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Mixup in hyperparameters for H_pert H_gene? #69

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mhorlacher opened this issue May 15, 2024 · 0 comments
Open

Mixup in hyperparameters for H_pert H_gene? #69

mhorlacher opened this issue May 15, 2024 · 0 comments

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@mhorlacher
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In "Supplementary Note 22: Hyperparameter Search" there's the following part:

"[...] the number of top similar genes in the co-expression network H_pert – {3, 5, 10, 20}; the number of top similar genes in the perturbation network H_gene – {3, 5, 10, 20}; [...]"

Is there a mix-up here? According to the main text, the co-expression network is used for deriving the gene embedding, while the GO-term network is used to derive the perturbation representation. What is the number of of neighbors used in the co-expression and GO-term networks for the final model?

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