diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 6af47c2..d1679fd 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ ci: repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 + rev: v4.5.0 hooks: - id: check-yaml - id: fix-encoding-pragma @@ -38,7 +38,7 @@ repos: - --profile=black - repo: https://github.com/asottile/pyupgrade - rev: v3.13.0 + rev: v3.15.0 hooks: - id: pyupgrade args: [--py38-plus] @@ -71,6 +71,6 @@ repos: - id: rst-inline-touching-normal - repo: https://github.com/pre-commit/mirrors-mypy - rev: 'v1.5.1' # Use the sha / tag you want to point at + rev: 'v1.6.0' # Use the sha / tag you want to point at hooks: - id: mypy diff --git a/paper/paper.md b/paper/paper.md index 84e7e98..3f6be27 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -73,6 +73,17 @@ available solvers. `sparse-lm` satisfies the need for a flexible and comprehensi library that enables easy experimentation and comparisons of different sparse linear regression algorithms within a single package. +Statistical regression models with structured sparsity (involving grouped covariates, +sparse grouped covariates, and hierarchical relationships between covariates terms) +parametrized via Group Lasso or Best Subset Selection based objetives have been used in a +wide range of scientific disciplines, including genomics [@Chen:2021], bioinformatics [@Ma:2007], +medicine [@Kim:2012], econometrics [@Athey:2017], chemistry [@Gu:2018], and materials science +[@Leong:2019]. The flexible implementation of sparse linear regression models in `sparse-lm` +allows researchers to easily experiment and choose the best regression model for their +specific problem. `sparse-lm` has already been used to build linear models with +structured sparsity in a handful of material science studies +[@Barroso-Luque:2022; @Zhong:2022; @Xie:2023, @Zhong:2023]. + # Background ![Schematic of a linear model with grouped covariates with hierarchical relations. @@ -137,18 +148,6 @@ introduce hierarchical structure into the model. Finally, we have also included $\ell_2$ regularization term controlled by the hyperparameter $\lambda$, which is useful when dealing with poorly conditioned design matrices. -Statistical regression models with structured sparsity (involving grouped covariates, -sparse grouped covariates, and hierarchical relationships between covariates terms) -parametrized via Group Lasso or Best Subset Selection based objetives have been used in a -wide range of scientific disciplines, including genomics [@Chen:2021], bioinformatics [@Ma:2007], -medicine [@Kim:2012], econometrics [@Athey:2017], chemistry [@Gu:2018], and materials science -[@Leong:2019]. The flexible implementation of sparse linear regression models in `sparse-lm` -allows researchers to easily experiment and choose the best regression model for their -specific problem. `sparse-lm` has already been used to build linear models with -structured sparsity in a handful of material science studies -[@Barroso-Luque:2022; @Zhong:2022; @Xie:2023, @Zhong:2023]. - - # Usage Since the linear regression models in `sparse-lm` are implemented to be compatible with diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..8a30e10 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,5 @@ +numpy >=1.23 +cvxpy >=1.2 +scikit-learn > 1.2 +scipy >=1.9 +joblib \ No newline at end of file