我针对您的问题分析了 4 种不同的解决方案，看起来对于任何大小的数组，numba jit 解决方案都是最好的。紧随其后的是@Alexander 的 cython 解决方案。
以下是结果（M 是x数组中的行数）：
M = 1000
function sparse_dense took 0.03 sec.
function sparse_loop took 0.07 sec.
function sparse_numba took 0.00 sec.
function sparse_cython took 0.09 sec.
M = 10000
function sparse_dense took 2.88 sec.
function sparse_loop took 0.68 sec.
function sparse_numba took 0.00 sec.
function sparse_cython took 0.01 sec.
M = 100000
function sparse_dense ran out of memory
function sparse_loop took 6.84 sec.
function sparse_numba took 0.09 sec.
function sparse_cython took 0.12 sec.
我用来分析这些方法的脚本是：
import numpy as np
from scipy.sparse import coo_matrix
from numba import autojit, jit, float64, int32
import pyximport
pyximport.install(setup_args={"script_args":["--compiler=mingw32"],
"include_dirs":np.get_include()},
reload_support=True)
def sparse_dense(a,b,c):
return coo_matrix(c.multiply(np.dot(a,b)))
def sparse_loop(a,b,c):
"""Multiply sparse matrix `c` by np.dot(a,b) by looping over non-zero
entries in `c` and using `np.dot()` for each entry."""
N = c.size
data = np.empty(N,dtype=float)
for i in range(N):
data[i] = c.data[i]*np.dot(a[c.row[i],:],b[:,c.col[i]])
return coo_matrix((data,(c.row,c.col)),shape=(a.shape[0],b.shape[1]))
#@autojit
def _sparse_mult4(a,b,cd,cr,cc):
N = cd.size
data = np.empty_like(cd)
for i in range(N):
num = 0.0
for j in range(a.shape[1]):
num += a[cr[i],j]*b[j,cc[i]]
data[i] = cd[i]*num
return data
_fast_sparse_mult4 = \
jit(float64[:,:](float64[:,:],float64[:,:],float64[:],int32[:],int32[:]))(_sparse_mult4)
def sparse_numba(a,b,c):
"""Multiply sparse matrix `c` by np.dot(a,b) using Numba's jit."""
assert c.shape == (a.shape[0],b.shape[1])
data = _fast_sparse_mult4(a,b,c.data,c.row,c.col)
return coo_matrix((data,(c.row,c.col)),shape=(a.shape[0],b.shape[1]))
def sparse_cython(a, b, c):
"""Computes c.multiply(np.dot(a,b)) using cython."""
from sparse_mult_c import sparse_mult_c
data = np.empty_like(c.data)
sparse_mult_c(a,b,c.data,c.row,c.col,data)
return coo_matrix((data,(c.row,c.col)),shape=(a.shape[0],b.shape[1]))
def unique_rows(a):
a = np.ascontiguousarray(a)
unique_a = np.unique(a.view([('', a.dtype)]*a.shape[1]))
return unique_a.view(a.dtype).reshape((unique_a.shape[0], a.shape[1]))
if __name__ == '__main__':
import time
for M in [1000,10000,100000]:
print 'M = %i' % M
N = M + 2
L = 10
x = np.random.rand(M,L)
t = np.random.rand(N,L).T
# number of non-zero entries in sparse r matrix
S = M*10
row = np.random.randint(M,size=S)
col = np.random.randint(N,size=S)
# remove duplicate rows and columns
row, col = unique_rows(np.dstack((row,col)).squeeze()).T
data = np.random.rand(row.size)
r = coo_matrix((data,(row,col)),shape=(M,N))
a2 = sparse_loop(x,t,r)
for f in [sparse_dense,sparse_loop,sparse_numba,sparse_cython]:
t0 = time.time()
try:
a = f(x,t,r)
except MemoryError:
print 'function %s ran out of memory' % f.__name__
continue
elapsed = time.time()-t0
try:
diff = abs(a-a2)
if diff.nnz > 0:
assert np.max(abs(a-a2).data) < 1e-5
except AssertionError:
print f.__name__
raise
print 'function %s took %.2f sec.' % (f.__name__,elapsed)
cython 函数是@Alexander 代码的略微修改版本：
# working from tutorial at: http://docs.cython.org/src/tutorial/numpy.html
cimport numpy as np
# Turn bounds checking back on if there are ANY problems!
cimport cython
@cython.boundscheck(False) # turn of bounds-checking for entire function
def sparse_mult_c(np.ndarray[np.float64_t, ndim=2] a,
np.ndarray[np.float64_t, ndim=2] b,
np.ndarray[np.float64_t, ndim=1] data,
np.ndarray[np.int32_t, ndim=1] rows,
np.ndarray[np.int32_t, ndim=1] cols,
np.ndarray[np.float64_t, ndim=1] out):
cdef int n = rows.shape[0]
cdef int k = a.shape[1]
cdef int i,j
cdef double num
for i in range(n):
num = 0.0
for j in range(k):
num += a[rows[i],j] * b[j,cols[i]]
out[i] = data[i]*num