-
-
Notifications
You must be signed in to change notification settings - Fork 85
/
Copy pathBenchmarkResult.R
580 lines (523 loc) · 21.4 KB
/
BenchmarkResult.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
#' @title Container for Benchmarking Results
#'
#' @include mlr_reflections.R
#'
#' @description
#' This is the result container object returned by [benchmark()].
#' A [BenchmarkResult] consists of the data of multiple [ResampleResult]s.
#' The contents of a `BenchmarkResult` and [ResampleResult] are almost identical and the stored [ResampleResult]s can be extracted via the `$resample_result(i)` method, where i is the index of the performed resample experiment.
#' This allows us to investigate the extracted [ResampleResult] and individual resampling iterations, as well as the predictions and models from each fold.
#'
#' [BenchmarkResult]s can be visualized via \CRANpkg{mlr3viz}'s `autoplot()` function.
#'
#' For statistical analysis of benchmark results and more advanced plots, see \CRANpkg{mlr3benchmark}.
#'
#' @note
#' All stored objects are accessed by reference.
#' Do not modify any extracted object without cloning it first.
#'
#' @template param_measures
#'
#' @section S3 Methods:
#' * `as.data.table(rr, ..., reassemble_learners = TRUE, convert_predictions = TRUE, predict_sets = "test", task_characteristics = FALSE)`\cr
#' [BenchmarkResult] -> [data.table::data.table()]\cr
#' Returns a tabular view of the internal data.
#' * `c(...)`\cr
#' ([BenchmarkResult], ...) -> [BenchmarkResult]\cr
#' Combines multiple objects convertible to [BenchmarkResult] into a new [BenchmarkResult].
#'
#' @template seealso_benchmark
#' @export
#' @examples
#' set.seed(123)
#' learners = list(
#' lrn("classif.featureless", predict_type = "prob"),
#' lrn("classif.rpart", predict_type = "prob")
#' )
#'
#' design = benchmark_grid(
#' tasks = list(tsk("sonar"), tsk("penguins")),
#' learners = learners,
#' resamplings = rsmp("cv", folds = 3)
#' )
#' print(design)
#'
#' bmr = benchmark(design)
#' print(bmr)
#'
#' bmr$tasks
#' bmr$learners
#'
#' # first 5 resampling iterations
#' head(as.data.table(bmr, measures = c("classif.acc", "classif.auc")), 5)
#'
#' # aggregate results
#' bmr$aggregate()
#'
#' # aggregate results with hyperparameters as separate columns
#' mlr3misc::unnest(bmr$aggregate(params = TRUE), "params")
#'
#' # extract resample result for classif.rpart
#' rr = bmr$aggregate()[learner_id == "classif.rpart", resample_result][[1]]
#' print(rr)
#'
#' # access the confusion matrix of the first resampling iteration
#' rr$predictions()[[1]]$confusion
#'
#' # reduce to subset with task id "sonar"
#' bmr$filter(task_ids = "sonar")
#' print(bmr)
BenchmarkResult = R6Class("BenchmarkResult",
public = list(
#' @description
#' Creates a new instance of this [R6][R6::R6Class] class.
#'
#' @param data (`ResultData`)\cr
#' An object of type `ResultData`, either extracted from another [ResampleResult], another
#' [BenchmarkResult], or manually constructed with [as_result_data()].
initialize = function(data = NULL) {
if (is.null(data)) {
private$.data = ResultData$new()
} else {
private$.data = assert_class(data, "ResultData")
}
},
#' @description
#' Opens the help page for this object.
help = function() {
open_help("mlr3::BenchmarkResult")
},
#' @description
#' Helper for print outputs.
#' @param ... (ignored).
format = function(...) {
sprintf("<%s>", class(self)[1L])
},
#' @description
#' Printer.
print = function() {
tab = self$aggregate(measures = list(), conditions = TRUE)
setattr(tab, "class", c("data.table", "data.frame"))
catf("%s of %i rows with %i resampling runs",
format(self), private$.data$iterations(), nrow(tab))
if (nrow(tab)) {
tab = remove_named(tab, c("uhash", "resample_result"))
print(tab, class = FALSE, row.names = FALSE, print.keys = FALSE, digits = 3)
}
},
#' @description
#' Fuses a second [BenchmarkResult] into itself, mutating the [BenchmarkResult] in-place.
