[New Model]: msaenet (Multi-Step Adaptive Elastic-Net)

[coforfe]

Hello,

There is a new algorithm (regression) available and specially suitable for p>>n cases:

msaenet: Multi-Step Adaptive Elastic-Net

Multi-step adaptive elastic-net (MSAENet) algorithm for feature selection in high-dimensional regressions proposed in Xiao and Xu (2015) (pdf).

Link in CRAN: msaenet

Thanks,
Carlos.

[topepo]

Looking at this, I will have train fit models that can tune over alphas and nsteps but use tune = "aic" for a single combination of those parameters. There doesn't seem to be a way to not tune, so I'll default to AIC (but there will be a single parameter set, so no tuning occurs).

[topepo]

If you can so some testing in the next day or so, that would be a good idea.

[coforfe]

Thanks.

Sorry, I have just installed the dev version and I do not see msaenetthere..

Regards,
Carlos.

[topepo]

You can get it by sourcing this file then using method = modelInfo. Thanks

[coforfe]

Thanks.
I could run it.

I run, several models without any error.

I have tried to replicate a msaenet example (binomial/classification) and compare it with the equivalent with caret. For the same dataset both get equivalent results.

Thanks,
Carlos.

[topepo]

When I tested, it seemed that the scale parameter had the largest effect on the results.

[coforfe]

Yes, I see the same effect with scale.

I did this, just for the sake of reproducibility:

With syntetic binary data generated with msaenet function:

Not centered and with tuneLength = 5

library(caret)
library(msaenet)

cctrl0 <- trainControl(number = 1, classProbs = TRUE,
                       summaryFunction = twoClassSummary)

dat = msaenet.sim.binomial(
  n = 300, p = 500, rho = 0.6,
  coef = rep(1, 10), snr = 3, p.train = 0.7,
  seed = 1001)

tr_Y <- as.factor(ifelse(dat$y.tr == 0, "Class1", "Class2"))

set.seed(1003)
msa_caret <- train(
                      x = dat$x.tr,
                      y = tr_Y,
                      method = modelInfo,
                      tuneLength = 5,
                      trControl = cctrl0,
                      metric = "ROC"
)
plot(msa_caret)

Centered and with tuneLength = 5

To check if by scaling the data it gets any improvement:

msa_caret_cent <- train(
  x = dat$x.tr,
  y = tr_Y,
  method = modelInfo,
  tuneLength = 5,
  trControl = cctrl0,
  metric = "ROC",
  preProc = c("center", "scale")
)
plot(msa_caret_cent)

This produces an error:

Error in get_types(x) : `x` must have column names

While in this other way:

Centered but without preProc and with tuneLength = 5

msa_caret_cent <- train(
  x = scale(dat$x.tr),
  y = tr_Y,
  method = modelInfo,
  tuneLength = 5,
  trControl = cctrl0,
  metric = "ROC",
)
plot(msa_caret_cent)

It works and improves ROCa little bit.

In both cases, the highest ROC is achieved with a scale = 2.

[topepo]

Who doesn't use column names? =]

Just added a check. I'm going to close this one out.

Thanks

[nanxstats]

@coforfe @topepo -- thanks a lot for adding my method and package to caret. This is awesome! Please just let me know if there is anything I can do to make the API better.

To share some of my experience: SCAD-net and MCP-net usually do better than elastic-net in terms of reducing false positive selections. I use EBIC myself to select the optimal step, but AIC and BIC are also good choices sometimes. scale can be important, and the adaptive weights transformation is a very interesting direction to explore.

-Nan