Question about diffusion map "gaussian" implementation

[jolespin]

Awesome, thank you for sharing this! I’ll definitely take a look at your preprint.

If you have a moment, would you be able to take a look at some of these questions I had about diffusion maps to see if you have any insight?

How to interpret Diffusion Maps?

I’m trying to adapt this to a very simple case which is the iris dataset: import anndata as ad import scanpy as sc from sklearn.neighbors import NearestNeighbors from scipy.sparse import csr_matrix from sklearn import datasets iris = datasets.load_iris() X_iris = pd.DataFrame( iris.data, columns=iris.feature_names, ) X_iris.index = X_iris.index.map(str) df_meta = pd.Series(iris.target).map(lambda x: iris.target_names[x]).to_frame("species") df_meta.index = df_meta.index.map(str) adat…