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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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ilisi scores #337

Closed aissav closed 1 year ago

aissav commented 2 years ago

Hi there,

We used your LISI evaluation code to evaluate the pancreatic integrated dataset and compare the scores with those obtained from the R LISI package. We observed that the iLISI and cLISI scores obtained from both methods (R and your implementation) are different (note that we used similar parameters for both methods).

I know that your implementation was based on the R package. Could you please tell us what could be the issue behind that?

Thank you very much.

LuckyMD commented 2 years ago

Hi @aissav,

Did you use the lisi_graph method or something else? lisi_graph is different from iLISI as it uses the knn graph computed for the dataset and doesn't recompute one. It uses graph-based distances to get more nearest neighbors when needed. This is explained in Supplementary Note 2 of the paper here. Hope that helps!