Here is the original explanation for more information by Hastie. Learn more. How to use glmnet in R for classification problems Ask Question. Asked 7 years, 1 month ago. Active 4 years, 7 months ago. Viewed 5k times. I want to use the glmnet in R to do classification problems. The sample data is as follows: y,x1,x2,x3,x4,x5,x6,x7,x8,x9,x10,x11 1,0. How can I restrict the output value to [0,1] thus I use it to do classification problems?
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OLS defines the function by which parameter estimates intercepts and slopes are calculated. It involves minimising the sum of squared residuals. L2 regularisation is a small addition to the OLS function that weights residuals in a particular way to make the parameters more stable.
The outcome is typically a model that fits the training data less well than OLS but generalises better because it is less sensitive to extreme variance in the data such as outliers. The glmnet package provides the functionality for ridge regression via glmnet.
Important things to know:. Because, unlike OLS regression done with lmridge regression involves tuning a hyperparameter, lambda, glmnet runs the model many times for different values of lambda.
We can automatically find a value for lambda that is optimal by using cv. The lowest point in the curve indicates the optimal lambda: the log value of lambda that best minimised the error in cross-validation. We can extract this values as:. And we can extract all of the fitted models like the object returned by glmnet via:. These are the two things we need to predict new data.
For example, predicting values and computing an R 2 value for the data we trained on:. By producing more stable parameters than OLS, ridge regression should be less prone to overfitting training data. Ridge regression might, therefore, predict training data less well than OLS, but better generalise to new data. Below is a simulation experiment I created to compare the prediction accuracy of ridge regression and OLS on training and test data.
Now run the simulations for varying numbers of training data and relative proportions of features takes some time :. For varying numbers of training data averaging over number of featureshow well do both models predict the training and test data? As hypothesised, OLS fits the training data better but Ridge regression better generalises to new test data.
Further, these effects are more pronounced when the number of training observations is low. For varying relative proportions of features averaging over numbers of training data how well do both models predict the training and test data?
Again, OLS has performed slightly better on training data, but Ridge better on test data. The effects are more pronounced when the number of features is relatively high compared to the number of training observations.
The following plot helps to visualise the relative advantage or disadvantage of Ridge to OLS over the number of observations and features:. OLS performs slightly better on the training data under similar conditions, indicating that it is more prone to overfitting training data than when ridge regularisation is employed. To leave a comment for the author, please follow the link and comment on their blog: blogR.
It only takes a minute to sign up. I'd like to pick the optimal lambda and alpha using the Glmnet package. I'm open to all models Ridge, Lasso, Elastic. Right now, I'm using the following code. Questions: How do I know what is the ideal alpha and lambda?
Is this the right approach and utilization of Glmnet?
What questions am I not considering that should be? The data:. It appears that the default in glmnet is to select lambda from a range of values from min. The range of values chosen by default is just a linear range on the log scale from a the minimum value like 0, or some value for which we set no features to zero to the maximum value, which they set to the smallest value for which the model would set all features to zero.
From the glmnet documentation :. The program then generates nlambda values linear on the log scale from lambda. Sign up to join this community. The best answers are voted up and rise to the top. Home Questions Tags Users Unanswered. Asked 2 years, 3 months ago. Active 1 year, 3 months ago.
Viewed 2k times. Active Oldest Votes. From the glmnet documentation : lambda can be provided, but is typically not and the program constructs a sequence. Will C Will C 71 4 4 bronze badges. Sign up or log in Sign up using Google. Sign up using Facebook. Sign up using Email and Password. Post as a guest Name. Email Required, but never shown.Fit a generalized linear model via penalized maximum likelihood.
The regularization path is computed for the lasso or elasticnet penalty at a grid of values for the regularization parameter lambda. Can deal with all shapes of data, including very large sparse data matrices. Fits linear, logistic and multinomial, poisson, and Cox regression models.
For either "binomial" or "multinomial"if y is presented as a vector, it will be coerced into a factor. The latter is a binary variable, with '1' indicating death, and '0' indicating right censored. The function Surv in package survival produces such a matrix. Response type see above. Either a character string representing one of the built-in families, or else a glm family object. Can be total counts if responses are proportion matrices. Default is 1 for each observation.
A vector of length nobs that is included in the linear predictor a nobs x nc matrix for the "multinomial" family. Useful for the "poisson" family e. Default is NULL. If supplied, then values must also be supplied to the predict function.
Smallest value for lambdaas a fraction of lambda. The default depends on the sample size nobs relative to the number of variables nvars. A very small value of lambda. This is undefined for "binomial" and "multinomial" models, and glmnet will exit gracefully when the percentage deviance explained is almost 1. A user supplied lambda sequence.
