Package: sparseSEM 4.1
Anhui Huang
sparseSEM: Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework
Provides elastic net penalized maximum likelihood estimator for structural equation models (SEM). The package implements `lasso` and `elastic net` (l1/l2) penalized SEM and estimates the model parameters with an efficient block coordinate ascent algorithm that maximizes the penalized likelihood of the SEM. Hyperparameters are inferred from cross-validation (CV). A Stability Selection (STS) function is also available to provide accurate causal effect selection. The software achieves high accuracy performance through a `Network Generative Pre-trained Transformer` (Network GPT) Framework with two steps: 1) pre-trains the model to generate a complete (fully connected) graph; and 2) uses the complete graph as the initial state to fit the `elastic net` penalized SEM.
Authors:
sparseSEM_4.1.tar.gz
sparseSEM_4.1.tar.gz(r-4.5-noble)sparseSEM_4.1.tar.gz(r-4.4-noble)
sparseSEM_4.1.tgz(r-4.4-emscripten)sparseSEM_4.1.tgz(r-4.3-emscripten)
sparseSEM.pdf |sparseSEM.html✨
sparseSEM/json (API)
# Install 'sparseSEM' in R: |
install.packages('sparseSEM', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 1 months agofrom:d46e74d47a. Checks:OK: 1 WARNING: 1. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Nov 27 2024 |
R-4.5-linux-x86_64 | WARNING | Nov 27 2024 |
Exports:elasticNetSEMelasticNetSEMcvelasticNetSEMpointenSEM_stability_selectionenSEM_stability_selection_parallelenSEM_STSlassoSEM
Dependencies:
Elastic Net Enabled Sparse-Aware Maximum Likelihood for Structural Equation Models in Inferring Gene Regulatory Networks
Rendered fromsparseSEM.Rmd
usingknitr::rmarkdown
on Nov 27 2024.Last update: 2023-08-09
Started: 2023-04-21
Elastic Net Penalized Structural Equation Models
Rendered fromNetwork-Inference-via-sparseSEM.Rmd
usingknitr::rmarkdown
on Nov 27 2024.Last update: 2023-08-09
Started: 2023-06-11
Readme and manuals
Help Manual
Help page | Topics |
---|---|
sparseSEM: Elastic Net Penalized Maximum Likelihood for Structural Equation Models with Network GPT Framework | sparseSEM-package sparseSEM |
True network edges | B |
The Elastic Net penalized SEM with Network GPT Framework | elasticNetSEM |
The Elastic Net penalty for SEM with user supplied (alphas, lambdas) for grid search | elasticNetSEMcv |
The Elastic Net penalty for SEM | elasticNetSEMpoint |
Stability Selection for the Elastic Net penalized SEM | enSEM_stability_selection |
Parallel Stability Selection for the Elastic Net penalized SEM | enSEM_stability_selection_parallel |
The Lasso penalty for SEM | lassoSEM |
Missing Network Node dependent variable data | Missing |
Genotype matrix | X |
Gene expression matrix | Y |
Yeast cis-QTL Gene Regulatory Network Dataset | yeast cisQTL GRN |