Tuning Over Multiple Learners

Tune over multiple learners for a single task.

tuning
resampling
classification
Authors

Jakob Richter

Bernd Bischl

Published

February 1, 2020

This use case shows how to tune over multiple learners for a single task. You will learn the following:

This is an advanced use case. What should you know before:

The Setup

Assume, you are given some ML task and what to compare a couple of learners, probably because you want to select the best of them at the end of the analysis. That’s a super standard scenario, it actually sounds so common that you might wonder: Why an (advanced) blog post about this? With pipelines? We will consider 2 cases: (a) Running the learners in their default, so without tuning, and (b) with tuning.

We load the mlr3verse package which pulls in the most important packages for this example. The mlr3learners package loads additional learners.

library(mlr3verse)
library(mlr3tuning)
library(mlr3learners)

We initialize the random number generator with a fixed seed for reproducibility, and decrease the verbosity of the logger to keep the output clearly represented.

set.seed(7832)
lgr::get_logger("mlr3")$set_threshold("warn")
lgr::get_logger("bbotk")$set_threshold("warn")

Let’s define our learners.

learners = list(
  lrn("classif.xgboost", id = "xgb", eval_metric = "logloss"),
  lrn("classif.ranger", id = "rf")
)
learners_ids = sapply(learners, function(x) x$id)

task = tsk("sonar") # some random data for this demo
inner_cv2 = rsmp("cv", folds = 2) # inner loop for nested CV
outer_cv5 = rsmp("cv", folds = 5) # outer loop for nested CV

Default Parameters

The Benchmark-Table Approach

Assume we don’t want to perform tuning and or with running all learner in their respective defaults. Simply run benchmark on the learners and the tasks. That tabulates our results nicely and shows us what works best.

grid = benchmark_grid(task, learners, outer_cv5)
bmr = benchmark(grid)
bmr$aggregate(measures = msr("classif.ce"))
   nr      resample_result task_id learner_id resampling_id iters classif.ce
1:  1 <ResampleResult[21]>   sonar        xgb            cv     5  0.2736353
2:  2 <ResampleResult[21]>   sonar         rf            cv     5  0.1973287

The Pipelines Approach

Ok, why would we ever want to change the simple approach above - and use pipelines / tuning for this? Three reasons:

  1. What we are doing with benchmark() is actually statistically flawed, insofar if we report the error of the numerically best method from the benchmark table as its estimated future performance. If we do that we have “optimized on the CV” (we basically ran a grid search over our learners!) and we know that this is will produce optimistically biased results. NB: This is a somewhat ridiculous criticism if we are going over only a handful of options, and the bias will be very small. But it will be noticeable if we do this over hundreds of learners, so it is important to understand the underlying problem. This is a somewhat subtle point, and this gallery post is more about technical hints for mlr3, so we will stop this discussion here.
  2. For some tuning algorithms, you might have a chance to more efficiently select from the set of algorithms than running the full benchmark. Because of the categorical nature of the problem, you will not be able to learn stuff like “If learner A works bad, I don’t have to try learner B”, but you can potentially save some resampling iterations. Assume you have so select from 100 candidates, experiments are expensive, and you use a 20-fold CV. If learner A has super-bad results in the first 5 folds of the CV, you might already want to stop here. “Racing” would be such a tuning algorithm.
  3. It helps us to foreshadow what comes later in this post where we tune the learners.

The pipeline just has a single purpose in this example: It should allow us to switch between different learners, depending on a hyperparameter. The pipe consists of three elements:

  • branch pipes incoming data to one of the following elements, on different data channels. We can name these channel on construction with options.
  • our learners (combined with gunion())
  • unbranch combines the forked paths at the end.
graph =
  po("branch", options = learners_ids) %>>%
  gunion(lapply(learners, po)) %>>%
  po("unbranch")
plot(graph, html = FALSE)

The pipeline has now quite a lot of available hyperparameters. It includes all hyperparameters from all contained learners. But as we don’t tune them here (yet), we don’t care (yet). But the first hyperparameter is special. branch.selection controls over which (named) branching channel our data flows.

