def test_discriminator_class_determinism(self):
d = GraphDiscriminator(gi.grammar, drop_rate=0.0)
smiles = get_smiles_from_database(5)
out1 = d({'smiles': smiles})['p_zinc']
out2 = d({'smiles': smiles})['p_zinc']
diff = torch.max((out1 - out2).abs())
assert diff < 1e-6, "Function is non-deterministic"
def test_discriminator_class_batch_independence(self):
d = GraphDiscriminator(gi.grammar, drop_rate=0.0)
smiles = get_smiles_from_database(5)
out1 = d({'smiles': smiles})['p_zinc']
out2 = d({'smiles': smiles[:1]})['p_zinc']
diff = torch.max((out1[0, :] - out2[0, :]).abs())
assert diff < 1e-6, "There is cross-talk between batches"
def test_discriminator_class(self):
d = GraphDiscriminator(gi.grammar, drop_rate=0.1)
smiles = get_smiles_from_database(5)
out = d(smiles)
assert out['p_zinc'].size(0) == len(smiles)
assert out['p_zinc'].size(1) == 2
assert len(out['p_zinc'].size()) == 2
assert out['smiles'] == smiles
def train_policy_gradient(molecules=True,
grammar=True,
smiles_source='ZINC',
EPOCHS=None,
BATCH_SIZE=None,
reward_fun_on=None,
reward_fun_off=None,
max_steps=277,
lr_on=2e-4,
lr_discrim=1e-4,
lr_schedule=None,
discrim_wt=2,
p_thresh=0.5,
drop_rate=0.0,
plot_ignore_initial=0,
randomize_reward=False,
save_file_root_name=None,
reward_sm=0.0,
preload_file_root_name=None,
anchor_file=None,
anchor_weight=0.0,
decoder_type='action',
plot_prefix='',
dashboard='policy gradient',
smiles_save_file=None,
on_policy_loss_type='best',
priors=True,
node_temperature_schedule=lambda x: 1.0,
rule_temperature_schedule=lambda x: 1.0,
eps=0.0,
half_float=False,
extra_repetition_penalty=0.0,
entropy_wgt=1.0):
root_location = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
root_location = root_location + '/../../'
def full_path(x):
return os.path.realpath(root_location + 'pretrained/' + x)
zinc_data = get_smiles_from_database(source=smiles_source)
zinc_set = set(zinc_data)
lookbacks = [BATCH_SIZE, 10 * BATCH_SIZE, 100 * BATCH_SIZE]
history_data = [deque(['O'], maxlen=lb) for lb in lookbacks]
if save_file_root_name is not None:
gen_save_file = save_file_root_name + '_gen.h5'
disc_save_file = save_file_root_name + '_disc.h5'
if preload_file_root_name is not None:
gen_preload_file = preload_file_root_name + '_gen.h5'
disc_preload_file = preload_file_root_name + '_disc.h5'
settings = get_settings(molecules=molecules, grammar=grammar)
codec = get_codec(molecules, grammar, settings['max_seq_length'])
discrim_model = GraphDiscriminator(codec.grammar, drop_rate=drop_rate)
if False and preload_file_root_name is not None:
try:
preload_path = full_path(disc_preload_file)
discrim_model.load_state_dict(torch.load(preload_path),
strict=False)
print('Discriminator weights loaded successfully!')
except Exception as e:
print('failed to load discriminator weights ' + str(e))
if EPOCHS is not None:
settings['EPOCHS'] = EPOCHS
if BATCH_SIZE is not None:
settings['BATCH_SIZE'] = BATCH_SIZE
alt_reward_calc = AdjustedRewardCalculator(reward_fun_on,
zinc_set,
lookbacks,
extra_repetition_penalty,
discrim_wt,
discrim_model=None)
reward_fun = lambda x: adj_reward(discrim_wt,
discrim_model,
reward_fun_on,
zinc_set,
history_data,
extra_repetition_penalty,
x,
alt_calc=alt_reward_calc)
task = SequenceGenerationTask(molecules=molecules,
grammar=grammar,
reward_fun=reward_fun,
batch_size=BATCH_SIZE,
max_steps=max_steps,
save_dataset=None)
node_policy = SoftmaxRandomSamplePolicy(temperature=torch.tensor(1.0),
eps=eps)
rule_policy = SoftmaxRandomSamplePolicy(temperature=torch.tensor(2.0),
eps=eps)
model = get_decoder(molecules,
grammar,
z_size=settings['z_size'],
decoder_hidden_n=200,
feature_len=codec.feature_len(),
max_seq_length=max_steps,
drop_rate=drop_rate,
batch_size=BATCH_SIZE,
decoder_type=decoder_type,
reward_fun=reward_fun,
task=task,
node_policy=node_policy,
rule_policy=rule_policy,
priors=priors)[0]
if preload_file_root_name is not None:
try:
preload_path = full_path(gen_preload_file)
model.load_state_dict(torch.load(preload_path, map_location='cpu'),
strict=False)
print('Generator weights loaded successfully!')
