README.md

This repo contains all of the scripts used in "Flexible mean field variational inference using mixtures of non-overlapping exponential families."

It also contains plotting scripts, although with different seeds, the output of the scripts may be slightly different from that in the paper. Overall, however, the results will be largely comparable. To make the finalized figures in the paper, I sometimes directly added labels to the figures, or combined the figures in inkscape but the data in the figures were in no way manipulated.

Below I describe each of the scripts in the code/ directory. Some of these scripts will generate data in the data/ directory and some of the scripts will use that data to generate figures. All of the scripts are assumed to be run from the code directory.

ldpred.py

Simulates data as described in the main text and then computes the correlation and MSE of the point estimates against the truth. The results are saved in data/ldpred/ The usage is:

python ldpred.py <sigma_sq_e> <number_of_repetitions>

The outputs are data/ldpred/cor_mat_<sigma_sq_e>.txt that contain the correlations and mse_mat_<sigma_sq_e>.txt that contain the MSE for each VI scheme. Additionally, it saves the raw data to be used with nimble_code.R and pyro_code_discrete.py. The plotting scripts assume that <number_of_repetitions> is 100.

nimble_code.R

Performs MCMC on the ldpred model data simulated by ldpred.py. The usage is:

Rscript nimble_code.R <1-indexed rep> <sigma_sq_e>

The output is data/ldpred/nimble_results_<1-indexed rep>_<sigma_sq_e>.txt, which contrains the correlation and MSE for this run. These runs can then be combined using parse_nimble.py. The plotting scripts assume that the <1-indexed rep>s run from 1-100.

parse_nimble.py

Combines all of the outputs from nimble_code.R, so that they can be used in ldpred_plotter.R.

pyro_code_discrete.py

Performs boosting black box VI using pyro on the ldpred model data simulated by ldpred.py. The usage is:

python pyro_code_discrete.py <1-indexed rep> <sigma_sq_e>

The output is data/ldpred/pyro_discrete_<sigma_sq_e>_rep_<1-indexed rep>_cor.txt and data/ldpred/pyro_discrete_<sigma_sq_e>_rep_<1-indexed rep>_mse.txt containing the correlation of the posterior mean and true betas and MSE respectively. The plotting scripts assume that the ``<1-indexed rep>```s run from 1-100.

parse_pyro.py

Combines all of the outputs from pyro_code_discrete.py, so that they can be used in ldpred_plotter.R.

ldpred_plotter.R

Takes the output of ldpred.py, parse_nimble.py, and parse_pyro.py and produces figures like Figure 1 and saves them in figs/.

sparse_pca.py

Analogous to ldpred.py, this simulates data for the sparse PCA model as described in the main text and then runs the various VI schemes on the results. The results (and the raw data) are saved in data/sparse_pca/ The usage is:

python sparse_pca.py <num_non_zero_variables> <rep_name>

In the paper num_non_zero_variables was always 100 and rep_name was used to generate 6 datasets. rep_name is optional. The ouputs are:

data/sparse_pca/data[_rep<rep_name>].npy: The simulated data matrix

data/sparse_pca/keep[_rep<rep_name>].npy: The indices of the non-zero effect sizes

data/sparse_pca/vi_mu_w_<sigma_sq_0>[_rep<rep_name>].npy: mu_w as defined in the appendix for the naive VI schemes

data/sparse_pca/vi_mu_w_sparse[_rep<rep_name>].npy: mu_w as defined in the appendix for the scheme based on the non-overlapping mixtures trick.

data/sparse_pca/vi_mu_z_<sigma_sq_0>[_rep<rep_name>].npy: Same as above but for mu_z.

data/sparse_pca/vi_mu_z_sparse[_rep<rep_name>].npy: Same as above but for mu_z.

data/sparse_pca/vi_psi_0_sparse[_rep<rep_name>].npy: psi_0 as defined in the appendix for the scheme based on the non-overlapping mixtures trick.

data/sparse_pca/vi_sigma_w_sparse[_rep<rep_name>].npy: sigma_w as defined in the appendix for the scheme based on the non-overlapping mixtures trick.

PCA_plotter_notebook.ipynb

Jupyter notebook to visualize and plot the figures in Figure 2 (additional formatting done in inkscape).

reconstruction_error.py

Reads in reps 1, 2, ..., 5 and prints the min, mean, and max reconstruction error.

make_pca_plots.py

Takes the data produced by sparse_pca.py and makes figures like those in Figure 5. Assumes that the <rep_name> above are 1, 2, ..., 5. Outputs files with self-explanatory names in figs/

threshold_plotter.R

Produces the plot in Figure 3 (additional text was added in inkscape).

data/

All of the outputs from scripts in the code directory and all of the necessary data to make the plots in the figs directory. The data are described above as ouputs of ldpred.py and sparse_pca.py Due to the size constraints on GitHub, this folder will be empty until the above scripts are run. Due to randomness in the simulation process the results will not exactly match those in the paper but will be comparable.

figs/

All of the raw figures used in the manuscript. Note that labels were often added directly to figures or figures were combined into multi-panel figures using inkscape.

Real Data Application

Data downloading and preprocessing were performed essentially exactly as described in in the kallisto tutorial implemented in this Google Collab notebook. To facilitate reproduction, large portions of this notebook are copied into code/real_data_PBMC_dataset.ipynb. Running the notebook should reproduce the figures in the paper.