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Density subsampling #106

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scottgigante opened this issue Jun 8, 2020 · 1 comment

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scottgigante commented Jun 8, 2020

Describe the solution you'd like
scprep.select.subsample(density=True, knn=3). Use nmslib if available?

Describe alternatives you've considered
Use sklearn.NearestNeighbors

scottgigante added the enhancement label

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scottgigante commented Jun 8, 2020

distances, _ = sklearn.NearestNeighbors(n_neighbors=3).fit(X).kneighbors()
distances = distances.max(axis=1)
p = distances / distances.sum()
X_subsample = scprep.select.select_rows(X, idx=np.random.choice(X.shape[0], n, p=p, replace=False)

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