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train_plus_transmembrane.py
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# Written by Seonwoo Min, Seoul National University (mswzeus@gmail.com)
# PLUS
import os
import sys
import argparse
import torch
import plus.config as config
from plus.data.alphabets import Protein
import plus.data.transmembrane as transmembrane
import plus.data.dataset as dataset
import plus.model.plus_rnn as plus_rnn
import plus.model.plus_tfm as plus_tfm
import plus.model.p_elmo as p_elmo
import plus.model.mlp as mlp
from plus.train import Trainer
from plus.utils import Print, set_seeds, set_output, load_models
parser = argparse.ArgumentParser('Train a Model on Transmembrane Datasets')
parser.add_argument('--data-config', help='path for data configuration file')
parser.add_argument('--model-config', help='path for model configuration file')
parser.add_argument('--lm-model-config', help='path for lm-model configuration file (for P-ELMo)')
parser.add_argument('--pr-model-config', help='path for pr-model configuration file (for P-ELMo and PLUS-RNN)')
parser.add_argument('--run-config', help='path for run configuration file')
parser.add_argument('--pretrained-model', help='path for pretrained model file')
parser.add_argument('--pretrained-lm-model', help='path for pretrained lm-model file (for P-ELMo)')
parser.add_argument('--pretrained-pr-model', help='path for pretrained pr-model file (for P-ELMo and PLUS-RNN)')
parser.add_argument('--device', help='device to use; multi-GPU if given multiple GPUs sperated by comma (default: cpu)')
parser.add_argument('--output-path', help='path for outputs (default: stdout and without saving)')
parser.add_argument('--output-index', help='prefix for outputs')
parser.add_argument('--sanity-check', default=False, action='store_true', help='sanity check flag')
def main():
set_seeds(2020)
args = vars(parser.parse_args())
alphabet = Protein()
cfgs = []
data_cfg = config.DataConfig(args["data_config"]); cfgs.append(data_cfg)
if args["lm_model_config"] is None:
model_cfg = config.ModelConfig(args["model_config"], input_dim=len(alphabet), num_classes=3)
cfgs += [model_cfg]
else:
lm_model_cfg = config.ModelConfig(args["lm_model_config"], idx="lm_model_config", input_dim=len(alphabet))
model_cfg = config.ModelConfig(args["model_config"], input_dim=len(alphabet),
lm_dim=lm_model_cfg.num_layers * lm_model_cfg.hidden_dim * 2, num_classes=3)
cfgs += [model_cfg, lm_model_cfg]
if model_cfg.model_type == "RNN":
pr_model_cfg = config.ModelConfig(args["pr_model_config"], idx="pr_model_config", model_type="MLP", num_classes=3)
if pr_model_cfg.projection: pr_model_cfg.set_input_dim(model_cfg.embedding_dim)
else: pr_model_cfg.set_input_dim(model_cfg.hidden_dim * 2)
cfgs.append(pr_model_cfg)
run_cfg = config.RunConfig(args["run_config"], sanity_check=args["sanity_check"]); cfgs.append(run_cfg)
output, save_prefix = set_output(args, "train_transmembrane_log")
os.environ['CUDA_VISIBLE_DEVICES'] = args["device"] if args["device"] is not None else ""
device, data_parallel = torch.device("cuda" if torch.cuda.is_available() else "cpu"), torch.cuda.device_count() > 1
config.print_configs(args, cfgs, device, output)
flag_rnn = (model_cfg.model_type == "RNN")
flag_lm_model = (args["lm_model_config"] is not None)
flag_lm_loss = (run_cfg.lm_loss_lambda != -1)
## load a train dataset
start = Print(" ".join(['start loading train datasets', data_cfg.path["train"]]), output)
dataset_train = transmembrane.load_transmembrane(data_cfg, "train", alphabet, args["sanity_check"])
dataset_train = dataset.Seq_dataset(*dataset_train, alphabet, run_cfg, flag_rnn, model_cfg.max_len, truncate=False)
collate_fn = dataset.collate_sequences if flag_rnn else None
iterator_train = torch.utils.data.DataLoader(dataset_train, run_cfg.batch_size_train, collate_fn=collate_fn, shuffle=True)
end = Print(" ".join(['loaded', str(len(dataset_train)), 'sequences']), output)
Print(" ".join(['elapsed time:', str(end - start)]), output, newline=True)
## load a dev dataset
start = Print(" ".join(['start loading dev datasets', data_cfg.path["dev"]]), output)
dataset_dev = transmembrane.load_transmembrane(data_cfg, "dev", alphabet, args["sanity_check"])
