ipss 1.1.2

Python implementation of integrated path stability selection (IPSS)

Integrated path stability selection (IPSS)

Fast, flexible feature selection with false discovery control

Associated papers

• Integrated path stability selection
  Accepted in Journal of the American Statistical Association and available on arXiv

• Nonparametric IPSS: Fast, flexible feature selection with false discovery control
  Published in Bioinformatics and available on arXiv

"Integrated path stability selection" introduces IPSS and applies it to regularized regression models like lasso.
"Nonparametric IPSS: Fast, flexible feature selection with false discovery control" extends IPSS to arbitrary feature importance scores, with a focus on scores from gradient boosting and random forests.

Installation

pip install ipss

Usage

from ipss import ipss

# load n-by-p feature matrix X and n-by-1 response vector y

# run ipss
ipss_output = ipss(X,y)

# select features based on target FDR
target_fdr = 0.1
q_values = ipss_output['q_values']
selected_features = [idx for idx, q_value in q_values.items() if q_value <= target_fdr]
print(f'Selected features (target FDR = {target_fdr}): {selected_features}')

Outputs

ipss_output = ipss(X,y) is a dictionary containing:

• efp_scores: Dictionary whose keys are feature indices and values are their efp scores (dict of length p).
• q_values: Dictionary whose keys are feature indices and values are their q-values (dict of length p).
• runtime: Runtime of the algorithm in seconds (float).
• selected_features: Indices of features selected by IPSS; empty list if target_fp and target_fdr are not specified (list of ints).
• stability_paths: Estimated selection probabilities at each parameter value (array of shape (n_alphas, p))

Selecting features

Each feature (column of X) is assigned:

• a q-value: the minimum false discovery rate (FDR) at which the feature is selected
• an efp score: the minimum expected number of false positives (E(FP)) at which the feature is selected

To select features:

• Control FDR by choosing all features with q_value ≤ target_fdr
  Example: Selecting features with q_value ≤ 0.1 controls the FDR at level 0.1
• Control E(FP) by choosing all features with efp_score ≤ target_fp
  Example: Selecting features with efp_score ≤ 2 controls the E(FP) at level 2

In general, we recommend selecting features using q_values or efp_scores after running ipss, rather than specifying target_fdr or target_fp as arguments (see General observations/recommendations).

Usage with custom feature importance scores

For custom feature importance scores, selector must be a function that takes X and y as inputs (as well as an optional dictionary of arguments selector_args specific to the feature importance function), and returns a list or NumPy array of importance scores, one per feature, that must align with the column order in X.

from ipss import ipss

# define custom feature importance function based on ridge regression
from sklearn.linear_model import Ridge
selector_args = {'alpha':1}
def ridge_selector(X, y, alpha):
	model = Ridge(alpha=alpha)
	model.fit(X,y)
	feature_importance_scores = np.abs(model.coef_)
	return feature_importance_scores

# load n-by-p feature matrix X and n-by-1 response vector y

# run ipss
ipss_output = ipss(X, y, selector=ridge_selector, selector_args=selector_args)

# select features based on target FDR
target_fdr = 0.1
q_values = ipss_output['q_values']
selected_features = [idx for idx, q_value in q_values.items() if q_value <= target_fdr]
print(f'Selected features (target FDR = {target_fdr}): {selected_features}')

Examples

The examples folder includes analyses of

• Simulated data: simple_example.py (Open in Google Colab).
• Cancer data: cancer.py (Open in Google Colab).

Full list of ipss arguments

Required arguments:

• X: Features (array of shape (n,p)), where n is the number of samples and p is the number of features.
• y: Response (array of shape (n,) or (n, 1)). ipss automatically detects if y is binary.

Optional arguments:

• selector: Base algorithm to use (str; default 'gb'). Options:
  • 'gb': Gradient boosting (uses XGBoost).
  • 'l1': L1-regularized linear or logistic regression (uses scikit-learn).
  • 'rf': Random forest (uses scikit-learn).
  • Custom function that computes feature importance scores (see usage example above).
• selector_args: Arguments for the base algorithm (dict; default None).
• preselect: Preselect/filter features prior to subsampling (bool; default True).
• preselect_args: Arguments for preselection algorithm (dict; default None).
• target_fp: Target number of false positives to control (positive float; default None).
• target_fdr: Target false discovery rate (FDR) (positive float; default None).
• B: Number of subsampling steps (int; default 100 for IPSSGB, 50 otherwise).
• n_alphas: Number of values in the regularization or threshold grid (int; default 25 if 'l1' else 100).
• ipss_function: Function to apply to selection probabilities (str; default 'h2' if 'l1' else 'h3'). Options:
  • 'h1': Linear function, h1(x) = 2x - 1 if x >= 0.5 else 0.
  • 'h2': Quadratic function, h2(x) = (2x - 1)**2 if x >= 0.5 else 0.
  • 'h3': Cubic function, h3(x) = (2x - 1)**3 if x >= 0.5 else 0.
• cutoff: Maximum value of the theoretical integral bound I(Lambda) (positive float; default 0.05).
• delta: Defines probability measure; see Associated papers (float; defaults depend on selector).
• standardize_X: Scale features to have mean 0, standard deviation 1 (bool; default None).
• center_y: Center response to have mean 0 (bool; default None).
• n_jobs: Number of jobs to run in parallel (int; default 1).

General observations/recommendations:

• IPSSGB is usually best for capturing nonlinear relationships between features and response
• IPSSL is usually best for capturing linear relationships between features and response
• For FDR control, we generally recommend computing q-values with ipss and then using them to select features at the desired FDR threshold (as in the Usage section above), rather than specifying target_fdr, which should be left as None. This provides greater flexibility when selecting features.
• For E(FP) control, we generally recommend computing efp scores with ipss and then using them to select features at the desired false positive threshold, rather than specifying target_fp, which should be left as None. This provides greater flexibility when selecting features.
• In general, all other parameters should not be changed
  • selector_args include, e.g., decision tree parameters for tree-based models
  • Results are robust to B provided it is greater than 25
  • 'h3' is less conservative than 'h2' which is less conservative than 'h1'.
  • Preselection can significantly reduce computation time.
  • Results are robust to cutoff provided it is between 0.025 and 0.1.
  • Results are robust to delta provided it is between 0 and 1.5.
  • Standardization is automatically applied for IPSSL. IPSSGB and IPSSRF are unaffected by this.
  • Centering y is automatically applied for IPSSL. IPSSGB and IPSSRF are unaffected by this.