main.py

import argparse
import os
import shutil
import sys
import time
import warnings
from random import sample
import csv

import numpy as np
import torch
import torch.nn as nn
import torch.optim as optim
from sklearn import metrics
from torch.autograd import Variable
from torch.optim.lr_scheduler import MultiStepLR

from cgcnn.data import CIFData
from cgcnn.data import collate_pool, get_train_val_test_loader
from cgcnn.model import CrystalGraphConvNet

parser = argparse.ArgumentParser(
    description='Crystal Graph Convolutional Neural Networks')
parser.add_argument('data_options', metavar='OPTIONS', nargs='+',
                    help='dataset options, started with the path to root dir, '
                         'then other options')
parser.add_argument('--task', choices=['regression', 'classification'],
                    default='regression', help='complete a regression or '
                    'classification task (default: regression)')
parser.add_argument('--disable-cuda', action='store_true',
                    help='Disable CUDA')
parser.add_argument('-j', '--workers', default=0, type=int, metavar='N',
                    help='number of data loading workers (default: 0)')
parser.add_argument('--epochs', default=30, type=int, metavar='N',
                    help='number of total epochs to run (default: 30)')
parser.add_argument('--start-epoch', default=0, type=int, metavar='N',
                    help='manual epoch number (useful on restarts)')
parser.add_argument('-b', '--batch-size', default=256, type=int,
                    metavar='N', help='mini-batch size (default: 256)')
parser.add_argument('--lr', '--learning-rate', default=0.01, type=float,
                    metavar='LR', help='initial learning rate (default: '
                                       '0.01)')
parser.add_argument('--lr-milestones', default=[100], nargs='+', type=int,
                    metavar='N', help='milestones for scheduler (default: '
                                      '[100])')
parser.add_argument('--momentum', default=0.9, type=float, metavar='M',
                    help='momentum')
parser.add_argument('--weight-decay', '--wd', default=0, type=float,
                    metavar='W', help='weight decay (default: 0)')
parser.add_argument('--print-freq', '-p', default=10, type=int,
                    metavar='N', help='print frequency (default: 10)')
parser.add_argument('--resume', default='', type=str, metavar='PATH',
                    help='path to latest checkpoint (default: none)')
train_group = parser.add_mutually_exclusive_group()
train_group.add_argument('--train-ratio', default=None, type=float, metavar='N',
                         help='number of training data to be loaded (default none)')
train_group.add_argument('--train-size', default=None, type=int, metavar='N',
                         help='number of training data to be loaded (default none)')
valid_group = parser.add_mutually_exclusive_group()
valid_group.add_argument('--val-ratio', default=0.1, type=float, metavar='N',
                         help='percentage of validation data to be loaded (default '
                         '0.1)')
valid_group.add_argument('--val-size', default=None, type=int, metavar='N',
                         help='number of validation data to be loaded (default '
                              '1000)')
test_group = parser.add_mutually_exclusive_group()
test_group.add_argument('--test-ratio', default=0.1, type=float, metavar='N',
                        help='percentage of test data to be loaded (default 0.1)')
test_group.add_argument('--test-size', default=None, type=int, metavar='N',
                        help='number of test data to be loaded (default 1000)')

parser.add_argument('--optim', default='SGD', type=str, metavar='SGD',
                    help='choose an optimizer, SGD or Adam, (default: SGD)')
parser.add_argument('--atom-fea-len', default=64, type=int, metavar='N',
                    help='number of hidden atom features in conv layers')
parser.add_argument('--h-fea-len', default=128, type=int, metavar='N',
                    help='number of hidden features after pooling')
parser.add_argument('--n-conv', default=3, type=int, metavar='N',
                    help='number of conv layers')
parser.add_argument('--n-h', default=1, type=int, metavar='N',
                    help='number of hidden layers after pooling')
parser.add_argument('--disable-save-torch', action='store_true',
                    help='Do not save CIF PyTorch data as .json files')
parser.add_argument('--clean-torch', action='store_true',
                    help='Clean CIF PyTorch data .json files')

args = parser.parse_args(sys.argv[1:])

args.cuda = not args.disable_cuda and torch.cuda.is_available()

if args.task == 'regression':
    best_mae_error = 1e10
else:
    best_mae_error = 0.