dataset_dev = dataset.Seq_dataset(*dataset_dev, alphabet, run_cfg, flag_rnn, model_cfg.max_len, truncate=False)
iterator_dev = torch.utils.data.DataLoader(dataset_dev, run_cfg.batch_size_eval, collate_fn=collate_fn)
end = Print(" ".join(['loaded', str(len(dataset_dev)), 'sequences']), output)
Print(" ".join(['elapsed time:', str(end - start)]), output, newline=True)
## initialize a model
start = Print('start initializing a model', output)
models_list = [] # list of lists [model, idx, flag_frz, flag_clip_grad, flag_clip_weight]
### model
if not flag_rnn: model = plus_tfm.PLUS_TFM(model_cfg)
elif not flag_lm_model: model = plus_rnn.PLUS_RNN(model_cfg)
else: model = p_elmo.P_ELMo(model_cfg)
models_list.append([model, "", flag_lm_model, flag_rnn, False])
### lm_model
if flag_lm_model:
lm_model = p_elmo.P_ELMo_lm(lm_model_cfg)
models_list.append([lm_model, "lm", True, False, False])
### pr_model
if flag_rnn:
pr_model = mlp.MLP(pr_model_cfg)
models_list.append([pr_model, "pr", False, False, False])
params, pr_params = [], []
for model, idx, frz, _, _ in models_list:
if frz: continue
elif idx != "pr": params += [p for p in model.parameters() if p.requires_grad]
else: pr_params += [p for p in model.parameters() if p.requires_grad]
load_models(args, models_list, device, data_parallel, output, tfm_cls=flag_rnn)
get_loss = plus_rnn.get_loss if flag_rnn else plus_tfm.get_loss
end = Print('end initializing a model', output)
Print("".join(['elapsed time:', str(end - start)]), output, newline=True)
## setup trainer configurations
start = Print('start setting trainer configurations', output)
optim = torch.optim.Adam([{'params':params, 'lr':run_cfg.learning_rate },
{'params':pr_params, 'lr':run_cfg.pr_learning_rate}])
tasks_list = [] # list of lists [idx, metrics_train, metrics_eval]
tasks_list.append(["cls", [], ["acc", "acc_p"]])
if flag_lm_loss: tasks_list.append(["lm", [], ["acc"]])
trainer = Trainer(models_list, get_loss, run_cfg, tasks_list, optim)
trainer_args = {}
trainer_args["data_parallel"] = data_parallel
trainer_args["paired"] = False
if flag_rnn: trainer_args["projection"] = pr_model_cfg.projection
if flag_rnn:
trainer_args["evaluate_cls"] = plus_rnn.evaluate_transmembrane
else:
trainer_args["evaluate_cls"] = plus_tfm.evaluate_cls_amino
trainer_args["evaluate"] = ["cls", plus_tfm.evaluate_transmembrane]
end = Print('end setting trainer configurations', output)
Print("".join(['elapsed time:', str(end - start)]), output, newline=True)
## train a model
start = Print('start training a model', output)
Print(trainer.get_headline(), output)
for epoch in range(run_cfg.num_epochs):
### train
dataset_train.set_augment(flag_lm_loss)
for B, batch in enumerate(iterator_train):
batch = [t.to(device) if type(t) is torch.Tensor else t for t in batch]
trainer.train(batch, trainer_args)
if B % 10 == 0: print('# epoch [{}/{}] train {:.1%} loss={:.4f}'.format(
epoch + 1, run_cfg.num_epochs, B / len(iterator_train), trainer.loss_train), end='\r', file=sys.stderr)
print(' ' * 150, end='\r', file=sys.stderr)
### evaluate cls
dataset_dev.set_augment(False)
trainer.set_exec_flags(["cls", 'lm'], [True, False])
for b, batch in enumerate(iterator_dev):
batch = [t.to(device) if type(t) is torch.Tensor else t for t in batch]
trainer.evaluate(batch, trainer_args)
if b % 10 == 0: print('# cls {:.1%} loss={:.4f}'.format(
b / len(iterator_dev), trainer.loss_eval), end='\r', file=sys.stderr)
print(' ' * 150, end='\r', file=sys.stderr)
### evaluate lm
if flag_lm_loss:
dataset_dev.set_augment(True)
trainer.set_exec_flags(["cls", 'lm'], [False, True])
for b, batch in enumerate(iterator_dev):
batch = [t.to(device) if type(t) is torch.Tensor else t for t in batch]
trainer.evaluate(batch, trainer_args)
if b % 10 == 0: print('# lm {:.1%} loss={:.4f}'.format(
b / len(iterator_dev), trainer.loss_eval), end='\r', file=sys.stderr)
print(' ' * 150, end='\r', file=sys.stderr)
### print log and save models
trainer.save(save_prefix)
Print(trainer.get_log(epoch + 1, args=trainer_args), output)
trainer.set_exec_flags(["cls", "lm"], [True, True])
trainer.reset()
if trainer.patience == 0: break
end = Print('end training a model', output)
Print("".join(['elapsed time:', str(end - start)]), output, newline=True)
if __name__ == '__main__':
main()