graph$param_set$ids()
 [1] "branch.selection"                "xgb.alpha"                       "xgb.approxcontrib"              
 [4] "xgb.base_score"                  "xgb.booster"                     "xgb.callbacks"                  
 [7] "xgb.colsample_bylevel"           "xgb.colsample_bynode"            "xgb.colsample_bytree"           
[10] "xgb.disable_default_eval_metric" "xgb.early_stopping_rounds"       "xgb.early_stopping_set"         
[13] "xgb.eta"                         "xgb.eval_metric"                 "xgb.feature_selector"           
[16] "xgb.feval"                       "xgb.gamma"                       "xgb.grow_policy"                
[19] "xgb.interaction_constraints"     "xgb.iterationrange"              "xgb.lambda"                     
[22] "xgb.lambda_bias"                 "xgb.max_bin"                     "xgb.max_delta_step"             
[25] "xgb.max_depth"                   "xgb.max_leaves"                  "xgb.maximize"                   
[28] "xgb.min_child_weight"            "xgb.missing"                     "xgb.monotone_constraints"       
[31] "xgb.normalize_type"              "xgb.nrounds"                     "xgb.nthread"                    
[34] "xgb.ntreelimit"                  "xgb.num_parallel_tree"           "xgb.objective"                  
[37] "xgb.one_drop"                    "xgb.outputmargin"                "xgb.predcontrib"                
[40] "xgb.predictor"                   "xgb.predinteraction"             "xgb.predleaf"                   
[43] "xgb.print_every_n"               "xgb.process_type"                "xgb.rate_drop"                  
[46] "xgb.refresh_leaf"                "xgb.reshape"                     "xgb.seed_per_iteration"         
[49] "xgb.sampling_method"             "xgb.sample_type"                 "xgb.save_name"                  
[52] "xgb.save_period"                 "xgb.scale_pos_weight"            "xgb.skip_drop"                  
[55] "xgb.strict_shape"                "xgb.subsample"                   "xgb.top_k"                      
[58] "xgb.training"                    "xgb.tree_method"                 "xgb.tweedie_variance_power"     
[61] "xgb.updater"                     "xgb.verbose"                     "xgb.watchlist"                  
[64] "xgb.xgb_model"                   "rf.alpha"                        "rf.always.split.variables"      
[67] "rf.class.weights"                "rf.holdout"                      "rf.importance"                  
[70] "rf.keep.inbag"                   "rf.max.depth"                    "rf.min.node.size"               
[73] "rf.min.prop"                     "rf.minprop"                      "rf.mtry"                        
[76] "rf.mtry.ratio"                   "rf.num.random.splits"            "rf.num.threads"                 
[79] "rf.num.trees"                    "rf.oob.error"                    "rf.regularization.factor"       
[82] "rf.regularization.usedepth"      "rf.replace"                      "rf.respect.unordered.factors"   
[85] "rf.sample.fraction"              "rf.save.memory"                  "rf.scale.permutation.importance"
[88] "rf.se.method"                    "rf.seed"                         "rf.split.select.weights"        
[91] "rf.splitrule"                    "rf.verbose"                      "rf.write.forest"                
graph$param_set$params$branch.selection
                 id    class lower upper levels        default
1: branch.selection ParamFct    NA    NA xgb,rf <NoDefault[3]>

We can now tune over this pipeline, and probably running grid search seems a good idea to “touch” every available learner. NB: We have now written down in (much more complicated code) what we did before with benchmark.

graph_learner = as_learner(graph)
graph_learner$id = "g"

search_space = ps(
  branch.selection = p_fct(c("rf", "xgb"))
)

instance = tune(
  method = "grid_search",
  task = task,
  learner = graph_learner,
  resampling = inner_cv2,
  measure = msr("classif.ce"),
  search_space = search_space
)

as.data.table(instance$archive)[, list(branch.selection, classif.ce)]
   branch.selection classif.ce
1:               rf  0.1778846
2:              xgb  0.3269231

But: Via this approach we can now get unbiased performance results via nested resampling and using the AutoTuner (which would make much more sense if we would select from 100 models and not 2).

at = auto_tuner(
  method = "grid_search",
  learner = graph_learner,
  resampling = inner_cv2,
  measure = msr("classif.ce"),
  search_space = search_space
)

rr = resample(task, at, outer_cv5, store_models = TRUE)

Access inner tuning result.

extract_inner_tuning_results(rr)[, list(iteration, branch.selection, classif.ce)]
   iteration branch.selection classif.ce
1:         1               rf  0.2349398
2:         2               rf  0.1626506
3:         3               rf  0.3012048
4:         4               rf  0.2813396
5:         5               rf  0.2932444

