Fortgeschrittene Computerintensive Methoden
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1 Fortgeschrittene Computerintensive Methoden Einheit 5: mlr - Machine Learning in R Bernd Bischl Matthias Schmid, Manuel Eugster, Bettina Grün, Friedrich Leisch Institut für Statistik LMU München SoSe 2015
2 mlr? No unifying interface for machine learning in R Experiments require lengthy, tedious and error-prone code Machine learning is (also) experimental science: We need powerful and flexible tools! mlr now exists for 3-4 years (or longer?), grown quite large Still heavily in development, but official releases are stable Was used for nearly all of my papers We cannot cover everything today, short intro + overview Focus: Resampling / model selection / benchmarking! Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 1 /??
3 mlr? Machine learning experiments are well structured Definition by plugging operators together (e.g., Weka or RapidMiner): mlr: abstractions, glue code and some own implementations Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 2 /??
4 The mlr Team Bernd Bischl (Muenchen) Michel Lang (Dortmund) Jakob Richter (Dortmund) Lars Kotthoff (Cork) Julia Schiffner (Duesseldorf) Eric Studerus (Basel) Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 3 /??
5 Package + Documentation Main project page on Github URL: Contains further links, tutorial, issue tracker. Official versions are released to CRAN. How to install install.packages("mlr") install_github("mlr", username = "berndbischl") Documentation Tutorial on project page (still growing) R docs and examples in HTML on project page (and in package) Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 4 /??
6 Disclaimer: Slides are here to remind me of what I want to show you. And the covered examples have to be short. Refer to tutorial, examples and technical docs later! Hence: Let s explore the web material a bit! Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 5 /??
7 Features I Clear S3 / object oriented interface Easy extension mechanism through S3 inheritance Abstract description of learners and data by properties Description of data and task Many convenience methods, generic building blocks for own experiments Resampling like bootstrapping, cross-validation and subsampling Easy tuning of hyperparameters Variable selection Benchmark experiments with 2 levels of resampling Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 6 /??
8 Features II Growing tutorial / examples Extensive unit-testing (testthat) Extensive argument checks to help user with errors Parallelization through parallelmap Local, socket, MPI and BatchJobs modes Parallelize experiments without touching code Job granularity can be changed, e.g., so jobs don t complete too early Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 7 /??
9 Remarks on S3 Not much needed (for usage) Makes extension process easy Extension is explained in tutorial If you simply use the package, you don t really need to care! Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 8 /??
10 Task Abstractions Regression, (cos-sens.) classification, clustering, survival tasks Internally: data frame with annotations: target column(s), weights, misclassification costs,... ) task = makeclassiftask(data = iris, target = "Species") print(task) ## Supervised task: iris ## Type: classif ## Target: Species ## Observations: 150 ## Features: ## numerics factors ordered ## ## Missings: FALSE ## Has weights: FALSE ## Has blocking: FALSE ## Classes: 3 ## setosa versicolor virginica ## ## Positive class: NA Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 9 /??
11 Learner Abstractions 49 classification, 6 clustering, 42 regression, 10 survival Reduction algorithms for cost-sensitive Internally: functions to train and predict, parameter set and annotations lrn = makelearner("classif.rpart") print(lrn) ## Learner classif.rpart from package rpart ## Type: classif ## Name: Decision Tree; Short name: rpart ## Class: classif.rpart ## Properties: twoclass,multiclass,missings,numerics,factors,ordered,prob,weights ## Predict-Type: response ## Hyperparameters: xval=0 Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 10 /??
12 Learner Abstractions getparamset(lrn) ## Type len Def Constr Req Trafo ## minsplit integer to Inf - - ## minbucket integer to Inf - - ## cp numeric to ## maxcompete integer to Inf - - ## maxsurrogate integer to Inf - - ## usesurrogate discrete - 2 0,1,2 - - ## surrogatestyle discrete - 0 0,1 - - ## maxdepth integer to ## xval integer to Inf - - ## parms untyped Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 11 /??
13 Learner Abstractions head(listlearners("classif", properties = c("prob", "multiclass"))) ## [1] "classif.bdk" "classif.boosting" ## [3] "classif.cforest" "classif.ctree" ## [5] "classif.extratrees" "classif.gbm" Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 12 /??
![boosting" ## [3] "classif.cforest" "classif.ctree" ## [5] "classif.](/docs-images/48/18887416/images/page_13.jpg "extratrees\" \"classif.")
14 Learner Abstractions head(listlearners(iris.task)) ## [1] "classif.bdk" "classif.boosting" ## [3] "classif.cforest" "classif.ctree" ## [5] "classif.extratrees" "classif.fnn" Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 13 /??
![cforest" "classif.ctree" ## [5] "classif.extratrees" "classif.](/docs-images/48/18887416/images/page_14.jpg "fnn\" Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive")
15 Performance Measures 21 classification, 7 regression, 1 survival Internally: performance function, aggregation function and annotations print(mmce) ## Name: Mean misclassification error ## Performance measure: mmce ## Properties: classif,classif.multi,req.pred,req.truth ## Minimize: TRUE ## Best: 0; Worst: 1 ## Aggregated by: test.mean ## Note: print(timetrain) ## Name: Time of fitting the model ## Performance measure: timetrain ## Properties: classif,classif.multi,regr,surv,costsens,cluster,req.model ## Minimize: TRUE ## Best: 0; Worst: Inf ## Aggregated by: test.mean ## Note: Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 14 /??
16 Performance Measures listmeasures("classif") ## [1] "f1" "featperc" "mmce" ## [4] "tn" "tp" "mcc" ## [7] "fn" "fp" "npv" ## [10] "bac" "timeboth" "acc" ## [13] "ppv" "multiclass.auc" "fnr" ## [16] "auc" "tnr" "ber" ## [19] "timepredict" "fpr" "gmean" ## [22] "tpr" "gpr" "fdr" ## [25] "timetrain" Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 15 /??
