python - 对称稀疏矩阵的高效切片

Question

我有一个稀疏对称矩阵列表 sigma 使得

len(sigma) = N

对于所有的i,j,k,

sigma[i].shape[0] == sigma[i].shape[1] = m  # Square
sigma[i][j,k] == sigma[i][k,j]  # Symmetric

我有一个索引数组 P 这样

P.shape[0] = N
P.shape[1] = k

我的目标是使用 P[i,:] 给出的索引提取 sigma[i] 的 k x k 密集子矩阵。这可以按如下方式完成

sub_matrices = np.empty([N,k,k])
for i in range(N):
    sub_matrices[i,:,:] = sigma[i][np.ix_(P[i,:], P[i,:])].todense()

但是请注意，虽然 k 很小，但 N(和 m)非常大。如果稀疏对称矩阵以 CSR 格式存储，这将花费很长时间。我觉得必须有更好的解决方案。例如，是否存在适合需要在两个维度上切片的对称矩阵的稀疏格式？

我正在使用 Python，但愿意接受任何我可以使用 Cython 接口(interface)的 C 库建议。

额外

请注意，我目前的 Cython 方法如下:

cimport cython
import numpy as np
cimport numpy as np

@cython.boundscheck(False) # turn off bounds-checking for entire function
cpdef sparse_slice_fast_cy(sigma,
                           long[:,:] P,
                           double[:,:,:] sub_matrices):
    """
    Inputs:
        sigma: A list (N,) of sparse sp.csr_matrix (m x m)
        P: A 2D array of integers (N, k)
        sub_matrices: A 3D array of doubles (N, k, k) containing the slicing
    """
    # Create variables for keeping code tidy
    cdef long N = P.shape[0]
    cdef long k = P.shape[1]

    cdef long i
    cdef long j
    cdef long index_pointer 
    cdef long sparse_row_pointer

    # Create objects for holding sparse matrix data
    cdef double[:] data
    cdef long[:] indices
    cdef long[:] indptr

    # Object for the ordered P
    cdef long[:] perm

    # Make sure sub_matrices is all 0
    sub_matrices[:] = 0

    for i in range(N):
        # Sort the P
        perm = np.argsort(P[i,:])

        # Get the sparse matrix values
        data     = sigma[i].data
        indices  = sigma[i].indices.astype(long)
        indptr   = sigma[i].indptr.astype(long)

        for j in range(k):
            # Loop over row P[i, perm[j]] in sigma searching for values
            # in P[i, :] vector i.e. compare
            #     sigma[P[i, perm[j], :]
            # against
            #     P[i,:]

            # To do this we need our sparse row vector with columns 
            #     indices[indptr[P[i, perm[j]]], indptr[P[i, perm[j]]+1]]
            # and data/values
            #     data[indptr[P[i, perm[j]]], indptr[P[i, perm[j]]+1]]
            # which comes from the csr matrix format.
            # We also need our sorted indexing vector
            #     P[i, perm[:]]

            # We begin by pointing at the top of both
            # our vectors and gradually move down them. In the event of 
            # an equality we add the data to sub_matrices[i,:,:] and 
            # increment the INDEXING VECTOR pointer, not the sparse
            # row vector pointer, as there can be multiple values that 
            # are the same in the indexing vector but not the sparse row
            # column vector (only 1 column can appear in 1 row!).
            index_pointer = 0
            sparse_row_pointer = indptr[P[i, perm[j]]]

            while ((index_pointer < k) and (sparse_row_pointer < indptr[P[i, perm[j]] + 1])):
                if indices[sparse_row_pointer] == P[i, perm[index_pointer]]:
                    # We can add data to sub_matrices
                    sub_matrices[i, perm[j], perm[index_pointer]] = \
                           data[sparse_row_pointer]

                    # Only increment the index pointer
                    index_pointer += 1
                elif indices[sparse_row_pointer] > P[i, perm[index_pointer]]:
                    # Need to increment index pointer
                    index_pointer += 1
                else:
                    # Need to increment sparse row pointer
                    sparse_row_pointer += 1

我相信 np.argsort 经常在相对较小的向量上调用时可能效率低下并且想换成 C 实现。我也没有利用可能在 N 稀疏矩阵上加速的并行处理。不幸的是，由于外部循环中存在 Python 强制转换，我不知道如何使用 prange。

