Fast group lasso regularised linear models in a sklearnstyle API.
Project description
The group lasso [1] regulariser is a well known method to achieve structured sparsity in machine learning and statistics. The idea is to create nonoverlapping groups of covariates, and recover regression weights in which only a sparse set of these covariate groups have nonzero components.
There are several reasons for why this might be a good idea. Say for example that we have a set of sensors and each of these sensors generate five measurements. We don’t want to maintain an unneccesary number of sensors. If we try normal LASSO regression, then we will get sparse components. However, these sparse components might not correspond to a sparse set of sensors, since they each generate five measurements. If we instead use group LASSO with measurements grouped by which sensor they were measured by, then we will get a sparse set of sensors.
An extension of the group lasso regulariser is the sparse group lasso regulariser [2], which imposes both groupwise sparsity and coefficientwise sparsity. This is done by combining the group lasso penalty with the traditional lasso penalty. In this library, I have implemented an efficient sparse group lasso solver being fully scikitlearn API compliant.
About this project
This project is developed by Yngve Mardal Moe and released under an MIT lisence. I am still working out a few things so changes might come rapidly.
Installation guide
Grouplasso requires Python 3.5+, numpy and scikitlearn. To install grouplasso via pip, simply run the command:
pip install grouplasso
Alternatively, you can manually pull this repository and run the setup.py file:
git clone https://github.com/yngvem/grouplasso.git cd grouplasso python setup.py
Documentation
You can read the full documentation on readthedocs.
Examples
Group lasso regression
The group lasso regulariser is implemented following the scikitlearn API, making it easy to use for those familiar with the Python ML ecosystem.
import numpy as np from group_lasso import GroupLasso # Dataset parameters num_data_points = 10_000 num_features = 500 num_groups = 25 assert num_features % num_groups == 0 # Generate data matrix X = np.random.standard_normal((num_data_points, num_features)) # Generate coefficients and intercept w = np.random.standard_normal((500, 1)) intercept = 2 # Generate groups and randomly set coefficients to zero groups = np.array([[group]*20 for group in range(25)]).ravel() for group in range(num_groups): w[groups == group] *= np.random.random() < 0.8 # Generate target vector: y = X@w + intercept noise = np.random.standard_normal(y.shape) noise /= np.linalg.norm(noise) noise *= 0.3*np.linalg.norm(y) y += noise # Generate group lasso object and fit the model gl = GroupLasso(groups=groups, reg=.05) gl.fit(X, y) estimated_w = gl.coef_ estimated_intercept = gl.intercept_[0] # Evaluate the model coef_correlation = np.corrcoef(w.ravel(), estimated_w.ravel())[0, 1] print( "True intercept: {intercept:.2f}. Estimated intercept: {estimated_intercept:.2f}".format( intercept=intercept, estimated_intercept=estimated_intercept ) ) print( "Correlation between true and estimated coefficients: {coef_correlation:.2f}".format( coef_correlation=coef_correlation ) )
True intercept: 2.00. Estimated intercept: 1.53 Correlation between true and estimated coefficients: 0.98
Group lasso as a transformer
Group lasso regression can also be used as a transformer
