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Penalized Regression, Part 2

Penalized Regression, Part 2. Penalized Regression. Recall in penalized regression, we re-write our loss function to include not only the squared error loss but a penalty term Our goal then becomes to minimize our a loss function (i.e. SS)

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Penalized Regression, Part 2

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  1. Penalized Regression, Part 2

  2. Penalized Regression Recall in penalized regression, we re-write our loss function to include not only the squared error loss but a penalty term Our goal then becomes to minimize our a loss function (i.e. SS) In the regression setting we can write M(q ) in terms of our regression parameters b as follows The penalty function takes the form

  3. Ridge Regression Last class we discussed ridge regression as an alternative to OLS when covariates are collinear Ridge regression can reduce the variability and improve accuracy of a regression model However, there is not a means of variable selection in ridge regression Ideally we want to be able to reduce the variability in a model but also be able to select which variables are most strongly associated with our outcome

  4. The Lasso versus Ridge Regression In ridge regression, the new function is Consider instead the estimator which minimizes The only change is to the penalty function and while the change is subtle, is has a big impact on our regression estimator

  5. The Lasso The name lasso stands for “Least Absolute Shrinkage and Selection Operator” Like ridge regression, penalizing the absolute values of the coefficients shrinks them towards zero But in the lasso, some coefficients are shrunk completely to zero Solutions where multiple coefficient estimates are identically zero are called sparse Thus the penalty performs a continuous variable selection, hence the name

  6. Geometry of Ridge versus Lasso2-dimensional case Solid areas represent the constraint regions The ellipses represent the contours of the least square error function

  7. The Lasso Because the lasso penalty has an absolute value operation, the objective function is not differentiable and therefore lacks a closed form As a result, we must use optimization algorithms to find the minimum Examples of these algorithms include -Quadratic programming (limit ~100 predictors) -Least Angle Regression/LAR (limit ~10,000 predictors)

  8. Selection of l Since lasso is not a linear estimator, we have no H matrix such that Thus determining the degrees of freedom are more difficult to estimate One means is to estimate the degrees of freedom based on the number of non-zero parameters in the model and then use AIC, BIC or Cp to select the best l Alternatively (and often more preferred) we could select l via cross-validation

  9. Forward Stagewise Selection Alternative method for variable subset selection designed to handle correlated predictors Iterative process that begins with all coefficients equal to zero and build regression function in successive small steps Similar algorithm to forward selection in that predictors added successively to the model However, it is much more cautious than forward stepwise model selection -e.g. for a model with 10 possible predictors stepwise takes 10 steps at most, stagewise may take 5000+

  10. Forward Stagewise Selection Stagewise algorithm: (1) Initialize model such that (2) Find the predictor Xj1 that is most correlated with r and add it to the model (here ) (3) Update -Note, h is a small constant controlling step-length (4) Update (5) Repeat steps 2 thru 4 until

  11. Stagewise versus Lasso Although the algorithms look entirely different, their results are very similar! They will trace very similar paths for addition of predictors to the model They both represent special cases of a method called least angle regression (LAR)

  12. Least Angle Regression LAR algorithm: (1) Initialize model such that Also initialize an empty “active set” A (subset of indices) (2) Find the predictor that is most correlated with r where ; update the active set to include (3) Move toward until some other covariate has the same correlation with r that does. Update the active set to include (4) Update rand move along towards the joint OLS direction for the regression of r on until a third covariate is as correlated with r as the first two predictors.Update the active set to include (5) Continue until all k covariates have been added to the model

  13. In Pictures Consider a case where we have 2 predictors… Efron et al. 2004

  14. Relationship Between LAR and Lasso LAR is a more general method than lasso A modification of the LAR algorithm produces the entire lasso path for l varied from 0 to infinity Modification occurs if a previously non-zero coefficient estimated to be zero at some point in the algorithm If this occurs, the LAR algorithm is modified such that the coefficient is removed from the active set and the joint direction is recomputed This modification is the most frequently implements version of LAR

  15. Relationship Bt/ LAR and Stagewise LAR is also a more general method than stagewise selection Can also reproduce stagewise results using modified LAR Start with the LAR algorithm and determine the best direction at each stage If the direction for any predictor in the active set doesn’t agree in sign with the correlation between r and Xj, adjust to move in the direction of corr(r, Xj) As step sizes go to 0, we get a modified version of the LAR algorithm

  16. Summary of the Three Methods • LARS • Uses least square directions in the active set of variables • Lasso • Uses the least square directions • If the variable crosses 0, it is removed from the active set • Forward stagewise • Uses non-negative least squares directions in the active set

  17. Degrees Freedom in LAR and lasso Consider fitting a LAR model with k < pparameters Equivalently use a lasso bound t that constrains the full regression fit General definition for the effective degrees of freedom (edf) for an adaptively fit model: For LARS at the kth step, the edf for the fit vector is exactly k For lasso, at any stage in the fit the effective degrees of freedom is approximately the number of predictors in the model

