mapalign
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satra
Diffusion map based embedding and alignment
To transform a new dataset based on the diffusion map model. Similar to the last part here: https://pydiffmap.readthedocs.io/en/master/usage.html ``` mydmap = dm.DiffusionMap.from_sklearn(n_evecs = 1, alpha = 0.5, epsilon = 'bgh',...
Currently the eigenvalues are not stored so we can’t measure importance of dimensions. I see in the backend there's the lambda values. Are these the scaled eigenvalues? Is there a...
Hello, I recently downloaded this package using pip in the terminal, and I encountered the error that Issue #20 referred to. It appears the last update to the PyPI module...
We were testing your package out and noted that it works with some versions of sklearn but not others. This appears to be due to the import statement in embed.py...
[Embeddings.zip](https://github.com/satra/mapalign/files/6576754/Embeddings.zip) I would like to ask two mutually related questions about the code: 1. Where can I found the theory and **rationale behind the automated computation of diffusion times** (line...
the exponentiation should not be necessary for estimating the diffusion time corresponding to a scaled eigenvalue.
Refactoring the kernel normalization and transition matrix computation as independent function will allow for more code re-use.
Hi @satra, in the current implementation, Markov matrix is calculated by taking sums along axis 1: `d_alpha = np.power(np.array(L_alpha.sum(axis=1)).flatten(), -1)` And multiplying each row by the respective inverse sum: `L_alpha...
I get a `NameError` ( global name 'rbf_kernel' is not defined) when trying to use the rbf kernel (`affinity='rbf'`). Maybe this is missing an import from sklearn (`sklearn.metrics.pairwise.rbf_kernel`) to be...
Sorry for disturbing you. I am very interested in the paper 'Situating the default-mode network along a principal gradient of macroscale cortical organization' which is based on mapalign, and code...
