hEFS: add paper link in some places (#157)

* add hEFS 2026 reference

* update roxygen

* update news

* add hEFS citation in README

* update docs

* fix non-ASCII character

* remove URL, doi is enough

Author: bblodfon

DESCRIPTION

@@ -54,7 +54,7 @@ Encoding: UTF-8
 Language: en-US
 NeedsCompilation: no
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 Collate:
     'ArchiveAsyncFSelect.R'
     'ArchiveAsyncFSelectFrozen.R'

NEWS.md

@@ -1,6 +1,7 @@
 # mlr3fselect (development version)
 
 * refactor: Remove rush backward compatibility.
+* docs: add hEFS reference.
 
 # mlr3fselect 1.5.1
 

R/EnsembleFSResult.R

@@ -21,7 +21,7 @@
 #'   Combines multiple [EnsembleFSResult] objects into a new [EnsembleFSResult].
 #'
 #' @references
-#' `r format_bib("das1999", "meinshausen2010")`
+#' `r format_bib("das1999", "meinshausen2010", "zobolas2026")`
 #'
 #' @export
 #' @examplesIf mlr3misc::require_namespaces("fastVoteR", quietly = TRUE)

R/bibentries.R

@@ -126,15 +126,23 @@ bibentries = c(
   ),
   hedou2024 = bibentry("article",
     #nolint next
-    author = "Hedou, Julien and Maric, Ivana and Bellan, Gregoire and Einhaus, Jakob and Gaudilliere, Dyani K. and Ladant, Francois Xavier and Verdonk, Franck and Stelzer, Ina A. and Feyaerts, Dorien and Tsai, Amy S. and Ganio, Edward A. and Sabayev, Maximilian and Gillard, Joshua and Amar, Jonas and Cambriel, Amelie and Oskotsky, Tomiko T. and Roldan, Alennie and Golob, Jonathan L. and Sirota, Marina and Bonham, Thomas A. and Sato, Masaki and Diop, Maigane and Durand, Xavier and Angst, Martin S. and Stevenson, David K. and Aghaeepour, Nima and Montanari, Andrea and Gaudilliere, Brice",
-    doi = "10.1038/s41587-023-02033-x",
-    issn = "1546-1696",
-    journal = "Nature Biotechnology 2024",
-    month = "jan",
-    pages = "1--13",
+    author    = "Hedou, Julien and Maric, Ivana and Bellan, Gregoire and Einhaus, Jakob and Gaudilliere, Dyani K. and Ladant, Francois Xavier and Verdonk, Franck and Stelzer, Ina A. and Feyaerts, Dorien and Tsai, Amy S. and Ganio, Edward A. and Sabayev, Maximilian and Gillard, Joshua and Amar, Jonas and Cambriel, Amelie and Oskotsky, Tomiko T. and Roldan, Alennie and Golob, Jonathan L. and Sirota, Marina and Bonham, Thomas A. and Sato, Masaki and Diop, Maigane and Durand, Xavier and Angst, Martin S. and Stevenson, David K. and Aghaeepour, Nima and Montanari, Andrea and Gaudilliere, Brice",
+    doi       = "10.1038/s41587-023-02033-x",
+    issn      = "1546-1696",
+    journal   = "Nature Biotechnology 2024",
+    month     = "jan",
+    pages     = "1--13",
     publisher = "Nature Publishing Group",
-    title = "Discovery of sparse, reliable omic biomarkers with Stabl",
-    url = "https://www.nature.com/articles/s41587-023-02033-x",
-    year = "2024"
+    title     = "Discovery of sparse, reliable omic biomarkers with Stabl",
+    url       = "https://www.nature.com/articles/s41587-023-02033-x",
+    year      = "2024"
+  ),
+  zobolas2026 = bibentry("article",
+    author  = "Zobolas, John and George, Anne-Marie and Lopez, Alberto and Fischer, Sebastian and Becker, Marc and Aittokallio, Tero",
+    doi     = "10.1186/s13040-026-00546-0",
+    issn    = "1756-0381",
+    journal = "BioData Mining",
+    title   = "Prognostic biomarker discovery in pancreatic cancer through hybrid ensemble feature selection and multi-omics data",
+    year    = "2026"
   )
 )

