Common MLJ Workflows

Data ingestion

import RDatasets
channing = RDatasets.dataset("boot", "channing")

julia> first(channing, 4)
4×5 DataFrame
 Row │ Sex   Entry  Exit   Time   Cens
     │ Cat…  Int32  Int32  Int32  Int32
─────┼──────────────────────────────────
   1 │ Male    782    909    127      1
   2 │ Male   1020   1128    108      1
   3 │ Male    856    969    113      1
   4 │ Male    915    957     42      1

Inspecting metadata, including column scientific types:

schema(channing)

┌───────┬───────────────┬──────────────────────────────────┐
│ names │ scitypes      │ types                            │
├───────┼───────────────┼──────────────────────────────────┤
│ Sex   │ Multiclass{2} │ CategoricalValue{String, UInt32} │
│ Entry │ Count         │ Int64                            │
│ Exit  │ Count         │ Int64                            │
│ Time  │ Count         │ Int64                            │
│ Cens  │ Count         │ Int64                            │
└───────┴───────────────┴──────────────────────────────────┘

Horizontally splitting data and shuffling rows.

Here y is the :Exit column and X everything else:

y, X =  unpack(channing, ==(:Exit), rng=123);

Here y is the :Exit column and X everything else except :Time:

y, X =  unpack(channing,
               ==(:Exit),
               !=(:Time);
               rng=123);
scitype(y)

AbstractVector{Count} (alias for AbstractArray{Count, 1})

schema(X)

┌───────┬───────────────┬──────────────────────────────────┐
│ names │ scitypes      │ types                            │
├───────┼───────────────┼──────────────────────────────────┤
│ Sex   │ Multiclass{2} │ CategoricalValue{String, UInt32} │
│ Entry │ Count         │ Int64                            │
│ Cens  │ Count         │ Int64                            │
└───────┴───────────────┴──────────────────────────────────┘

Fixing wrong scientific types in X:

X = coerce(X, :Exit=>Continuous, :Entry=>Continuous, :Cens=>Multiclass)
schema(X)

┌───────┬─────────────────┬──────────────────────────────────┐
│ names │ scitypes        │ types                            │
├───────┼─────────────────┼──────────────────────────────────┤
│ Sex   │ Multiclass{2}   │ CategoricalValue{String, UInt32} │
│ Entry │ Continuous      │ Float64                          │
│ Cens  │ Multiclass{462} │ CategoricalValue{Int64, UInt32}  │
└───────┴─────────────────┴──────────────────────────────────┘

Loading a built-in supervised dataset:

table = load_iris();
schema(table)

┌──────────────┬───────────────┬──────────────────────────────────┐
│ names        │ scitypes      │ types                            │
├──────────────┼───────────────┼──────────────────────────────────┤
│ sepal_length │ Continuous    │ Float64                          │
│ sepal_width  │ Continuous    │ Float64                          │
│ petal_length │ Continuous    │ Float64                          │
│ petal_width  │ Continuous    │ Float64                          │
│ target       │ Multiclass{3} │ CategoricalValue{String, UInt32} │
└──────────────┴───────────────┴──────────────────────────────────┘

Loading a built-in data set already split into X and y:

X, y = @load_iris;
selectrows(X, 1:4) # selectrows works whenever `Tables.istable(X)==true`.

(sepal_length = [5.1, 4.9, 4.7, 4.6],
 sepal_width = [3.5, 3.0, 3.2, 3.1],
 petal_length = [1.4, 1.4, 1.3, 1.5],
 petal_width = [0.2, 0.2, 0.2, 0.2],)

y[1:4]

4-element CategoricalArray{String,1,UInt32}:
 "setosa"
 "setosa"
 "setosa"
 "setosa"

Splitting data vertically after row shuffling:

channing_train, channing_test = partition(channing, 0.6, rng=123);

Or, if already horizontally split:

(Xtrain, Xtest), (ytrain, ytest)  = partition((X, y), 0.6, multi=true,  rng=123)

