Keras版GCN源码解析

        直接上代码:

        后面会在这份源码的基础上做实验;

        TensorFlow版的GCN源码也看过了,但是看不太懂,欢迎交流GCN相关内容。

1 setup.py

from setuptools import setup
from setuptools import find_packages

setup(name='kegra',           # 生成的包名称
      version='0.0.1',        # 版本号
      description='Deep Learning on Graphs with Keras',           # 包的简要描述
      author='Thomas Kipf',         # 包的作者
      author_email='thomas.kipf@gmail.com',           # 包作者的邮箱地址
      url='https://tkipf.github.io',            # 程序的官网地址
      download_url='...',           # 程序的下载地址
      license='MIT',          # 程序的授权信息
      install_requires=['keras'],         # 需要安装的依赖包
      extras_require={        # 额外用于模型存储的依赖包
          'model_saving': ['json', 'h5py'],
      },
      package_data={'kegra': ['README.md']},
      # fine_packages()函数默认在和setup.py同一目录下搜索各个含有__init__.py的包
      packages=find_packages())

2 utils.py

# 如果某个版本中出现了某个新的功能特性,而且这个特性和当前版本中使用的不兼容,
# 也就是说它在当前版本中不是语言标准,那么我们如果想要使用的话就要从__future__模块导入
from __future__ import print_function       # print()函数

import scipy.sparse as sp       # python中稀疏矩阵相关库
import numpy as np      # python中操作数组的函数
from scipy.sparse.linalg.eigen.arpack import eigsh, ArpackNoConvergence     # 稀疏矩阵中查找特征值/特征向量的函数


# 将标签转换为one-hot编码形式
def encode_onehot(labels):
    # set()函数创建一个不重复元素集合
    classes = set(labels)
    # np.identity()函数创建方针,返回主对角线元素为1,其余元素为0的数组
    # enumerate()函数用于将一个可遍历的数据对象(如列表、元组或字符串)组合为一个索引序列
    # 同时列出数据和数据下标,一般用在for循环中
    classes_dict = {c: np.identity(len(classes))[i, :] for i, c in enumerate(classes)}
    # map()函数根据提供的函数对指定序列做映射
    # map(function, iterable)
    # 第一个参数function以参数序列中的每一个元素调用function函数,返回包含每次function函数返回值的新列表
    labels_onehot = np.array(list(map(classes_dict.get, labels)), dtype=np.int32)
    return labels_onehot


# 加载数据
def load_data(path="data/cora/", dataset="cora"):
    """Load citation network dataset (cora only for now)"""
    # str.format()函数用于格式化字符串
    print('Loading {} dataset...'.format(dataset))
    # np.genfromtxt()函数用于从.csv文件或.tsv文件中生成数组
    # np.genfromtxt(fname, dtype, delimiter, usecols, skip_header)
    # frame:文件名
    # dtype:数据类型
    # delimiter:分隔符
    # usecols:选择读哪几列,通常将属性集读为一个数组,将标签读为一个数组
    # skip_header:是否跳过表头
    idx_features_labels = np.genfromtxt("{}{}.content".format(path, dataset), dtype=np.dtype(str))
    # 提取样本的特征,并将其转换为csr矩阵(压缩稀疏行矩阵),用行索引、列索引和值表示矩阵
    features = sp.csr_matrix(idx_features_labels[:, 1:-1], dtype=np.float32)
    # 提取样本的标签,并将其转换为one-hot编码形式
    labels = encode_onehot(idx_features_labels[:, -1])

    # build graph
    # 样本的id数组
    idx = np.array(idx_features_labels[:, 0], dtype=np.int32)
    # 有样本id到样本索引的映射字典
    idx_map = {j: i for i, j in enumerate(idx)}
    # 样本之间的引用关系数组
    edges_unordered = np.genfromtxt("{}{}.cites".format(path, dataset), dtype=np.int32)
    # 将样本之间的引用关系用样本索引之间的关系表示
    edges = np.array(list(map(idx_map.get, edges_unordered.flatten())),
                     dtype=np.int32).reshape(edges_unordered.shape)
    # 构建图的邻接矩阵,用坐标形式的稀疏矩阵表示,非对称邻接矩阵
    adj = sp.coo_matrix((np.ones(edges.shape[0]), (edges[:, 0], edges[:, 1])),
                        shape=(labels.shape[0], labels.shape[0]), dtype=np.float32)

