', end='')
np.random.seed(hparams['rng_seed_model'])
hmm = ssm.HMM(
hparams['n_arhmm_states'], obs_dim,
observations=obs_type, observation_kwargs=obs_kwargs,
transitions=transitions, transition_kwargs=transition_kwargs)
hmm.initialize(latents['train'])
hmm.observations.initialize(latents['train'], **obs_init_kwargs)
# save out hparams as csv and dict
hparams['training_completed'] = False
export_hparams(hparams, exp)
print('done')
# ####################
# ### TRAIN MODEL ###
# ####################
# TODO: move fitting into own function
# TODO: adopt early stopping strategy from ssm
# precompute normalizers
n_datapoints = {}
n_datapoints_sess = {}
for dtype in {'train', 'val', 'test'}:
n_datapoints[dtype] = np.vstack(latents[dtype]).size
n_datapoints_sess[dtype] = {}
for d in range(n_datasets):
n_datapoints_sess[dtype][d] = np.vstack(latents_sess[d][dtype]).size
for epoch in range(hparams['n_iters'] + 1):
# Note: the 0th epoch has no training (randomly initialized model is evaluated) so we cycle
# through `n_iters` training epochs
print('epoch %03i/%03i' % (epoch, hparams['n_iters']))
if epoch > 0:
hmm.fit(latents['train'], method='em', num_iters=1, initialize=False)
# export aggregated metrics on train/val data
tr_ll = hmm.log_likelihood(latents['train']) / n_datapoints['train']
val_ll = hmm.log_likelihood(latents['val']) / n_datapoints['val']
exp.log({
'epoch': epoch, 'dataset': -1, 'tr_loss': tr_ll, 'val_loss': val_ll, 'trial': -1})
# export individual session metrics on train/val data
for d in range(data_generator.n_datasets):
tr_ll = hmm.log_likelihood(latents_sess[d]['train']) / n_datapoints_sess['train'][d]
val_ll = hmm.log_likelihood(latents_sess[d]['val']) / n_datapoints_sess['val'][d]
exp.log({
'epoch': epoch, 'dataset': d, 'tr_loss': tr_ll, 'val_loss': val_ll, 'trial': -1})
# export individual session metrics on test data
for d in range(n_datasets):
for i, b in enumerate(trial_idxs_sess[d]['test']):
n = latents_sess[d]['test'][i].size
test_ll = hmm.log_likelihood(latents_sess[d]['test'][i]) / n
exp.log({'epoch': epoch, 'dataset': d, 'test_loss': test_ll, 'trial': b})
exp.save()
# reconfigure model/states by usage
zs = [hmm.most_likely_states(x) for x in latents['train']]
usage = np.bincount(np.concatenate(zs), minlength=hmm.K)
perm = np.argsort(usage)[::-1]
hmm.permute(perm)
# save model
filepath = os.path.join(hparams['expt_dir'], 'version_%i' % exp.version, 'best_val_model.pt')
with open(filepath, 'wb') as f:
pickle.dump(hmm, f)
# ######################
# ### EVALUATE ARHMM ###
# ######################
# export states
if hparams['export_states']:
export_states(hparams, data_generator, hmm)
# export training plots
if hparams['export_train_plots']:
print('creating training plots...', end='')
version_dir = os.path.join(hparams['expt_dir'], 'version_%i' % hparams['version'])
save_file = os.path.join(version_dir, 'loss_training')
export_train_plots(hparams, 'train', loss_type='ll', save_file=save_file)
save_file = os.path.join(version_dir, 'loss_validation')
export_train_plots(hparams, 'val', loss_type='ll', save_file=save_file)
print('done')
# update hparams upon successful training
hparams['training_completed'] = True
export_hparams(hparams, exp)
# get rid of unneeded logging info
_clean_tt_dir(hparams)
def main(hparams, *args):
if not isinstance(hparams, dict):
hparams = vars(hparams)
if hparams['model_type'] == 'conv':
# blend outer hparams with architecture hparams
hparams = {**hparams['architecture_params'], **hparams}
# print hparams to console
_print_hparams(hparams)
if hparams['model_type'] == 'conv' and hparams['n_ae_latents'] > hparams[
'max_latents']:
raise ValueError(
'Number of latents higher than max latents, architecture will not work'
)
# Start at random times (so test tube creates separate folders)
np.random.seed(random.randint(0, 1000))
time.sleep(np.random.uniform(3))
