Rmosek
: Primal vs Dual with \(l_1\) regularizationLast updated: 2018-05-12
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Environment: empty
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
✔ Seed:
set.seed(12345)
The command set.seed(12345)
was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
✔ Repository version: ddf9062
wflow_publish
or wflow_git_commit
). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: analysis/.DS_Store
Ignored: analysis/BH_robustness_cache/
Ignored: analysis/FDR_Null_cache/
Ignored: analysis/FDR_null_betahat_cache/
Ignored: analysis/Rmosek_cache/
Ignored: analysis/StepDown_cache/
Ignored: analysis/alternative2_cache/
Ignored: analysis/alternative_cache/
Ignored: analysis/ash_gd_cache/
Ignored: analysis/average_cor_gtex_2_cache/
Ignored: analysis/average_cor_gtex_cache/
Ignored: analysis/brca_cache/
Ignored: analysis/cash_deconv_cache/
Ignored: analysis/cash_fdr_1_cache/
Ignored: analysis/cash_fdr_2_cache/
Ignored: analysis/cash_fdr_3_cache/
Ignored: analysis/cash_fdr_4_cache/
Ignored: analysis/cash_fdr_5_cache/
Ignored: analysis/cash_fdr_6_cache/
Ignored: analysis/cash_plots_cache/
Ignored: analysis/cash_sim_1_cache/
Ignored: analysis/cash_sim_2_cache/
Ignored: analysis/cash_sim_3_cache/
Ignored: analysis/cash_sim_4_cache/
Ignored: analysis/cash_sim_5_cache/
Ignored: analysis/cash_sim_6_cache/
Ignored: analysis/cash_sim_7_cache/
Ignored: analysis/correlated_z_2_cache/
Ignored: analysis/correlated_z_3_cache/
Ignored: analysis/correlated_z_cache/
Ignored: analysis/create_null_cache/
Ignored: analysis/cutoff_null_cache/
Ignored: analysis/design_matrix_2_cache/
Ignored: analysis/design_matrix_cache/
Ignored: analysis/diagnostic_ash_cache/
Ignored: analysis/diagnostic_correlated_z_2_cache/
Ignored: analysis/diagnostic_correlated_z_3_cache/
Ignored: analysis/diagnostic_correlated_z_cache/
Ignored: analysis/diagnostic_plot_2_cache/
Ignored: analysis/diagnostic_plot_cache/
Ignored: analysis/efron_leukemia_cache/
Ignored: analysis/fitting_normal_cache/
Ignored: analysis/gaussian_derivatives_2_cache/
Ignored: analysis/gaussian_derivatives_3_cache/
Ignored: analysis/gaussian_derivatives_4_cache/
Ignored: analysis/gaussian_derivatives_5_cache/
Ignored: analysis/gaussian_derivatives_cache/
Ignored: analysis/gd-ash_cache/
Ignored: analysis/gd_delta_cache/
Ignored: analysis/gd_lik_2_cache/
Ignored: analysis/gd_lik_cache/
Ignored: analysis/gd_w_cache/
Ignored: analysis/knockoff_10_cache/
Ignored: analysis/knockoff_2_cache/
Ignored: analysis/knockoff_3_cache/
Ignored: analysis/knockoff_4_cache/
Ignored: analysis/knockoff_5_cache/
Ignored: analysis/knockoff_6_cache/
Ignored: analysis/knockoff_7_cache/
Ignored: analysis/knockoff_8_cache/
Ignored: analysis/knockoff_9_cache/
Ignored: analysis/knockoff_cache/
Ignored: analysis/knockoff_var_cache/
Ignored: analysis/marginal_z_alternative_cache/
Ignored: analysis/marginal_z_cache/
Ignored: analysis/mosek_reg_2_cache/
Ignored: analysis/mosek_reg_4_cache/
Ignored: analysis/mosek_reg_5_cache/
Ignored: analysis/mosek_reg_6_cache/
Ignored: analysis/mosek_reg_cache/
Ignored: analysis/pihat0_null_cache/
Ignored: analysis/plot_diagnostic_cache/
Ignored: analysis/poster_obayes17_cache/
Ignored: analysis/real_data_simulation_2_cache/
Ignored: analysis/real_data_simulation_3_cache/
Ignored: analysis/real_data_simulation_4_cache/
Ignored: analysis/real_data_simulation_5_cache/
Ignored: analysis/real_data_simulation_cache/
Ignored: analysis/rmosek_primal_dual_2_cache/
Ignored: analysis/rmosek_primal_dual_cache/
Ignored: analysis/seqgendiff_cache/
Ignored: analysis/simulated_correlated_null_2_cache/
Ignored: analysis/simulated_correlated_null_3_cache/
Ignored: analysis/simulated_correlated_null_cache/
Ignored: analysis/simulation_real_se_2_cache/
Ignored: analysis/simulation_real_se_cache/
Ignored: analysis/smemo_2_cache/
Ignored: data/LSI/
Ignored: docs/.DS_Store
Ignored: docs/figure/.DS_Store
Ignored: output/fig/
Unstaged changes:
Deleted: analysis/cash_plots_fdp.Rmd
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
File | Version | Author | Date | Message |
---|---|---|---|---|
rmd | cc0ab83 | Lei Sun | 2018-05-11 | update |
html | 0f36d99 | LSun | 2017-12-21 | Build site. |
html | 853a484 | LSun | 2017-11-07 | Build site. |
html | 4f032ad | LSun | 2017-11-05 | transfer |
html | 7c74e1a | LSun | 2017-06-23 | Build site. |
rmd | b9c4ac9 | LSun | 2017-06-23 | wflow_publish(“rmosek_primal_dual_2.rmd”) |
Following previous simulation, we are adding \(l_1\) regularization to the primal form such that
\[ \begin{array}{rl} \min\limits_{f \in \mathbb{R}^m, \ \ g \in \mathbb{R}^n} & -\sum\limits_{i = 1}^n\log\left(g_i\right) + \sum\limits_{j = 1}^m\lambda_j\left|f_j\right| \\ \text{s.t.} & Af + a = g\\ & g \geq 0 \ . \end{array} \]
Its dual form is
\[ \begin{array}{rl} \min\limits_{\nu \in \mathbb{R}^n} & a^T\nu-\sum\limits_{i = 1}^n\log\left(\nu_i\right) \\ \text{s.t.} & \left|A^T\nu\right| \leq \lambda\\ & \nu\geq0 \ . \end{array} \]
Right now we haven’t figured out how to program the \(l_1\) regularized primal form in Rmosek
, so here we are only comparing the dual form with or without regularization.
Let \(\lambda\) be
\[ \lambda_i = \begin{cases} 0 & i \text{ odd ;}\\ a / \rho^{i/2} & i \text{ even .}\\ \end{cases} \] with \(a = 10\), \(\rho = 0.5\). \(n = 10^4\), \(m = 10\), \(A\) and \(a\) are generated in the same way.
The dual optimization in all \(1000\) simulation trials reaches the optimal solution both with and without regularization.
sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.0.1 Rcpp_0.12.16 digest_0.6.15
[4] rprojroot_1.3-2 R.methodsS3_1.7.1 backports_1.1.2
[7] git2r_0.21.0 magrittr_1.5 evaluate_0.10.1
[10] stringi_1.1.6 whisker_0.3-2 R.oo_1.21.0
[13] R.utils_2.6.0 rmarkdown_1.9 tools_3.4.3
[16] stringr_1.3.0 yaml_2.1.18 compiler_3.4.3
[19] htmltools_0.3.6 knitr_1.20
This reproducible R Markdown analysis was created with workflowr 1.0.1