import numpy as np from sklearn.pipeline import Pipeline from sklearn.linear_model import Ridge from group_lasso import GroupLasso # Dataset parameters num_data_points = 10_000 num_features = 500 num_groups = 25 assert num_features % num_groups == 0 # Generate data matrix X = np.random.standard_normal((num_data_points, num_features)) # Generate coefficients and intercept w = np.random.standard_normal((500, 1)) intercept = 2 # Generate groups and randomly set coefficients to zero groups = np.array([[group]*20 for group in range(25)]).ravel() for group in range(num_groups): w[groups == group] *= np.random.random() < 0.8 # Generate target vector: y = X@w + intercept noise = np.random.standard_normal(y.shape) noise /= np.linalg.norm(noise) noise *= 0.3*np.linalg.norm(y) y += noise # Generate group lasso object and fit the model # We use an artificially high regularisation coefficient since # we want to use group lasso as a variable selection algorithm. gl = GroupLasso(groups=groups, group_reg=0.1, l1_reg=0.05) gl.fit(X, y) new_X = gl.transform(X) # Evaluate the model predicted_y = gl.predict(X) R_squared = 1  np.sum((y  predicted_y)**2)/np.sum(y**2) print("The rows with zerovalued coefficients have now been removed from the dataset.") print("The new shape is:", new_X.shape) print("The R^2 statistic for the group lasso model is: {R_squared:.2f}".format(R_squared=R_squared)) print("This is very low since the regularisation is so high." # Use group lasso in a scikitlearn pipeline pipe = Pipeline( memory=None, steps=[ ('variable_selection', GroupLasso(groups=groups, reg=.1)), ('regressor', Ridge(alpha=0.1)) ] ) pipe.fit(X, y) predicted_y = pipe.predict(X) R_squared = 1  np.sum((y  predicted_y)**2)/np.sum(y**2) print("The R^2 statistic for the pipeline is: {R_squared:.2f}".format(R_squared=R_squared))
The rows with zerovalued coefficients have now been removed from the dataset. The new shape is: (10000, 280) The R^2 statistic for the group lasso model is: 0.17 This is very low since the regularisation is so high. The R^2 statistic for the pipeline is: 0.72
Further work
 Fully test with sparse arrays and make examples
 Make it easier to work with categorical data
 Poisson regression
Implementation details
The problem is solved using the FISTA optimiser [3] with a gradientbased adaptive restarting scheme [4]. No line search is currently implemented, but I hope to look at that later.
Although fast, the FISTA optimiser does not achieve as low loss values as the significantly slower second order interior point methods. This might, at first glance, seem like a problem. However, it does recover the sparsity patterns of the data, which can be used to train a new model with the given subset of the features.
Also, even though the FISTA optimiser is not meant for stochastic optimisation, it has to my experience not suffered a large fall in performance when the mini batch was large enough. I have therefore implemented minibatch optimisation using FISTA, and thus been able to fit models based on data with ~500 columns and 10 000 000 rows on my moderately priced laptop.
Finally, we note that since FISTA uses Nesterov acceleration, is not a descent algorithm. We can therefore not expect the loss to decrease monotonically.
References
[1]  Yuan, M. and Lin, Y. (2006), Model selection and estimation in regression with grouped variables. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 68: 4967. doi:10.1111/j.14679868.2005.00532.x 
[2]  Simon, N., Friedman, J., Hastie, T., & Tibshirani, R. (2013). A sparsegroup lasso. Journal of Computational and Graphical Statistics, 22(2), 231245. 
[3]  Beck, A. and Teboulle, M. (2009), A Fast Iterative ShrinkageThresholding Algorithm for Linear Inverse Problems. SIAM Journal on Imaging Sciences 2009 2:1, 183202. doi:10.1137/080716542 
[4]  O’Donoghue, B. & Candès, E. (2015), Adaptive Restart for Accelerated Gradient Schemes. Found Comput Math 15: 715. doi:10.1007/s102080139150 
Project details
Release history Release notifications  RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Filename, size  File type  Python version  Upload date  Hashes 

Filename, size group_lasso1.2.1py3noneany.whl (14.9 kB)  File type Wheel  Python version py3  Upload date  Hashes View 
Filename, size grouplasso1.2.1.tar.gz (135.3 kB)  File type Source  Python version None  Upload date  Hashes View 
Hashes for group_lasso1.2.1py3noneany.whl
Algorithm  Hash digest  

SHA256  eee8eff9707eec820759832a56e69e2b6916bae8956c730f6d6f5fe63b482c27 

MD5  bf69058e92b570b55430e32161fd431e 

BLAKE2256  575b620f994d27fcbcead88484ea313e45cab432d76a90708f0a5598919022c5 