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MrVI does not store temporary distance matrices efficiently #3166

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PierreBoyeau opened this issue Jan 27, 2025 · 1 comment
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MrVI does not store temporary distance matrices efficiently #3166

PierreBoyeau opened this issue Jan 27, 2025 · 1 comment
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@PierreBoyeau
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MrVI temporarilly represents outputs as xarrays, typed not as numpy arrays, but as Jax arrays. This causes significant memory overhead, especially when computing cell-specific distance matrices for a large number of samples.
@VladimirShitov VladimirShitov mentioned this issue Feb 10, 2025
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@justjhong justjhong mentioned this issue Feb 19, 2025
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canergen added a commit that referenced this issue Feb 20, 2025
@PierreBoyeau @ori-kron-wis
@pre-commit-ci @justjhong @canergen
fix: MrVI compatible with large sample sizes (#3146)
c3926eb 
Fixes #3145, #3166

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Co-authored-by: Ori Kronfeld <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Justin Hong <[email protected]>
Co-authored-by: Can Ergen <[email protected]>
@justjhong
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Resolved in #3146

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@justjhong @PierreBoyeau