Comments (2)
hsidky
commented on June 29, 2024
Hi,
The main issue is that your kernel bandwidth is too large. Per Coifman et al., they suggest twice the slope of a log-log plot of the sum of the similarity matrix. There is a convenience function in dmaps to sum the similarity matrix: diffMap.sum_similarity_matrix(epsilon).
You should get a good result with a kernel bandwidth of about 0.1.
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teshaTe
commented on June 29, 2024
Great, Thank you very much for the help!
I also read the article from another post: https://sidky.io/blog/diffusion-maps-part-2/
everything become more clear) Again thank you for your help!
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