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def test_qm9():
adj, nf, ef, labels = qm9.load_data('numpy', amount=1000)
correctly_padded(adj, nf, ef)
assert adj.shape[0] == labels.shape[0]
# Test that it doesn't crash
qm9.load_data('networkx', amount=1000)
qm9.load_data('sdf', amount=1000)
def test_qm9():
adj, nf, ef, labels = qm9.load_data('numpy', amount=1000)
correctly_padded(adj, nf, ef)
assert adj.shape[0] == labels.shape[0]
# Test that it doesn't crash
qm9.load_data('networkx', amount=1000)
qm9.load_data('sdf', amount=1000)
import matplotlib.pyplot as plt
import numpy as np
from keras.callbacks import EarlyStopping
from keras.layers import Input, Dense
from keras.models import Model
from keras.optimizers import Adam
from sklearn.model_selection import train_test_split
from spektral.datasets import qm9
from spektral.layers import EdgeConditionedConv, GlobalAvgPool
from spektral.utils import label_to_one_hot
# Load data
A, X, E, y = qm9.load_data(return_type='numpy',
nf_keys='atomic_num',
ef_keys='type',
self_loops=True,
amount=1000) # Set to None to train on whole dataset
y = y[['cv']].values # Heat capacity at 298.15K
# Preprocessing
uniq_X = np.unique(X)
uniq_X = uniq_X[uniq_X != 0]
X = label_to_one_hot(X, uniq_X)
uniq_E = np.unique(E)
uniq_E = uniq_E[uniq_E != 0]
E = label_to_one_hot(E, uniq_E)
# Parameters
N = X.shape[-2] # Number of nodes in the graphs
import tensorflow as tf
from keras.layers import Input, Dense
from keras.models import Model
from keras.optimizers import Adam
from sklearn.model_selection import train_test_split
from spektral.datasets import qm9
from spektral.layers import GlobalAvgPool, EdgeConditionedConv
from spektral.utils import Batch, batch_iterator
from spektral.utils import label_to_one_hot
np.random.seed(0)
SW_KEY = 'dense_1_sample_weights:0' # Keras automatically creates a placeholder for sample weights, which must be fed
# Load data
A, X, E, y = qm9.load_data(return_type='numpy',
nf_keys='atomic_num',
ef_keys='type',
self_loops=True,
auto_pad=False,
amount=1000) # Set to None to train on whole dataset
y = y[['cv']].values # Heat capacity at 298.15K
# Preprocessing
uniq_X = np.unique([v for x in X for v in np.unique(x)])
X = [label_to_one_hot(x, uniq_X) for x in X]
uniq_E = np.unique([v for e in E for v in np.unique(e)])
uniq_E = uniq_E[uniq_E != 0]
E = [label_to_one_hot(e, uniq_E) for e in E]
# Parameters
F = X[0].shape[-1] # Dimension of node features
],
'methods': [],
'classes': []
},
{
'page': 'datasets/delaunay.md',
'functions': [
datasets.delaunay.generate_data
],
'methods': [],
'classes': []
},
{
'page': 'datasets/qm9.md',
'functions': [
datasets.qm9.load_data
],
'methods': [],
'classes': []
},
{
'page': 'datasets/mnist.md',
'functions': [
datasets.mnist.load_data
],
'methods': [],
'classes': []
},
{
'page': 'brain.md',
'functions': [
brain.get_fc_graphs