def main():
    global args, best_mae_error

    # load data
    dataset = CIFData(*args.data_options,
                      disable_save_torch=args.disable_save_torch)
    collate_fn = collate_pool
    train_loader, val_loader, test_loader = get_train_val_test_loader(
        dataset=dataset,
        collate_fn=collate_fn,
        batch_size=args.batch_size,
        train_ratio=args.train_ratio,
        num_workers=args.workers,
        val_ratio=args.val_ratio,
        test_ratio=args.test_ratio,
        pin_memory=args.cuda,
        train_size=args.train_size,
        val_size=args.val_size,
        test_size=args.test_size,
        return_test=True)

    # Make sure >1 class is present
    if args.task == 'classification':
        total_train = 0
        total_val = 0
        total_test = 0
        for i, (_, target, _) in enumerate(train_loader):
            for target_i in target.squeeze():
                total_train += target_i
        if bool(total_train == 0):
            raise ValueError('All 0s in train')
        elif bool(total_train == 1):
            raise ValueError('All 1s in train')
        for i, (_, target, _) in enumerate(val_loader):
            if len(target) == 1:
                raise ValueError('Only single entry in val')
            for target_i in target.squeeze():
                total_val += target_i
        if bool(total_val == 0):
            raise ValueError('All 0s in val')
        elif bool(total_val == 1):
            raise ValueError('All 1s in val')
        for i, (_, target, _) in enumerate(test_loader):
            if len(target) == 1:
                raise ValueError('Only single entry in test')
            for target_i in target.squeeze():
                total_test += target_i
        if bool(total_test == 0):
            raise ValueError('All 0s in test')
        elif bool(total_test == 1):
            raise ValueError('All 1s in test')

    # make output folder if needed
    if not os.path.exists('output'):
        os.mkdir('output')

    # make and clean torch files if needed
    torch_data_path = os.path.join(args.data_options[0], 'cifdata')
    if args.clean_torch and os.path.exists(torch_data_path):
        shutil.rmtree(torch_data_path)
    if os.path.exists(torch_data_path):
        if not args.clean_torch:
            warnings.warn('Found cifdata folder at ' +
                          torch_data_path+'. Will read in .jsons as-available')
    else:
        os.mkdir(torch_data_path)

    # obtain target value normalizer
    if args.task == 'classification':
        normalizer = Normalizer(torch.zeros(2))
        normalizer.load_state_dict({'mean': 0., 'std': 1.})
    else:
        if len(dataset) < 500:
            warnings.warn('Dataset has less than 500 data points. '
                          'Lower accuracy is expected. ')
            sample_data_list = [dataset[i] for i in range(len(dataset))]
        else:
            sample_data_list = [dataset[i] for i in
                                sample(range(len(dataset)), 500)]
        _, sample_target, _ = collate_pool(sample_data_list)
        normalizer = Normalizer(sample_target)

    # build model
    structures, _, _ = dataset[0]
    orig_atom_fea_len = structures[0].shape[-1]
    nbr_fea_len = structures[1].shape[-1]
    model = CrystalGraphConvNet(orig_atom_fea_len, nbr_fea_len,
                                atom_fea_len=args.atom_fea_len,
                                n_conv=args.n_conv,
                                h_fea_len=args.h_fea_len,
                                n_h=args.n_h,
                                classification=True if args.task ==
                                'classification' else False)
    if args.cuda:
        model.cuda()

    # define loss func and optimizer
    if args.task == 'classification':
        criterion = nn.NLLLoss()
    else:
        criterion = nn.MSELoss()
    if args.optim == 'SGD':
        optimizer = optim.SGD(model.parameters(), args.lr,
                              momentum=args.momentum,
                              weight_decay=args.weight_decay)
    elif args.optim == 'Adam':
        optimizer = optim.Adam(model.parameters(), args.lr,
                               weight_decay=args.weight_decay)
    else:
        raise NameError('Only SGD or Adam is allowed as --optim')