(((sepal_length = [6.7, 5.7, 7.2, 4.4, 5.6, 6.5, 4.4, 6.1, 5.4, 4.9  …  6.4, 5.5, 5.4, 4.8, 6.5, 4.9, 6.5, 6.7, 5.6, 6.4], sepal_width = [3.3, 2.8, 3.0, 2.9, 2.5, 3.0, 3.0, 2.9, 3.9, 2.5  …  3.1, 2.3, 3.7, 3.1, 3.0, 2.4, 2.8, 3.3, 2.9, 2.8], petal_length = [5.7, 4.1, 5.8, 1.4, 3.9, 5.2, 1.3, 4.7, 1.7, 4.5  …  5.5, 4.0, 1.5, 1.6, 5.5, 3.3, 4.6, 5.7, 3.6, 5.6], petal_width = [2.1, 1.3, 1.6, 0.2, 1.1, 2.0, 0.2, 1.4, 0.4, 1.7  …  1.8, 1.3, 0.2, 0.2, 1.8, 1.0, 1.5, 2.5, 1.3, 2.2]), (sepal_length = [6.0, 5.8, 6.7, 5.1, 5.0, 6.3, 5.7, 6.4, 6.1, 5.0  …  6.4, 6.8, 6.9, 6.1, 6.7, 5.0, 7.6, 6.3, 5.1, 5.0], sepal_width = [2.7, 2.6, 3.0, 3.8, 3.4, 2.8, 2.5, 3.2, 2.8, 3.5  …  2.7, 3.2, 3.1, 2.8, 2.5, 3.5, 3.0, 2.5, 3.8, 3.6], petal_length = [5.1, 4.0, 5.2, 1.9, 1.5, 5.1, 5.0, 4.5, 4.7, 1.6  …  5.3, 5.9, 5.4, 4.0, 5.8, 1.3, 6.6, 5.0, 1.6, 1.4], petal_width = [1.6, 1.2, 2.3, 0.4, 0.2, 1.5, 2.0, 1.5, 1.2, 0.6  …  1.9, 2.3, 2.1, 1.3, 1.8, 0.3, 2.1, 1.9, 0.2, 0.2])), (CategoricalValue{String, UInt32}["virginica", "versicolor", "virginica", "setosa", "versicolor", "virginica", "setosa", "versicolor", "setosa", "virginica"  …  "virginica", "versicolor", "setosa", "setosa", "virginica", "versicolor", "versicolor", "virginica", "versicolor", "virginica"], CategoricalValue{String, UInt32}["versicolor", "versicolor", "virginica", "setosa", "setosa", "virginica", "virginica", "versicolor", "versicolor", "setosa"  …  "virginica", "virginica", "virginica", "versicolor", "virginica", "setosa", "virginica", "virginica", "setosa", "setosa"]))

Model Search

Reference: Model Search

Searching for a supervised model:

X, y = @load_boston
ms = models(matching(X, y))

64-element Vector{NamedTuple{(:name, :package_name, :is_supervised, :abstract_type, :deep_properties, :docstring, :fit_data_scitype, :human_name, :hyperparameter_ranges, :hyperparameter_types, :hyperparameters, :implemented_methods, :inverse_transform_scitype, :is_pure_julia, :is_wrapper, :iteration_parameter, :load_path, :package_license, :package_url, :package_uuid, :predict_scitype, :prediction_type, :reporting_operations, :reports_feature_importances, :supports_class_weights, :supports_online, :supports_training_losses, :supports_weights, :transform_scitype, :input_scitype, :target_scitype, :output_scitype)}}:
 (name = ARDRegressor, package_name = ScikitLearn, ... )
 (name = AdaBoostRegressor, package_name = ScikitLearn, ... )
 (name = BaggingRegressor, package_name = ScikitLearn, ... )
 (name = BayesianRidgeRegressor, package_name = ScikitLearn, ... )
 (name = ConstantRegressor, package_name = MLJModels, ... )
 (name = DecisionTreeRegressor, package_name = BetaML, ... )
 (name = DecisionTreeRegressor, package_name = DecisionTree, ... )
 (name = DeterministicConstantRegressor, package_name = MLJModels, ... )
 (name = DummyRegressor, package_name = ScikitLearn, ... )
 (name = ElasticNetCVRegressor, package_name = ScikitLearn, ... )
 ⋮
 (name = RidgeRegressor, package_name = MultivariateStats, ... )
 (name = RidgeRegressor, package_name = ScikitLearn, ... )
 (name = RobustRegressor, package_name = MLJLinearModels, ... )
 (name = SGDRegressor, package_name = ScikitLearn, ... )
 (name = SVMLinearRegressor, package_name = ScikitLearn, ... )
 (name = SVMNuRegressor, package_name = ScikitLearn, ... )
 (name = SVMRegressor, package_name = ScikitLearn, ... )
 (name = TheilSenRegressor, package_name = ScikitLearn, ... )
 (name = XGBoostRegressor, package_name = XGBoost, ... )