R/embedded_ensemble_fselect.R

@@ -39,7 +39,7 @@
 #' @returns an [EnsembleFSResult] object.
 #'
 #' @source
-#' `r format_bib("meinshausen2010", "hedou2024")`
+#' `r format_bib("meinshausen2010", "hedou2024", "zobolas2026")`
 #' @export
 #' @examples
 #' \donttest{

R/ensemble_fselect.R

@@ -60,7 +60,7 @@
 #' @returns an [EnsembleFSResult] object.
 #'
 #' @source
-#' `r format_bib("saeys2008", "abeel2010", "pes2020")`
+#' `r format_bib("saeys2008", "abeel2010", "pes2020", "zobolas2026")`
 #' @export
 #' @examples
 #' \donttest{

README.Rmd

@@ -137,4 +137,4 @@ If you use **mlr3fselect** in your work, please cite the package:
 
 The **ensemble feature selection** components (hEFS) are described in the following study:
 
-> Zobolas, J., George, A.-M., López, A., Fischer, S., Becker, M., & Aittokallio, T. (2025). Optimizing prognostic biomarker discovery in pancreatic cancer through hybrid ensemble feature selection and multi-omics data. arXiv. https://arxiv.org/pdf/2509.02648
+> Zobolas, J., George, AM., López, A., Fischer, S., Becker, M., & Aittokallio, T. Prognostic biomarker discovery in pancreatic cancer through hybrid ensemble feature selection and multi-omics data. BioData Mining (2026). https://doi.org/10.1186/s13040-026-00546-0

README.md

@@ -105,10 +105,11 @@ instance = fsi(
 instance
 ```
 
-    ## <FSelectInstanceBatchSingleCrit>
-    ## * State:  Not optimized
-    ## * Objective: <ObjectiveFSelectBatch:classif.svm_on_spam>
-    ## * Terminator: <TerminatorEvals>
+    ## 
+    ## ── <FSelectInstanceBatchSingleCrit> ────────────────────────────────────────────────────────────────
+    ## • State: Not optimized
+    ## • Objective: <ObjectiveFSelectBatch> (classif.svm_on_spam)
+    ## • Terminator: <TerminatorEvals>
 
 We select a simple random search as the optimization algorithm.
 
@@ -117,10 +118,11 @@ fselector = fs("random_search", batch_size = 5)
 fselector
 ```
 
-    ## <FSelectorBatchRandomSearch>: Random Search
-    ## * Parameters: batch_size=5
-    ## * Properties: single-crit, multi-crit
-    ## * Packages: mlr3fselect
+    ## 
+    ## ── <FSelectorBatchRandomSearch>: Random Search ─────────────────────────────────────────────────────
+    ## • Parameters: batch_size=5
+    ## • Properties: single-crit and multi-crit
+    ## • Packages: mlr3fselect
 
 To start the feature selection, we simply pass the instance to the
 fselector.
@@ -202,7 +204,7 @@ If you use **mlr3fselect** in your work, please cite the package:
 The **ensemble feature selection** components (hEFS) are described in
 the following study:
 
-> Zobolas, J., George, A.-M., López, A., Fischer, S., Becker, M., &
-> Aittokallio, T. (2025). Optimizing prognostic biomarker discovery in
-> pancreatic cancer through hybrid ensemble feature selection and
-> multi-omics data. arXiv. <https://arxiv.org/pdf/2509.02648>
+> Zobolas, J., George, AM., López, A., Fischer, S., Becker, M., &
+> Aittokallio, T. Prognostic biomarker discovery in pancreatic cancer
+> through hybrid ensemble feature selection and multi-omics data.
+> BioData Mining (2026). <https://doi.org/10.1186/s13040-026-00546-0>