Given a 3d array X with dimensions (K,n,m) that can be considered as a stack of K (n,m) matrices and a 1d vector b (dim n), the goal is to obtain the resulting vector r (dim n) each component of which is calculated as:
It is easy to see that the expression under the k-summation (i.e. two internal sums) is just a dot product X_k b X_k (and, therefore, can easily be calculated using numpy). So, the desired vector r is
where X_k is the k-th 2d (n,m) 'layer' of 3d array X.
I.e. the current solution is
r = 0
for k in range(K):
r += x[k,:,:] # (b # x[k, :, :])
Can r be efficiently calculated avoiding a for-loop by k?
Or maybe there is another efficient way to calculate r?
(I tried np.tensordot but since it is just pure summation by k I didn't get a correct result yet.)
This looks like a perfect usecase for einsum:
r = np.einsum('kij,l,klj->i', x, b, x)
which will vectorize the operation, e.g. it's more optimal than a for loop.
Related
I'm trying to make a matrix/vector multiplication, but my matrix is stored in a way # operator cannot be used.
My matrix Z is actually a list on size N containing the columns of the matrix which are all PETSc4py.Vec of size NN, where NN≫N (eg. NN=10000 and N=10). As N is small, I can make a for loop on it, so for instance, if I want to compute r =Z.T # u with u a vector of size NN, I do
r = np.zeros(N)
for i,z in enumerate(Z):
r[i] = u * z # scalar product
Now I have a vector u of size N and I want to make the multiplication w = Z # u, I can't apply the same method because it would involve a loop of size NN which I'm trying to avoid.
I could convert my "matrix" Z to a NumPy matrix, but I'm also trying to avoid it...
I represented on the figure 1 the way the matrix is stored. A red line represents a vector that should be read for a the matrix-vector multiplication.
Is there a mathematical way (or a magic trick !) to compute this operation without making the big loop ?
Thanks
I need to multiply each row of an array A with all rows of an array B element-wise. For instance, let's say we have the following arrays:
A = np.array([[1,5],[3,6]])
B = np.array([[4,2],[8,2]])
I want to get the following array C:
C = np.array([[4,10],[8,10],[12,12],[24,12]])
I could do this by using for loop but I think there could be a better way to do it.
EDIT: I thought of repeating and tiling but my arrays are not that small. It could create some memory problem.
Leverage broadcasting extending dims for A to 3D with None/np.newaxis, perform the elementwise multiplication and reshape back to 2D -
(A[:,None]*B).reshape(-1,B.shape[1])
which essentially would be -
(A[:,None,:]*B[None,:,:]).reshape(-1,B.shape[1])
Schematically put, it's :
A : M x 1 x N
B : 1 x K x N
out : M x K x N
Final reshape to merge last two axes and give us (M x K*N) shaped 2D array.
We can also use einsum to perform the extension to 3D and elementwise multiplication in one function call -
np.einsum('ij,kj->ikj',A,B).reshape(-1,B.shape[1])
I wanted to define my own addition operator that takes an Nx1 vector (call it A) and a 1xN vector (B) such that the element in the i^th row and j^th column is the sum of the i^th element in A and the j^th element in B. An example is illustrated here.
I was able to write the following code for the function (and it is correct as far as I know).
def test_fn(a, b):
a_len = a.shape[0]
b_len = b.shape[1]
prod = np.array([[0]*a_len]*b_len)
for i in range(a_len):
for j in range(b_len):
prod[i, j] = a[i, 0] + b[0, j]
return prod
However, the vectors I am working with contain thousands of elements, and the function above is quite slow. I was wondering if there was a better way to approach this problem, or if there was a numpy function that could be of use. Any help would be appreciated.
According to numpy's broadcasting rules, you can use a+b to implement your own defined operator.
The first rule of broadcasting is that if all input arrays do not have the same number of dimensions, a “1” will be repeatedly prepended to the shapes of the smaller arrays until all the arrays have the same number of dimensions.
The second rule of broadcasting ensures that arrays with a size of 1 along a particular dimension act as if they had the size of the array with the largest shape along that dimension. The value of the array element is assumed to be the same along that dimension for the “broadcast” array.
I have a linear system in which all the matrices are block diagonal. They have N blocks identical in shape.
Matrices are stored in compressed format as numpy arrays with shape (N, n, m), while the shape of the vectors is (N, m).
I currently implemented the matrix-vector product as
import numpy as np
def mvdot(m, v):
return (m * np.expand_dims(v, -2)).sum(-1)
Thanks to broadcasting rules, if all the blocks of a matrix are the same I have to store it only once in an array with shape (1, n, m): the product with a vector (N, m) still gives the correct (N, n) vector.
