theislab / theislab/moscot

Pull/push in a batch-wise fashion

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#592 3 comments 0 reactions 2 assignees View on GitHub

@MUCDK is already working on this.

Since Aug 11, 2023.

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Description

Hi there! For a simple TemporalProblem, I've held out some genes (from the embedding computation, simple PCA) and computed the coupling. I would now like to use the coupling to predict expression values of the held out genes (at either t_1 or t_2, both possible), as a means of validation. However, when calling tp.push(source=8.0, target=8.5, data=gexp_sc, scale_by_marginals=True), where gexp_sc is the gene expression matrix of held-out genes on the source cells, my kernel dies. I assume that's because the matrix multiplication is carried out using a dense formulation, all at once. Is it somehow possible to do this in a batch-wise fashion, i.e. by only loading small chunks of the coupling into memory at once?

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