另一点需要注意的是，Cython 方法似乎使用了大量内存，但我不知道它被分配到哪里。

最新版本

根据ead的建议，下面是最新版本的Cython代码

cimport cython
import numpy as np
cimport numpy as np

@cython.boundscheck(False) # turn off bounds-checking for entire function
cpdef sparse_slice_fast_cy(sigma,
                           np.ndarray[np.int32_t, ndim=2] P,
                           np.float64_t[:,:,:] sub_matrices,
                           int symmetric):
    """
    Inputs:
        sigma: A list (N,) of sparse sp.csr_matrix (m x m)
        P: A 2D array of integers (N, k)
        sub_matrices: A 3D array of doubles (N, k, k) containing the slicing
        symmetric: 1 if the sigma matrices are symmetric
    """
    # Create variables for keeping code tidy
    cdef np.int32_t N = P.shape[0]
    cdef np.int32_t k = P.shape[1]

    cdef np.int32_t i
    cdef np.int32_t j
    cdef np.int32_t index_pointer 
    cdef np.int32_t sparse_row_pointer

    # Create objects for holding sparse matrix data
    cdef np.float64_t[:] data
    cdef np.int32_t[:] indices

    cdef np.int32_t[:] indptr

    # Object for the ordered P
    cdef np.int32_t[:,:] perm = np.argsort(P, axis=1).astype(np.int32)

    # Make sure sub_matrices is all 0
    sub_matrices[:] = 0

    for i in range(N):
        # Get the sparse matrix values
        data     = sigma[i].data
        indices  = sigma[i].indices
        indptr   = sigma[i].indptr

        for j in range(k):
            # Loop over row P[i, perm[j]] in sigma searching for values
            # in P[i, :] vector i.e. compare
            #     sigma[P[i, perm[j], :]
            # against
            #     P[i,:]

            # To do this we need our sparse row vector with columns 
            #     indices[indptr[P[i, perm[j]]], indptr[P[i, perm[j]]+1]]
            # and data/values
            #     data[indptr[P[i, perm[j]]], indptr[P[i, perm[j]]+1]]
            # which comes from the csr matrix format.
            # We also need our sorted indexing vector
            #     P[i, perm[:]]

            # We begin by pointing at the top of both
            # our vectors and gradually move down them. In the event of 
            # an equality we add the data to sub_matrices[i,:,:] and 
            # increment the INDEXING VECTOR pointer, not the sparse
            # row vector pointer, as there can be multiple values that 
            # are the same in the indexing vector but not the sparse row
            # column vector (only 1 column can appear in 1 row!).

            if symmetric:
                index_pointer = j  # Only search upper triangular
            else:
                index_pointer = 0
            sparse_row_pointer = indptr[P[i, perm[i, j]]]

            while ((index_pointer < k) and (sparse_row_pointer < indptr[P[i, perm[i, j]] + 1])):
                if indices[sparse_row_pointer] == P[i, perm[i, index_pointer]]:
                    # We can add data to sub_matrices
                    sub_matrices[i, perm[i, j], perm[i, index_pointer]] = \
                           data[sparse_row_pointer]

                    if symmetric:
                        sub_matrices[i, perm[i, index_pointer], perm[i, j]] = \
                               data[sparse_row_pointer]

                    # Only increment the index pointer
                    index_pointer += 1
                elif indices[sparse_row_pointer] > P[i, perm[i, index_pointer]]:
                    # Need to increment index pointer
                    index_pointer += 1
                else:
                    # Need to increment sparse row pointer
                    sparse_row_pointer += 1

平行版

下面是一个并行版本，虽然它似乎没有提供任何加速并且代码不再那么好看:

# See https://stackoverflow.com/questions/48805636/efficient-slicing-of-symmetric-sparse-matrices
cimport cython
import numpy as np
cimport numpy as np
from libc.stdlib cimport malloc, free
from cython.parallel import prange

@cython.boundscheck(False) # turn off bounds-checking for entire function
cpdef sparse_slice_fast_cy(sigma,
                           np.ndarray[np.int32_t, ndim=2] P,
                           np.float64_t[:,:,:] sub_matrices,
                           int symmetric):
    """
    Inputs:
        sigma: A list (N,) of sparse sp.csr_matrix (m x m)
        P: A 2D array of integers (N, k)
        sub_matrices: A 3D array of doubles (N, k, k) containing the slicing
        symmetric: 1 if the sigma matrices are symmetric
    """
    # Create variables for keeping code tidy
    cdef np.int32_t N = P.shape[0]
    cdef np.int32_t k = P.shape[1]

    cdef np.int32_t i
    cdef np.int32_t j
    cdef np.int32_t index_pointer 
    cdef np.int32_t sparse_row_pointer