# create test-tube experiment
hparams, sess_ids, exp = create_tt_experiment(hparams)
if hparams is None:
print('Experiment exists! Aborting fit')
return
# build data generator
data_generator = build_data_generator(hparams, sess_ids)
# ####################
# ### CREATE MODEL ###
# ####################
def set_n_labels(data_generator, hparams):
data, _ = data_generator.next_batch('val')
sh = data['labels'].shape
hparams['n_labels'] = sh[2] # [1, n_t, n_labels]
print('constructing model...', end='')
torch.manual_seed(hparams['rng_seed_model'])
torch_rng_seed = torch.get_rng_state()
hparams['model_build_rng_seed'] = torch_rng_seed
hparams['n_datasets'] = len(sess_ids)
if hparams['model_class'] == 'ae':
from behavenet.models import AE as Model
elif hparams['model_class'] == 'vae':
from behavenet.models import VAE as Model
elif hparams['model_class'] == 'beta-tcvae':
from behavenet.models import BetaTCVAE as Model
elif hparams['model_class'] == 'ps-vae':
from behavenet.models import PSVAE as Model
set_n_labels(data_generator, hparams)
elif hparams['model_class'] == 'msps-vae':
from behavenet.models import MSPSVAE as Model
set_n_labels(data_generator, hparams)
elif hparams['model_class'] == 'cond-vae':
from behavenet.models import ConditionalVAE as Model
set_n_labels(data_generator, hparams)
elif hparams['model_class'] == 'cond-ae':
from behavenet.models import ConditionalAE as Model
set_n_labels(data_generator, hparams)
elif hparams['model_class'] == 'cond-ae-msp':
from behavenet.models import AEMSP as Model
set_n_labels(data_generator, hparams)
else:
raise NotImplementedError(
'The model class "%s" is not currently implemented' %
hparams['model_class'])
model = Model(hparams)
model.to(hparams['device'])
# load pretrained weights if specified
model = load_pretrained_ae(model, hparams)
# Parallelize over gpus if desired
if hparams['n_parallel_gpus'] > 1:
from behavenet.models import CustomDataParallel
model = CustomDataParallel(model)
model.version = exp.version
torch_rng_seed = torch.get_rng_state()
hparams['training_rng_seed'] = torch_rng_seed
# save out hparams as csv and dict
hparams['training_completed'] = False
export_hparams(hparams, exp)
print('done')
# ###################
# ### TRAIN MODEL ###
# ###################
print(model)
fit(hparams, model, data_generator, exp, method='ae')
# update hparams upon successful training
hparams['training_completed'] = True
export_hparams(hparams, exp)
# get rid of unneeded logging info
_clean_tt_dir(hparams)
# export training plots
if hparams['export_train_plots']:
print('creating training plots...', end='')
version_dir = os.path.join(hparams['expt_dir'],
'version_%i' % hparams['version'])
if hparams['model_class'] == 'msps-vae':
from behavenet.plotting.cond_ae_utils import plot_mspsvae_training_curves
save_file = os.path.join(version_dir, 'loss_training')
plot_mspsvae_training_curves(
hparams,
alpha=hparams['ps_vae.alpha'],
beta=hparams['ps_vae.beta'],
delta=hparams['ps_vae.delta'],
rng_seed_model=hparams['rng_seed_model'],
n_latents=hparams['n_ae_latents'] - hparams['n_background'] -
hparams['n_labels'],
n_background=hparams['n_background'],
n_labels=hparams['n_labels'],
dtype='train',
save_file=save_file,
format='png',
version_dir=version_dir)
save_file = os.path.join(version_dir, 'loss_validation')
plot_mspsvae_training_curves(
hparams,
alpha=hparams['ps_vae.alpha'],
beta=hparams['ps_vae.beta'],
delta=hparams['ps_vae.delta'],
rng_seed_model=hparams['rng_seed_model'],
n_latents=hparams['n_ae_latents'] - hparams['n_background'] -
hparams['n_labels'],
n_background=hparams['n_background'],
n_labels=hparams['n_labels'],
dtype='val',
save_file=save_file,
format='png',
version_dir=version_dir)
else:
save_file = os.path.join(version_dir, 'loss_training')
export_train_plots(hparams, 'train', save_file=save_file)
save_file = os.path.join(version_dir, 'loss_validation')
export_train_plots(hparams, 'val', save_file=save_file)