    # build symmetric adjacency matrix
    # 将非对称邻接矩阵转变为对称邻接矩阵
    adj = adj + adj.T.multiply(adj.T > adj) - adj.multiply(adj.T > adj)
    # 打印消息:数据集有多少个节点、多少条边、每个样本有多少维特征
    print('Dataset has {} nodes, {} edges, {} features.'.format(adj.shape[0], edges.shape[0], features.shape[1]))
    # 返回特征的密集矩阵表示、邻接矩阵和标签的one-hot编码
    return features.todense(), adj, labels


# 对邻接矩阵进行归一化处理
def normalize_adj(adj, symmetric=True):
    # 如果邻接矩阵为对称矩阵,得到对称归一化邻接矩阵
    # D^(-1/2) * A * D^(-1/2)
    if symmetric:
        # A.sum(axis=1):计算矩阵的每一行元素之和,得到节点的度矩阵D
        # np.power(x, n):数组元素求n次方,得到D^(-1/2)
        # sp.diags()函数根据给定的对象创建对角矩阵,对角线上的元素为给定对象中的元素
        d = sp.diags(np.power(np.array(adj.sum(1)), -0.5).flatten(), 0)
        # tocsr()函数将矩阵转化为压缩稀疏行矩阵
        a_norm = adj.dot(d).transpose().dot(d).tocsr()
    # 如果邻接矩阵不是对称矩阵,得到随机游走正则化拉普拉斯算子
    # D^(-1) * A
    else:
        d = sp.diags(np.power(np.array(adj.sum(1)), -1).flatten(), 0)
        a_norm = d.dot(adj).tocsr()
    return a_norm


# 在邻接矩阵中加入自连接
def preprocess_adj(adj, symmetric=True):
    adj = adj + sp.eye(adj.shape[0])
    # 对加入自连接的邻接矩阵进行对称归一化处理
    adj = normalize_adj(adj, symmetric)
    return adj


# 构造样本掩码
def sample_mask(idx, l):
    """
    :param idx: 有标签样本的索引列表
    :param l: 所有样本数量
    :return: 布尔类型数组,其中有标签样本所对应的位置为True,无标签样本所对应的位置为False
    """
    # np.zeros()函数创建一个给定形状和类型的用0填充的数组
    mask = np.zeros(l)
    mask[idx] = 1
    return np.array(mask, dtype=np.bool)


# 数据集划分
def get_splits(y):
    # 训练集索引列表
    idx_train = range(140)
    # 验证集索引列表
    idx_val = range(200, 500)
    # 测试集索引列表
    idx_test = range(500, 1500)
    # 训练集样本标签
    y_train = np.zeros(y.shape, dtype=np.int32)
    # 验证集样本标签
    y_val = np.zeros(y.shape, dtype=np.int32)
    # 测试集样本标签
    y_test = np.zeros(y.shape, dtype=np.int32)
    y_train[idx_train] = y[idx_train]
    y_val[idx_val] = y[idx_val]
    y_test[idx_test] = y[idx_test]
    # 训练数据的样本掩码
    train_mask = sample_mask(idx_train, y.shape[0])
    return y_train, y_val, y_test, idx_train, idx_val, idx_test, train_mask


# 定义分类交叉熵
def categorical_crossentropy(preds, labels):
    """
    :param preds:模型对样本的输出数组
    :param labels:样本的one-hot标签数组
    :return:样本的平均交叉熵损失
    """
    # np.extract(condition, x)函数,根据某个条件从数组中抽取元素
    # np.mean()函数默认求数组中所有元素均值
    return np.mean(-np.log(np.extract(labels, preds)))


# 定义准确率函数
def accuracy(preds, labels):
    # np.argmax(x)函数取出x中元素最大值所对应的索引
    # np.equal(x1, x2)函数用于在元素级比较两个数组是否相等
    return np.mean(np.equal(np.argmax(labels, 1), np.argmax(preds, 1)))


# 评估样本划分的损失函数和准确率
def evaluate_preds(preds, labels, indices):
    """
    :param preds:对于样本的预测值
    :param labels:样本的标签one-hot向量
    :param indices:样本的索引集合
    :return:交叉熵损失函数列表、准确率列表
    """
    split_loss = list()
    split_acc = list()

    for y_split, idx_split in zip(labels, indices):
        # 计算每一个样本划分的交叉熵损失函数
        split_loss.append(categorical_crossentropy(preds[idx_split], y_split[idx_split]))
        # 计算每一个样本划分的准确率
        split_acc.append(accuracy(preds[idx_split], y_split[idx_split]))

    return split_loss, split_acc


# 对拉普拉斯矩阵进行归一化处理
def normalized_laplacian(adj, symmetric=True):
    # 对称归一化的邻接矩阵,D ^ (-1/2) * A * D ^ (-1/2)
    adj_normalized = normalize_adj(adj, symmetric)
    # 得到对称规范化的图拉普拉斯矩阵,L = I - D ^ (-1/2) * A * D ^ (-1/2)
    laplacian = sp.eye(adj.shape[0]) - adj_normalized
    return laplacian