#' If the second [BenchmarkResult] `bmr` is `NULL`, simply returns `self`.
#' Note that you can alternatively use the combine function [c()] which calls this method internally.
#'
#' @param bmr ([BenchmarkResult])\cr
#' A second [BenchmarkResult] object.
#'
#' @return
#' Returns the object itself, but modified **by reference**.
#' You need to explicitly `$clone()` the object beforehand if you want to keep
#' the object in its previous state.
combine = function(bmr) {
if (!is.null(bmr)) {
assert_benchmark_result(bmr)
if (private$.data$iterations() && self$task_type != bmr$task_type) {
stopf("BenchmarkResult is of task type '%s', but must be '%s'", bmr$task_type, self$task_type)
}
private$.data$combine(get_private(bmr)$.data)
}
invisible(self)
},
#' @description
#' Marshals all stored models.
#' @param ... (any)\cr
#' Additional arguments passed to [`marshal_model()`].
marshal = function(...) {
private$.data$marshal(...)
},
#' @description
#' Unmarshals all stored models.
#' @param ... (any)\cr
#' Additional arguments passed to [`unmarshal_model()`].
unmarshal = function(...) {
private$.data$unmarshal(...)
},
#' @description
#' Returns a table with one row for each resampling iteration, including
#' all involved objects: [Task], [Learner], [Resampling], iteration number
#' (`integer(1)`), and [Prediction]. If `ids` is set to `TRUE`, character
#' column of extracted ids are added to the table for convenient
#' filtering: `"task_id"`, `"learner_id"`, and `"resampling_id"`.
#'
#' Additionally calculates the provided performance measures and binds the
#' performance scores as extra columns. These columns are named using the id of
#' the respective [Measure].
#'
#' @param ids (`logical(1)`)\cr
#' Adds object ids (`"task_id"`, `"learner_id"`, `"resampling_id"`) as
#' extra character columns to the returned table.
#'
#' @param conditions (`logical(1)`)\cr
#' Adds condition messages (`"warnings"`, `"errors"`) as extra
#' list columns of character vectors to the returned table
#'
#' @param predictions (`logical(1)`)\cr
#' Additionally return prediction objects, one column for each `predict_set` of all learners combined.
#' Columns are named `"prediction_train"`, `"prediction_test"` and `"prediction_internal_valid"`,
#' if present.
#'
#' @return [data.table::data.table()].
score = function(measures = NULL, ids = TRUE, conditions = FALSE, predictions = TRUE) {
measures = assert_measures(as_measures(measures, task_type = self$task_type))
assert_flag(ids)
assert_flag(conditions)
assert_flag(predictions)
tab = score_measures(self, measures, view = NULL)
tab = merge(private$.data$data$uhashes, tab, by = "uhash", sort = FALSE)
tab[, "nr" := .GRP, by = "uhash"]
if (ids) {
set(tab, j = "task_id", value = ids(tab$task))
set(tab, j = "learner_id", value = ids(tab$learner))
set(tab, j = "resampling_id", value = ids(tab$resampling))
}
if (conditions) {
set(tab, j = "warnings", value = map(tab$learner, "warnings"))
set(tab, j = "errors", value = map(tab$learner, "errors"))
}
if (predictions && nrow(tab)) {
predict_sets = intersect(
mlr_reflections$predict_sets,
unlist(map(self$learners$learner, "predict_sets"), use.names = FALSE)
)
predict_cols = sprintf("prediction_%s", predict_sets)
for (i in seq_along(predict_sets)) {
set(tab, j = predict_cols[i],
value = map(tab$prediction, function(p) as_prediction(p[[predict_sets[i]]], check = FALSE))
)
}
} else {
predict_cols = character()
}
set_data_table_class(tab, "bmr_score")
cns = c("uhash", "nr", "task", "task_id", "learner", "learner_id", "resampling", "resampling_id",
"iteration", predict_cols, "warnings", "errors", ids(measures))
cns = intersect(cns, names(tab))
tab[, cns, with = FALSE]
},
#' @description
#' Calculates the observation-wise loss via the loss function set in the
#' [Measure]'s field `obs_loss`.
#' Returns a `data.table()` with the columns `row_ids`, `truth`, `response` and
#' one additional numeric column for each measure, named with the respective measure id.
#' If there is no observation-wise loss function for the measure, the column is filled with
#' `NA` values.