print('done')
def main(hparams, *args):
if not isinstance(hparams, dict):
hparams = vars(hparams)
# print hparams to console
_print_hparams(hparams)
if hparams['model_type'] == 'conv':
# blend outer hparams with architecture hparams
hparams = {**hparams, **hparams['architecture_params']}
if hparams['model_type'] == 'conv' and hparams['n_ae_latents'] > hparams[
'max_latents']:
raise ValueError(
'Number of latents higher than max latents, architecture will not work'
)
# Start at random times (so test tube creates separate folders)
np.random.seed(random.randint(0, 1000))
time.sleep(np.random.uniform(1))
# create test-tube experiment
hparams, sess_ids, exp = create_tt_experiment(hparams)
if hparams is None:
print('Experiment exists! Aborting fit')
return
# build data generator
data_generator = build_data_generator(hparams, sess_ids)
# ####################
# ### CREATE MODEL ###
# ####################
print('constructing model...', end='')
torch.manual_seed(hparams['rng_seed_model'])
torch_rnd_seed = torch.get_rng_state()
hparams['model_build_rnd_seed'] = torch_rnd_seed
hparams['n_datasets'] = len(sess_ids)
model = AE(hparams)
model.to(hparams['device'])
model.version = exp.version
torch_rnd_seed = torch.get_rng_state()
hparams['training_rnd_seed'] = torch_rnd_seed
# save out hparams as csv and dict
hparams['training_completed'] = False
export_hparams(hparams, exp)
print('done')
# ####################
# ### TRAIN MODEL ###
# ####################
fit(hparams, model, data_generator, exp, method='ae')
# export training plots
if hparams['export_train_plots']:
print('creating training plots...', end='')
version_dir = os.path.join(hparams['expt_dir'],
'version_%i' % hparams['version'])
save_file = os.path.join(version_dir, 'loss_training')
export_train_plots(hparams, 'train', save_file=save_file)
save_file = os.path.join(version_dir, 'loss_validation')
export_train_plots(hparams, 'val', save_file=save_file)
print('done')
# update hparams upon successful training
hparams['training_completed'] = True
export_hparams(hparams, exp)
# get rid of unneeded logging info
_clean_tt_dir(hparams)
def main(hparams, *args):
if not isinstance(hparams, dict):
hparams = vars(hparams)
# print hparams to console
_print_hparams(hparams)
# Start at random times (so test tube creates separate folders)
np.random.seed(random.randint(0, 1000))
time.sleep(np.random.uniform(1))
# create test-tube experiment
hparams, sess_ids, exp = create_tt_experiment(hparams)
if hparams is None:
print('Experiment exists! Aborting fit')
return
# build data generator
data_generator = build_data_generator(hparams, sess_ids)
ex_trial = data_generator.datasets[0].batch_idxs['train'][0]
i_sig = hparams['input_signal']
o_sig = hparams['output_signal']
if hparams['model_class'] == 'neural-arhmm':
hparams['input_size'] = data_generator.datasets[0][ex_trial][
i_sig].shape[1]
hparams['output_size'] = hparams['n_arhmm_states']
elif hparams['model_class'] == 'arhmm-neural':
hparams['input_size'] = hparams['n_arhmm_states']
hparams['output_size'] = data_generator.datasets[0][ex_trial][
o_sig].shape[1]
elif hparams['model_class'] == 'neural-ae':
hparams['input_size'] = data_generator.datasets[0][ex_trial][
i_sig].shape[1]
hparams['output_size'] = hparams['n_ae_latents']
elif hparams['model_class'] == 'neural-ae-me':
hparams['input_size'] = data_generator.datasets[0][ex_trial][
i_sig].shape[1]
hparams['output_size'] = hparams['n_ae_latents']
elif hparams['model_class'] == 'ae-neural':
hparams['input_size'] = hparams['n_ae_latents']
hparams['output_size'] = data_generator.datasets[0][ex_trial][
o_sig].shape[1]
elif hparams['model_class'] == 'neural-labels':
hparams['input_size'] = data_generator.datasets[0][ex_trial][
i_sig].shape[1]
hparams['output_size'] = hparams['n_labels']
elif hparams['model_class'] == 'labels-neural':
hparams['input_size'] = hparams['n_labels']