Typical usage is to have the program compute its own lambda sequence based on nlambda and lambda. Supplying a value of lambda overrides this. Avoid supplying a single value for lambda for predictions after CV use predict instead. Supply instead a decreasing sequence of lambda values.
Logical flag for x variable standardization, prior to fitting the model sequence.LASSO Regression in R (Part One)
The coefficients are always returned on the original scale. If variables are in the same units already, you might not wish to standardize. Convergence threshold for coordinate descent. Each inner coordinate-descent loop continues until the maximum change in the objective after any coefficient update is less than thresh times the null deviance. Defaults value is 1E Limit the maximum number of variables in the model.
Useful for very large nvarsif a partial path is desired. Indices of variables to be excluded from the model. Default is none. Equivalent to an infinite penalty factor next item. Separate penalty factors can be applied to each coefficient. This is a number that multiplies lambda to allow differential shrinkage. Can be 0 for some variables, which implies no shrinkage, and that variable is always included in the model.
It only takes a minute to sign up. Is there a way to manually add an intercept term manually into the glmnet function of R rather than using the built-in intercept feature? I tried adding a column of ones to my x matrix, making it a x matrix, and then ran.
I also tried running. This code also results in a 0 value for the intercept term for all lambda values. Has anyone had success manually inputting an intercept term into glmnet? Sign up to join this community. The best answers are voted up and rise to the top.
Home Questions Tags Users Unanswered. Asked 5 years, 1 month ago. Active 5 years, 1 month ago. Viewed times. I would alternatively like to be able to change the penalty for the intercept -- I have a unit conversion issue where the L2 norm should weight the intercept differently than the slope.
Then we take whichever model has the best performance as the final model. A subtler method, known as stepwise selectionreduces the chances of over-fitting by only looking at the most promising models. A hybrid approach is to consider use both forward and backward selection. This is done by creating two lists of variables at each step, one from forward and one from backward selection.
Then variables from both lists are tested to see if adding or subtracting from the current model would improve the fit or not. Otherwise there will be conflicts as there are functions named select and filter in both. Alternatively, specify the library in the function call with dplyr::select.
One of the main weaknesses of the GLM, including all linear models in this chapter, is that the features need to be selected by hand. Stepwise selection helps to improve this process, but fails when the inputs are correlated and often has a strong dependence on seemingly arbitrary choices of evaluation metrics such as using AIC or BIC and forward or backward directions. The Bias Variance Trade-off is about finding the lowest error by changing the flexibility of the model.
Penalization methods use a parameter to control for this flexibility directly. Earlier on we said that the linear model minimizes the sum of square terms, known as the residual sum of squares RSS.
This loss function can be modified so that models which include more and larger coefficients are considered as worse. Ridge regression adds a penalty term which is proportional to the square of the sum of the coefficients. Just as with Ridge regression, we want to favor simpler models; however, we also want to select variables. This is the same as forcing some coefficients to be equal to 0.
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Instead of taking the square of the coefficients L2 normwe take the absolute value L1 norm. Note : While any response family is possible with penalized regression, in R, only the Gaussian family is possible in the library glmnetand so this is the only type of question that the SOA can ask. The Elastic Net uses a penalty term which is between the L1 and L2 norms. The loss function is then. Luckily, none of this needs to be memorized.
On the exam, read the documentation in R to refresh your memory. For the Elastic Net, the function is glmnetand so running? Shortcut : When using complicated functions on the exam, use? We will use the glmnet package in order to perform ridge regression and the lasso. The main function in this package is glmnetwhich can be used to fit ridge regression models, lasso models, and more. This function has slightly different syntax from other model-fitting functions that we have encountered thus far in this book.
I have been about to run the glmnet. However, I have a tough time understanding the output. My goal is to get the list of genes and their respective coefficients so I can rank the list of gene based on how relevant they are at separating my two group of labels.
Here you can see no variables were dropped or they would have. At least I would when modeling expression. When using predict. Also check this post it contains some other relevant information. I explained also how it works in a blog post. Learn more. Extract data from glmnet output data Ask Question.
Asked 2 years, 10 months ago. Active 2 years, 10 months ago. Viewed times. Additionally, anyone know if there is a way to use L0-norm for feature selection in R? Thank you so much! Son nguyen. Son nguyen Son nguyen 29 3 3 bronze badges. Active Oldest Votes. Length Width 1. Width 2. Sign up or log in Sign up using Google.
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Podcast Ben answers his first question on Stack Overflow.