Implement reordering function to assess feature significance? about cca_zoo HOT 7 OPEN

Apologies for never having responded! Must have caught me at a busy time. Not done anything myself, as ever welcome any contributions that are of practical use to people :)

from cca_zoo.

Implementation in Python:

# compute the absolute correlation matrix between the original and resampled 
# v weights
def cor_matrix(X,Y):
    X = (X - X.mean(axis=0)) / X.std(axis=0)
    Y = (Y - Y.mean(axis=0)) / Y.std(axis=0)
    cor_matrix = np.dot(X.T, Y) / X.shape[0]
    return cor_matrix

def reorderCCA(v_org,v_res,u_org,u_res,cors_org,cors_res):

    cor_matrix_abs = np.abs(cor_matrix(v_org,v_res))
    res_match = np.argmax(cor_matrix_abs,axis=1)
    res_cor = np.amax(cor_matrix_abs,axis=1)
    res_match_count = len(np.unique(res_match))
    
    # now reorder the u and v weights from the resampled CCA based on the correlation matches
    u_res_ordered = u_res[:,res_match]
    v_res_ordered = v_res[:,res_match]
    cors_final = cors_res[res_match]
    
    # for each v variate get the 'mean' sign for both original and resampled v
    signs_org = np.sign(np.mean(np.sign(v_org),axis=0))
    signs_res = np.sign(np.mean(np.sign(v_res_ordered),axis=0))
    
    # compute element wise product
    signs_prod = (signs_org * signs_res).reshape(-1,1)
    
    # change the signs of u and v of the resampled cca
    u_final = (u_res_ordered.T * signs_prod).T
    v_final = (v_res_ordered.T * signs_prod).T
    
    # if you can't exclusively assign one resampled v to one original v, return
    # nans
    if res_match_count < u_org.shape[1]:
        u_na = np.empty(u_org.shape)
        u_na[:] = np.nan
        v_na = np.empty(v_org.shape)
        v_na[:] = np.nan    
        cors_na = np.repeat(np.nan,u_org.shape[1])
        res_match_na = np.repeat(np.nan,u_org.shape[1])
        res_cor_na = np.repeat(np.nan,u_org.shape[1])
        res_one_reorder = [u_na,v_na,cors_na,res_match_na,res_cor_na]
    else: 
        res_one_reorder = [u_final,v_final,cors_final,res_match,res_cor]

    return res_one_reorder

from cca_zoo.

I am not sure if this function makes sense. Xia et al. refer to this paper (Mišić et al.)

Matching Decompositions From Original and Resampled Matrices
The decompositions of both permuted and bootstrap-resampled
data matrices are not guaranteed to produce a set of LVs comparable with the ones derived from the original data matrix, because
both types of resampling could induce arbitrary axis rotation (a
change in the order of LVs) or axis reflection (a sign change for
the weights). As a result, Procrustes rotations are used to match
the resampled LVs to the original LVs (McIntosh and Lobaugh
2004).

But here Procrustes Rotations are used to match resampled to original variates. I am not sure if the function above from Xia et al. is Procrustes Rotation?

from cca_zoo.

I guess the whole issue could also be renamed to: "Implement Procrustes Rotation for resampling purposes (bootstrapping, permutation)".

For completeness:

Here's the implementation from pyls:
https://github.com/netneurolab/pypyls/blob/d8a19d564cc5804249527b68c937df3a5fd8c7cc/pyls/compute.py#L240

This package might help:
https://procrustes.readthedocs.io/en/latest/

Maybe also this:
https://github.com/MaxHalford/prince#generalized-procrustes-analysis-gpa

from cca_zoo.

Any update on this? I might start to work on this with my colleagues on this :)

Also posted a question on this on CrossValidated

from cca_zoo.

Spent some time making sure everything works with scikit-learn permutation testing stuff so that might be relevant/helpful

from cca_zoo.

In a nutshell: If we are only considering one variate, we can simply take the absolute values of the loadings/weights. But once you got more variates, you may end up in situations where you have a different order of the variates but still similar weights (similar relationship of variables when only considering each variate in isolation). In this case, Procrustes rotation may help. Not sure, however, what some statisticians would say about this because a different order of variates might inherently also be an indicator of bad reliability.

from cca_zoo.