How to use scib benchmark-metrics evaluate the adata after BBKNN integretion

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1

The paper showed we can use benchmark metrics to evaluate the adata after BBKNN integration. But I can only use some default functions in the benchmark-metrics package to get the batch-remove grades. For bio-conservation grades, I can’t find appropriate functions to apply.

2

Hey @wangflmi

Have you checked scib-metrics tutorials? There are several examples overthere on how to run scib-metrics benchmarker to produce batch-remove & bio-conservation grades

See for example:

4

Hi@ori-kron-wis,

The tutorials seemed only show the embedding-based methods, I could not find the example for the graph-based one, like BBKNN.

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Can you see if this helps you:

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