Handling missing data in decomposition about tensorly HOT 12 CLOSED

Just FYI - I have (scipy/numpy) code that handles this (see link below). Agree it would be a nice addition to tensorly!

https://github.com/ahwillia/tensortools/blob/master/tensortools/least_squares.py

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Agreed, let's make that happen!

Robust tensor PCA in TensorLy already handles missing values, ideally this should be the case for all decompositions.

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Hi! Has it been worked on? If not I would like to start working on it

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Nice posts. Would you like to create a pull request to add support for missing values?

Currently the Robust Tensor PCA handles missing values but Tucker and CP don't.
There are a number of things that we want to add, like having the option of choosing the solver as @ahwillia suggested.

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I'd love to do a PR. Sadly, at this point of time, I don't know where the masking would need to be done in the code. Would you have a clue? If the factorisation can be reduced to least squares, this should be trivial.

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You're welcome to take a crack at it @ShivangiM!

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Hi @ShivangiM, any luck with this?

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@JeanKossaifi not yet, been busy lately.

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Hi all

I am wondering if robust_pca has been implemented as intended in terms of handling the missing values.

I understand the requested format for the missing value mask, but it seems that in the underlying data array X, the missing data cannot be a nan value, so it seems that you have to use a numerical value for missing data points in X.

However, I have noticed that the results are sensitive to the particular numerical value used for missing points, which I think cannot be the intended behavior? Is there an assumed value that missing points must have?

Sorry for lack of code, am on a mobile as not allowed GitHub at work!

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Hi, I am trying to use CP for decomposition on my experiment (a part of data missing), and I notice that function parafac provides parameter "mask" for handling the missing values.

I am successful when the tensor is 2-dimensions, e.g. tl.tensor([[1., 2.], [3., 4.]]), and the mask array is same with the tensor while its value is 0/1.

However, when I repeat this process when the tensor is in higher-dimension, e.g. tl.tensor([ [[1., 2.], [3., 4.]], [[5.,6.],[7.,8.]] ]), it doesn't work.

The error is as followed:

Traceback (most recent call last):
  File "t.py", line 40, in <module>
    factors = parafac(X, rank=2, mask=kk)
  File "/home/a/Documents/tensorly/tensorly/decomposition/candecomp_parafac.py", line 185, in parafac
    tensor = tensor*mask + tl.kruskal_to_tensor((None, factors), mask=1-mask)
  File "/home/a/Documents/tensorly/tensorly/kruskal_tensor.py", line 188, in kruskal_to_tensor
    full_tensor = T.sum(khatri_rao([factors[0]*weights]+factors[1:], mask=mask), axis=1)
  File "/home/a/Documents/tensorly/tensorly/tenalg/_khatri_rao.py", line 98, in khatri_rao
    return T.kr(matrices, weights=weights, mask=mask)
  File "/home/a/Documents/tensorly/tensorly/backend/__init__.py", line 160, in inner
    return _get_backend_method(name)(*args, **kwargs)
  File "/home/a/Documents/tensorly/tensorly/backend/numpy_backend.py", line 69, in kr
    return np.einsum(operation, *matrices).reshape((-1, n_columns))*mask
ValueError: operands could not be broadcast together with shapes (16,2) (2,2,2,2) 

It seems that the direct problem is in
np.einsum(operation, *matrices).reshape((-1, n_columns))*mask.
I doubt that it is because matrix multi need to use np.dot() and change this code into
np.dot(np.einsum(operation, *matrices).reshape((-1, n_columns)),mask)
and the problem becomes:

Traceback (most recent call last):
  File "t.py", line 40, in <module>
    factors = parafac(X, rank=2, mask=kk)
  File "/home/a/Documents/tensorly/tensorly/decomposition/candecomp_parafac.py", line 185, in parafac
    tensor = tensor*mask + tl.kruskal_to_tensor((None, factors), mask=1-mask)
  File "/home/a/Documents/tensorly/tensorly/kruskal_tensor.py", line 190, in kruskal_to_tensor
    return fold(full_tensor, 0, shape)
  File "/home/a/Documents/tensorly/tensorly/base.py", line 77, in fold
    return T.moveaxis(T.reshape(unfolded_tensor, full_shape), 0, mode)
  File "/home/a/Documents/tensorly/tensorly/backend/__init__.py", line 160, in inner
    return _get_backend_method(name)(*args, **kwargs)
  File "<__array_function__ internals>", line 6, in reshape
  File "/home/a/.local/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 301, in reshape
    return _wrapfunc(a, 'reshape', newshape, order=order)
  File "/home/a/.local/lib/python3.6/site-packages/numpy/core/fromnumeric.py", line 61, in _wrapfunc
    return bound(*args, **kwds)
ValueError: cannot reshape array of size 64 into shape (2,2,2,2)

I don't really understand it indeed. What should I do for my goal? I am very hopeful for help and it is better if there is example in code. Thanks very much for anyone's suggestions.

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@milanlanlan I would suggest opening a separate issue report for this. It looks like mask needs to be reshaped, or else multiplied before the reshape (I'm not sure which).

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Fixed by #173

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