def main():
# Initialize arguments -- Just
args = init_argparse('pdbbind')
# Initialize file paths
args = init_file_paths(args)
# Initialize logger
init_logger(args)
# Initialize device and data type
device, dtype = init_cuda(args)
# Initialize dataloader
args, datasets, num_species, charge_scale = initialize_datasets(args, args.datadir, 'pdbbind',
force_download=args.force_download,
ignore_check=args.ignore_check
)
# Construct PyTorch dataloaders from datasets
dataloaders = {split: DataLoader(dataset,
batch_size=args.batch_size,
shuffle=args.shuffle if (split == 'train') else False,
num_workers=args.num_workers,
collate_fn=collate_fn)
for split, dataset in datasets.items()}
# Initialize model
model = CormorantPDBBind(args.maxl, args.max_sh, args.num_cg_levels, args.num_channels, num_species,
args.cutoff_type, args.hard_cut_rad, args.soft_cut_rad, args.soft_cut_width,
args.weight_init, args.level_gain, args.charge_power, args.basis_set,
charge_scale, args.gaussian_mask, args.top, args.input,
cgprod_bounded = True,
device=device, dtype=dtype)
# Initialize the scheduler and optimizer
optimizer = init_optimizer(args, model)
scheduler, restart_epochs = init_scheduler(args, optimizer)
# Define a loss function. Just use L2 loss for now.
loss_fn = torch.nn.functional.mse_loss
# Apply the covariance and permutation invariance tests.
cormorant_tests(model, dataloaders['train'], args, charge_scale=charge_scale)
# Instantiate the training class
trainer = Engine(args, dataloaders, model, loss_fn, optimizer, scheduler, restart_epochs, device, dtype, clip_value=None)
print('Initialized the trainer with clip value:',trainer.clip_value)
# Load from checkpoint file. If no checkpoint file exists, automatically does nothing.
trainer.load_checkpoint()
# Train model.
trainer.train()
# Test predictions on best model and also last checkpointed model.
trainer.evaluate()
def main():
# Initialize arguments
args = init_cormorant_argparse('lba')
# Initialize file paths
args = init_cormorant_file_paths(args)
# Initialize logger
init_logger(args)
# Initialize device and data type
device, dtype = init_cuda(args)
# Initialize dataloader
if args.format == 'npz':
args, datasets, num_species, charge_scale = initialize_datasets(args, args.datadir, 'lba', args.ddir_suffix)
else:
args, datasets, num_species, charge_scale = initialize_lba_data(args, args.datadir)
# Further differences for Siamese networks
if args.siamese:
collate_fn = collate_lba_siamese
else:
collate_fn = collate_lba
# Construct PyTorch dataloaders from datasets
dataloaders = {split: DataLoader(dataset, batch_size=args.batch_size,
shuffle=args.shuffle if (split == 'train') else False,
num_workers=args.num_workers, collate_fn=collate_fn)
for split, dataset in datasets.items()}
# Initialize model
if args.siamese:
model = ENN_LBA_Siamese(args.maxl, args.max_sh, args.num_cg_levels, args.num_channels, num_species,
args.cutoff_type, args.hard_cut_rad, args.soft_cut_rad, args.soft_cut_width,
args.weight_init, args.level_gain, args.charge_power, args.basis_set,
charge_scale, args.gaussian_mask,
device=device, dtype=dtype)
else:
model = ENN_LBA(args.maxl, args.max_sh, args.num_cg_levels, args.num_channels, num_species,
args.cutoff_type, args.hard_cut_rad, args.soft_cut_rad, args.soft_cut_width,
args.weight_init, args.level_gain, args.charge_power, args.basis_set,
charge_scale, args.gaussian_mask,
device=device, dtype=dtype)
# Initialize the scheduler and optimizer
optimizer = init_optimizer(args, model)
scheduler, restart_epochs = init_scheduler(args, optimizer)
