[BioC] How to best include hyperparameter optimization in MLInterfaces?
Vincent Carey
stvjc at channing.harvard.edu
Mon Apr 15 12:54:56 CEST 2013
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.
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