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test_progsnn_atlas.py
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from argparse import ArgumentParser
import datetime
import os
import numpy as np
from tqdm import tqdm
import torch
import torch.utils.data
from torch import nn
from torch.nn import functional as F
import pickle
import pytorch_lightning as pl
from pytorch_lightning.loggers import WandbLogger
from pytorch_lightning.callbacks.early_stopping import EarlyStopping
from pytorch_lightning.loggers import TensorBoardLogger
from pathlib import Path
from models.gsae_model import GSAE
from models.progsnn import ProGSNN_ATLAS
from torch_geometric.loader import DataLoader
from torchvision import transforms
from deshaw_processing.de_shaw_Dataset import DEShaw, Scattering
if __name__ == '__main__':
parser = ArgumentParser()
parser.add_argument('--dataset', default='deshaw', type=str)
parser.add_argument('--input_dim', default=None, type=int)
parser.add_argument('--latent_dim', default=64, type=int)
parser.add_argument('--hidden_dim', default=256, type=int)
parser.add_argument('--embedding_dim', default=128, type=int)
parser.add_argument('--lr', default=0.001, type=float)
parser.add_argument('--alpha', default=2, type=float)
parser.add_argument('--beta', default=0.0005, type=float)
parser.add_argument('--beta_loss', default=0.5, type=float)
parser.add_argument('--gamma', default=0.0005, type=float)
parser.add_argument('--n_epochs', default=40, type=int)
parser.add_argument('--len_epoch', default=None)
parser.add_argument('--probs', default=0.2)
parser.add_argument('--nhead', default=1)
parser.add_argument('--layers', default=1)
parser.add_argument('--task', default='reg')
parser.add_argument('--batch_size', default=64, type=int)
parser.add_argument('--n_gpus', default=1, type=int)
parser.add_argument('--save_dir', default='train_logs/', type=str)
parser.add_argument('--residue_num', default=None, type=int)
parser.add_argument('--protein', default=None, type=str)
# add args from trainer
# parser = pl.Trainer.add_argparse_args(parser)
# parse params
args = parser.parse_args()
#55 residues
if args.protein == '1bx7':
#Change to analyis of 1bgf_A_protein
with open('1bx7_A_analysis/graphsrog_new.pkl', 'rb') as file:
full_dataset = pickle.load(file)
#46 residues
if args.protein == '1ab1':
with open('1ab1_A_analysis(1)/graphsrog.pkl', 'rb') as file:
full_dataset = pickle.load(file)
#60 residues
if args.protein == '1bxy':
with open('1bxy_A_analysis/graphsrog_new.pkl', 'rb') as file:
full_dataset = pickle.load(file)
if args.protein == '1ptq':
with open('1ptq_A_analysis/graphsrog_new.pkl', 'rb') as file:
full_dataset = pickle.load(file)
if args.protein == '1fd3':
with open('1fd3_A_analysis/graphsrog.pkl', 'rb') as file:
full_dataset = pickle.load(file)
# for data in full_dataset:
# y = float(data.y)
# data.y = y
train_size = int(0.8 * len(full_dataset))
val_size = len(full_dataset) - train_size
train_set, val_set = torch.utils.data.random_split(full_dataset, [train_size, val_size])
train_loader = DataLoader(train_set, batch_size=args.batch_size,
shuffle=False, num_workers=15)
# valid loader
valid_loader = DataLoader(val_set, batch_size=args.batch_size,
shuffle=False, num_workers=15)
full_loader = DataLoader(full_dataset,
batch_size=args.batch_size,
shuffle=False,
num_workers=15)
# logger
now = datetime.datetime.now()
date_suffix = now.strftime("%Y-%m-%d-%M")
save_dir = args.save_dir + 'progsnn_logs_run_{}_{}/'.format(args.dataset,date_suffix)
if not os.path.exists(save_dir):
os.makedirs(save_dir)
wandb_logger = WandbLogger(name='run_progsnn',
project='progsnn',
log_model=True,
save_dir=save_dir)
wandb_logger.log_hyperparams(args)
wandb_logger.experiment.log({"logging timestamp":date_suffix})
# print(train_loader)
# print([item for item in full_dataset])
# early stopping
early_stop_callback = EarlyStopping(
monitor='val_loss',
min_delta=0.00,
patience=5,
verbose=True,
mode='min'
)
# args.input_dim = train_set[0].x.shape[-1]
args.input_dim = 3
# print(train_set[0].x.shape[-1])
# print(full_dataset[0][0].shape)
args.prot_graph_size = max(
[item.edge_index.shape[1] for item in full_dataset])
print(args.prot_graph_size)
# import pdb; pdb.set_trace()
args.len_epoch = len(train_loader)
args.residue_num = full_dataset[0].x.shape[0]
# init module
model = ProGSNN_ATLAS(args)
# # most basic trainer, uses good defaults
# trainer = pl.Trainer(
# max_epochs=args.n_epochs,
# #gpus=args.n_gpus,
# callbacks=[early_stop_callback],
# logger = wandb_logger
# )
# trainer.fit(model=model,
# train_dataloaders=train_loader,
# val_dataloaders=valid_loader,
# )
#test model
trained_weights = torch.load('train_logs/progsnn_logs_run_atlas_2024-08-20-49/model_atlas_1ptq.npy')
model.load_state_dict(trained_weights)
model = model.eval()
attention_maps_col = []
attention_maps_row = []
# import pdb; pdb.set_trace()
# get test set prediction
times = np.array([data.time for data in full_dataset])
test_latent = []
latent_embeddings = []
coords_recon_lst = []
with torch.no_grad():
for x in tqdm(full_loader):
print("Looping through test set..")
y_hat, z_rep, _, _, _, att_map_row,coords_recon, _, _ = model(x)
# import pdb; pdb.set_trace()
# attention_maps_col.append(att_map_col)
# attention_maps_row.append(att_map_row)
coords_recon_lst.append(coords_recon)
test_latent.append(y_hat)
latent_embeddings.append(z_rep)
print(test_latent)
test_predictions = torch.cat(test_latent, dim=0)
# print("Saving attention maps..")
# with open(f'attention_maps_{args.protein}.pkl', 'wb') as file:
# pickle.dump(attention_maps_row, file)
print("Saving latent embeddings..")
with open(f'latent_embeddings{args.protein}_notime.pkl', 'wb') as file:
pickle.dump(latent_embeddings, file)
print("Saving times..")
with open(f'times_{args.protein}_notime.pkl', 'wb') as file:
pickle.dump(times, file)
# print("Saving coordinates..")
# with open(f'coords_{args.protein}_notime.pkl', 'wb') as file:
# pickle.dump(coords_recon_lst, file)