#' Note that some measures such as RMSE, do have an `$obs_loss`, but they require an
#' additional transformation after aggregation, in this example taking the square-root.
#' @param predict_sets (`character()`)\cr
#' The predict sets.
obs_loss = function(measures = NULL, predict_sets = "test") {
measures = assert_measures(as_measures(measures, task_type = self$task_type))
map_dtr(self$resample_results$resample_result,
function(rr) {
rr$obs_loss(measures, predict_sets)
}, .idcol = "resample_result")
},
#' @description
#' Returns a result table where resampling iterations are combined into
#' [ResampleResult]s. A column with the aggregated performance score is
#' added for each [Measure], named with the id of the respective measure.
#'
#' The method for aggregation is controlled by the [Measure], e.g. micro
#' aggregation, macro aggregation or custom aggregation. Most measures
#' default to macro aggregation.
#'
#' Note that the aggregated performances just give a quick impression which
#' approaches work well and which approaches are probably underperforming.
#' However, the aggregates do not account for variance and cannot replace
#' a statistical test.
#' See \CRANpkg{mlr3viz} to get a better impression via boxplots or
#' \CRANpkg{mlr3benchmark} for critical difference plots and
#' significance tests.
#'
#' For convenience, different flags can be set to extract more
#' information from the returned [ResampleResult].
#'
#' @param uhashes (`logical(1)`)\cr
#' Adds the uhash values of the [ResampleResult] as extra character
#' column `"uhash"`.
#'
#' @param ids (`logical(1)`)\cr
#' Adds object ids (`"task_id"`, `"learner_id"`, `"resampling_id"`) as
#' extra character columns for convenient subsetting.
#'
#' @param params (`logical(1)`)\cr
#' Adds the hyperparameter values as extra list column `"params"`. You
#' can unnest them with [mlr3misc::unnest()].
#'
#' @param conditions (`logical(1)`)\cr
#' Adds the number of resampling iterations with at least one warning as
#' extra integer column `"warnings"`, and the number of resampling
#' iterations with errors as extra integer column `"errors"`.
#'
#' @return [data.table::data.table()].
aggregate = function(measures = NULL, ids = TRUE, uhashes = FALSE, params = FALSE, conditions = FALSE) {
measures = if (is.null(measures)) {
default_measures(self$task_type)
} else {
assert_measures(as_measures(measures))
}
assert_flag(ids)
assert_flag(uhashes)
assert_flag(params)
assert_flag(conditions)
create_rr = function(view) {
if (length(view)) ResampleResult$new(private$.data, view = copy(view)) else list()
}
rdata = private$.data$data
tab = rdata$fact[rdata$uhashes, list(
nr = .GRP,
iters = .N,
task_hash = .SD$task_hash[1L],
learner_hash = .SD$learner_hash[1L],
learner_phash = .SD$learner_phash[1L],
resampling_hash = .SD$resampling_hash[1L],
resample_result = list(create_rr(.BY[[1L]])),
warnings = if (conditions) sum(map_int(.SD$learner_state, function(s) sum(s$log$class == "warning"))) else NA_integer_,
errors = if (conditions) sum(map_int(.SD$learner_state, function(s) sum(s$log$class == "error"))) else NA_integer_
), by = "uhash", on = "uhash", nomatch = NULL]
if (ids) {
tab = merge(tab, rdata$tasks[, list(task_hash = .SD$task_hash, task_id = ids(.SD$task))],
by = "task_hash", sort = FALSE)
tab = merge(tab, rdata$learners[, list(learner_phash = .SD$learner_phash, learner_id = ids(.SD$learner))],
by = "learner_phash", sort = FALSE)
tab = merge(tab, rdata$resamplings[, list(resampling_hash = .SD$resampling_hash, resampling_id = ids(.SD$resampling))],
by = "resampling_hash", sort = FALSE)
}
if (!uhashes) {
set(tab, j = "uhash", value = NULL)
}
if (params) {
tab = merge(tab, rdata$learner_components, by = "learner_hash", sort = FALSE)
setnames(tab, "learner_param_vals", "params")
}
if (!conditions) {
tab = remove_named(tab, c("warnings", "errors"))
}
if (nrow(tab) > 0L) {
scores = map_dtr(tab$resample_result, function(rr) as.list(resample_result_aggregate(rr, measures)))
} else {
scores = setDT(named_list(ids(measures), double()))
}
tab = insert_named(tab, scores)
set_data_table_class(tab, "bmr_aggregate")
cns = c("uhash", "nr", "resample_result", "task_id", "learner_id", "resampling_id", "iters",
"warnings", "errors", "params", names(scores))
cns = intersect(cns, names(tab))
tab[, cns, with = FALSE]
},
#' @description
#' Subsets the benchmark result. If `task_ids` is not `NULL`, keeps all
#' tasks with provided task ids and discards all others tasks.