except Exception as e:
print('failed to load generator weights ' + str(e))
anchor_model = None
# construct the loader to feed the discriminator
def make_callback(data):
def hc(inputs, model, outputs, loss_fn, loss):
graphs = outputs['graphs']
smiles = [g.to_smiles() for g in graphs]
for s in smiles: # only store unique instances of molecules so discriminator can't guess on frequency
if s not in data:
data.append(s)
return hc
class TemperatureCallback:
def __init__(self, policy, temperature_function):
self.policy = policy
self.counter = 0
self.temp_fun = temperature_function
def __call__(self, inputs, model, outputs, loss_fn, loss):
self.counter += 1
target_temp = self.temp_fun(self.counter)
self.policy.set_temperature(target_temp)
# need to have something there to begin with, else the DataLoader constructor barfs
def get_rl_fitter(model,
loss_obj,
train_gen,
save_path,
fit_plot_prefix='',
model_process_fun=None,
lr=None,
lr_schedule=lr_schedule,
extra_callbacks=[],
loss_display_cap=float('inf'),
anchor_model=None,
anchor_weight=0):
nice_params = filter(lambda p: p.requires_grad, model.parameters())
optimizer = optim.Adam(nice_params, lr=lr, eps=1e-4)
if lr_schedule is None:
lr_schedule = lambda x: 1.0
scheduler = lr_scheduler.LambdaLR(optimizer, lr_schedule)
if dashboard is not None:
metric_monitor = MetricPlotter(
plot_prefix=fit_plot_prefix,
loss_display_cap=loss_display_cap,
dashboard_name=dashboard,
plot_ignore_initial=plot_ignore_initial,
process_model_fun=model_process_fun,
smooth_weight=reward_sm,
save_location=os.path.dirname(save_path))
else:
metric_monitor = None
checkpointer = Checkpointer(valid_batches_to_checkpoint=10,
save_path=save_path,
save_always=True)
fitter = fit_rl(train_gen=train_gen,
model=model,
optimizer=optimizer,
scheduler=scheduler,
epochs=EPOCHS,
loss_fn=loss_obj,
grad_clip=5,
half_float=half_float,
anchor_model=anchor_model,
anchor_weight=anchor_weight,
callbacks=[metric_monitor, checkpointer] +
extra_callbacks)
return fitter
class GeneratorToIterable:
def __init__(self, gen):
self.gen = gen
# we assume the generator is finite
self.len = 0
for _ in gen():
self.len += 1
def __len__(self):
return self.len
def __iter__(self):
return self.gen()
def my_gen():
for _ in range(1000):
yield to_gpu(torch.zeros(BATCH_SIZE, settings['z_size']))
# the on-policy fitter
gen_extra_callbacks = [make_callback(d) for d in history_data]
if smiles_save_file is not None:
smiles_save_path = os.path.realpath(root_location + 'pretrained/' +
smiles_save_file)
gen_extra_callbacks.append(MoleculeSaver(smiles_save_path, gzip=True))
print('Saved SMILES to {}'.format(smiles_save_file))
if node_temperature_schedule is not None:
gen_extra_callbacks.append(
TemperatureCallback(node_policy, node_temperature_schedule))
if rule_temperature_schedule is not None:
gen_extra_callbacks.append(
TemperatureCallback(rule_policy, rule_temperature_schedule))
fitter1 = get_rl_fitter(
model,
PolicyGradientLoss(
on_policy_loss_type,
