epierson9 / multiphenotype_methods

Methods for inferring low-dimensional representations of high-dimensional phenotype spaces.

This code contains methods for inferring low-dimensional representations of high-dimensional phenotype spaces.

To see an example, please look at toy_data_example.ipynb.

We are happy to make this code available for any commercial or non-commercial actor to use. This code is available under the MIT License (see LICENSE.md).

multiphenotype_methods's Issues

More consistency in how we pass data around / how we keep it in the object?

PW writes: "I don't understand when we pass data around and when we keep it in the object. Seems good to either always pass data around, or put it in the object at the top level?"

Clarify/restructure include_age_in_encoder_input versus need_ages

PW: I still think we need to clarify these variables, otherwise there's a good chance we'll introduce some bug in the future. For example, need_ages says it's whether age is needed to compute loss or other quantities. include_age_in_encoder_input says it's whether age is used to approximate the posterior over Z. The posterior over Z seems to count as an "other quantity" so why is it handled separately from need_ages?