ms[6]

(name = "DecisionTreeRegressor",
 package_name = "BetaML",
 is_supervised = true,
 abstract_type = Deterministic,
 deep_properties = (),
 docstring = "```julia\nmutable struct DecisionTreeRegressor <: M...",
 fit_data_scitype =
     Tuple{Table{<:AbstractVector{<:Union{Missing, Known}}}, AbstractVector{<:Continuous}},
 human_name = "decision tree regressor",
 hyperparameter_ranges =
     (nothing, nothing, nothing, nothing, nothing, nothing),
 hyperparameter_types =
     ("Int64", "Float64", "Int64", "Int64", "Function", "Random.AbstractRNG"),
 hyperparameters = (:max_depth,
                    :min_gain,
                    :min_records,
                    :max_features,
                    :splitting_criterion,
                    :rng),
 implemented_methods = [:fit, :predict],
 inverse_transform_scitype = Unknown,
 is_pure_julia = true,
 is_wrapper = false,
 iteration_parameter = nothing,
 load_path = "BetaML.Trees.DecisionTreeRegressor",
 package_license = "MIT",
 package_url = "https://github.com/sylvaticus/BetaML.jl",
 package_uuid = "024491cd-cc6b-443e-8034-08ea7eb7db2b",
 predict_scitype = AbstractVector{<:Continuous},
 prediction_type = :deterministic,
 reporting_operations = (),
 reports_feature_importances = false,
 supports_class_weights = false,
 supports_online = false,
 supports_training_losses = false,
 supports_weights = false,
 transform_scitype = Unknown,
 input_scitype = Table{<:AbstractVector{<:Union{Missing, Known}}},
 target_scitype = AbstractVector{<:Continuous},
 output_scitype = Unknown)

models("Tree");

23-element Vector{NamedTuple{(:name, :package_name, :is_supervised, :abstract_type, :deep_properties, :docstring, :fit_data_scitype, :human_name, :hyperparameter_ranges, :hyperparameter_types, :hyperparameters, :implemented_methods, :inverse_transform_scitype, :is_pure_julia, :is_wrapper, :iteration_parameter, :load_path, :package_license, :package_url, :package_uuid, :predict_scitype, :prediction_type, :reporting_operations, :reports_feature_importances, :supports_class_weights, :supports_online, :supports_training_losses, :supports_weights, :transform_scitype, :input_scitype, :target_scitype, :output_scitype)}}:
 (name = ABODDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = AdaBoostStumpClassifier, package_name = DecisionTree, ... )
 (name = COFDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = DNNDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = DecisionTreeClassifier, package_name = BetaML, ... )
 (name = DecisionTreeClassifier, package_name = DecisionTree, ... )
 (name = DecisionTreeRegressor, package_name = BetaML, ... )
 (name = DecisionTreeRegressor, package_name = DecisionTree, ... )
 (name = EvoTreeClassifier, package_name = EvoTrees, ... )
 (name = EvoTreeCount, package_name = EvoTrees, ... )
 ⋮
 (name = ExtraTreesRegressor, package_name = ScikitLearn, ... )
 (name = GeneralImputer, package_name = BetaML, ... )
 (name = KNNDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = LOFDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = OneRuleClassifier, package_name = OneRule, ... )
 (name = RandomForestClassifier, package_name = BetaML, ... )
 (name = RandomForestClassifier, package_name = DecisionTree, ... )
 (name = RandomForestRegressor, package_name = BetaML, ... )
 (name = RandomForestRegressor, package_name = DecisionTree, ... )