entropy_wgt=entropy_wgt), # last_reward_wgt=reward_sm),
GeneratorToIterable(my_gen),
full_path(gen_save_file),
plot_prefix + 'on-policy',
model_process_fun=model_process_fun,
lr=lr_on,
extra_callbacks=gen_extra_callbacks,
anchor_model=anchor_model,
anchor_weight=anchor_weight)
#
# # get existing molecule data to add training
pre_dataset = EvenlyBlendedDataset(
2 * [history_data[0]] + history_data[1:],
labels=False) # a blend of 3 time horizons
dataset = EvenlyBlendedDataset([pre_dataset, zinc_data], labels=True)
discrim_loader = DataLoader(dataset, shuffle=True, batch_size=50)
class MyLoss(nn.Module):
def __init__(self):
super().__init__()
self.celoss = nn.CrossEntropyLoss()
def forward(self, x):
# tmp = discriminator_reward_mult(x['smiles'])
# tmp2 = F.softmax(x['p_zinc'], dim=1)[:,1].detach().cpu().numpy()
# import numpy as np
# assert np.max(np.abs(tmp-tmp2)) < 1e-6
return self.celoss(x['p_zinc'].to(device),
x['dataset_index'].to(device))
fitter2 = get_rl_fitter(discrim_model,
MyLoss(),
IterableTransform(
discrim_loader, lambda x: {
'smiles': x['X'],
'dataset_index': x['dataset_index']
}),
full_path(disc_save_file),
plot_prefix + ' discriminator',
lr=lr_discrim,
model_process_fun=None)
def on_policy_gen(fitter, model):
while True:
# model.policy = SoftmaxRandomSamplePolicy()#bias=codec.grammar.get_log_frequencies())
yield next(fitter)
return model, fitter1, fitter2 #,on_policy_gen(fitter1, model)
def train_policy_gradient_ppo(molecules=True,
grammar=True,
smiles_source='ZINC',
EPOCHS=None,
BATCH_SIZE=None,
reward_fun_on=None,
reward_fun_off=None,
max_steps=277,
lr_on=2e-4,
lr_discrim=1e-4,
discrim_wt=2,
p_thresh=0.5,
drop_rate=0.0,
plot_ignore_initial=0,
randomize_reward=False,
save_file_root_name=None,
reward_sm=0.0,
preload_file_root_name=None,
anchor_file=None,
anchor_weight=0.0,
decoder_type='action',
plot_prefix='',
dashboard='policy gradient',
smiles_save_file=None,
on_policy_loss_type='best',
priors=True,
node_temperature_schedule=lambda x: 1.0,
rule_temperature_schedule=lambda x: 1.0,
eps=0.0,
half_float=False,
extra_repetition_penalty=0.0):
root_location = os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe())))
root_location = root_location + '/../../'
def full_path(x):
return os.path.realpath(root_location + 'pretrained/' + x)
if save_file_root_name is not None:
gen_save_file = save_file_root_name + '_gen.h5'
disc_save_file = save_file_root_name + '_disc.h5'
if preload_file_root_name is not None:
gen_preload_file = preload_file_root_name + '_gen.h5'
disc_preload_file = preload_file_root_name + '_disc.h5'
settings = get_settings(molecules=molecules, grammar=grammar)
codec = get_codec(molecules, grammar, settings['max_seq_length'])
discrim_model = GraphDiscriminator(codec.grammar, drop_rate=drop_rate)
if False and preload_file_root_name is not None:
try:
preload_path = full_path(disc_preload_file)
discrim_model.load_state_dict(torch.load(preload_path),
strict=False)
print('Discriminator weights loaded successfully!')