Access inner tuning archives.

extract_inner_tuning_archives(rr)[, list(iteration, branch.selection, classif.ce, resample_result)]
    iteration branch.selection classif.ce      resample_result
 1:         1               rf  0.2349398 <ResampleResult[21]>
 2:         1              xgb  0.2469880 <ResampleResult[21]>
 3:         2               rf  0.1626506 <ResampleResult[21]>
 4:         2              xgb  0.2530120 <ResampleResult[21]>
 5:         3              xgb  0.3795181 <ResampleResult[21]>
 6:         3               rf  0.3012048 <ResampleResult[21]>
 7:         4              xgb  0.3714859 <ResampleResult[21]>
 8:         4               rf  0.2813396 <ResampleResult[21]>
 9:         5              xgb  0.3353414 <ResampleResult[21]>
10:         5               rf  0.2932444 <ResampleResult[21]>

Model-Selection and Tuning with Pipelines

Now let’s select from our given set of models and tune their hyperparameters. One way to do this is to define a search space for each individual learner, wrap them all with the AutoTuner, then call benchmark() on them. As this is pretty standard, we will skip this here, and show an even neater option, where you can tune over models and hyperparameters in one go. If you have quite a large space of potential learners and combine this with an efficient tuning algorithm, this can save quite some time in tuning as you can learn during optimization which options work best and focus on them. NB: Many AutoML systems work in a very similar way.

Define the Search Space

Remember, that the pipeline contains a joint set of all contained hyperparameters. Prefixed with the respective PipeOp ID, to make names unique.

