C2s attention returns genenames and optimisation#329
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martinaoliver merged 21 commits intomainfrom Feb 10, 2026
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Avoid calling unstable pyensembl endpoint for hsapiens
compile transcriptformer
Update torch versions
Fix issues of requests-cache due to pybiomart
C2sen fixes and extensions
Revert logger
C2sen updates
Set max_genes to 200 to avoid OOM issues
Improve memory usage of C2S
Include tahoe-1x
adjust requirements for documentation
keep process data sparse for c2s
Return gene level attn
maxiallard
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Feb 10, 2026
bputzeys
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Feb 11, 2026
C2s attention returns genenames and optimisation (#329)
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Three updates for optimisation and compatibility with attention map analysis
***NOTE: This function is not being called in bioagents for inference with c2s - is only being used to retrieve attention maps