Spektral 示例代码记录

第一个版本

# 用来测试系统好坏, 以及数据集格式
from spektral.datasets import Citation
import numpy as np
import pickle as pkl
import networkx as nx
import scipy.sparse as sp
from scipy.sparse.linalg.eigen.arpack import eigsh
import sys


def parse_index_file(filename):
    """Parse index file."""
    index = []
    for line in open(filename):
        index.append(int(line.strip()))
    return index


def sample_mask(idx, l):
    """Create mask."""
    mask = np.zeros(l)
    mask[idx] = 1
    return np.array(mask, dtype=np.bool)


def load_data(dataset_str):
    """
    Loads input data from gcn/data directory
    ind.dataset_str.x => the feature vectors of the training instances as scipy.sparse.csr.csr_matrix object;
    ind.dataset_str.tx => the feature vectors of the test instances as scipy.sparse.csr.csr_matrix object;
    ind.dataset_str.allx => the feature vectors of both labeled and unlabeled training instances
        (a superset of ind.dataset_str.x) as scipy.sparse.csr.csr_matrix object;
    ind.dataset_str.y => the one-hot labels of the labeled training instances as numpy.ndarray object;
    ind.dataset_str.ty => the one-hot labels of the test instances as numpy.ndarray object;
    ind.dataset_str.ally => the labels for instances in ind.dataset_str.allx as numpy.ndarray object;
    ind.dataset_str.graph => a dict in the format {index: [index_of_neighbor_nodes]} as collections.defaultdict
        object;
    ind.dataset_str.test.index => the indices of test instances in graph, for the inductive setting as list object.
    All objects above must be saved using python pickle module.
    :param dataset_str: Dataset name
    :return: All data input files loaded (as well the training/test data).
    """
    names = ['x', 'y', 'tx', 'ty', 'allx', 'ally', 'graph']
    objects = []
    for i in range(len(names)):
        with open("/home/stone/.spektral/datasets/Citation/cora/ind.{}.{}".format(dataset_str, names[i]), 'rb') as f:
            if sys.version_info > (3, 0):
                objects.append(pkl.load(f, encoding='latin1'))
            else:
                objects.append(pkl.load(f))

    x, y, tx, ty, allx, ally, graph = tuple(objects)
    test_idx_reorder = parse_index_file("/home/stone/.spektral/datasets/Citation/cora/ind.{}.test.index".format(dataset_str))
    test_idx_range = np.sort(test_idx_reorder)

    if dataset_str == 'citeseer':
        # Fix citeseer dataset (there are some isolated nodes in the graph)
        # Find isolated nodes, add them as zero-vecs into the right position
        test_idx_range_full = range(min(test_idx_reorder), max(test_idx_reorder)+1)
        tx_extended = sp.lil_matrix((len(test_idx_range_full), x.shape[1]))
        tx_extended[test_idx_range-min(test_idx_range), :] = tx
        tx = tx_extended
        ty_extended = np.zeros((len(test_idx_range_full), y.shape[1]))
        ty_extended[test_idx_range-min(test_idx_range), :] = ty
        ty = ty_extended

    features = sp.vstack((allx, tx)).tolil()
    features[test_idx_reorder, :] = features[test_idx_range, :]
    adj = nx.adjacency_matrix(nx.from_dict_of_lists(graph))

    labels = np.vstack((ally, ty))
    labels[test_idx_reorder, :] = labels[test_idx_range, :]

    idx_test = test_idx_range.tolist()
    idx_train = range(len(y))
    idx_val = range(len(y), len(y)+500)

    train_mask = sample_mask(idx_train, labels.shape[0])
    val_mask = sample_mask(idx_val, labels.shape[0])
    test_mask = sample_mask(idx_test, labels.shape[0])

    y_train = np.zeros(labels.shape)
    y_val = np.zeros(labels.shape)
    y_test = np.zeros(labels.shape)
    y_train[train_mask, :] = labels[train_mask, :]
    y_val[val_mask, :] = labels[val_mask, :]
    y_test[test_mask, :] = labels[test_mask, :]

    return adj, features, labels, train_mask, val_mask, test_mask


def sparse_to_tuple(sparse_mx):
    """Convert sparse matrix to tuple representation."""
    def to_tuple(mx):
        if not sp.isspmatrix_coo(mx):
            mx = mx.tocoo()
        coords = np.vstack((mx.row, mx.col)).transpose()
        values = mx.data
        shape = mx.shape
        return coords, values, shape

    if isinstance(sparse_mx, list):
        for i in range(len(sparse_mx)):
            sparse_mx[i] = to_tuple(sparse_mx[i])
    else:
        sparse_mx = to_tuple(sparse_mx)

    return sparse_mx


def preprocess_features(features):
    """Row-normalize feature matrix and convert to tuple representation"""
    rowsum = np.array(features.sum(1))
    r_inv = np.power(rowsum, -1).flatten()
    r_inv[np.isinf(r_inv)] = 0.
    r_mat_inv = sp.diags(r_inv)
    features = r_mat_inv.dot(features)
    return sparse_to_tuple(features)


