mlr3 optimized average of ensemble - r

I try to optimize the averaged prediction of two logistic regressions in a classification task using a superlearner.
My measure of interest is classif.auc
The mlr3 help file tells me (?mlr_learners_avg)
Predictions are averaged using weights (in order of appearance in the
data) which are optimized using nonlinear optimization from the
package "nloptr" for a measure provided in measure (defaults to
classif.acc for LearnerClassifAvg and regr.mse for LearnerRegrAvg).
Learned weights can be obtained from $model. Using non-linear
optimization is implemented in the SuperLearner R package. For a more
detailed analysis the reader is referred to LeDell (2015).
I have two questions regarding this information:
When I look at the source code I think LearnerClassifAvg$new() defaults to "classif.ce", is that true?
I think I could set it to classif.auc with param_set$values <- list(measure="classif.auc",optimizer="nloptr",log_level="warn")
The help file refers to the SuperLearner package and LeDell 2015. As I understand it correctly, the proposed "AUC-Maximizing Ensembles through Metalearning" solution from the paper above is, however, not impelemented in mlr3? Or do I miss something? Could this solution be applied in mlr3? In the mlr3 book I found a paragraph regarding calling an external optimization function, would that be possible for SuperLearner?

As far as I understand it, LeDell2015 proposes and evaluate a general strategy that optimizes AUC as a black-box function by learning optimal weights. They do not really propose a best strategy or any concrete defaults so I looked into the defaults of the SuperLearner package's AUC optimization strategy.
Assuming I understood the paper correctly:
The LearnerClassifAvg basically implements what is proposed in LeDell2015 namely, it optimizes the weights for any metric using non-linear optimization. LeDell2015 focus on the special case of optimizing AUC. As you rightly pointed out, by setting the measure to "classif.auc" you get a meta-learner that optimizes AUC. The default with respect to which optimization routine is used deviates between mlr3pipelines and the SuperLearner package, where we use NLOPT_LN_COBYLA and SuperLearner ... uses the Nelder-Mead method via the optim function to minimize rank loss (from the documentation).
So in order to get exactly the same behaviour, you would need to implement a Nelder-Mead bbotk::Optimizer similar to here that simply wraps stats::optim with method Nelder-Mead and carefully compare settings and stopping criteria. I am fairly confident that NLOPT_LN_COBYLA delivers somewhat comparable results, LeDell2015 has a comparison of the different optimizers for further reference.
Thanks for spotting the error in the documentation. I agree, that the description is a little unclear and I will try to improve this!

Related

How to estimate gamma and cost parameters for SVM quickly

I want to train SVMs in R and I know there are functions such as e1071::tune.svm() that can be used to find the optimal parameters for the SVM. However, it seems there are some formulas out there (e.g. used in this report) that can give you a reasonable estimate of these parameters.
Since a grid-search for the parameters can take quite a lot of time on larger datasets and usually, one has to provide a range of possible values anyway, I wondered whether there is a package that implements formulas to get a quick estimate for the gamma and cost parameters for the SVM?
So far, I've found out that caret::train() might use such an approach to estimate sigma (which should be the reciprocal of 2*gamma^2) but I haven't tried it yet, since other calculations are still running (and will be, probably for the next days). Is there also an implementation to estimate cost or at least give a range of reasonable values?
I have found a similar question that asks for alternatives to grid-search in general. However, I would be interested in an R implementation of such alternatives and also, I hope things have developed further since the more general question was posted years ago.

