[BioC] How to best include hyperparameter optimization in MLInterfaces?

[Vincent Carey]

On Mon, Apr 15, 2013 at 4:43 AM, Andreas Bernthaler [guest]
<guest at bioconductor.org> wrote:
>
> Hi,
>
> I am currently working with MLInterfaces and have a question regarding the optimization of hyperparameters of the learning functions (that are given to MLearn by the .methods parameter). Is it somehow possible to do optimization of hyperparameters, e.g the k in knn? Or in other words is it intended to have hyperparameter optimization included in MLInterfaces?
>

I have no immediate plans to introduce this in MLInterfaces.  The CMA
package does address
hyperparameter tuning.

> Thank you very much!
>
>  -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8
>  [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats4    grid      stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] multicore_0.1-7       BIAutils_0.2.00       RPostgreSQL_0.3-3     DBI_0.2-5             TangoR_1.0.19         R.oo_1.10.1
>  [7] R.methodsS3_1.4.2     BIProlif_0.1.69       xtable_1.7-0          XML_3.95-0.1          drc_2.3-0             plotrix_3.4-5
> [13] nlme_3.1-105          magic_1.5-2           abind_1.4-0           alr3_2.0.5            car_2.0-15            nnet_7.3-5
> [19] RODBC_1.3-6           ROCR_1.0-4            gplots_2.11.0         KernSmooth_2.23-8     caTools_1.13          bitops_1.0-5
> [25] gdata_2.12.0          gtools_2.7.0          lattice_0.20-10       logging_0.6-92        snow_0.3-10           Cairo_1.5-2
> [31] MLInterfaces_1.38.0   sfsmisc_1.0-23        annotate_1.36.0       AnnotationDbi_1.20.3  rda_1.0.2-2           rpart_4.0-3
> [37] genefilter_1.40.0     MASS_7.3-22           Biobase_2.18.0        BiocGenerics_0.4.0    ClassDiscovery_2.13.4 PreProcess_2.12.2
> [43] oompaBase_2.15.0      mclust_4.0            cluster_1.14.3
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.4   Matrix_1.0-10    mboost_2.1-3     parallel_2.15.1  RSQLite_0.11.2   splines_2.15.1   survival_2.36-14 tools_2.15.1
>
> --
> Sent via the guest posting facility at bioconductor.org.