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Diffusion operator construction #200

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qubit0 opened this issue May 6, 2022 · 0 comments

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qubit0 commented May 6, 2022

I am trying to understand how the diffusion operator is constructed. I can follow up to cell-cell distance matrix i.e.
$D_{pca} = pca(D,0.70)$

After that affinity matrix caculated using a Gaussian kernel. Here, we have to choose sigma.

How is sigma chosen?
Where in the python source code, can I find the adapative tuning of sigma?
What is magic_operator.graph.kernel ? How is it constructed? If we set non-zero values to zero here than does it become an adjacency matrix for the graph?
magic_operator.graph.diff_op is a row normalized Markov matrix M(i,j), right ?

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