Refactoring moscot to include moscot.neural
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@selmanozleyen is already working on this.
Since Nov 7, 2024.
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- Python
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Description
We want to have a moscot.neural module which implements the discrete problems as equivalent neural problems. Therefore, we consecutively do the following steps:
- remove Protocol classes https://github.com/theislab/moscot/issues/765
- Move
GENOTLinProblemto neural module #778 - moscot.neural.base should have
NeuralOTProblem(currentlyCondOTProblem, instead ofOTProblemin discrete case), and theNeuralOutput(instead of theOTTOutputin discrete case), this can be adapted from the current implementation. Therefore, restructure the output into aBaseOutputwhich is the parent class ofDiscreteOTOutputandNeuralOTOutput#778
moscot.neural.solvers in future times should include
-
GenotLin, -
GenotQuad, - and
OTCFM,
start with GenotLin, because it's implemented already, and extend it to GenotQuad. OTCFM will be added later.
- Port the dataloader (or roughly the idea of the dataloader) from CellFlow, and extend it to include quadratic terms.
- Let's also distinguish between the data representation which we compute the coupling in, and the one which are input/output to the flow
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