My questions are:
how to implement an efficient matrix-matrix product that yields the matrix with shape (N, n, m) from two matrices with shapes (N, n, p) and (N, p, m)?
is there a way to perform these operations with a numpy built-in (possibly faster) function? Functions like np.linalg.inv make me think that numpy was designed to support this compressed format for block diagonal matrices.
If I understand your question correctly, you have two arrays of shape (N,n,p) and (N,p,m), respectively, and their product should be of shape (N,n,m) where element [i,:,:] is the matrix product of M1[i,:,:] and M2[i,:,:]. This can be achieved using numpy.einsum:
import numpy as np
N = 7
n,p,m = 3,4,5
M1 = np.random.rand(N,n,p)
M2 = np.random.rand(N,p,m)
Mprod = np.einsum('ijk,ikl->ijl',M1,M2)
# check if all the submatrices are what we expect
all([np.allclose(np.dot(M1[k,...],M2[k,...]),Mprod[k,...]) for k in range(N)])
# True
Numpy's einsum is an incredibly versatile construction for complicated linear operations, and it's usually pretty efficient with two operands. The idea is to rewrite your operation in an indexed way: what you need is to multiply M1[i,j,k] with M2[i,k,l] for each i,j,l, and sum over k. This is exactly what the above call to einsum does: it collapses the index k, and performs the necessary products and assignments along the remaining dimensions in the given order.
The matrix-vector product can be done similarly:
M = np.random.rand(N,n,m)
v = np.random.rand(N,m)
Mvprod = np.einsum('ijk,ik->ij',M,v)
It's possible that numpy.dot can be coerced with the proper transposes and dimension tricks to directly do what you want, but I couldn't make that work.
Both of the above operations can be done in the same function call by allowing an implicit number of dimensions within einsum:
def mvdot(M1,M2):
return np.einsum('ijk,ik...->ij...',M1,M2)
Mprod = mvdot(M1,M2)
Mvprod = mvdot(M,v)
In case the input argument M2 is a block matrix, there will be a leading dimension appended to the result, creating a block matrix. In case M2 is a "block vector", the result will be a block vector.
Since Python 3.5 and above, the previous example can be simplified using the matrix multiplication operator # (numpy.matmul) which treats this case as a stack of matrices residing in the last two indexes and broadcast accordingly:
import numpy as np
N = 7
n,p,m = 3,4,5
M1 = np.random.rand(N,n,p)
M2 = np.random.rand(N,p,m)
Mprod = M1 # M2 # similar to np.matmul(M1, M2)
all([np.allclose(np.dot(M1[k,...],M2[k,...]),Mprod[k,...]) for k in range(N)])
#True
I have some data represented by input_x. It is a tensor of unknown size (should be inputted by batch) and each item there is of size n. input_x undergoes tf.nn.embedding_lookup, so that embed now has dimensions [?, n, m] where m is the embedding size and ? refers to the unknown batch size.
This is described here:
input_x = tf.placeholder(tf.int32, [None, n], name="input_x")
embed = tf.nn.embedding_lookup(W, input_x)
I'm now trying to multiply each sample in my input data (which is now expanded by embedding dimension) by a matrix variable, U, and I can't seem to get how to do that.
I first tried using tf.matmul but it gives an error due to mismatch in shapes. I then tried the following, by expanding the dimension of U and applying batch_matmul (I also tried the function from tf.nn.math_ops., the result was the same):
U = tf.Variable( ... )
U1 = tf.expand_dims(U,0)
h=tf.batch_matmul(embed, U1)
This passes the initial compilation, but then when actual data is applied, I get the following error:
In[0].dim(0) and In[1].dim(0) must be the same: [64,58,128] vs [1,128,128]
I also know why this is happening - I replicated the dimension of U and it is now 1, but the minibatch size, 64, doesn't fit.
How can I do that matrix multiplication on my tensor-matrix input correctly (for unknown batch size)?
Previous answers are obsolete. Currently tf.matmul() support tensors with rank > 2:
The inputs must be matrices (or tensors of rank > 2, representing
batches of matrices), with matching inner dimensions, possibly after
transposition.
Also tf.batch_matmul() was removed and tf.matmul() is the right way to do batch multiplication. The main idea can be understood from the following code:
import tensorflow as tf
batch_size, n, m, k = 10, 3, 5, 2
A = tf.Variable(tf.random_normal(shape=(batch_size, n, m)))
B = tf.Variable(tf.random_normal(shape=(batch_size, m, k)))
tf.matmul(A, B)
Now you will receive a tensor of the shape (batch_size, n, k). Here is what is going on here. Assume you have batch_size of matrices nxm and batch_size of matrices mxk. Now for each pair of them you calculate nxm X mxk which gives you an nxk matrix. You will have batch_size of them.