except Exception as e:
print('failed to load discriminator weights ' + str(e))
zinc_data = get_smiles_from_database(source=smiles_source)
zinc_set = set(zinc_data)
lookbacks = [BATCH_SIZE, 10 * BATCH_SIZE, 100 * BATCH_SIZE]
history_data = [deque(['O'], maxlen=lb) for lb in lookbacks]
def originality_mult(smiles_list):
out = []
for s in smiles_list:
if s in zinc_set:
out.append(0.5)
elif s in history_data[0]:
out.append(0.5)
elif s in history_data[1]:
out.append(0.70)
elif s in history_data[2]:
out.append(0.85)
else:
out.append(1.0)
return np.array(out)
def sigmoid(x):
return 1 / (1 + np.exp(-x))
def discriminator_reward_mult(smiles_list):
orig_state = discrim_model.training
discrim_model.eval()
discrim_out_logits = discrim_model(smiles_list)['p_zinc']
discrim_probs = F.softmax(discrim_out_logits, dim=1)
prob_zinc = discrim_probs[:, 1].detach().cpu().numpy()
if orig_state:
discrim_model.train()
return prob_zinc
def apply_originality_penalty(x, orig_mult):
assert x <= 1, "Reward must be no greater than 0"
if x > 0.5: # want to punish nearly-perfect scores less and less
out = math.pow(x, 1 / orig_mult)
else: # continuous join at 0.5
penalty = math.pow(0.5, 1 / orig_mult) - 0.5
out = x + penalty
out -= extra_repetition_penalty * (1 - 1 / orig_mult)
return out
def adj_reward(x):
if discrim_wt > 1e-5:
p = discriminator_reward_mult(x)
else:
p = 0
rwd = np.array(reward_fun_on(x))
orig_mult = originality_mult(x)
# we assume the reward is <=1, first term will dominate for reward <0, second for 0 < reward < 1
# reward = np.minimum(rwd/orig_mult, np.power(np.abs(rwd),1/orig_mult))
reward = np.array([
apply_originality_penalty(x, om) for x, om in zip(rwd, orig_mult)
])
out = reward + discrim_wt * p * orig_mult
return out
def adj_reward_old(x):
p = discriminator_reward_mult(x)
w = sigmoid(-(p - p_thresh) / 0.01)
if randomize_reward:
rand = np.random.uniform(size=p.shape)
w *= rand
reward = np.maximum(reward_fun_on(x), p_thresh)
weighted_reward = w * p + (1 - w) * reward
out = weighted_reward * originality_mult(x) #
return out
if EPOCHS is not None:
settings['EPOCHS'] = EPOCHS
if BATCH_SIZE is not None:
settings['BATCH_SIZE'] = BATCH_SIZE
task = SequenceGenerationTask(molecules=molecules,
grammar=grammar,
reward_fun=adj_reward,
batch_size=BATCH_SIZE,
max_steps=max_steps,
save_dataset=None)
node_policy = SoftmaxRandomSamplePolicy(temperature=torch.tensor(1.0),
eps=eps)
rule_policy = SoftmaxRandomSamplePolicy(temperature=torch.tensor(1.0),
eps=eps)
model = get_decoder(molecules,
grammar,
z_size=settings['z_size'],
decoder_hidden_n=200,
feature_len=codec.feature_len(),
max_seq_length=max_steps,
drop_rate=drop_rate,
batch_size=BATCH_SIZE,
decoder_type=decoder_type,
reward_fun=adj_reward,
task=task,
node_policy=node_policy,
rule_policy=rule_policy,
priors=priors)[0]
if preload_file_root_name is not None:
try:
preload_path = full_path(gen_preload_file)
model.load_state_dict(torch.load(preload_path, map_location='cpu'),
strict=False)
print('Generator weights loaded successfully!')