    # optionally resume from a checkpoint
    if args.resume:
        if os.path.isfile(args.resume):
            print("=> loading checkpoint '{}'".format(args.resume))
            checkpoint = torch.load(args.resume)
            args.start_epoch = checkpoint['epoch']
            best_mae_error = checkpoint['best_mae_error']
            model.load_state_dict(checkpoint['state_dict'])
            optimizer.load_state_dict(checkpoint['optimizer'])
            normalizer.load_state_dict(checkpoint['normalizer'])
            print("=> loaded checkpoint '{}' (epoch {})"
                  .format(args.resume, checkpoint['epoch']))
        else:
            print("=> no checkpoint found at '{}'".format(args.resume))

    scheduler = MultiStepLR(optimizer, milestones=args.lr_milestones,
                            gamma=0.1)

    for epoch in range(args.start_epoch, args.epochs):
        # train for one epoch
        train(train_loader, model, criterion, optimizer, epoch, normalizer)

        # evaluate on validation set
        mae_error = validate(val_loader, model, criterion, normalizer)

        if mae_error != mae_error:
            print('Exit due to NaN')
            sys.exit(1)

        scheduler.step()

        # remember the best mae_eror and save checkpoint
        if args.task == 'regression':
            is_best = mae_error < best_mae_error
            best_mae_error = min(mae_error, best_mae_error)
        else:
            is_best = mae_error > best_mae_error
            best_mae_error = max(mae_error, best_mae_error)
        save_checkpoint({
            'epoch': epoch + 1,
            'state_dict': model.state_dict(),
            'best_mae_error': best_mae_error,
            'optimizer': optimizer.state_dict(),
            'normalizer': normalizer.state_dict(),
            'args': vars(args)
        }, is_best)

    # test best model
    best_checkpoint = torch.load(os.path.join('output', 'model_best.pth.tar'))
    model.load_state_dict(best_checkpoint['state_dict'])
    print('---------Evaluate Best Model on Train Set---------------')
    validate(train_loader, model, criterion, normalizer, test=True,
             csv_name='train_results.csv')
    print('---------Evaluate Best Model on Val Set---------------')
    validate(val_loader, model, criterion, normalizer, test=True,
             csv_name='val_results.csv')
    print('---------Evaluate Best Model on Test Set---------------')
    validate(test_loader, model, criterion, normalizer, test=True,
             csv_name='test_results.csv')


def train(train_loader, model, criterion, optimizer, epoch, normalizer):
    batch_time = AverageMeter()
    data_time = AverageMeter()
    losses = AverageMeter()
    if args.task == 'regression':
        mae_errors = AverageMeter()
    else:
        accuracies = AverageMeter()
        precisions = AverageMeter()
        recalls = AverageMeter()
        fscores = AverageMeter()
        auc_scores = AverageMeter()

    # switch to train mode
    model.train()

    end = time.time()
    for i, (input_, target, _) in enumerate(train_loader):
        # measure data loading time
        data_time.update(time.time() - end)

        if args.cuda:
            input_var = (tensor.to("cuda") for tensor in input_)
        else:
            input_var = input_

        # normalize target
        if args.task == 'regression':
            target_normed = normalizer.norm(target)
        else:
            target_normed = target.view(-1).long()
        if args.cuda:
            target_var = Variable(target_normed.cuda(non_blocking=True))
        else:
            target_var = Variable(target_normed)

        # compute output
        output = model(*input_var)
        loss = criterion(output, target_var)

        # measure accuracy and record loss
        if args.task == 'regression':
            mae_error = mae(normalizer.denorm(output.data.cpu()), target)
            losses.update(loss.data.cpu(), target.size(0))
            mae_errors.update(mae_error, target.size(0))
        else:
            accuracy, precision, recall, fscore, auc_score = \
                class_eval(output.data.cpu(), target)
            losses.update(loss.data.cpu().item(), target.size(0))
            accuracies.update(accuracy, target.size(0))
            precisions.update(precision, target.size(0))
            recalls.update(recall, target.size(0))
            fscores.update(fscore, target.size(0))
            auc_scores.update(auc_score, target.size(0))