as.data.table(graph$param_set)[, list(id, class, lower, upper, nlevels)]
                                 id    class lower upper nlevels
 1:                branch.selection ParamFct    NA    NA       2
 2:                       xgb.alpha ParamDbl     0   Inf     Inf
 3:               xgb.approxcontrib ParamLgl    NA    NA       2
 4:                  xgb.base_score ParamDbl  -Inf   Inf     Inf
 5:                     xgb.booster ParamFct    NA    NA       3
 6:                   xgb.callbacks ParamUty    NA    NA     Inf
 7:           xgb.colsample_bylevel ParamDbl     0     1     Inf
 8:            xgb.colsample_bynode ParamDbl     0     1     Inf
 9:            xgb.colsample_bytree ParamDbl     0     1     Inf
10: xgb.disable_default_eval_metric ParamLgl    NA    NA       2
11:       xgb.early_stopping_rounds ParamInt     1   Inf     Inf
12:          xgb.early_stopping_set ParamFct    NA    NA       3
13:                         xgb.eta ParamDbl     0     1     Inf
14:                 xgb.eval_metric ParamUty    NA    NA     Inf
15:            xgb.feature_selector ParamFct    NA    NA       5
16:                       xgb.feval ParamUty    NA    NA     Inf
17:                       xgb.gamma ParamDbl     0   Inf     Inf
18:                 xgb.grow_policy ParamFct    NA    NA       2
19:     xgb.interaction_constraints ParamUty    NA    NA     Inf
20:              xgb.iterationrange ParamUty    NA    NA     Inf
21:                      xgb.lambda ParamDbl     0   Inf     Inf
22:                 xgb.lambda_bias ParamDbl     0   Inf     Inf
23:                     xgb.max_bin ParamInt     2   Inf     Inf
24:              xgb.max_delta_step ParamDbl     0   Inf     Inf
25:                   xgb.max_depth ParamInt     0   Inf     Inf
26:                  xgb.max_leaves ParamInt     0   Inf     Inf
27:                    xgb.maximize ParamLgl    NA    NA       2
28:            xgb.min_child_weight ParamDbl     0   Inf     Inf
29:                     xgb.missing ParamDbl  -Inf   Inf     Inf
30:        xgb.monotone_constraints ParamUty    NA    NA     Inf
31:              xgb.normalize_type ParamFct    NA    NA       2
32:                     xgb.nrounds ParamInt     1   Inf     Inf
33:                     xgb.nthread ParamInt     1   Inf     Inf
34:                  xgb.ntreelimit ParamInt     1   Inf     Inf
35:           xgb.num_parallel_tree ParamInt     1   Inf     Inf
36:                   xgb.objective ParamUty    NA    NA     Inf
37:                    xgb.one_drop ParamLgl    NA    NA       2
38:                xgb.outputmargin ParamLgl    NA    NA       2
39:                 xgb.predcontrib ParamLgl    NA    NA       2
40:                   xgb.predictor ParamFct    NA    NA       2
41:             xgb.predinteraction ParamLgl    NA    NA       2
42:                    xgb.predleaf ParamLgl    NA    NA       2
43:               xgb.print_every_n ParamInt     1   Inf     Inf
44:                xgb.process_type ParamFct    NA    NA       2
45:                   xgb.rate_drop ParamDbl     0     1     Inf
46:                xgb.refresh_leaf ParamLgl    NA    NA       2
47:                     xgb.reshape ParamLgl    NA    NA       2
48:          xgb.seed_per_iteration ParamLgl    NA    NA       2
49:             xgb.sampling_method ParamFct    NA    NA       2
50:                 xgb.sample_type ParamFct    NA    NA       2
51:                   xgb.save_name ParamUty    NA    NA     Inf
52:                 xgb.save_period ParamInt     0   Inf     Inf
53:            xgb.scale_pos_weight ParamDbl  -Inf   Inf     Inf
54:                   xgb.skip_drop ParamDbl     0     1     Inf
55:                xgb.strict_shape ParamLgl    NA    NA       2
56:                   xgb.subsample ParamDbl     0     1     Inf
57:                       xgb.top_k ParamInt     0   Inf     Inf
58:                    xgb.training ParamLgl    NA    NA       2
59:                 xgb.tree_method ParamFct    NA    NA       5
60:      xgb.tweedie_variance_power ParamDbl     1     2     Inf
61:                     xgb.updater ParamUty    NA    NA     Inf
62:                     xgb.verbose ParamInt     0     2       3
63:                   xgb.watchlist ParamUty    NA    NA     Inf
64:                   xgb.xgb_model ParamUty    NA    NA     Inf
65:                        rf.alpha ParamDbl  -Inf   Inf     Inf
66:       rf.always.split.variables ParamUty    NA    NA     Inf
67:                rf.class.weights ParamUty    NA    NA     Inf
68:                      rf.holdout ParamLgl    NA    NA       2
69:                   rf.importance ParamFct    NA    NA       4
70:                   rf.keep.inbag ParamLgl    NA    NA       2
71:                    rf.max.depth ParamInt     0   Inf     Inf
72:                rf.min.node.size ParamInt     1   Inf     Inf
73:                     rf.min.prop ParamDbl  -Inf   Inf     Inf
74:                      rf.minprop ParamDbl  -Inf   Inf     Inf
75:                         rf.mtry ParamInt     1   Inf     Inf
76:                   rf.mtry.ratio ParamDbl     0     1     Inf
77:            rf.num.random.splits ParamInt     1   Inf     Inf
78:                  rf.num.threads ParamInt     1   Inf     Inf
79:                    rf.num.trees ParamInt     1   Inf     Inf
80:                    rf.oob.error ParamLgl    NA    NA       2
81:        rf.regularization.factor ParamUty    NA    NA     Inf
82:      rf.regularization.usedepth ParamLgl    NA    NA       2
83:                      rf.replace ParamLgl    NA    NA       2
84:    rf.respect.unordered.factors ParamFct    NA    NA       3
85:              rf.sample.fraction ParamDbl     0     1     Inf
86:                  rf.save.memory ParamLgl    NA    NA       2
87: rf.scale.permutation.importance ParamLgl    NA    NA       2
88:                    rf.se.method ParamFct    NA    NA       2
89:                         rf.seed ParamInt  -Inf   Inf     Inf
90:         rf.split.select.weights ParamUty    NA    NA     Inf
91:                    rf.splitrule ParamFct    NA    NA       3
92:                      rf.verbose ParamLgl    NA    NA       2
93:                 rf.write.forest ParamLgl    NA    NA       2
                                 id    class lower upper nlevels

We decide to tune the mtry parameter of the random forest and the nrounds parameter of xgboost. Additionally, we tune branching parameter that selects our learner.

We also have to reflect the hierarchical order of the parameter sets (admittedly, this is somewhat inconvenient). We can only set the mtry value if the pipe is configured to use the random forest (ranger). The same applies for the xgboost parameter.

search_space = ps(
  branch.selection = p_fct(c("rf", "xgb")),
  rf.mtry = p_int(1L, 20L, depends = branch.selection == "rf"),
  xgb.nrounds = p_int(1, 500, depends = branch.selection == "xgb"))