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Reduce mem footprint of get_latent_representation
#84
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Tests currently failing due to an issue in scvi-tools, which has been fixed. Just need to make sure the CI here installs from main. |
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For another solution: In resolVI, I have a second batch size, which are macrobatches and every macrobatch is copied (and median etc is computed). We could do it here, but I imagine the time difference to be very low here and wouldn't do it. |
ebezzi
approved these changes
Feb 7, 2024
canergen
reviewed
Feb 7, 2024
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Helps with the memory footprint of this method since embeddings are not transferred to CPU until all batches have been processed. Technically leads to an increase in runtime due to having a call to
device_getper batch instead of a larger one at the end, since I believejax.device_getblocks computation. I think this is a better alternative than running out of GPU memory, and the increase in runtime can be mitigated by increasing the batch size