Notice that something like this is also valid:
A = tf.Variable(tf.random_normal(shape=(a, b, n, m)))
B = tf.Variable(tf.random_normal(shape=(a, b, m, k)))
tf.matmul(A, B)
and will give you a shape (a, b, n, k)
1. I want to multiply a batch of matrices with a batch of matrices of the same length, pairwise
M = tf.random_normal((batch_size, n, m))
N = tf.random_normal((batch_size, m, p))
# python >= 3.5
MN = M # N
# or the old way,
MN = tf.matmul(M, N)
# MN has shape (batch_size, n, p)
2. I want to multiply a batch of matrices with a batch of vectors of the same length, pairwise
We fall back to case 1 by adding and removing a dimension to v.
M = tf.random_normal((batch_size, n, m))
v = tf.random_normal((batch_size, m))
Mv = (M # v[..., None])[..., 0]
# Mv has shape (batch_size, n)
3. I want to multiply a single matrix with a batch of matrices
In this case, we cannot simply add a batch dimension of 1 to the single matrix, because tf.matmul does not broadcast in the batch dimension.
3.1. The single matrix is on the right side
In that case, we can treat the matrix batch as a single large matrix, using a simple reshape.
M = tf.random_normal((batch_size, n, m))
N = tf.random_normal((m, p))
MN = tf.reshape(tf.reshape(M, [-1, m]) # N, [-1, n, p])
# MN has shape (batch_size, n, p)
3.2. The single matrix is on the left side
This case is more complicated. We can fall back to case 3.1 by transposing the matrices.
MT = tf.matrix_transpose(M)
NT = tf.matrix_transpose(N)
NTMT = tf.reshape(tf.reshape(NT, [-1, m]) # MT, [-1, p, n])
MN = tf.matrix_transpose(NTMT)
However, transposition can be a costly operation, and here it is done twice on an entire batch of matrices. It may be better to simply duplicate M to match the batch dimension:
MN = tf.tile(M[None], [batch_size, 1, 1]) # N
Profiling will tell which option works better for a given problem/hardware combination.
4. I want to multiply a single matrix with a batch of vectors
This looks similar to case 3.2 since the single matrix is on the left, but it is actually simpler because transposing a vector is essentially a no-op. We end-up with
M = tf.random_normal((n, m))
v = tf.random_normal((batch_size, m))
MT = tf.matrix_transpose(M)
Mv = v # MT
What about einsum?
All of the previous multiplications could have been written with the tf.einsum swiss army knife. For example the first solution for 3.2 could be written simply as
MN = tf.einsum('nm,bmp->bnp', M, N)
However, note that einsum is ultimately relying on tranpose and matmul for the computation.
So even though einsum is a very convenient way to write matrix multiplications, it hides the complexity of the operations underneath — for example it is not straightforward to guess how many times an einsum expression will transpose your data, and therefore how costly the operation will be. Also, it may hide the fact that there could be several alternatives for the same operation (see case 3.2) and might not necessarily choose the better option.
For this reason, I would personally use explicit formulas like those above to better convey their respective complexity. Although if you know what you are doing and like the simplicity of the einsum syntax, then by all means go for it.
The matmul operation only works on matrices (2D tensors). Here are two main approaches to do this, both assume that U is a 2D tensor.
Slice embed into 2D tensors and multiply each of them with U individually. This is probably easiest to do using tf.scan() like this:
h = tf.scan(lambda a, x: tf.matmul(x, U), embed)
On the other hand if efficiency is important it may be better to reshape embed to be a 2D tensor so the multiplication can be done with a single matmul like this:
embed = tf.reshape(embed, [-1, m])
h = tf.matmul(embed, U)
h = tf.reshape(h, [-1, n, c])
where c is the number of columns in U. The last reshape will make sure that h is a 3D tensor where the 0th dimension corresponds to the batch just like the original x_input and embed.
As answered by #Stryke, there are two ways to achieve this: 1. Scanning, and 2. Reshaping
tf.scan requires lambda functions and is generally used for recursive operations. Some examples for the same are here: https://rdipietro.github.io/tensorflow-scan-examples/
I personally prefer reshaping, since it is more intuitive. If you are trying to matrix multiply each matrix in the 3D tensor by the matrix that is the 2D tensor, like Cijl = Aijk * Bkl, you can do it with a simple reshape.
A' = tf.reshape(Aijk,[i*j,k])
C' = tf.matmul(A',Bkl)
C = tf.reshape(C',[i,j,l])
It seems that in TensorFlow 1.11.0 the docs for tf.matmul incorrectly say that it works for rank >= 2.
Instead, the best clean alternative I've found is to use tf.tensordot(a, b, (-1, 0)) (docs).
This function gets the dot product of any axis of array a and any axis of array b in its general form tf.tensordot(a, b, axis). Providing axis as (-1, 0) gets the standard dot product of two arrays.