GitHub - mlr-org/mlr3: mlr3: Machine Learning in R - next generation (original) (raw)

mlr3

Package website: release |dev

Efficient, object-oriented programming on the building blocks of machine learning. Successor of mlr.

Resources (for users and developers)

• We have written a book. This should be the central entry point to the package.
• The mlr-org website includes for example agallery with case studies.
• Reference manual
• FAQ
• Ask questions on Stackoverflow (tag #mlr3)
• Extension Learners
  • Recommended core regression, classification, and survival learners are in mlr3learners
  • All others are inmlr3extralearners
  • Use the learner search to get a simple overview
• Cheatsheets
  • Overview of cheatsheets
  • mlr3
  • mlr3tuning
  • mlr3pipelines
• Videos:
  • useR2019 talk on mlr3
  • useR2019 talk on mlr3pipelines and mlr3tuning
  • useR2020 tutorial on mlr3, mlr3tuning and mlr3pipelines
• Courses/Lectures
  • The course Introduction to Machine learning (I2ML) is a free and open flipped classroom course on the basics of machine learning. mlr3 is used in thedemosandexercises.
• Templates/Tutorials
  • mlr3-targets: Tutorial showcasing how to use {mlr3} withtargets for reproducible ML workflow automation.
• List of extension packages
• mlr-outreach contains public talks and slides resources.
• Wiki: Contains mainly information for developers.

Installation

Install the last release from CRAN:

Install the development version from GitHub:

install.packages("pak")

pak::pak("mlr-org/mlr3")

If you want to get started with mlr3, we recommend installing themlr3verse meta-package which installsmlr3 and some of the most important extension packages:

install.packages("mlr3verse")

Example

Constructing Learners and Tasks

library(mlr3)

create learning task

task_penguins = as_task_classif(species ~ ., data = palmerpenguins::penguins) task_penguins

## <TaskClassif:palmerpenguins::penguins> (344 x 8)
## * Target: species
## * Properties: multiclass
## * Features (7):
##   - int (3): body_mass_g, flipper_length_mm, year
##   - dbl (2): bill_depth_mm, bill_length_mm
##   - fct (2): island, sex

load learner and set hyperparameter

learner = lrn("classif.rpart", cp = .01)

Basic train + predict

train/test split

split = partition(task_penguins, ratio = 0.67)

train the model

learner$train(task_penguins, split$train_set)

predict data

prediction = learner$predict(task_penguins, split$test_set)

calculate performance

prediction$confusion

##            truth
## response    Adelie Chinstrap Gentoo
##   Adelie       146         5      0
##   Chinstrap      6        63      1
##   Gentoo         0         0    123

measure = msr("classif.acc") prediction$score(measure)

## classif.acc 
##   0.9651163

Resample

3-fold cross validation

resampling = rsmp("cv", folds = 3L)

run experiments

rr = resample(task_penguins, learner, resampling)

access results

rr$score(measure)[, .(task_id, learner_id, iteration, classif.acc)]

##                     task_id    learner_id iteration classif.acc
## 1: palmerpenguins::penguins classif.rpart         1   0.8956522
## 2: palmerpenguins::penguins classif.rpart         2   0.9478261
## 3: palmerpenguins::penguins classif.rpart         3   0.9649123

## classif.acc 
##   0.9361302

Extension Packages

Consult thewiki for short descriptions and links to the respective repositories.

For beginners, we strongly recommend to install and load themlr3verse package for a better user experience.

Why a rewrite?

mlr was first released toCRAN in 2013. Its core design and architecture date back even further. The addition of many features has led to a feature creep which makesmlr hard to maintain and hard to extend. We also think that while mlr was nicely extensible in some parts (learners, measures, etc.), other parts were less easy to extend from the outside. Also, many helpful R libraries did not exist at the timemlr was created, and their inclusion would result in non-trivial API changes.

Design principles

• Only the basic building blocks for machine learning are implemented in this package.
• Focus on computation here. No visualization or other stuff. That can go in extra packages.
• Overcome the limitations of R’s S3 classes with the help ofR6.
• Embrace R6 for a clean OO-design, object state-changes and reference semantics. This might be less “traditional R”, but seems to fit mlr nicely.
• Embrace data.tablefor fast and convenient data frame computations.
• Combine data.table and R6, for this we will make heavy use of list columns in data.tables.
• Defensive programming and type safety. All user input is checked withcheckmate. Return types are documented, and mechanisms popular in base R which “simplify” the result unpredictably (e.g., sapply() or dropargument in [.data.frame) are avoided.
• Be light on dependencies. mlr3 requires the following packages at runtime:
  • parallelly: Helper functions for parallelization. No extra recursive dependencies.
  • future.apply: Resampling and benchmarking is parallelized with thefuture abstraction interfacing many parallel backends.
  • backports: Ensures backward compatibility with older R releases. Developed by members of the mlr team. No recursive dependencies.
  • checkmate: Fast argument checks. Developed by members of the mlr team. No extra recursive dependencies.
  • mlr3misc: Miscellaneous functions used in multiple mlr3 extension packages. Developed by themlr team.
  • paradox: Descriptions for parameters and parameter sets. Developed by themlr team. No extra recursive dependencies.
  • R6: Reference class objects. No recursive dependencies.
  • data.table: Extension of R’s data.frame. No recursive dependencies.
  • digest (viamlr3misc): Hash digests. No recursive dependencies.
  • uuid: Create unique string identifiers. No recursive dependencies.
  • lgr: Logging facility. No extra recursive dependencies.
  • mlr3measures: Performance measures. No extra recursive dependencies.
  • mlbench: A collection of machine learning data sets. No dependencies.
  • palmerpenguins: A classification data set about penguins, used on examples and provided as a toy task. No dependencies.
• Reflections: Objects are queryable for properties and capabilities, allowing you to program on them.
• Additional functionality that comes with extra dependencies:
  • To capture output, warnings and exceptions,evaluate andcallr can be used.

Contributing to mlr3

This R package is licensed under theLGPL-3. If you encounter problems using this software (lack of documentation, misleading or wrong documentation, unexpected behavior, bugs, …) or just want to suggest features, please open an issue in the issue tracker. Pull requests are welcome and will be included at the discretion of the maintainers.

Please consult the wiki for astyle guide, aroxygen guide and a pull request guide.

Citing mlr3

If you use mlr3, please cite our JOSS article:

@Article{mlr3,
  title = {{mlr3}: A modern object-oriented machine learning framework in {R}},
  author = {Michel Lang and Martin Binder and Jakob Richter and Patrick Schratz and Florian Pfisterer and Stefan Coors and Quay Au and Giuseppe Casalicchio and Lars Kotthoff and Bernd Bischl},
  journal = {Journal of Open Source Software},
  year = {2019},
  month = {dec},
  doi = {10.21105/joss.01903},
  url = {https://joss.theoj.org/papers/10.21105/joss.01903},
}