# 重新调整对称归一化的图拉普拉斯矩阵,得到其简化版本
def rescale_laplacian(laplacian):
    try:
        print('Calculating largest eigenvalue of normalized graph Laplacian...')
        # 计算对称归一化图拉普拉斯矩阵的最大特征值
        largest_eigval = eigsh(laplacian, 1, which='LM', return_eigenvectors=False)[0]
    # 如果计算过程不收敛
    except ArpackNoConvergence:
        print('Eigenvalue calculation did not converge! Using largest_eigval=2 instead.')
        largest_eigval = 2

    # 调整后的对称归一化图拉普拉斯矩阵,L~ = 2 / Lambda * L - I
    scaled_laplacian = (2. / largest_eigval) * laplacian - sp.eye(laplacian.shape[0])
    return scaled_laplacian


# 计算直到k阶的切比雪夫多项式
def chebyshev_polynomial(X, k):
    # 返回一个稀疏矩阵列表
    """Calculate Chebyshev polynomials up to order k. Return a list of sparse matrices."""
    print("Calculating Chebyshev polynomials up to order {}...".format(k))

    T_k = list()
    T_k.append(sp.eye(X.shape[0]).tocsr())      # T0(X) = I
    T_k.append(X)       # T1(X) = L~

    # 定义切比雪夫递归公式
    def chebyshev_recurrence(T_k_minus_one, T_k_minus_two, X):
        """
        :param T_k_minus_one: T(k-1)(L~)
        :param T_k_minus_two: T(k-2)(L~)
        :param X: L~
        :return: Tk(L~)
        """
        # 将输入转化为csr矩阵(压缩稀疏行矩阵)
        X_ = sp.csr_matrix(X, copy=True)
        # 递归公式:Tk(L~) = 2L~ * T(k-1)(L~) - T(k-2)(L~)
        return 2 * X_.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], X))

    # 返回切比雪夫多项式列表
    return T_k


# 将稀疏矩阵转化为元组表示
def sparse_to_tuple(sparse_mx):
    if not sp.isspmatrix_coo(sparse_mx):
        # 将稀疏矩阵转化为coo矩阵形式
        # coo矩阵采用三个数组分别存储行、列和非零元素值的信息
        sparse_mx = sparse_mx.tocoo()
    # np.vstack()函数沿着数组的某条轴堆叠数组
    # 获取非零元素的位置索引
    coords = np.vstack((sparse_mx.row, sparse_mx.col)).transpose()
    # 获取矩阵的非零元素
    values = sparse_mx.data
    # 获取矩阵的形状
    shape = sparse_mx.shape
    return coords, values, shape

3 graph.py

# 如果某个版本中出现了某个新的功能特性,而且这个特性和当前版本中使用的不兼容,
# 也就是说它在当前版本中不是语言标准,那么我们如果想要使用的话就要从__future__模块导入
from __future__ import print_function       # print()函数

from keras import activations, initializers, constraints
from keras import regularizers
from keras.engine import Layer
import keras.backend as K


# 定义基本的图卷积类
# Keras自定义层要实现build方法、call方法和compute_output_shape(input_shape)方法
class GraphConvolution(Layer):
    """Basic graph convolution layer as in https://arxiv.org/abs/1609.02907"""
    # 构造函数
    def __init__(self, units, support=1,
                 activation=None,
                 use_bias=True,
                 kernel_initializer='glorot_uniform',
                 bias_initializer='zeros',
                 kernel_regularizer=None,
                 bias_regularizer=None,
                 activity_regularizer=None,
                 kernel_constraint=None,
                 bias_constraint=None,
                 **kwargs):
        if 'input_shape' not in kwargs and 'input_dim' in kwargs:
            # pop()函数用于删除列表中某元素,并返回该元素的值
            kwargs['input_shape'] = (kwargs.pop('input_dim'),)
        super(GraphConvolution, self).__init__(**kwargs)
        self.units = units
        self.activation = activations.get(activation)
        self.use_bias = use_bias
        self.kernel_initializer = initializers.get(kernel_initializer)
        self.bias_initializer = initializers.get(bias_initializer)
        # 施加在权重上的正则项
        self.kernel_regularizer = regularizers.get(kernel_regularizer)
        # 施加在偏置向量上的正则项
        self.bias_regularizer = regularizers.get(bias_regularizer)
        # 施加在输出上的正则项
        self.activity_regularizer = regularizers.get(activity_regularizer)
        # 对主权重矩阵进行约束
        self.kernel_constraint = constraints.get(kernel_constraint)
        # 对偏置向量进行约束
        self.bias_constraint = constraints.get(bias_constraint)
        self.supports_masking = True

