Hi Team,
Earlier docs for scVI mention that the number of epochs should scale downwards with number of obs/cells. E.g: “([For] > 100,000 cells) you may only need ~10 epochs.” I cannot find similar advice on the modern docs. Is this advice still valid and should even fewer epochs be used for even larger datasets?
Thank you in advance,
Tim
I don’t think it’s relevant anymore, and it really depends on what you are doing.
You will need to train until convergence, and you can use the early_stopping parameter for that, but if you are starting from an already trained large model and only finetune it with your cells, yes might be that only a few epochs will be enough.
Thank you. If I am training a completely new model, what could be unintended consequences of not using the ‘early_stopping’ parameter to ensure convergence?
It will just train for as many epochs as you enter, possibly leading to overfitting.
You should check your loss curves while doing this.