    # Create objects for holding sparse matrix data
    cdef np.float64_t[:] data_mem_view
    cdef np.int32_t[:] indices_mem_view
    cdef np.int32_t[:] indptr_mem_view

    cdef np.float64_t **data = <np.float64_t **> malloc(N * sizeof(np.float64_t *))
    cdef np.int32_t **indices = <np.int32_t **> malloc(N * sizeof(np.int32_t *))
    cdef np.int32_t **indptr = <np.int32_t **> malloc(N * sizeof(np.int32_t *))

    for i in range(N):
        data_mem_view = sigma[i].data
        data[i] = &(data_mem_view[0])

        indices_mem_view = sigma[i].indices
        indices[i] = &(indices_mem_view[0])

        indptr_mem_view = sigma[i].indptr
        indptr[i] = &(indptr_mem_view[0])

    # Object for the ordered P
    cdef np.int32_t[:,:] perm = np.argsort(P, axis=1).astype(np.int32)

    # Make sure sub_matrices is all 0
    sub_matrices[:] = 0

    for i in prange(N, nogil=True):
        for j in range(k):
            # Loop over row P[i, perm[j]] in sigma searching for values
            # in P[i, :] vector i.e. compare
            #     sigma[P[i, perm[j], :]
            # against
            #     P[i,:]
            # To do this we need our sparse row vector with columns 
            #     indices[indptr[P[i, perm[j]]], indptr[P[i, perm[j]]+1]]
            # and data/values
            #     data[indptr[P[i, perm[j]]], indptr[P[i, perm[j]]+1]]
            # which comes from the csr matrix format.
            # We also need our sorted indexing vector
            #     P[i, perm[:]]

            # We begin by pointing at the top of both
            # our vectors and gradually move down them. In the event of 
            # an equality we add the data to sub_matrices[i,:,:] and 
            # increment the INDEXING VECTOR pointer, not the sparse
            # row vector pointer, as there can be multiple values that 
            # are the same in the indexing vector but not the sparse row
            # column vector (only 1 column can appear in 1 row!).

            if symmetric:
                index_pointer = j  # Only search upper triangular
            else:
                index_pointer = 0
            sparse_row_pointer = indptr[i][P[i, perm[i, j]]]

            while ((index_pointer < k) and 
                   (sparse_row_pointer < indptr[i][P[i, perm[i, j]] + 1])):
                if indices[i][sparse_row_pointer] == P[i, perm[i, index_pointer]]:
                    # We can add data to sub_matrices
                    sub_matrices[i, perm[i, j], perm[i, index_pointer]] = \
                           data[i][sparse_row_pointer]

                    if symmetric:
                        sub_matrices[i, perm[i, index_pointer], perm[i, j]] = \
                               data[i][sparse_row_pointer]

                    # Only increment the index pointer
                    index_pointer = index_pointer + 1
                elif indices[i][sparse_row_pointer] > P[i, perm[i, index_pointer]]:
                    # Need to increment index pointer
                    index_pointer = index_pointer + 1
                else:
                    # Need to increment sparse row pointer
                    sparse_row_pointer = sparse_row_pointer + 1

    # Free malloc'd data
    free(data)
    free(indices)
    free(indptr)

测试

测试代码运行

cythonize -i sparse_slice.pyx

其中 sparse_slice.pyx 是文件名。然后你可以使用这个脚本:

import time
import numpy as np
import scipy as sp
import scipy.sparse
from sparse_slice import sparse_slice_fast_cy

k = 100
N = 20000
m = 10000
samples = 20

# Create sigma matrices
## The sampling of random sparse takes a while so just do a few and 
## then populate with these.
now = time.time()
sigma_samples = []
for i in range(samples):
    sigma_samples.append(sp.sparse.rand(m, m, density=0.001, format='csr'))
    sigma_samples[-1] = sigma_samples[-1] + sigma_samples[-1].T  # Symmetric

