# Training split conditioned on batch\_key

**URL:** <https://discourse.scverse.org/t/training-split-conditioned-on-batch-key/2283>\
**Category:** scvi-tools\
**Tags:** scvi\
**Created:** [May 16, 2024, 3:51pm UTC](https://discourse.scverse.org/t/training-split-conditioned-on-batch-key/2283 "2024-05-16T15:51:03Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Florian\_Deckert](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/florian_deckert/32/76_2.png) [@Florian\_Deckert](https://discourse.scverse.org/u/Florian_Deckert)\
**Post date:** [May 16, 2024, 3:51pm UTC](https://discourse.scverse.org/t/training-split-conditioned-on-batch-key/2283/1 "2024-05-16T15:51:03Z")

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Hello SCVI-Team,

I am currently working with public scRNAseq Atlas data (HCA, HLCA, etc.). It is crucial to account for not only patient-specific but also technical effects such as study, sample preparation, and assay type. Typically, I utilize the `patient_id` as the `batch_key` and address sources of technical noise with the `categorical_covariate_keys` parameter during model setup. This approach generally works well with some additional preprocessing steps.

However, I’ve noticed significant variations in the total number of cells per patient across different studies. This variability poses a risk of underrepresentation or absence of certain patients and/or studies (and their respective covariates) in the training and validation datasets.

Would it be advisable to split the data per patient ID into training and validation sets, or could this approach potentially compromise the model training?

I greatly appreciate your insights.

Best wishes, Florian

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**Author:** ![Florian\_Deckert](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/florian_deckert/32/76_2.png) [@Florian\_Deckert](https://discourse.scverse.org/u/Florian_Deckert)\
**Post date:** [May 16, 2024, 4:30pm UTC](https://discourse.scverse.org/t/training-split-conditioned-on-batch-key/2283/2 "2024-05-16T16:30:47Z")

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I have reviewed the splitting indices in `model.train_indices` and `model.validation_indices` and confirmed that the random shuffling and splitting effectively distribute data without considering the patient ID. Each patient (or study) approximately maintains a 0.9/0.1 ratio for the training/validation datasets, which aligns with our expectations (In hindsight, it was unreasonable to assume otherwise.).

However, would you advise to monitor any additional parameters to ensure proper learning when observing strong differences in total cell numbers between covariant?

Thank you once again for your support.  
Best regards, Florian

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**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [May 17, 2024, 12:08pm UTC](https://discourse.scverse.org/t/training-split-conditioned-on-batch-key/2283/3 "2024-05-17T12:08:07Z")

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Hi, we have scVI criticism. The think you could monitor is whether the CV per cell is different for different batches. This could point to this batch being modeled worse. It is hard to tell without much more information whether this is due to technical effects (library sizes, ambient genes etc) or model training though.

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**Author:** ![Florian\_Deckert](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/florian_deckert/32/76_2.png) [@Florian\_Deckert](https://discourse.scverse.org/u/Florian_Deckert)\
**Post date:** [May 22, 2024, 2:26pm UTC](https://discourse.scverse.org/t/training-split-conditioned-on-batch-key/2283/4 "2024-05-22T14:26:11Z")

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@cane11 Thank you very much! I just slowly start to really understand some fundamental concepts of VAE and your input is highly appreciated. I will read up the Posterior Predictive checks (PPC) section of scvi-criticism, it looks great 🙂