        # compute gradient and do SGD step
        optimizer.zero_grad()
        loss.backward()
        optimizer.step()

        # measure elapsed time
        batch_time.update(time.time() - end)
        end = time.time()

        if i % args.print_freq == 0:
            if args.task == 'regression':
                print('Epoch: [{0}][{1}/{2}]\t'
                      'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
                      'Data {data_time.val:.3f} ({data_time.avg:.3f})\t'
                      'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
                      'MAE {mae_errors.val:.3f} ({mae_errors.avg:.3f})'.format(
                          epoch+1, i+1, len(train_loader), batch_time=batch_time,
                          data_time=data_time, loss=losses, mae_errors=mae_errors)
                      )
            else:
                print('Epoch: [{0}][{1}/{2}]\t'
                      'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
                      'Data {data_time.val:.3f} ({data_time.avg:.3f})\t'
                      'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
                      'Accu {accu.val:.3f} ({accu.avg:.3f})\t'
                      'Precision {prec.val:.3f} ({prec.avg:.3f})\t'
                      'Recall {recall.val:.3f} ({recall.avg:.3f})\t'
                      'F1 {f1.val:.3f} ({f1.avg:.3f})\t'
                      'AUC {auc.val:.3f} ({auc.avg:.3f})'.format(
                          epoch+1, i+1, len(train_loader), batch_time=batch_time,
                          data_time=data_time, loss=losses, accu=accuracies,
                          prec=precisions, recall=recalls, f1=fscores,
                          auc=auc_scores)
                      )


def validate(val_loader, model, criterion, normalizer, test=False, csv_name='test_results.csv'):
    batch_time = AverageMeter()
    losses = AverageMeter()
    if args.task == 'regression':
        mae_errors = AverageMeter()
    else:
        accuracies = AverageMeter()
        precisions = AverageMeter()
        recalls = AverageMeter()
        fscores = AverageMeter()
        auc_scores = AverageMeter()
    if test:
        test_targets = []
        test_preds = []
        test_cif_ids = []

    # switch to evaluate mode
    model.eval()

    end = time.time()
    for i, (input_, target, batch_cif_ids) in enumerate(val_loader):
        if args.cuda:
            with torch.no_grad():
                input_var = (tensor.to("cuda") for tensor in input_)
        else:
            with torch.no_grad():
                input_var = input_
        if args.task == 'regression':
            target_normed = normalizer.norm(target)
        else:
            target_normed = target.view(-1).long()
        if args.cuda:
            with torch.no_grad():
                target_var = Variable(target_normed.cuda(non_blocking=True))
        else:
            with torch.no_grad():
                target_var = Variable(target_normed)

        # compute output
        output = model(*input_var)
        loss = criterion(output, target_var)

        # measure accuracy and record loss
        if args.task == 'regression':
            mae_error = mae(normalizer.denorm(output.data.cpu()), target)
            losses.update(loss.data.cpu().item(), target.size(0))
            mae_errors.update(mae_error, target.size(0))
            if test:
                test_pred = normalizer.denorm(output.data.cpu())
                test_target = target
                test_preds += test_pred.view(-1).tolist()
                test_targets += test_target.view(-1).tolist()
                test_cif_ids += batch_cif_ids
        else:
            accuracy, precision, recall, fscore, auc_score = \
                class_eval(output.data.cpu(), target)
            losses.update(loss.data.cpu().item(), target.size(0))
            accuracies.update(accuracy, target.size(0))
            precisions.update(precision, target.size(0))
            recalls.update(recall, target.size(0))
            fscores.update(fscore, target.size(0))
            auc_scores.update(auc_score, target.size(0))
            if test:
                test_pred = torch.exp(output.data.cpu())
                test_target = target
                assert test_pred.shape[1] == 2
                test_preds += test_pred[:, 1].tolist()
                test_targets += test_target.view(-1).tolist()
                test_cif_ids += batch_cif_ids

