mlr3 package updates - q1/2022

Quarterly mlr3 package updates. This posts gives an overview by listing the recent release notes of mlr3 packages from the last quarter. Cover photo by Atle Mo.

R
News
Author

Sebastian Fischer

Published

April 25, 2022

Due to the high amount of packages in the mlr3 ecosystem, it is hard to keep up with the latest changes across all packages. This posts gives an overview by listing the recent release notes of mlr3 packages from the last quarter. Note that only CRAN packages are listed here and the sort order is alphabetically.

bbotk

Description: Black-Box Optimization Toolkit

0.5.2

  • refactor: The $print() method of OptimInstance omits unnecessary columns now.
  • fix: The $clear() method of OptimInstance raised an error.
  • fix: The $clear() method of Archive missed to reset the $start_time field.
  • feat: Optimizer and Terminator objects have the optional field $label now.
  • feat: as.data.table() functions for objects of class Dictionary have been extended with additional columns.
  • feat: Add a as.data.table.DictionaryTerminator() function.

0.5.1

  • fix: The return of the $.status() method of TerminatorRunTime and TerminatorClockTime was not in a consistent unit. The return is in seconds from now on.
  • fix: The number of evaluations was recorded as 0 in the log messages when the search space was empty.
  • feat: Add a as.data.table.DictionaryOptimizer() function.
  • feat: New $help() method which opens the manual page of an Optimizer.

0.5.0

  • feat: Add $nds_selection() method to Archive.
  • feat: New Codomain class that allows extra parameters.
  • refactor: Objective values were automatically named. From now on, only unnamed returns of ObjectiveRFun are named.
  • fix: OptimInstance, Archive and Objective objects were not cloned properly.
  • refactor: The fields $param_classes, $properties and $packages of Optimizer objects are read-only now.
  • feat: The branin() function is exported now.

mlr3

Description: Machine Learning in R - Next Generation

0.13.3

  • Most objects now have a new (optional) field label, i.e. Task, TaskGenerator, Learner, Resampling, and Measure.
  • as.data.table() methods for objects of class Dictonary have been extended with additional columns.
  • as_task_classif.formula() and as_task_regr.formula() now remove additional atrributes attached to the data which caused some some learners to break.
  • Packages are now loaded prior to calling the $train() and $predict() methods of a Learner. This ensures that package loading errors are properly propagated and not affected by encapsulation (#771).

0.13.2

  • Setting a fallback learner for a learner with encapsulation in its default settings now automatically sets encapsulation to "evaluate" (#763).
  • as_task_classif() and as_task_regr() now support the construction of tasks using the formula interface, e.g. as_task_regr(mpg ~ ., data = mtcars) (#761).
  • The row role "validation" has been renamed to "holdout". In the next release, mlr3 will start switching to the now more common terms "train"/"validation" instead of "train"/"test" for the sets created during resampling.

0.13.1

  • Improved performance for many operations on ResampleResult and BenchmarkResult.
  • resample() and benchmark() got a new argument clone to control which objects to clone before performing computations.
  • Tasks are checked for infinite values during the conversion from data.frame to Task in as_task_classif() and as_task_regr(). A warning is signaled if any column contains infinite values.

mlr3filters

Description: Filter-based feature selection for mlr3

0.5.0

  • Add references to benchmark paper and praznik paper (#104)
  • New filter FilterSelectedFeatures which makes use of embedded feature selection methods of learners. See the help page for more details (#102)
  • Allow NA as task type. This makes it possible to use other tasks than "regr" or "classif" for certain filters, e.g. FilterVariance (#106)

mlr3fselect

Description: Wrapper feature selection for mlr3

0.7.0

  • feat: Allow to pass FSelector objects as method in fselect() and auto_fselector().
  • feat: Added $label to FSelectors.
  • docs: New examples with fselect() function.
  • feat: $help() method which opens manual page of a FSelector.
  • feat: Added a as.data.table.DictionaryFSelector function.
  • feat: Added min_features parameter to FSelectorSequential.

0.6.1

  • Add store_models flag to fselect().
  • Remove store_x_domain flag.

mlr3hyperband

Description: Hyperband for ‘mlr3’

0.4.0

  • feat: New adjust_minimum_budget flag in OptimizerSuccessiveHalving. The minimum budget is adjusted in the base stage to use the maximum budget in last stage.
  • feat: New repetitions parameter to specify the exact number of repetitions. Replaced the repeats parameter.

0.3.0

  • feat: TunerHyperband evaluates configurations of same budget across brackets in parallel now.
  • feat: New repeats parameter to repeat runs of successive halving and hyperband until termination.
  • fix: Bug where maximization measures were minimized.

mlr3proba

Description: Probabilistic Supervised Learning for ‘mlr3’

0.4.9

  • Fixed bug in surv.logloss causing IPCW weighting to not be applied correctly

0.4.8

  • Bug fixes in AUC measures

0.4.7

  • Add right-censored log loss
  • Fix bug in {rpart} where model was being discarded when set to be kept. Parameter model now called keep_model.