# Define a loss function. Just use L2 loss for now.
loss_fn = torch.nn.functional.mse_loss
# Apply the covariance and permutation invariance tests.
cormorant_tests(model, dataloaders['train'], args, charge_scale=charge_scale, siamese = args.siamese)
# Instantiate the training class
trainer = Engine(args, dataloaders, model, loss_fn, optimizer, scheduler, restart_epochs, device, dtype, clip_value=None)
# Load from checkpoint file. If no checkpoint file exists, automatically does nothing.
trainer.load_checkpoint()
# Train model.
trainer.train()
# Test predictions on best model and also last checkpointed model.
trainer.evaluate()
def main():
# Initialize arguments -- Just
args = init_argparse('qm9')
# Initialize file paths
args = init_file_paths(args)
# Initialize logger
init_logger(args)
# Initialize device and data type
device, dtype = init_cuda(args)
# Initialize dataloader
args, datasets, num_species, charge_scale = initialize_datasets(
args,
args.datadir,
'qm9',
subtract_thermo=args.subtract_thermo,
force_download=args.force_download)
# unit conversion (U0, U, G, H are not converted when loaded from our or the MoleculeNet data because the identifiers differ)
qm9_to_eV = {
'U0': 27.2114,
'U': 27.2114,
'G': 27.2114,
'H': 27.2114,
'zpve': 27211.4,
'gap': 27.2114,
'h**o': 27.2114,
'lumo': 27.2114
}
for dataset in datasets.values():
dataset.convert_units(qm9_to_eV)
# Construct PyTorch dataloaders from datasets
dataloaders = {
split: DataLoader(dataset,
batch_size=args.batch_size,
shuffle=args.shuffle if
(split == 'train') else False,
num_workers=args.num_workers,
collate_fn=collate_fn)
for split, dataset in datasets.items()
}
# Initialize model
model = CormorantQM9(args.maxl,
args.max_sh,
args.num_cg_levels,
args.num_channels,
num_species,
args.cutoff_type,
args.hard_cut_rad,
args.soft_cut_rad,
args.soft_cut_width,
args.weight_init,
args.level_gain,
args.charge_power,
args.basis_set,
charge_scale,
args.gaussian_mask,
args.top,
args.input,
args.num_mpnn_levels,
device=device,
dtype=dtype)
# Initialize the scheduler and optimizer
optimizer = init_optimizer(args, model)
scheduler, restart_epochs = init_scheduler(args, optimizer)
# Define a loss function. Just use L2 loss for now.
loss_fn = torch.nn.functional.mse_loss
# Apply the covariance and permutation invariance tests.
cormorant_tests(model,
dataloaders['train'],
args,
charge_scale=charge_scale)
# Instantiate the training class
trainer = Engine(args, dataloaders, model, loss_fn, optimizer, scheduler,
restart_epochs, device, dtype)
# Load from checkpoint file. If no checkpoint file exists, automatically does nothing.
trainer.load_checkpoint()
# Train model.
trainer.train()
# Test predictions on best model and also last checkpointed model.
trainer.evaluate()
def main():
# Initialize arguments
args = init_cormorant_argparse('res')
# Initialize file paths
args = init_cormorant_file_paths(args)
# Initialize logger
init_logger(args)
# Initialize device and data type
device, dtype = init_cuda(args)
# Initialize dataloader
args, datasets, num_species, charge_scale = initialize_datasets(
args, args.datadir, 'res', args.ddir_suffix)
# Construct PyTorch dataloaders from datasets
dataloaders = {
split: DataLoader(dataset,
batch_size=args.batch_size,
shuffle=args.shuffle if
(split == 'train') else False,
num_workers=args.num_workers,
collate_fn=collate_fn)
for split, dataset in datasets.items()
}
# Initialize model
model = ENN_RES(args.maxl,
args.max_sh,
args.num_cg_levels,
args.num_channels,
num_species,
args.cutoff_type,
args.hard_cut_rad,
args.soft_cut_rad,
args.soft_cut_width,
args.weight_init,
args.level_gain,
args.charge_power,
args.basis_set,
charge_scale,
args.gaussian_mask,
args.top,
args.input,
args.num_mpnn_levels,
num_classes=20,
cgprod_bounded=False,
cg_agg_normalization='relu',
cg_pow_normalization='relu',
device=device,
dtype=dtype)
# Initialize the scheduler and optimizer
optimizer = init_optimizer(args, model)
scheduler, restart_epochs = init_scheduler(args, optimizer)