## Now make the sigma list from these.
sigma = []
for i in range(N):
    j = np.random.randint(samples)
    sigma.append(sigma_samples[j])
print('Time to make sigma: {}'.format(time.time() - now))

# Create indexer
now = time.time()
P = np.empty([N, k]).astype(int)
for i in range(N):
    P[i, :] = np.random.choice(np.arange(m), k, replace=True)
print('Time to make P: {}'.format(time.time() - now))

# Create objects for holding the slices
sub_matrices_slow = np.empty([N, k, k])
sub_matrices_fast = np.empty([N, k, k])

# Run both slicings
## Slow
now = time.time()
for i in range(N):
    sub_matrices_slow[i,:,:] = sigma[i][np.ix_(P[i,:], P[i,:])].todense()
print('Time to make sub_matrices_slow: {}'.format(time.time() - now))

## Fast
symmetric = 1
now = time.time()
sparse_slice_fast_cy(sigma, P.astype(np.int32), sub_matrices_fast, symmetric)
print('Time to make sub_matrices_fast: {}'.format(time.time() - now))

assert(np.all((sub_matrices_slow - sub_matrices_fast)**2 < 1e-6))

Answer 1

现在无法测试，但有两个建议:

A) 在 i-loop 上一次对所有行进行排序:

# Object for the ordered P
cdef long[:,:] perm = np.argsort(P, axis=1)

也许您需要将 P 作为 np.ndarray[np.int64_t, ndim=2] P(或任何类型)传递以避免复制。您必须通过 perm[i,X] 而不是 perm[X] 访问数据。

B) 定义

cdef np.int32_t[:] indices
cdef np.int32_t[:] indptr

因此您不需要通过“.astype”复制数据，即

for i in range(N):
    data     = sigma[i].data
    indices  = sigma[i].indices
    indptr   = sigma[i].indptr

我认为因为 sigma[i] 有 O(m) 元素，复制是你函数的瓶颈:你得到运行时间 O(N *(m+k^2)) 而不是 `O(N*k^2) - 最好避免它。

否则功能看起来还不错。

为了让 prange 与 i 循环一起工作，您应该通过创建一种指向 data、indices 和 indptr 的第一个元素的指针数组，并在廉价的预处理步骤中填充它们。可以让它工作，但问题是并行化的 yield 有多少——很可能是这种情况，问题是内存限制的——必须看时间安排。

您还可以通过仅处理上三角矩阵来使用对称性:

  ...
  index_pointer = j #only upper triangle!
  ....
  ....
     # We can add data to sub_matrices
     #upper triangle sub-matrix:
     sub_matrices[i, perm[j], perm[index_pointer]] = \
                       data[sparse_row_pointer]
     #lower triangle sub-matrix:
     sub_matrices[i, perm[index_pointer], perm[j]] = \
                       data[sparse_row_pointer]
  ....

我会从 B) 开始，看看结果如何...

---

编辑:

关于内存使用:可以通过以下方式测量峰值内存使用

 /usr/bin/time -f "peak_used_memory:%M(in Kb)" python test.py

我使用 N=2000 运行我的测试并得到 (python3.6+cython0.27.1):

                             peak memory usage
only slow                       245Mb
only fast                       245Mb
slow+fast no check              402Mb
slow+fast+assert                576Mb

因此有 50Mb 的开销，两个函数使用了 200Mb，另外还有 176Mb 用于评估断言。对于 N 的其他值，我也可以看到相同的行为。

所以我想说 cython 没有大量的内存使用。

---

此任务很可能(至少部分)受内存限制，因此并行化不会有太大帮助。您应该减少加载到缓存的内存量。

一种可能是不使用perm - 毕竟它也需要加载到缓存中。你可以做到，如果

1. 您可以接受矩阵 sigma 中的任何行/列排列，而不仅仅是对 P 进行排序并使用它。
2. 每行的元素很少，因此对每个元素进行线性搜索就可以了。
3. 对每个元素进行二分查找

我想在最好的情况下你可以赢大约 20-30%。

有时 cython 生成的代码不容易针对 c 编译器进行优化，直接用 C 编写然后用 python 包装它通常会取得更好的结果。

但只有当此操作确实是您程序的瓶颈时，我才会这样做。

---

顺便声明一下

cdef np.int64_t[:,:] perm = np.argsort(P, axis=1)

您不需要额外复印。