def normalize_adj(adj):
    """Symmetrically normalize adjacency matrix."""
    adj = sp.coo_matrix(adj)
    rowsum = np.array(adj.sum(1))
    d_inv_sqrt = np.power(rowsum, -0.5).flatten()
    d_inv_sqrt[np.isinf(d_inv_sqrt)] = 0.
    d_mat_inv_sqrt = sp.diags(d_inv_sqrt)
    return adj.dot(d_mat_inv_sqrt).transpose().dot(d_mat_inv_sqrt).tocoo()


def preprocess_adj(adj):
    """Preprocessing of adjacency matrix for simple GCN model and conversion to tuple representation."""
    adj_normalized = normalize_adj(adj + sp.eye(adj.shape[0]))
    return sparse_to_tuple(adj_normalized)


def construct_feed_dict(features, support, labels, labels_mask, placeholders):
    """Construct feed dictionary."""
    feed_dict = dict()
    feed_dict.update({placeholders['labels']: labels})
    feed_dict.update({placeholders['labels_mask']: labels_mask})
    feed_dict.update({placeholders['features']: features})
    feed_dict.update({placeholders['support'][i]: support[i] for i in range(len(support))})
    feed_dict.update({placeholders['num_features_nonzero']: features[1].shape})
    return feed_dict


def chebyshev_polynomials(adj, k):
    """Calculate Chebyshev polynomials up to order k. Return a list of sparse matrices (tuple representation)."""
    print("Calculating Chebyshev polynomials up to order {}...".format(k))

    adj_normalized = normalize_adj(adj)
    laplacian = sp.eye(adj.shape[0]) - adj_normalized
    largest_eigval, _ = eigsh(laplacian, 1, which='LM')
    scaled_laplacian = (2. / largest_eigval[0]) * laplacian - sp.eye(adj.shape[0])

    t_k = list()
    t_k.append(sp.eye(adj.shape[0]))
    t_k.append(scaled_laplacian)

    def chebyshev_recurrence(t_k_minus_one, t_k_minus_two, scaled_lap):
        s_lap = sp.csr_matrix(scaled_lap, copy=True)
        return 2 * s_lap.dot(t_k_minus_one) - t_k_minus_two

    for i in range(2, k+1):
        t_k.append(chebyshev_recurrence(t_k[-1], t_k[-2], scaled_laplacian))

    return sparse_to_tuple(t_k)

A, X, y, train_mask, val_mask, test_mask = load_data('cora')


N = A.shape[0] # A 为形状为 (N, N) 的网络邻接矩阵
F = X.shape[-1] # X 为形状为 (N, F) 的节点特征
n_classes = y.shape[-1] # y 表示形状为 (N, n_classes) 的标签
print(n_classes)
# print(A, X, y, train_mask, val_mask, test_mask,sep="\n--------------\n")

from spektral.layers import GCNConv
from tensorflow.keras.models import Model
from tensorflow.keras.layers import Input, Dropout

A = GCNConv.preprocess(A).astype('f4') # 预处理邻接矩阵
print("\n-----------\n",A)
X_in = Input(shape=(F, )) # X 节点特征
A_in = Input((N, ), sparse=True) # 邻接矩阵

X_1 = GCNConv(16, 'relu')([X_in, A_in]) # 图卷积
X_1 = Dropout(0.5)(X_1)
X_2 = GCNConv(n_classes, 'softmax')([X_1, A_in]) # 分类

model = Model(inputs=[X_in, A_in], outputs=X_2)



model.compile(optimizer='adam', # 梯度下降
              loss='categorical_crossentropy', # 分类的常用损失函数
              weighted_metrics=['acc']) # 打印准确率

model.summary() # 显示当前网络的结构

# Prepare data
X = X.toarray()
A = A.astype('f4')
validation_data = ([X, A], y, val_mask)
# Train model
model.fit([X, A], y,
          epochs=200,
          sample_weight=train_mask,
          validation_data=validation_data,
          batch_size=N,
          shuffle=False)

# Evaluate model
eval_results = model.evaluate([X, A],
                              y,
                              sample_weight=test_mask,
                              batch_size=N)

print(eval_results)

第二个版本

需要import的库

import numpy as np
import tensorflow as tf
from tensorflow.keras.callbacks import EarlyStopping
from tensorflow.keras.losses import CategoricalCrossentropy
from tensorflow.keras.optimizers import Adam

from spektral.data.loaders import SingleLoader
from spektral.datasets.citation import Citation
from spektral.layers import GCNConv
from spektral.models.gcn import GCN
from spektral.transforms import AdjToSpTensor, LayerPreprocess

参数设定

learning_rate = 1e-2
seed = 0
epochs = 200
patience = 10
data = "cora"
tf.random.set_seed(seed=seed)  # make weight initialization reproducible
#随机种子

Load data

dataset = Citation(
    data, normalize_x=True, transforms=[LayerPreprocess(GCNConv), AdjToSpTensor()]
)
#AdjToSpTensor()把邻接矩阵变成稀疏量
#LayerPreprocess将卷基层的预处理用于邻接矩阵