hparams['output_size'] = data_generator.datasets[0][ex_trial][
o_sig].shape[1]
else:
raise ValueError('%s is an invalid model class' %
hparams['model_class'])
if hparams['model_class'] == 'neural-ae' or hparams['model_class'] == 'neural-ae' \
or hparams['model_class'] == 'ae-neural':
hparams['ae_model_path'] = os.path.join(
os.path.dirname(data_generator.datasets[0].paths['ae_latents']))
hparams['ae_model_latents_file'] = data_generator.datasets[0].paths[
'ae_latents']
elif hparams['model_class'] == 'neural-arhmm' or hparams[
'model_class'] == 'arhmm-neural':
hparams['arhmm_model_path'] = os.path.dirname(
data_generator.datasets[0].paths['arhmm_states'])
hparams['arhmm_model_states_file'] = data_generator.datasets[0].paths[
'arhmm_states']
# Store which AE was used for the ARHMM
tags = pickle.load(
open(os.path.join(hparams['arhmm_model_path'], 'meta_tags.pkl'),
'rb'))
hparams['ae_model_latents_file'] = tags['ae_model_latents_file']
# ####################
# ### CREATE MODEL ###
# ####################
print('constructing model...', end='')
torch.manual_seed(hparams['rng_seed_model'])
torch_rng_seed = torch.get_rng_state()
hparams['model_build_rng_seed'] = torch_rng_seed
model = Decoder(hparams)
model.to(hparams['device'])
model.version = exp.version
torch_rng_seed = torch.get_rng_state()
hparams['training_rng_seed'] = torch_rng_seed
# save out hparams as csv and dict for easy reloading
hparams['training_completed'] = False
export_hparams(hparams, exp)
print('done')
# ####################
# ### TRAIN MODEL ###
# ####################
fit(hparams, model, data_generator, exp, method='nll')
# update hparams upon successful training
hparams['training_completed'] = True
export_hparams(hparams, exp)
# get rid of unneeded logging info
_clean_tt_dir(hparams)
def main(hparams, *args):
if not isinstance(hparams, dict):
hparams = vars(hparams)
if hparams['model_type'] == 'conv':
# blend outer hparams with architecture hparams
hparams = {**hparams, **hparams['architecture_params']}
# print hparams to console
_print_hparams(hparams)
# Start at random times (so test tube creates separate folders)
np.random.seed(random.randint(0, 1000))
time.sleep(np.random.uniform(1))
# create test-tube experiment
hparams, sess_ids, exp = create_tt_experiment(hparams)
if hparams is None:
print('Experiment exists! Aborting fit')
return
# build data generator
data_generator = build_data_generator(hparams, sess_ids)
# ####################
# ### CREATE MODEL ###
# ####################
print('constructing model...', end='')
torch.manual_seed(hparams['rng_seed_model'])
torch_rnd_seed = torch.get_rng_state()
hparams['model_build_rnd_seed'] = torch_rnd_seed
hparams['n_datasets'] = len(sess_ids)
data, _ = data_generator.next_batch('train')
sh = data['labels'].shape
hparams['n_labels'] = sh[2] # [1, n_t, n_labels]
model = ConvDecoder(hparams)
model.to(hparams['device'])
# Load pretrained weights if specified
# model = load_pretrained_ae(model, hparams)
model.version = exp.version
torch_rnd_seed = torch.get_rng_state()
hparams['training_rnd_seed'] = torch_rnd_seed
# save out hparams as csv and dict
hparams['training_completed'] = False
export_hparams(hparams, exp)
print('done')
# ###################
# ### TRAIN MODEL ###
# ###################
fit(hparams, model, data_generator, exp, method='conv-decoder')
# export training plots
if hparams['export_train_plots']:
print('creating training plots...', end='')
version_dir = os.path.join(hparams['expt_dir'],
'version_%i' % hparams['version'])
save_file = os.path.join(version_dir, 'loss_training')
export_train_plots(hparams, 'train', save_file=save_file)
save_file = os.path.join(version_dir, 'loss_validation')
export_train_plots(hparams, 'val', save_file=save_file)
print('done')
# update hparams upon successful training
hparams['training_completed'] = True
export_hparams(hparams, exp)
# get rid of unneeded logging info
_clean_tt_dir(hparams)