  18. Software Packages What if we consider lasso, forward stagewise, or LAR as alternatives? There are 2 packages in R that will allow us to do this -lars -glmnet The lars package has the advantage of being able to fit all three model types (plus a typical forward stepwise selection algorithm) However, the glmnet package can fit lasso regression models for different types of regression -linear, logistic, cox-proportional hazards, multinomial, and poisson

  19. Body Fat Example Recall our regression model > summary(mod13) Call: lm(formula = PBF ~ Age + Wt + Ht + Neck + Chest + Abd + Hip + Thigh + Knee + Ankle + Bicep + Arm + Wrist, data = bodyfat, x = T) Coefficients: Estimate Std. Error t value Pr(>|t|) (Intercept) -18.18849 17.34857 -1.048 0.29551 Age 0.06208 0.03235 1.919 0.05618 . Wt -0.08844 0.05353 -1.652 0.09978 . Ht -0.06959 0.09601 -0.725 0.46925 Neck -0.47060 0.23247 -2.024 0.04405 * Chest -0.02386 0.09915 -0.241 0.81000 Abd 0.95477 0.08645 11.04 < 2e-16 *** Hip -0.20754 0.14591 -1.422 0.15622 Thigh 0.23610 0.14436 1.636 0.10326 Knee 0.01528 0.24198 0.063 0.94970 Ankle 0.17400 0.22147 0.786 0.43285 Bicep 0.18160 0.17113 1.061 0.28966 Arm 0.45202 0.19913 2.270 0.02410 * Wrist -1.62064 0.53495 -3.030 0.00272 ** Residual standard error: 4.305 on 238 degrees of freedom. Multiple R-squared: 0.749, Adjusted R-squared: 0.7353 . F-statistic: 54.65 on 13 and 238 DF, p-value: < 2.2e-16

  20. Body Fat Example LAR: >library(lars) >par(mfrow=c(2,2)) >object <- lars(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), type="lasso") >plot(object, breaks=F) >object2 <- lars(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), type="lar") >plot(object2, breaks=F) >object3 <- lars(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), type=“for") >plot(object3, breaks=F) >object4 <- lars(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), type=“stepwise") >plot(object4, breaks=F)

  21. Body Fat Example A closer look at the model: >object <- lars(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), type="lasso") > names(object) [1] "call" "type" "df" "lambda" "R2" "RSS" "Cp" "actions" [9] "entry" "Gamrat" "arc.length" "Gram" "beta" "mu" "normx" "meanx" > object$beta Age Wt Ht Neck Chest Abd Hip Thigh Knee Ankle 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.0000000 0.000000000 0.00000000 0.00000000 0.0000000 1 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.5164924 0.000000000 0.00000000 0.00000000 0.0000000 2 0.00000000 0.00000000 -0.04395065 0.00000000 0.00000000 0.5314218 0.000000000 0.00000000 0.00000000 0.0000000 3 0.01710504 0.00000000 -0.13752803 0.00000000 0.00000000 0.5621288 0.000000000 0.00000000 0.00000000 0.0000000 4 0.04880181 0.00000000 -0.15894236 0.00000000 0.00000000 0.6550929 0.000000000 0.00000000 0.00000000 0.0000000 5 0.04994577 0.00000000 -0.15905246 -0.02624509 0.00000000 0.6626603 0.000000000 0.00000000 0.00000000 0.0000000 6 0.06499276 0.00000000 -0.15911969 -0.25799496 0.00000000 0.7079872 0.000000000 0.00000000 0.00000000 0.0000000 7 0.06467180 0.00000000 -0.15921694 -0.26404701 0.00000000 0.7118167 -0.004720494 0.00000000 0.00000000 0.0000000 8 0.06022586 -0.01117359 -0.14998300 -0.29599536 0.00000000 0.7527298 -0.022557736 0.00000000 0.00000000 0.0000000 9 0.05710956 -0.02219531 -0.14039586 -0.32675736 0.00000000 0.7842966 -0.035675017 0.00000000 0.00000000 0.0000000 10 0.05853733 -0.04577935 -0.11203059 -0.39386199 0.00000000 0.8425758 -0.101022340 0.09657784 0.00000000 0.0000000 11 0.06132775 -0.07889636 -0.07798153 -0.45141574 0.00000000 0.9142944 -0.171178163 0.20141924 0.00000000 0.1259630 12 0.06214695 -0.08452690 -0.07220347 -0.46528070 -0.01582661 0.9402896 -0.194491760 0.22553958 0.00000000 0.1586161 13 0.06207865 -0.08844468 -0.06959043 -0.47060001 -0.02386415 0.9547735 -0.207541123 0.23609984 0.01528121 0.1739954 Bicep Arm Wrist 0 0.00000000 0.0000000 0.000000 1 0.00000000 0.0000000 0.000000 2 0.00000000 0.0000000 0.000000 3 0.00000000 0.0000000 0.000000 4 0.00000000 0.0000000 -1.169755 5 0.00000000 0.0000000 -1.198047 6 0.00000000 0.2175660 -1.535349 7 0.00000000 0.2236663 -1.538953 8 0.00000000 0.2834326 -1.535810 9 0.04157133 0.3117864 -1.534938 10 0.09096070 0.3635421 -1.522325 11 0.15173471 0.4229317 -1.587661 12 0.17055965 0.4425212 -1.607395 13 0.18160242 0.4520249 -1.620639