# Define cross-entropy as the loss function.
loss_fn = torch.nn.functional.cross_entropy
# Apply the covariance and permutation invariance tests.
cormorant_tests(model,
dataloaders['train'],
args,
charge_scale=charge_scale)
# Instantiate the training class
trainer = Engine(args,
dataloaders,
model,
loss_fn,
optimizer,
scheduler,
restart_epochs,
device,
dtype,
task='classification',
clip_value=None)
print('Initialized a', trainer.task, 'trainer.')
# Load from checkpoint file. If no checkpoint file exists, automatically does nothing.
trainer.load_checkpoint()
# Train model.
trainer.train()
# Test predictions on best model and also last checkpointed model.
trainer.evaluate()
def main():
# Initialize arguments
args = init_cormorant_argparse('msp')
# Initialize file paths
args = init_cormorant_file_paths(args)
# Initialize logger
init_logger(args)
# Initialize device and data type
device, dtype = init_cuda(args)
# Initialize dataloader # Use initialize_msp_data to load LMDB directly (needs much more memory)
if args.format.lower().startswith('lmdb'):
init = initialize_msp_data(args, args.datadir)
else:
init = initialize_datasets(args, args.datadir, 'msp', args.ddir_suffix)
args, datasets, num_species, charge_scale = init
# Construct PyTorch dataloaders from datasets
dataloaders = {
split: DataLoader(dataset,
batch_size=args.batch_size,
shuffle=args.shuffle if
(split == 'train') else False,
num_workers=args.num_workers,
collate_fn=collate_msp)
for split, dataset in datasets.items()
}
# Initialize model
model = ENN_MSP(args.maxl,
args.max_sh,
args.num_cg_levels,
args.num_channels,
num_species,
args.cutoff_type,
args.hard_cut_rad,
args.soft_cut_rad,
args.soft_cut_width,
args.weight_init,
args.level_gain,
args.charge_power,
args.basis_set,
charge_scale,
args.gaussian_mask,
num_classes=args.num_classes,
device=device,
dtype=dtype)
# Initialize the scheduler and optimizer
optimizer = init_optimizer(args, model)
scheduler, restart_epochs = init_scheduler(args, optimizer)
# Define cross-entropy as the loss function.
loss_fn = torch.nn.functional.cross_entropy
gc.collect()
# Apply the covariance and permutation invariance tests.
cormorant_tests(model,
dataloaders['train'],
args,
charge_scale=charge_scale,
siamese=True)
# Instantiate the training class
trainer = Engine(args,
dataloaders,
model,
loss_fn,
optimizer,
scheduler,
restart_epochs,
device,
dtype,
task='classification',
clip_value=None)
print('Initialized a', trainer.task, 'trainer.')
# Load from checkpoint file. If no checkpoint file exists, automatically does nothing.
trainer.load_checkpoint()
# Train model.
trainer.train()
# Test predictions on best model and also last checkpointed model.
trainer.evaluate()
from cormorant.data.utils import initialize_datasets
from cormorant.data.collate import collate_fn
import logging
logging.basicConfig(level=logging.INFO)
datasets, num_species, max_charge = initialize_datasets('/tmp/test', 'qm9')
train = datasets['train']
batch = [train[i] for i in [5, 123, 5436, 43132]]
batch_coll = collate_fn(batch)
breakpoint()