        self.support = support
        assert support >= 1

    # 计算输出的形状
    # 如果自定义层更改了输入张量的形状,则应该在这里定义形状变化的逻辑
    # 让Keras能够自动推断各层的形状
    def compute_output_shape(self, input_shapes):
        # 特征矩阵形状
        features_shape = input_shapes[0]
        # 输出形状为(批大小, 输出维度)
        output_shape = (features_shape[0], self.units)
        return output_shape  # (batch_size, output_dim)

    # 定义层中的参数
    def build(self, input_shapes):
        # 特征矩阵形状
        features_shape = input_shapes[0]
        assert len(features_shape) == 2
        # 特征维度
        input_dim = features_shape[1]

        self.kernel = self.add_weight(shape=(input_dim * self.support,
                                             self.units),
                                      initializer=self.kernel_initializer,
                                      name='kernel',
                                      regularizer=self.kernel_regularizer,
                                   constraint=self.kernel_constraint)
        # 如果存在偏置
        if self.use_bias:
            self.bias = self.add_weight(shape=(self.units,),
                                        initializer=self.bias_initializer,
                                        name='bias',
                                        regularizer=self.bias_regularizer,
                                        constraint=self.bias_constraint)
        else:
            self.bias = None
        # 必须设定self.bulit = True
        self.built = True

    # 编写层的功能逻辑
    def call(self, inputs, mask=None):
        features = inputs[0]        # 特征
        basis = inputs[1:]      # 对称归一化的邻接矩阵

        # 多个图的情况
        supports = list()
        for i in range(self.support):
            # A * X
            supports.append(K.dot(basis[i], features))
        # 将多个图的结果按行拼接
        supports = K.concatenate(supports, axis=1)
        # A * X * W
        output = K.dot(supports, self.kernel)

        if self.bias:
            # A * X * W + b
            output += self.bias
        return self.activation(output)

    # 定义当前层的配置信息
    def get_config(self):
        config = {'units': self.units,
                  'support': self.support,
                  'activation': activations.serialize(self.activation),
                  'use_bias': self.use_bias,
                  'kernel_initializer': initializers.serialize(
                      self.kernel_initializer),
                  'bias_initializer': initializers.serialize(
                      self.bias_initializer),
                  'kernel_regularizer': regularizers.serialize(
                      self.kernel_regularizer),
                  'bias_regularizer': regularizers.serialize(
                      self.bias_regularizer),
                  'activity_regularizer': regularizers.serialize(
                      self.activity_regularizer),
                  'kernel_constraint': constraints.serialize(
                      self.kernel_constraint),
                  'bias_constraint': constraints.serialize(self.bias_constraint)
        }

        base_config = super(GraphConvolution, self).get_config()
        return dict(list(base_config.items()) + list(config.items()))

4 train.py

from __future__ import print_function

from keras.layers import Input, Dropout
from keras.models import Model
from keras.optimizers import Adam
from keras.regularizers import l2

from kegra.layers.graph import GraphConvolution
from kegra.utils import *

import time

# 超参数
# Define parameters
DATASET = 'cora'
# 过滤器
FILTER = 'localpool'  # 'chebyshev'
# 最大多项式的度
MAX_DEGREE = 2  # maximum polynomial degree
# 是否对称正则化
SYM_NORM = True  # symmetric (True) vs. left-only (False) normalization
# 迭代次数
NB_EPOCH = 20000
# 提前停止参数
PATIENCE = 10  # early stopping patience

# 加载数据
# Get data
X, A, y = load_data(dataset=DATASET)        # 特征、邻接矩阵、标签
# 训练集样本标签、验证集样本标签、测试集样本标签、训练集索引列表
# 验证集索引列表、测试集索引列表、训练数据的样本掩码
y_train, y_val, y_test, idx_train, idx_val, idx_test, train_mask = get_splits(y)

