Metrics discrepancy between Tutorial_Multiomics.ipynb and Supplementary Table 4

[nc1m]

Hello,

After running Tutorial_Multiomics.ipynb and comparing the outputs to Supplementary Table 4, I found that the evaluation metrics in the tutorial are consistently higher.
Could you clarify whether this difference is due to the clustering algorithm used in the tutorial or to updates in the code (e.g., preprocessing changes, parameter defaults, or random seeds)?

Thank you!

[nc1m]

I found a similar case between Tutorial_ZeroShot_Integration.ipynb and Supplementary Figure 12.