![auc" "fnr" ## [16] "auc" "tnr" "ber" ## [19] "timepredict" "fpr" "gmean" ## [22] "tpr" "gpr"](/docs-images/48/18887416/images/page_16.jpg "\"fdr\" ## [25] \"timetrain\" Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden")
17 Overview of Implemented Learners Classification LDA, QDA, RDA, MDA Trees and forests Boosting (different variants) SVMs (different variants)... Regression Linear, lasso and ridge Boosting Trees and forests Gaussian processes... Clustering K-Means EM DBscan X-Means... Much better documented on web page, let s go there! Survival Analysis Cox-PH Cox-Boost Random survival forest Penalized regression... Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 16 /??
18 Example ex1.r: Training and prediction Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 17 /??
19 Resampling Hold-Out Cross-validation Bootstrap Subsampling Stratification Blocking and quite a few extensions Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 18 /??
20 Resampling Resampling techniques: CV, Bootstrap, Subsampling,... cv3f = makeresampledesc("cv", iters = 3, stratify = TRUE) 10-fold CV of rpart on iris lrn = makelearner("classif.rpart") cv10f = makeresampledesc("cv", iters = 10) measures = list(mmce, acc) resample(lrn, task, cv10f, measures)$aggr ## mmce.test.mean acc.test.mean ## crossval(lrn, task)$aggr ## mmce.test.mean ## Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 19 /??
21 Example ex2.r: Resampling Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 20 /??
22 Benchmarking Compare multiple learners on multiple tasks Fair comparisons: same training and test sets for each learner data("sonar", package = "mlbench") tasks = list( makeclassiftask(data = iris, target = "Species"), makeclassiftask(data = Sonar, target = "Class") ) learners = list( makelearner("classif.rpart"), makelearner("classif.randomforest"), makelearner("classif.ksvm") ) benchmark(learners, tasks, cv10f, mmce) ## task.id learner.id mmce.test.mean ## 1 iris classif.rpart ## 2 iris classif.randomforest ## 3 iris classif.ksvm ## 4 Sonar classif.rpart ## 5 Sonar classif.randomforest ## 6 Sonar classif.ksvm Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 21 /??
23 Example ex3.r: Benchmarking Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 22 /??
24 Visualizations plotlearnerprediction(makelearner("classif.randomforest"), task, features = c("sepal.length", "Sepal.Width")) 4.5 classif.randomforest: Train: mmce=0.0933; CV: mmce.test.mean= Sepal.Width Species setosa versicolor virginica Sepal.Length Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 23 /??
25 Example ex4.r: ROC analysis Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 24 /??
26 Remarks on model selection I Basic machine learning Fit parameters of model to predict new data Generalisation error commonly estimated by resampling, e.g. 10-fold cross-validation 2nd, 3rd,... level of inference Comparing inducers or hyperparameters is harder Feature selection either in 2nd level or adds a 3rd one... Statistical comparisons on the 2nd stage are non-trivial Still active research Very likely that high performance computing is needed Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 25 /??
27 Tuning / Grid Search / Random search Tuning Used to find best hyperparameters for a method in a data-dependend way Must be done for some methods, like SVMs Grid search Basic method: Exhaustively try all combinations of finite grid Inefficient, combinatorial explosion Searches large, irrelevant areas Reasonable for continuous parameters? Still often default method Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 26 /??
28 Tuning / Grid Search / Random search Random search Randomly draw parameters mlr supports all types and depencies here Scales better then grid search Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 27 /??
29 Example ex5.r: Basic tuning: grid search Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 28 /??
30 Remarks on Model Selection II Salzberg (1997): On comparing classifiers: Pitfalls to avoid and a recommended approach Many articles do not contain sound statistical methodology Compare against enough reasonable algorithms Do not just report mean performance values Do not cheat through repeated tuning Use double cross-validation for tuning and evaluation Apply the correct test (assumptions?) Adapt for multiple testing Think about independence and distributions Do not rely solely on UCI We might overfit on it Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 29 /??
31 Nested Resampling Ensures unbiased results for meta model optimization Use this for tuning and feature selection Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 30 /??
32 Example ex6.r: Tuning + nested resampling via wrappers Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 31 /??
33 Parallelization Activate with parallelmap::parallelstart Backends: local, multicore, socket, mpi and BatchJobs parallelstart("batchjobs") benchmark([...]) parallelstop() Parallelization levels parallelgetregisteredlevels() ## mlr: mlr.benchmark, mlr.resample, mlr.selectfeatures, mlr.tuneparams Defaults to first possible / most outer loop Few iterations in benchmark (loop over learners tasks), many in resampling parallelstart("multicore", level = "mlr.resample") Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 32 /??
34 Parallelization parallelmap is documented here: BatchJobs is documented here: Make sure to read the Wiki page for Dortmund! Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 33 /??
35 Example ex7.r: Parallelization Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 34 /??
36 Outlook / Not Shown Today I Regression Survival analysis Clustering Regular cost-sensitive learning (class-specific costs) Cost-sensitive learning (example-dependent costs) Smarter tuning algorithms CMA-ES, iterated F-facing, model-based optimization... Multi-critera optimization... Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 35 /??
37 Outlook / Not Shown Today II Variable selection Filters: Simply imported available R methods Wrappers: Forward, backward, stochastic search, GAs Bagging for arbitary base learners Generic imputation for missing values Wrapping / tuning of preprocessing Over / Undersampling for unbalanced class sizes mlr connection to OpenML... Bernd Bischl SoSe 2015 Fortgeschrittene Computerintensive Methoden 5 36 /??
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