cgcnn_main.py

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

import numpy as np
import pandas as pd
import math
from sklearn import metrics
from sklearn.model_selection import KFold
import torch
import torch.nn as nn
import torch.optim as optim
from torch.autograd import Variable
from torch.optim.lr_scheduler import MultiStepLR
from torch.utils.data.dataloader import default_collate
from torch.utils.data.sampler import SubsetRandomSampler
from torch.utils.data import Dataset, DataLoader

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

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('--demo', default=0, type=int,
                    help='Quick demo mode, 1000 samples')
parser.add_argument('--hybrid', default=0, type=int,
                    help='Hybrid training mode')
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)')
parser.add_argument('--data-size', default=None, type=int, metavar='N',
                    help='number of data to be loaded (default none)')
parser.add_argument('--train-size', default=None, type=int, metavar='N',
                    help='number of training data to be loaded (default none)')
parser.add_argument('--val-size', default=0, type=int, metavar='N',
                    help='number of validation data to be loaded (default '
                    '1000)')
parser.add_argument('--test-size', default=1000, 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('--validation', default=None, type=str, metavar='validation', 
                    help='choose cross validation')
parser.add_argument('-k', default=10, type=int, metavar='N',
                    help='k fold validation')

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 cgcnn():
    global args, best_mae_error
    try:
        remove_checkpoint()
    except:
        pass
    root_dir = args.data_options[0]
    id_prop_file = os.path.join(root_dir, 'id_prop.csv')
    if args.demo == 1:
        sample_number = 1000
        args.epochs = 2
    else:
        sample_number = len(pd.read_csv(id_prop_file))
    if args.data_size:
        assert args.data_size <= sample_number, 'Not that many samples!'
        sample_number = args.data_size
    collate_fn = collate_pool

    if not args.validation:
        # load data
        dataset = CIFData(*args.data_options, sample_number=sample_number, random_seed=123)
        train_loader, val_loader, test_loader = get_train_val_test_loader(
            dataset=dataset, collate_fn=collate_fn, batch_size=args.batch_size,
            train_size=args.train_size, num_workers=args.workers,
            val_size=args.val_size, test_size=args.test_size,
            pin_memory=args.cuda, return_test=True)
        build_model(dataset, collate_fn, train_loader, val_loader, test_loader)
    elif args.validation == 'cv':
        cv(args.k, sample_number, collate_fn)
    elif args.validation == 'fcv':
        fcv(args.k, sample_number, collate_fn)
    elif args.validation == 'holdout':
        dataset = CIFData(*args.data_options, sample_number=sample_number, random_seed=None)
        train_loader, val_loader, test_loader = get_train_val_test_loader(
            dataset=dataset, collate_fn=collate_fn, batch_size=args.batch_size,
            train_size=1000, num_workers=args.workers,
            val_size=args.val_size, test_size=100,
            pin_memory=args.cuda, return_test=True)
        build_model(dataset, collate_fn, train_loader, val_loader, test_loader)

        # dataset = CIFData(*args.data_options, sample_number=sample_number, random_seed=123)
        # train_loader, val_loader, test_loader = get_train_val_test_loader(
        #     dataset=dataset, collate_fn=collate_fn, batch_size=args.batch_size,
        #     train_size=2000, num_workers=args.workers,
        #     val_size=100, test_size=100,
        #     pin_memory=args.cuda, return_test=True)
        # build_model(dataset, collate_fn, train_loader, val_loader, test_loader)
    elif args.validation == 'iecv':
        cv(5, sample_number, collate_fn)
        result = pd.read_csv('cgcnn_result.csv', names=['prediction', 'target'])
        cv_result = evaluation_plot(result.target, result.prediction)

        fcv(100, sample_number, collate_fn, lite=True)
        result = pd.read_csv('cgcnn_result.csv', names=['prediction', 'target'])
        fcv_result = evaluation_plot(result.target, result.prediction)

        print(cv_result[0])
        print(fcv_result[0])
        alpha = 0.5
        beta = 1 - alpha
        print(math.sqrt(alpha * cv_result[0]**2 + beta * fcv_result[0]**2))
        
def cv(k, sample_number, collate_fn):
    global args, best_mae_error
    seed = 7
    dataset = CIFData(*args.data_options, sample_number=sample_number, random_seed=seed)

    np.random.seed(seed)
    kfold = KFold(n_splits=k, shuffle=True, random_state=seed)

    for i, (train_indices, test_indices) in enumerate(kfold.split(X = np.zeros((sample_number, 1)))):
        train_sampler = SubsetRandomSampler(train_indices)
        val_sampler = SubsetRandomSampler(list())
        test_sampler = SubsetRandomSampler(test_indices)
        train_loader = DataLoader(dataset, batch_size=args.batch_size,
                                sampler=train_sampler,
                                num_workers=args.workers,
                                collate_fn=collate_fn, pin_memory=False)
        val_loader = DataLoader(dataset, batch_size=args.batch_size,
                                sampler=val_sampler,
                                num_workers=args.workers,
                                collate_fn=collate_fn, pin_memory=False)
        test_loader = DataLoader(dataset, batch_size=args.batch_size,
                                sampler=test_sampler,
                                num_workers=args.workers,
                                collate_fn=collate_fn, pin_memory=False)

        print('{} of {} fold \r'.format(i+1, k))
        build_model(dataset, collate_fn, train_loader, val_loader, test_loader)

def fcv(k, sample_number, collate_fn, lite=False):
    global args, best_mae_error