        # measure elapsed time
        batch_time.update(time.time() - end)
        end = time.time()

        if test:
            print_name = 'Test'
        else:
            print_name = 'Validation'

        if i % args.print_freq == 0:
            if args.task == 'regression':
                print(print_name+': [{0}/{1}]\t'
                      'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
                      'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
                      'MAE {mae_errors.val:.3f} ({mae_errors.avg:.3f})'.format(
                          i+1, len(val_loader), batch_time=batch_time, loss=losses,
                          mae_errors=mae_errors))
            else:
                print(print_name+': [{0}/{1}]\t'
                      'Time {batch_time.val:.3f} ({batch_time.avg:.3f})\t'
                      'Loss {loss.val:.4f} ({loss.avg:.4f})\t'
                      'Accu {accu.val:.3f} ({accu.avg:.3f})\t'
                      'Precision {prec.val:.3f} ({prec.avg:.3f})\t'
                      'Recall {recall.val:.3f} ({recall.avg:.3f})\t'
                      'F1 {f1.val:.3f} ({f1.avg:.3f})\t'
                      'AUC {auc.val:.3f} ({auc.avg:.3f})'.format(
                          i+1, len(val_loader), batch_time=batch_time, loss=losses,
                          accu=accuracies, prec=precisions, recall=recalls,
                          f1=fscores, auc=auc_scores))

    if test:
        star_label = '**'
        with open(os.path.join('output', csv_name), 'w') as f:
            writer = csv.writer(f)
            for cif_id, target, pred in zip(test_cif_ids, test_targets,
                                            test_preds):
                writer.writerow((cif_id, target, pred))
    else:
        star_label = '*'
    if args.task == 'regression':
        print(' {star} MAE {mae_errors.avg:.3f}'.format(star=star_label,
                                                        mae_errors=mae_errors))
        return mae_errors.avg
    else:
        print(' {star} AUC {auc.avg:.3f}'.format(star=star_label,
                                                 auc=auc_scores))
        return auc_scores.avg


class Normalizer(object):
    """Normalize a Tensor and restore it later. """

    def __init__(self, tensor):
        """tensor is taken as a sample to calculate the mean and std"""
        self.mean = torch.mean(tensor)
        self.std = torch.std(tensor)

    def norm(self, tensor):
        return (tensor - self.mean) / self.std

    def denorm(self, normed_tensor):
        return normed_tensor * self.std + self.mean

    def state_dict(self):
        return {'mean': self.mean,
                'std': self.std}

    def load_state_dict(self, state_dict):
        self.mean = state_dict['mean']
        self.std = state_dict['std']


def mae(prediction, target):
    """
    Computes the mean absolute error between prediction and target

    Parameters
    ----------

    prediction: torch.Tensor (N, 1)
    target: torch.Tensor (N, 1)
    """
    return torch.mean(torch.abs(target - prediction))


def class_eval(prediction, target):
    prediction = np.exp(prediction.numpy())
    target = target.numpy()
    pred_label = np.argmax(prediction, axis=1)
    target_label = np.squeeze(target)
    if not target_label.shape:
        target_label = np.asarray([target_label])
    if prediction.shape[1] == 2:
        precision, recall, fscore, _ = metrics.precision_recall_fscore_support(
            target_label, pred_label, average='binary')
        auc_score = metrics.roc_auc_score(target_label, prediction[:, 1])
        accuracy = metrics.accuracy_score(target_label, pred_label)
    else:
        raise NotImplementedError
    return accuracy, precision, recall, fscore, auc_score


class AverageMeter(object):
    """Computes and stores the average and current value"""

    def __init__(self):
        self.reset()

    def reset(self):
        self.val = 0
        self.avg = 0
        self.sum = 0
        self.count = 0

    def update(self, val, n=1):
        self.val = val
        self.sum += val * n
        self.count += n
        self.avg = self.sum / self.count


def save_checkpoint(state, is_best, filename=os.path.join('output', 'checkpoint.pth.tar')):
    torch.save(state, filename)
    if is_best:
        shutil.copyfile(filename, os.path.join('output', 'model_best.pth.tar'))


def adjust_learning_rate(optimizer, epoch, k):
    """Sets the learning rate to the initial LR decayed by 10 every k epochs"""
    assert type(k) is int
    lr = args.lr * (0.1 ** (epoch // k))
    for param_group in optimizer.param_groups:
        param_group['lr'] = lr


if __name__ == '__main__':
    main()