  22. Body Fat Example A closer look at the model: > names(object) [1] "call" "type" "df" "lambda" "R2" "RSS" "Cp" "actions" [9] "entry" "Gamrat" "arc.length" "Gram" "beta" "mu" "normx" "meanx" > object$df Intercept 1 2 3 4 5 6 7 8 9 10 11 12 13 14 > object$Cp 0 1 2 3 4 5 6 7 8 9 10 698.4 93.62 85.47 65.41 30.12 30.51 19.39 20.91 18.68 17.41 12.76 11 12 13 10.47 12.06 14.00

  23. Body Fat Example Glmnet: >fit<-glmnet(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), alpha=1) >fit.cv<-cv.glmnet(x=as.matrix(bodyfat[,3:15]), y=as.vector(bodyfat[,2]), alpha=1) >plot(fit.cv, sign.lambda=-1) >fit<-glmnet(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), alpha=1, 0.02123575)

  24. Body Fat Example Glmnet: >fit<-glmnet(x=as.matrix(bodyfat[,3:15]),y=as.vector(bodyfat[,2]), alpha=1) >names(fit) [1] "a0" "beta" "df" "dim" "lambda" "dev.ratio" "nulldev" "npasses" "jerr" [10] "offset" "call" "nobs" > fit$lambda [1] 6.793883455 6.190333574 5.640401401 5.139323686 4.682760334 4.266756812 3.887709897 3.542336464 3.227645056 [10] 2.940909965 2.679647629 2.441595119 2.224690538 2.027055162 1.846977168 1.682896807 1.533392893 1.397170495 [19] 1.273049719 1.159955490 1.056908242 0.963015426 0.877463790 0.799512325 0.728485854 0.663769178 0.604801754 [28] 0.551072833 0.502117041 0.457510347 0.416866389 0.379833128 0.346089800 0.315344136 0.287329832 0.261804242 [37] 0.238546274 0.217354481 0.198045308 0.180451508 0.164420694 0.149814013 0.136504949 0.124378225 0.113328806 [46] 0.103260988 0.094087566 0.085729086 0.078113150 0.071173793 0.064850910 0.059089734 0.053840365 0.049057335 [55] 0.044699216 0.040728261 0.037110075 0.033813318 0.030809436 0.028072411 0.025578535 0.023306209 0.021235749 [64] 0.019349224 0.017630292 0.016064066 0.014636978 0.013336669 0.012151876 0.011072337 0.010088701 0.009192449 [73] 0.008375817 0.007631733 0.006953750 0.006335998 0.005773126 0.005260257

  25. Body Fat Example Glmnet: >fit.cv<-cv.glmnet(x=as.matrix(bodyfat[,3:15]), y=as.vector(bodyfat[,2]), alpha=1) > names(fit.cv) [1] "lambda" "cvm" "cvsd" "cvup" "cvlo" "nzero" "name" "glmnet.fit" [9] "lambda.min" "lambda.1se" > fit.cv$lambda.min [1] 0.02123575

  26. Ridge versus Lasso Coefficient Paths Ridge

  27. Trace Plot

  28. Lasso LARS Stagewise Stepwise

  29. Body Fat Example

  30. If we remove the outliers and clean up the data before analysis…

  31. Body Fat Example What can we do in SAS? SAS can also do cross-validation However, it only fits linear regression Here’s the basic SAS code ods graphics on; proc glmselect data=bf plots=all; model pbf=age wt ht neck chest abd hip thigh knee ankle bicep arm wrist/selection=lasso(stop=none choose=AIC); run; ods graphics off;

  32. The GLMSELECT Procedure LASSO Selection Summary Effect Effect Number Step Entered Removed Effects In AIC 0 Intercept 1 1 1325.7477 ----------------------------------------------------------------------------------------------- Abd 2 2 1070.4404 Ht 3 3 1064.8357 Age 4 4 1049.4793 Wrist 5 5 1019.1226 Neck 6 6 1019.6222 Arm 7 7 1009.0982 Hip 8 8 1010.6285 Wt 9 9 1008.4396 Bicep 10 10 1007.1631 Thigh 11 11 1002.3524 Ankle 12 12 999.8569* Chest 13 13 1001.4229 13 Knee 14 14 1003.3574

  33. Penalized regression methods are most useful when -high collinearity exists -when p >> n Keep in mind you still need to look at the data first Could also consider other forms of penalized regression, though in practice alternatives are not used

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