    # k step forward validation
    minimum_ratio=0.1
    maximum_ratio=1 - 1 / k
    fold_sample_number = math.floor(sample_number / k)
    minimum_sample_number = round(minimum_ratio * sample_number)
    maxmum_sample_number = round(maximum_ratio * sample_number)
    dataset = CIFData(*args.data_options, sample_number=sample_number, random_seed=None)

    for i, split in enumerate(range(fold_sample_number, sample_number, fold_sample_number if not lite else fold_sample_number*10)):
        if split < minimum_sample_number:
            continue
        if split > maxmum_sample_number:
            break
        
        print("Training end in %s out of %s \r" % (split, sample_number))

        total_size = len(dataset)
        indices = list(range(total_size))
        train_sampler = SubsetRandomSampler(indices[:split])
        val_sampler = SubsetRandomSampler(list())
        test_sampler = SubsetRandomSampler(indices[split:split+fold_sample_number])

        train_loader = DataLoader(dataset, batch_size=args.batch_size,
                                sampler=train_sampler,
                                num_workers=args.workers,
                                collate_fn=collate_fn, pin_memory=False)
        val_loader = DataLoader(dataset, batch_size=args.batch_size,
                                sampler=val_sampler,
                                num_workers=args.workers,
                                collate_fn=collate_fn, pin_memory=False)
        test_loader = DataLoader(dataset, batch_size=args.batch_size,
                                sampler=test_sampler,
                                num_workers=args.workers,
                                collate_fn=collate_fn, pin_memory=False)

        build_model(dataset, collate_fn, train_loader, val_loader, test_loader)

def build_model(dataset, collate_fn, train_loader, val_loader, test_loader):
    global args, best_mae_error

    # 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
        reg_sched = 0.2
        reg_sched_epoch = math.floor(args.epochs * reg_sched)

        if not args.hybrid or epoch <= reg_sched_epoch:
            train(train_loader, model, criterion, optimizer, epoch, normalizer, l1_reg=False)
        else:
            train(train_loader, model, criterion, optimizer, epoch, normalizer, l1_reg=True)

        # 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
    print('---------Evaluate Model on Test Set---------------')
    if not args.validation and args.val_size > 0:
        try:
            best_checkpoint = torch.load('model_best.pth.tar')
            model.load_state_dict(best_checkpoint['state_dict'])
        except:
            print('No pre trained model')
    validate(test_loader, model, criterion, normalizer, test=True, file_name='{}_{}'.format(args.k, args.validation) if args.validation else 'test')
    
    # remove_checkpoint()

def train(train_loader, model, criterion, optimizer, epoch, normalizer, l1_reg=False):
    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 = (Variable(input[0].cuda(async=True)),
                         Variable(input[1].cuda(async=True)),
                         input[2].cuda(async=True),
                         [crys_idx.cuda(async=True) for crys_idx in input[3]])
        else:
            input_var = (Variable(input[0]),
                         Variable(input[1]),
                         input[2],
                         input[3])
        # 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(async=True))
        else:
            target_var = Variable(target_normed)

        # compute output
        output = model(*input_var)
        if not l1_reg:
            loss = criterion(output, target_var)
        else:
            l1_regularization = torch.Tensor(0)
            for param in model.parameters():
                l1_regularization += torch.norm(param, 1)
            loss = criterion(output, target_var) + l1_regularization

        # measure accuracy and record loss
        if args.task == 'regression':
            mae_error = mae(normalizer.denorm(output.data.cpu()), target)
            losses.update(criterion(output, target_var).item(), 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()[0], 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, i, 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, i, 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, file_name=''):
    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 = (Variable(input[0].cuda(async=True)),
                            Variable(input[1].cuda(async=True)),
                            input[2].cuda(async=True),
                            [crys_idx.cuda(async=True) for crys_idx in input[3]])
        else:
            with torch.no_grad():
                input_var = (Variable(input[0]),
                            Variable(input[1]),
                            input[2],
                            input[3])
        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(async=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.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()[0], 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 i % args.print_freq == 0:
            if args.task == 'regression':
                print('Test: [{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, len(val_loader), batch_time=batch_time, loss=losses,
                       mae_errors=mae_errors))
            else:
                print('Test: [{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, len(val_loader), batch_time=batch_time, loss=losses,
                       accu=accuracies, prec=precisions, recall=recalls,
                       f1=fscores, auc=auc_scores))

    if test:
        star_label = '**'
        import csv
        # with open('mae_{}.csv'.format(file_name), 'a') as f:
        #     writer = csv.writer(f)
        #     writer.writerow(['{mae_errors.avg:.4f}'.format(mae_errors=mae_errors)])
        if os.path.exists('cgcnn_result.csv'):
            os.remove('cgcnn_result.csv')
        with open('cgcnn_result.csv', 'a') 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))
        result = pd.read_csv('cgcnn_result.csv', names=['prediction', 'target'])
        evaluation_plot(result.target, result.prediction)
    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 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='checkpoint.pth.tar'):
    torch.save(state, filename)
    if is_best:
        shutil.copyfile(filename, 'model_best.pth.tar')

def remove_checkpoint():
    os.remove('checkpoint.pth.tar')
    os.remove('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

def evaluation_plot(y, cv_prediction):
    y = np.array(y).ravel()
    cv_prediction = np.array(cv_prediction).ravel()
    
    cv_prediction = np.nan_to_num(cv_prediction)
    
    mae = metrics.mean_absolute_error(y, cv_prediction)
    r2 = metrics.r2_score(y, cv_prediction)
    rmse = math.sqrt(metrics.mean_squared_error(y, cv_prediction))
    return mae, rmse, r2

if __name__ == '__main__':
    cgcnn()