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AllenCellModeling / pytorch_integrated_cell

Integrated Cell project implemented in pytorch
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Discussion: vanilla is ok #79

Closed donovanr closed 3 years ago

donovanr commented 4 years ago

Issue summary

don't be ashamed

Details

You all seem a little abashed that this is a “plain vanilla” beta-VAE and not some kind of breakthrough in the ML space. This is FINE! It is almost always better to use the simplest possible alternative. The merit of this paper is the cell biological application, and the way that the beta-VAE makes it possible to put quantitative values (and probabilities of specific observations) on things that are very hard to describe in anything other than qualitative terms. We are aiming for a computational biology audience, not a CS/ML audience.

TODO

tknijnen commented 4 years ago

Indeed. This issue can be closed as it does not have any action items it seems.

donovanr commented 4 years ago

the action item is to change the manuscript text to highlight this as a feature.

donovanr commented 4 years ago

@gregjohnso adding you since this seems pretty decoupled from other stuff. I'd say a paragraph citing some lit about how reliable VAEs are compared to GANs, the multi-task benefits, etc would do it. Maybe citing success of vanilla architecture in other areas from say general stuff like faces to other areas of comp bio like scvi?