A more refined search:

models() do model
    matching(model, X, y) &&
    model.prediction_type == :deterministic &&
    model.is_pure_julia
end;

Searching for an unsupervised model:

models(matching(X))

58-element Vector{NamedTuple{(:name, :package_name, :is_supervised, :abstract_type, :deep_properties, :docstring, :fit_data_scitype, :human_name, :hyperparameter_ranges, :hyperparameter_types, :hyperparameters, :implemented_methods, :inverse_transform_scitype, :is_pure_julia, :is_wrapper, :iteration_parameter, :load_path, :package_license, :package_url, :package_uuid, :predict_scitype, :prediction_type, :reporting_operations, :reports_feature_importances, :supports_class_weights, :supports_online, :supports_training_losses, :supports_weights, :transform_scitype, :input_scitype, :target_scitype, :output_scitype)}}:
 (name = ABODDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = ABODDetector, package_name = OutlierDetectionPython, ... )
 (name = AEDetector, package_name = OutlierDetectionNetworks, ... )
 (name = AffinityPropagation, package_name = ScikitLearn, ... )
 (name = AgglomerativeClustering, package_name = ScikitLearn, ... )
 (name = Birch, package_name = ScikitLearn, ... )
 (name = CBLOFDetector, package_name = OutlierDetectionPython, ... )
 (name = COFDetector, package_name = OutlierDetectionNeighbors, ... )
 (name = COFDetector, package_name = OutlierDetectionPython, ... )
 (name = COPODDetector, package_name = OutlierDetectionPython, ... )
 ⋮
 (name = PPCA, package_name = MultivariateStats, ... )
 (name = RODDetector, package_name = OutlierDetectionPython, ... )
 (name = RandomForestImputer, package_name = BetaML, ... )
 (name = SODDetector, package_name = OutlierDetectionPython, ... )
 (name = SOSDetector, package_name = OutlierDetectionPython, ... )
 (name = SimpleImputer, package_name = BetaML, ... )
 (name = SpectralClustering, package_name = ScikitLearn, ... )
 (name = Standardizer, package_name = MLJModels, ... )
 (name = TSVDTransformer, package_name = TSVD, ... )

Getting the metadata entry for a given model type:

info("PCA")
info("RidgeRegressor", pkg="MultivariateStats") # a model type in multiple packages

(name = "RidgeRegressor",
 package_name = "MultivariateStats",
 is_supervised = true,
 abstract_type = Deterministic,
 deep_properties = (),
 docstring = "```\nRidgeRegressor\n```\n\nA model type for construct...",
 fit_data_scitype =
     Tuple{Table{<:AbstractVector{<:Continuous}}, AbstractVector{Continuous}},
 human_name = "ridge regressor",
 hyperparameter_ranges = (nothing, nothing),
 hyperparameter_types = ("Union{Real, AbstractVecOrMat}", "Bool"),
 hyperparameters = (:lambda, :bias),
 implemented_methods = [:clean!, :fit, :fitted_params, :predict],
 inverse_transform_scitype = Unknown,
 is_pure_julia = true,
 is_wrapper = false,
 iteration_parameter = nothing,
 load_path = "MLJMultivariateStatsInterface.RidgeRegressor",
 package_license = "MIT",
 package_url = "https://github.com/JuliaStats/MultivariateStats.jl",
 package_uuid = "6f286f6a-111f-5878-ab1e-185364afe411",
 predict_scitype = AbstractVector{Continuous},
 prediction_type = :deterministic,
 reporting_operations = (),
 reports_feature_importances = false,
 supports_class_weights = false,
 supports_online = false,
 supports_training_losses = false,
 supports_weights = false,
 transform_scitype = Unknown,
 input_scitype = Table{<:AbstractVector{<:Continuous}},
 target_scitype = AbstractVector{Continuous},
 output_scitype = Unknown)

Extracting the model document string:

doc("DecisionTreeClassifier", pkg="DecisionTree")

DecisionTreeClassifier

A model type for constructing a CART decision tree classifier, based on DecisionTree.jl, and implementing the MLJ model interface.