0.4.6

  • Patch for upstream breakages
  • Add TaskSurv$kaplan method
  • {survivalmodels} now imported (previously suggested)

0.4.5

  • Improved reduction from survival matrix predictions to ranking predictions
  • Fixed cindex bug when all predictions equal
  • Fix for valgrind

0.4.4

  • Minor change to how distributions are created to better support improper distributions
  • Fixed bug in simsurv task that made it impossible to predict the target

0.4.3

  • Massive speed-up in distrcompositor PipeOp/pipeline
  • More informative error given if $distr called for a learner that does not support this return type
  • Fix massive bottleneck in scoring rule measures
  • Add Density coercions as_task_dens and as_prediction_dens
  • Measures now use parameter sets like learners. This streamlines the interface but unfortunately means ids can no longer be set dynamically.
  • Add parameters t_max and p_max to Graf, Schmid and Integrated Log-loss as an alternative to times. t_max is equivalent to times = seq(t_max) and p_max is the proportion of censoring to integrate up to in the dataset.
  • Fix bug in Rcpp code that was causing erroneous values for calculating the cindex in datasets greater than 20,000 observations.

mlr3spatial

Description: Support for Spatial Objects Within the ‘mlr3’ Ecosystem

0.1.2

  • refactor: stars objects are directly converted to terra objects now.

0.1.1

  • fix: compatibility to terra update.

mlr3spatiotempcv

Description: Spatiotemporal resampling methods for mlr3

1.0.1

  • Fixed a issue which caused coordinates to appear in the feature set when a data.frame was supplied (#166, @be-marc)
  • Add autoplot() support for "groups" column role in rsmp("cv")

mlr3tuning

Description: Tuning for ‘mlr3’

0.13.0

  • feat: Allow to pass Tuner objects as method in tune() and auto_tuner().
  • docs: Link Tuner to help page of bbotk::Optimizer.
  • feat: Tuner objects have the optional field $label now.
  • feat: as.data.table() functions for objects of class Dictionary have been extended with additional columns.

0.12.1

  • feat: Add a as.data.table.DictionaryTuner function.
  • feat: New $help() method which opens the manual page of an Tuner.

0.12.0

  • feat: as_search_space() function to create search spaces from Learner and ParamSet objects. Allow to pass TuningSpace objects as search_space in TuningInstanceSingleCrit and TuningInstanceMultiCrit.
  • feat: The mlr3::HotstartStack can now be removed after tuning with the keep_hotstart_stack flag.
  • feat: The Archive stores errors and warnings of the learners.
  • feat: When no measure is provided, the default measure is used in auto_tuner() and tune_nested().

0.11.0

  • fix: $assign_result() method in TuningInstanceSingleCrit when search space is empty.
  • feat: Default measure is used when no measure is supplied to TuningInstanceSingleCrit.

0.10.0

  • Fixes bug in TuningInstanceMultiCrit$assign_result().
  • Hotstarting of learners with previously fitted models.
  • Remove deep clones to speed up tuning.
  • Add store_models flag to auto_tuner().
  • Add "noisy" property to ObjectiveTuning.

mlr3tuningspaces

Description: Search Spaces for Hyperparameter Tuning

0.2.0

  • feat: Add a as.data.table.TuningSpace() function.
  • feat: TuningSpace objects have the optional field $label now.
  • feat: New $help() method which opens the manual page of a TuningSpace.
  • feat: Add search space for glmnet and kknn to default collection.
  • feat: New as_search_space() function to create search spaces from TuningSpace objects.

0.1.1

  • fix: The subsample hyperparameter is tuned on a logarithmic scale now. The lower bound of alpha is reduced from 1e-4 to 1e-3. The tuning range of the lambda hyperparameter was 0.1 to 1. From now on, lambda is tuned from 1e-3 to 1e3 on a logarithmic scale.

0.1.0

  • refactor: update citations.
  • feat: Add mtry.ratio hyperparameter to tuning spaces of the ranger learner.
  • feat: Add $print() method to TuningSpace objects.

mlr3verse

Description: Easily Install and Load the ‘mlr3’ Package Family

0.2.4

  • Updated reexports.

mlr3viz

Description: Visualizations for ‘mlr3’

0.5.8

  • Compatibility fixes.

paradox

0.9.0

  • Added default_values() function to extract default values from ParamSet objects.

0.8.0

  • Parameters now have a new (optional) field description.
  • Improved printing of parameters in documentation (#355).
  • A warning is now signaled if the package ParamHelpers is also loaded.
  • Fixed some links.