We convert the binary masks to sample weights so that we can compute the average loss over the nodes (following original implementation by Kipf & Welling)

def mask_to_weights(mask):
    return mask.astype(np.float32) / np.count_nonzero(mask)

#############################
weights_tr, weights_va, weights_te = (
    mask_to_weights(mask)
    for mask in (dataset.mask_tr, dataset.mask_va, dataset.mask_te)
)
##weight和mask都是2708  
#n_node_feature 1433
#n_label 7
#n_nodes 2708
#该数据集共2708个样本点,1433维

model = GCN(n_labels=dataset.n_labels, n_input_channels=dataset.n_node_features)
model.compile(
    optimizer=Adam(learning_rate),
    loss=CategoricalCrossentropy(reduction="sum"),
    weighted_metrics=["acc"],
)

def __init__(
        self,
        n_labels,
        channels=16,
        activation="relu",
        output_activation="softmax",
        use_bias=False,
        dropout_rate=0.5,
        l2_reg=2.5e-4,
        n_input_channels=None,
        **kwargs,
    ):
     - `n_labels`: number of channels in output;
    - `channels`: number of channels in first GCNConv layer;
    - `activation`: activation of the first GCNConv layer;
    - `output_activation`: activation of the second GCNConv layer;
    - `use_bias`: whether to add a learnable bias to the two GCNConv layers;
    - `dropout_rate`: `rate` used in `Dropout` layers;
    - `l2_reg`: l2 regularization strength;
    - `n_input_channels`: number of input channels, required for tf 2.1;
    - `**kwargs`: passed to `Model.__init__`.

Train model

loader_tr = SingleLoader(dataset, sample_weights=weights_tr)
loader_va = SingleLoader(dataset, sample_weights=weights_va)
model.fit(
    loader_tr.load(),
    steps_per_epoch=loader_tr.steps_per_epoch,   #1
    validation_data=loader_va.load(),
# def load(self):
#        output = self.collate(self.dataset)
#        return tf.data.Dataset.from_tensors(output).repeat(self.epochs)
    validation_steps=loader_va.steps_per_epoch,  #1
    epochs=epochs, 
    callbacks=[EarlyStopping(patience=patience, restore_best_weights=True)],
)

Evaluate model

print("Evaluating model.")
loader_te = SingleLoader(dataset, sample_weights=weights_te)
eval_results = model.evaluate(loader_te.load(), steps=loader_te.steps_per_epoch)
print("Done.\n" "Test loss: {}\n" "Test accuracy: {}".format(*eval_results))

完整代码

"""
This example implements the experiments on citation networks from the paper:

Semi-Supervised Classification with Graph Convolutional Networks (https://arxiv.org/abs/1609.02907)
Thomas N. Kipf, Max Welling
"""
import numpy as np
import tensorflow as tf
from tensorflow.keras.callbacks import EarlyStopping
from tensorflow.keras.losses import CategoricalCrossentropy
from tensorflow.keras.optimizers import Adam

from spektral.data.loaders import SingleLoader
from spektral.datasets.citation import Citation
from spektral.layers import GCNConv
from spektral.models.gcn import GCN
from spektral.transforms import AdjToSpTensor, LayerPreprocess

learning_rate = 1e-2
seed = 0
epochs = 200
patience = 10
data = "cora"

tf.random.set_seed(seed=seed)  # make weight initialization reproducible

# Load data
dataset = Citation(
    data, normalize_x=True, transforms=[LayerPreprocess(GCNConv), AdjToSpTensor()]
)


# We convert the binary masks to sample weights so that we can compute the
# average loss over the nodes (following original implementation by
# Kipf & Welling)
def mask_to_weights(mask):
    return mask.astype(np.float32) / np.count_nonzero(mask)


weights_tr, weights_va, weights_te = (
    mask_to_weights(mask)
    for mask in (dataset.mask_tr, dataset.mask_va, dataset.mask_te)
)

model = GCN(n_labels=dataset.n_labels, n_input_channels=dataset.n_node_features)
model.compile(
    optimizer=Adam(learning_rate),
    loss=CategoricalCrossentropy(reduction="sum"),
    weighted_metrics=["acc"],
)

# Train model
loader_tr = SingleLoader(dataset, sample_weights=weights_tr)
loader_va = SingleLoader(dataset, sample_weights=weights_va)
model.fit(
    loader_tr.load(),
    steps_per_epoch=loader_tr.steps_per_epoch,
    validation_data=loader_va.load(),
    validation_steps=loader_va.steps_per_epoch,
    epochs=epochs,
    callbacks=[EarlyStopping(patience=patience, restore_best_weights=True)],
)

# Evaluate model
print("Evaluating model.")
loader_te = SingleLoader(dataset, sample_weights=weights_te)
eval_results = model.evaluate(loader_te.load(), steps=loader_te.steps_per_epoch)
print("Done.\n" "Test loss: {}\n" "Test accuracy: {}".format(*eval_results))