# 对特征进行归一化处理
# Normalize X
X /= X.sum(1).reshape(-1, 1)

# 当过滤器为局部池化过滤器时
if FILTER == 'localpool':
    """ Local pooling filters (see 'renormalization trick' in Kipf & Welling, arXiv 2016) """
    print('Using local pooling filters...')
    # 加入自连接的邻接矩阵
    A_ = preprocess_adj(A, SYM_NORM)
    support = 1
    # 特征矩阵和邻接矩阵
    graph = [X, A_]
    G = [Input(shape=(None, None), batch_shape=(None, None), sparse=True)]

# 当过滤器为切比雪夫多项式时
elif FILTER == 'chebyshev':
    """ Chebyshev polynomial basis filters (Defferard et al., NIPS 2016)  """
    print('Using Chebyshev polynomial basis filters...')
    # 对拉普拉斯矩阵进行归一化处理,得到对称规范化的拉普拉斯矩阵
    L = normalized_laplacian(A, SYM_NORM)
    # 重新调整对称归一化的图拉普拉斯矩阵,得到其简化版本
    L_scaled = rescale_laplacian(L)
    # 计算直到MAX_DEGREE阶的切比雪夫多项式
    T_k = chebyshev_polynomial(L_scaled, MAX_DEGREE)
    #
    support = MAX_DEGREE + 1
    # 特征矩阵、直到MAX_DEGREE阶的切比雪夫多项式列表
    graph = [X]+T_k     # 列表相加
    G = [Input(shape=(None, None), batch_shape=(None, None), sparse=True) for _ in range(support)]

else:
    raise Exception('Invalid filter type.')

# shape为形状元组,不包括batch_size
# 例如shape=(32, )表示预期的输入将是一批32维的向量
X_in = Input(shape=(X.shape[1],))

# 定义模型架构
# 注意:我们将图卷积网络的参数作为张量列表传递
# 更优雅的做法需要重写Layer基类
# Define model architecture
# NOTE: We pass arguments for graph convolutional layers as a list of tensors.
# This is somewhat hacky, more elegant options would require rewriting the Layer base class.
H = Dropout(0.5)(X_in)
H = GraphConvolution(16, support, activation='relu', kernel_regularizer=l2(5e-4))([H]+G)
H = Dropout(0.5)(H)
Y = GraphConvolution(y.shape[1], support, activation='softmax')([H]+G)

# 编译模型
# Compile model
model = Model(inputs=[X_in]+G, outputs=Y)
model.compile(loss='categorical_crossentropy', optimizer=Adam(lr=0.01))

# 训练过程中的辅助变量
# Helper variables for main training loop
wait = 0
preds = None
best_val_loss = 99999

# 训练模型
# Fit
for epoch in range(1, NB_EPOCH+1):

    # 统计系统时钟的时间戳
    # Log wall-clock time
    t = time.time()

    # 每一次迭代过程
    # Single training iteration (we mask nodes without labels for loss calculation)
    model.fit(graph, y_train, sample_weight=train_mask,     # 向sample_weight参数传递train_mask用于样本掩码
              batch_size=A.shape[0], epochs=1, shuffle=False, verbose=0)

    # 预测模型在整个数据集上的输出
    # Predict on full dataset
    preds = model.predict(graph, batch_size=A.shape[0])

    # 模型在验证集上的损失和准确率
    # Train / validation scores
    train_val_loss, train_val_acc = evaluate_preds(preds, [y_train, y_val],
                                                   [idx_train, idx_val])
    print("Epoch: {:04d}".format(epoch),
          "train_loss= {:.4f}".format(train_val_loss[0]),       # 在训练集上的损失
          "train_acc= {:.4f}".format(train_val_acc[0]),     # 在训练集上的准确率
          "val_loss= {:.4f}".format(train_val_loss[1]),     # 在验证集上的损失
          "val_acc= {:.4f}".format(train_val_acc[1]),       # 在验证集上的准确率
          "time= {:.4f}".format(time.time() - t))       # 本次迭代的运行时间

    # 提取停止
    # Early stopping
    if train_val_loss[1] < best_val_loss:
        best_val_loss = train_val_loss[1]
        wait = 0
    else:
        # 当模型在测试集上的损失连续10次迭代没有优化时,则提取停止
        if wait >= PATIENCE:
            print('Epoch {}: early stopping'.format(epoch))
            break
        wait += 1

# 模型在测试集上的损失和准确率
# Testing
test_loss, test_acc = evaluate_preds(preds, [y_test], [idx_test])
print("Test set results:",
      "loss= {:.4f}".format(test_loss[0]),
      "accuracy= {:.4f}".format(test_acc[0]))

 

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