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geneformer tokenizer fails on scperturb datasets #324

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amva13 opened this issue Oct 22, 2024 · 4 comments
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geneformer tokenizer fails on scperturb datasets #324

amva13 opened this issue Oct 22, 2024 · 4 comments
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amva13 commented Oct 22, 2024

https://github.com/mims-harvard/TDC/tree/geneformer_server
@amva13 amva13 self-assigned this Oct 22, 2024
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amva13 commented Oct 29, 2024

update - works totally OK for general anndata frame. need some custom processing code for scperturb. doable in next few weeks.

TDC/tdc/test/test_model_server.py

Line 103 in 2daa6ca

x = tokenizer.tokenize_cell_vectors(adata,

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amva13 commented Jan 20, 2025

putting up PR for thi

@amva13 amva13 mentioned this issue Jan 20, 2025
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amva13 commented Jan 20, 2025

to be closed by #345

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amva13 commented Jan 21, 2025

fix merged

@amva13 amva13 closed this as completed Jan 21, 2025
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