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multiVI fails with invalid tensor #2581
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Hi, the errors you are referring to are issues about MPS Apple hardware. We have seen the issue you are facing in multiVI in newer scvi-tools version. The main reason in our hands is that we have changed the default see in newer scvi-tools version. Do you fix the seed and still face the problem? Can you share the toy dataset (how large is it - ncells and file size)? It would be interesting to explore what updates in the TrainingPlan remove these errors. |
thanks for your answer! here is the toy dataset (approx 2000 cells by 4000 features) i didn't include a seed but i will try that and let you know. |
Unfortunately, no success with explicit scvi.settings.seed |
Hi @bio-la, sorry you're running into this issue. It looks like the issue might be slightly different than the Discourse threads you linked since the CI is running on Ubuntu, not macOS, so I'm guessing this is an issue unrelated to a PyTorch MPS build. Could you try passing in a lower learning rate (maybe |
thanks for your suggestions. here are my comments:
I'm using this dataset
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Hi, @martinkim0 any news on this? thanks! |
We are on it. I have one solution (gradient clipping) that solves similar problems in totalVI (AdversarialTrainingplan is not stable). We first need to make sure that it doesn't reduce quality in downstream tasks. |
Hi @bio-la, currently we enable an adversarial classifier even if only a single batch is present in the dataset. This is a bug. We will have a fix soonish. To overcome the error for now, you can pass |
awesome! will wait for the changes to be merged and let you know. thank you! |
Hi scvi team, thanks for the excellent tools! I'm reaching out with an issue running MultiVI with versions scvi-tools >=0.20.3
the error is the same reported here and here.
i set up two actions to reproduce the error. I'm running the same script with the same toy dataset, only changing the scvi-tools version in the environment. (you can see all the dependencies in the conda list step). the action is ran on ubuntu but i have the same issue on an intel chip.
this action, with scvi-tools=1.1.1 fails with the same error as described before
https://github.com/DendrouLab/panpipes/actions/runs/8114022415/job/22178710942?pr=201
this action, with scvi-tools=0.20.3, runs successfully. https://github.com/DendrouLab/panpipes/actions/runs/8114022411/job/22178710284?pr=201
thanks for your help!
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