#' Same procedure for `learner_ids` and `resampling_ids`.
#'
#' @param task_ids (`character()`)\cr
#' Ids of [Task]s to keep.
#' @param task_hashes (`character()`)\cr
#' Hashes of [Task]s to keep.
#' @param learner_ids (`character()`)\cr
#' Ids of [Learner]s to keep.
#' @param learner_hashes (`character()`)\cr
#' Hashes of [Learner]s to keep.
#' @param resampling_ids (`character()`)\cr
#' Ids of [Resampling]s to keep.
#' @param resampling_hashes (`character()`)\cr
#' Hashes of [Resampling]s to keep.
#'
#' @return
#' Returns the object itself, but modified **by reference**.
#' You need to explicitly `$clone()` the object beforehand if you want to keeps
#' the object in its previous state.
filter = function(task_ids = NULL, task_hashes = NULL, learner_ids = NULL, learner_hashes = NULL,
resampling_ids = NULL, resampling_hashes = NULL) {
learner_phashes = NULL
filter_if_not_null = function(column, hashes) {
if (is.null(hashes)) {
fact
} else {
fact[unique(hashes), on = column, nomatch = NULL]
}
}
if (!is.null(task_ids)) {
task = task_hash = NULL
task_hashes = union(task_hashes, private$.data$data$tasks[ids(task) %in% task_ids, task_hash])
}
if (!is.null(learner_ids)) {
learner = learner_phash = NULL
learner_phashes = private$.data$data$learners[ids(learner) %in% learner_ids, learner_phash]
}
if (!is.null(resampling_ids)) {
resampling = resampling_hash = NULL
resampling_hashes = union(resampling_hashes, private$.data$data$resamplings[ids(resampling) %in% resampling_ids, resampling_hash])
}
fact = private$.data$data$fact
fact = filter_if_not_null("task_hash", task_hashes)
fact = filter_if_not_null("learner_hash", learner_hashes)
fact = filter_if_not_null("learner_phash", learner_phashes)
fact = filter_if_not_null("resampling_hash", resampling_hashes)
private$.data$data$fact = fact
private$.data$sweep()
invisible(self)
},
#' @description
#' Retrieve the i-th [ResampleResult], by position or by unique hash `uhash`.
#' `i` and `uhash` are mutually exclusive.
#'
#' @param i (`integer(1)`)\cr
#' The iteration value to filter for.
#'
#' @param uhash (`logical(1)`)\cr
#' The `ushash` value to filter for.
#'
#' @return [ResampleResult].
resample_result = function(i = NULL, uhash = NULL) {
if (!xor(is.null(i), is.null(uhash))) {
stopf("Either `i` or `uhash` must be provided")
}
uhashes = private$.data$uhashes()
if (is.null(i)) {
needle = assert_choice(uhash, uhashes)
} else {
i = assert_int(i, lower = 1L, upper = length(uhashes), coerce = TRUE)
needle = uhashes[i]
}
ResampleResult$new(private$.data, view = needle)
},
#' @description
#' Shrinks the [BenchmarkResult] by discarding parts of the internally stored data.
#' Note that certain operations might stop work, e.g. extracting
#' importance values from learners or calculating measures requiring the task's data.
#'
#' @param backends (`logical(1)`)\cr
#' If `TRUE`, the [DataBackend] is removed from all stored [Task]s.
#' @param models (`logical(1)`)\cr
#' If `TRUE`, the stored model is removed from all [Learner]s.
#'
#' @return
#' Returns the object itself, but modified **by reference**.
#' You need to explicitly `$clone()` the object beforehand if you want to keeps
#' the object in its previous state.
discard = function(backends = FALSE, models = FALSE) {
private$.data$discard(backends = backends, models = models)
}
),
active = list(
#' @field task_type (`character(1)`)\cr
#' Task type of objects in the `BenchmarkResult`.
