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theislab / scarches

Reference mapping for single-cell genomics
https://docs.scarches.org/en/latest/
BSD 3-Clause "New" or "Revised" License
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scPoli Model for Unsupervised Use #224

Open ShreyParikh07 opened 8 months ago

ShreyParikh07 commented 8 months ago

Version history

scarches: 0.5.10

Issue

When attempting to initialize the scPoli model for unsupervised learning, the constructor seems to require a label_indices=[] argument to be passed as an empty list, which should be optional in unsupervised scenarios.

moinfar commented 6 months ago

Hi, To use scPoli in unsupervised settings, please note that you should:

  1. Set all values in the passed cell_type_keys to a dummy value (e.g. 'Unknown') and pass the unknown_ct_names=['Unknown'] parameter to scPoli.
  2. Additionally, Set labeled_indices=[]

The second requirement may be relaxed in an upcoming merge request. Please note that scPoli without cell-type information is equivalent to trVAE with batches handled using embedding vectors rather than one-hot encodings.