ToDos Deadline - Githubissues

Everybody:

Tim:

[ ] #68
[x] Run GP on some test data as a POC
[ ] Fill in Table in Appendix with established methods
[ ] Make Plots Features (x-axs) vs Factor Norms (y-axis) for Non-negativity vs. HS & SNS & Laplace for non-negative DGP
[x] 1st plot: 2 UMAPs of latent space z (one colored by time, one colored by diff stage). Inference w/o any covariates
[x] 2nd plot: 2 UMAPs of latent space z (one colored by time, one colored by diff stage). Inference only with time in GP
[x] 3rd plot: 2 UMAPs of latent space z (one colored by time, one colored by diff stage). Inference with time and diff stage in GP
[x] Gridsearch over lengthscales [0.001, 0.01, 0.1, 1, 2, 5, 10]
[ ] Predict only 1 or 2 factors from the GP, estimate other factors separately

Arber:

[x] Refactor generative models with multiple plate combinations (SnS etc...)
[x] Write subsection about DGP of synthetic data
[x] Add benchmark results on sparsity and recon error as a table (prec, rec, f1, rmse)

Martin:

[x] Make Plots Features (x-axis) vs R2 Reconstruction (y-axis) for different Sparsity Priors
[x] CLL Data
[ ] Depending on GPU, repeat all plots but with samples/views/missings on y-axis
[ ] Make Heatmaps: Features x Samples vs Time until Convergence for different Priors

Not assigned (for grabs):

bioFAM / cellij