R alternatives to JAGS/BUGS

Is there an R-Package I could use for Bayesian parameter estimation as an alternative to JAGS? I found an old question regarding JAGS/BUGS alternatives in R, however, the last post is already 9 years old. So maybe there are new and flexible gibbs sampling packages available in R? I want to use it to get parameter estimates for novel hierarchical hidden markov models with random effects and covariates etc. I highly value the flexibility of JAGS and think that JAGS is simply great, however, I want to write R functions that facilitate model specification and am looking for a package that I can use for parameter estimation.
There are some alternatives:
stan, with rstan R package. Stan looks well optimized but cannot do certain type of models (like binomial/poisson mixture model), since he cannot sample a discrete variable (or something like that...).
nimble
if you want highly optimized sampling based on C++, you may want to check Rcpp based solutions from Dirk Eddelbuettel

R Supervised Latent Dirichlet Allocation Package

I'm using this LDA package for R. Specifically I am trying to do supervised latent dirichlet allocation (slda). In the linked package, there's an slda.em function. However what confuses me is that it asks for alpha, eta and variance parameters. As far as I understand, I thought these parameters are unknowns in the model. So my question is, did the author of the package mean to say that these are initial guesses for the parameters? If yes, there doesn't seem to be a way of accessing them from the result of running slda.em.
Aside from coding the extra EM steps in the algorithm, is there a suggested way to guess reasonable values for these parameters?
Since you are trying to generate a supervised model, the typical approach would be to use cross validation to determine the model parameters. So you hold out some of the data as your test set, train the a model on the remaining data, and evaluate the model performance, repeating k times. You then continue to repeat with different model parameters to determine which result in the best model performance.
In the specific case of slda, I would run demo(slda) to see the author's implementation of it. When you run the demo, you'll see that he sets alpha=1.0, eta=0.1, and variance=0.25. I'd suggest using these as your starting point, and then use cross validation to determine better parameters if you need to improve model performance.

Weights argument in R gbm function

What is the weights argument for in the R gbm function? Does it implement cost-sensitive stochastic gradient boosting?
You may have already read this, but the documentation says that the weights parameter is defined in this way:
an optional vector of weights to be used in the fitting process. Must
be positive but do not need to be normalized. If keep.data=FALSE in
the initial call to gbm then it is the user’s responsibility to
resupply the weights to gbm.more.
Thus my interpretation would be that they are standard observation weights as in any statistical model.
Is it cost-sensitive? Good question. I first noticed that one of the main citations for the package is:
B. Kriegler (2007). Cost-Sensitive Stochastic Gradient Boosting Within a Quantitative Regression Framework.
so I figured it does imply cost-sensitivity, but there's not an explicit use of that term in the vignette, so if it was not apparent.
I did a little bit of a deeper dive though and found some more resources. You can find the equations describing the weights towards the end of this article which describes the package.
I also found this question being asked way back in 2009 in a mailing list, and while there was no response, I finally found a a scholarly article discussing the use of gbm and other R packages for cost-sensitive gradient boosting.
The conclusion is that gbm's quantile loss function is differentiable and can be used in cost-sensitive applications wherein over/under-estimation have different error costs, however other quantitative loss functions (aside from quantile) may be necessary/appropriate in some applications of cost-sensitive gradient boosting.
That paper is centered around gbm but also discusses other packages and if your focus is on cost-sensitive gradient boosting then you may want to look at the others they mention in the paper as well.

Does R support switching between optimizers like STATA does?

I need to implement the model show here:
http://www.ssc.upenn.edu/~fdiebold/papers/paper55/DRAfinal.pdf
The model estimation step on p.315 notes that:
"We maximize the likelihood by iterating the Marquart and
Berndt–Hall–Hall–Hausman algorithms, using numerical derivatives, optimal
stepsize, and a convergence criterion of 10^-6 for the change in the norm of the
parameter vector from one iteration to the next."
Now I know that stata supports switching between optimizers,
http://www.stata.com/manuals13/rmaximize.pdf
see bottom of p2.
Is there an R package or Matlab function/s that can do the same thing?
Specifically I need to be able to switch between BHHH and Levenberg-Marquardt.
Kind Regards
Baz
For R, check out the CRAN Task View on Optimization. Searching that page, it looks like BHHH and Marquardt are available in separate packages (minpack.lm and maxLik, respectively). You could write your own code to handle switching between them.

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