except Exception as e:
print('failed to load generator weights ' + str(e))
anchor_model = None
from generative_playground.molecules.rdkit_utils.rdkit_utils import NormalizedScorer
import numpy as np
scorer = NormalizedScorer()
if reward_fun_off is None:
reward_fun_off = reward_fun_on
# construct the loader to feed the discriminator
def make_callback(data):
def hc(inputs, model, outputs, loss_fn, loss):
graphs = outputs['graphs']
smiles = [g.to_smiles() for g in graphs]
for s in smiles: # only store unique instances of molecules so discriminator can't guess on frequency
if s not in data:
data.append(s)
return hc
class TemperatureCallback:
def __init__(self, policy, temperature_function):
self.policy = policy
self.counter = 0
self.temp_fun = temperature_function
def __call__(self, inputs, model, outputs, loss_fn, loss):
self.counter += 1
target_temp = self.temp_fun(self.counter)
self.policy.set_temperature(target_temp)
# need to have something there to begin with, else the DataLoader constructor barfs
def get_rl_fitter(model,
loss_obj,
train_gen,
save_path,
fit_plot_prefix='',
model_process_fun=None,
lr=None,
extra_callbacks=[],
loss_display_cap=float('inf'),
anchor_model=None,
anchor_weight=0):
nice_params = filter(lambda p: p.requires_grad, model.parameters())
optimizer = optim.Adam(nice_params, lr=lr, eps=1e-4)
scheduler = lr_scheduler.StepLR(optimizer, step_size=100, gamma=0.99)
if dashboard is not None:
metric_monitor = MetricPlotter(
plot_prefix=fit_plot_prefix,
loss_display_cap=loss_display_cap,
dashboard_name=dashboard,
plot_ignore_initial=plot_ignore_initial,
process_model_fun=model_process_fun,
smooth_weight=reward_sm)
else:
metric_monitor = None
checkpointer = Checkpointer(valid_batches_to_checkpoint=1,
save_path=save_path,
save_always=True)
fitter = fit_rl(train_gen=train_gen,
model=model,
optimizer=optimizer,
scheduler=scheduler,
epochs=EPOCHS,
loss_fn=loss_obj,
grad_clip=5,
half_float=half_float,
anchor_model=anchor_model,
anchor_weight=anchor_weight,
callbacks=[metric_monitor, checkpointer] +
extra_callbacks)
return fitter
def my_gen():
for _ in range(1000):
yield to_gpu(torch.zeros(BATCH_SIZE, settings['z_size']))
# the on-policy fitter
gen_extra_callbacks = [make_callback(d) for d in history_data]
if smiles_save_file is not None:
smiles_save_path = os.path.realpath(root_location + 'pretrained/' +
smiles_save_file)
gen_extra_callbacks.append(MoleculeSaver(smiles_save_path, gzip=True))
print('Saved SMILES to {}'.format(smiles_save_file))
if node_temperature_schedule is not None:
gen_extra_callbacks.append(
TemperatureCallback(node_policy, node_temperature_schedule))
if rule_temperature_schedule is not None:
gen_extra_callbacks.append(
TemperatureCallback(rule_policy, rule_temperature_schedule))
fitter1 = get_rl_fitter(
model,
PolicyGradientLoss(on_policy_loss_type), # last_reward_wgt=reward_sm),
GeneratorToIterable(my_gen),
full_path(gen_save_file),
plot_prefix + 'on-policy',
model_process_fun=model_process_fun,
lr=lr_on,
extra_callbacks=gen_extra_callbacks,
anchor_model=anchor_model,
anchor_weight=anchor_weight)
#
# # get existing molecule data to add training
pre_dataset = EvenlyBlendedDataset(
2 * [history_data[0]] + history_data[1:],
labels=False) # a blend of 3 time horizons
dataset = EvenlyBlendedDataset([pre_dataset, zinc_data], labels=True)
discrim_loader = DataLoader(dataset, shuffle=True, batch_size=50)
class MyLoss(nn.Module):
def __init__(self):
super().__init__()
self.celoss = nn.CrossEntropyLoss()
def forward(self, x):
# tmp = discriminator_reward_mult(x['smiles'])
# tmp2 = F.softmax(x['p_zinc'], dim=1)[:,1].detach().cpu().numpy()
# import numpy as np
# assert np.max(np.abs(tmp-tmp2)) < 1e-6
return self.celoss(x['p_zinc'].to(device),
x['dataset_index'].to(device))
fitter2 = get_rl_fitter(discrim_model,
MyLoss(),
IterableTransform(
discrim_loader, lambda x: {
'smiles': x['X'],
'dataset_index': x['dataset_index']
}),
full_path(disc_save_file),
plot_prefix + ' discriminator',
lr=lr_discrim,
model_process_fun=None)
def on_policy_gen(fitter, model):
while True:
# model.policy = SoftmaxRandomSamplePolicy()#bias=codec.grammar.get_log_frequencies())
yield next(fitter)
return model, fitter1, fitter2 #,on_policy_gen(fitter1, model)