#' All stored objects ([Task], [Learner], [Prediction]) in a single `BenchmarkResult` are
#' required to have the same task type, e.g., `"classif"` or `"regr"`.
#' This is `NA` for empty [BenchmarkResult]s.
task_type = function(rhs) {
assert_ro_binding(rhs)
private$.data$task_type
},
#' @field tasks ([data.table::data.table()])\cr
#' Table of included [Task]s with three columns:
#'
#' * `"task_hash"` (`character(1)`),
#' * `"task_id"` (`character(1)`), and
#' * `"task"` ([Task]).
tasks = function(rhs) {
assert_ro_binding(rhs)
tab = private$.data$tasks()
set(tab, j = "task_id", value = ids(tab$task))
setcolorder(tab, c("task_hash", "task_id", "task"))[]
},
#' @field learners ([data.table::data.table()])\cr
#' Table of included [Learner]s with three columns:
#'
#' * `"learner_hash"` (`character(1)`),
#' * `"learner_id"` (`character(1)`), and
#' * `"learner"` ([Learner]).
#'
#' Note that it is not feasible to access learned models via this field, as the training task would be ambiguous.
#' For this reason the returned learner are reset before they are returned.
#' Instead, select a row from the table returned by `$score()`.
learners = function(rhs) {
assert_ro_binding(rhs)
tab = private$.data$learners(states = FALSE)
set(tab, j = "learner_id", value = ids(tab$learner))
setcolorder(tab, c("learner_hash", "learner_id", "learner"))[]
},
#' @field resamplings ([data.table::data.table()])\cr
#' Table of included [Resampling]s with three columns:
#'
#' * `"resampling_hash"` (`character(1)`),
#' * `"resampling_id"` (`character(1)`), and
#' * `"resampling"` ([Resampling]).
resamplings = function(rhs) {
assert_ro_binding(rhs)
tab = private$.data$resamplings()
set(tab, j = "resampling_id", value = ids(tab$resampling))
setcolorder(tab, c("resampling_hash", "resampling_id", "resampling"))[]
},
#' @field resample_results ([data.table::data.table()])\cr
#' Returns a table with three columns:
#' * `uhash` (`character()`).
#' * `resample_result` ([ResampleResult]).
resample_results = function(rhs) {
assert_ro_binding(rhs)
rdata = private$.data$data
create_rr = function(view) {
if (length(view)) ResampleResult$new(private$.data, view = copy(view)) else list()
}
rdata$fact[rdata$uhashes, list(
nr = .GRP,
resample_result = list(create_rr(.BY[[1L]]))
), by = "uhash"]
},
#' @field n_resample_results (`integer(1)`)\cr
#' Returns the total number of stored [ResampleResult]s.
n_resample_results = function(rhs) {
assert_ro_binding(rhs)
length(private$.data$uhashes())
},
#' @field uhashes (`character()`)\cr
#' Set of (unique) hashes of all included [ResampleResult]s.
uhashes = function(rhs) {
assert_ro_binding(rhs)
private$.data$uhashes()
}
),
private = list(
# @field data (`ResultData`)\cr
# Internal data storage object of type `ResultData`.
.data = NULL,
deep_clone = function(name, value) {
if (name == ".data") value$clone(deep = TRUE) else value
}
)
)
#' @export
as.data.table.BenchmarkResult = function(x, ..., hashes = FALSE, predict_sets = "test", task_characteristics = FALSE) { # nolint
assert_flag(task_characteristics)
tab = get_private(x)$.data$as_data_table(view = NULL, predict_sets = predict_sets)
tab = tab[, c("uhash", "task", "learner", "resampling", "iteration", "prediction"), with = FALSE]
if (task_characteristics) {
set(tab, j = "characteristics", value = map(tab$task, "characteristics"))
tab = unnest(tab, "characteristics")
}
tab[]
}
#' @export
c.BenchmarkResult = function(...) { # nolint
bmrs = lapply(list(...), as_benchmark_result)
init = BenchmarkResult$new()
Reduce(function(lhs, rhs) lhs$combine(rhs), bmrs, init = init)
}
#' @export
print.bmr_score = function(x, ...) {
print_data_table(x, c("uhash", "task", "learner", "resampling", "prediction"))
}
#' @export
print.bmr_aggregate = function(x, ...) {
print_data_table(x, "resample_result")
}