From MLJ, the type can be imported using

DecisionTreeClassifier = @load DecisionTreeClassifier pkg=DecisionTree

Do model = DecisionTreeClassifier() to construct an instance with default hyper-parameters. Provide keyword arguments to override hyper-parameter defaults, as in DecisionTreeClassifier(max_depth=...).

DecisionTreeClassifier implements the CART algorithm, originally published in Breiman, Leo; Friedman, J. H.; Olshen, R. A.; Stone, C. J. (1984): "Classification and regression trees". Monterey, CA: Wadsworth & Brooks/Cole Advanced Books & Software..

Training data

In MLJ or MLJBase, bind an instance model to data with

mach = machine(model, X, y)

where

X: any table of input features (eg, a DataFrame) whose columns each have one of the following element scitypes: Continuous, Count, or <:OrderedFactor; check column scitypes with schema(X)
y: is the target, which can be any AbstractVector whose element scitype is <:OrderedFactor or <:Multiclass; check the scitype with scitype(y)

Train the machine using fit!(mach, rows=...).

Hyper-parameters

max_depth=-1: max depth of the decision tree (-1=any)
min_samples_leaf=1: max number of samples each leaf needs to have
min_samples_split=2: min number of samples needed for a split
min_purity_increase=0: min purity needed for a split
n_subfeatures=0: number of features to select at random (0 for all, -1 for square root of number of features)
post_prune=false: set to true for post-fit pruning
merge_purity_threshold=1.0: (post-pruning) merge leaves having combined purity >= merge_purity_threshold
display_depth=5: max depth to show when displaying the tree
feature_importance: method to use for computing feature importances. One of (:impurity, :split)
rng=Random.GLOBAL_RNG: random number generator or seed

Operations

predict(mach, Xnew): return predictions of the target given features Xnew having the same scitype as X above. Predictions are probabilistic, but uncalibrated.
predict_mode(mach, Xnew): instead return the mode of each prediction above.

Fitted parameters

The fields of fitted_params(mach) are:

tree: the tree or stump object returned by the core DecisionTree.jl algorithm
encoding: dictionary of target classes keyed on integers used internally by DecisionTree.jl; needed to interpret pretty printing of tree (obtained by calling fit!(mach, verbosity=2) or from report - see below)
features: the names of the features encountered in training, in an order consistent with the output of print_tree (see below)

Report

The fields of report(mach) are:

classes_seen: list of target classes actually observed in training
print_tree: method to print a pretty representation of the fitted tree, with single argument the tree depth; interpretation requires internal integer-class encoding (see "Fitted parameters" above).
features: the names of the features encountered in training, in an order consistent with the output of print_tree (see below)

Examples

using MLJ
Tree = @load DecisionTreeClassifier pkg=DecisionTree
tree = Tree(max_depth=4, min_samples_split=3)

X, y = @load_iris
mach = machine(tree, X, y) |> fit!

Xnew = (sepal_length = [6.4, 7.2, 7.4],
        sepal_width = [2.8, 3.0, 2.8],
        petal_length = [5.6, 5.8, 6.1],
        petal_width = [2.1, 1.6, 1.9],)
yhat = predict(mach, Xnew) # probabilistic predictions
predict_mode(mach, Xnew)   # point predictions
pdf.(yhat, "virginica")    # probabilities for the "verginica" class

fitted_params(mach).tree # raw tree or stump object from DecisionTrees.jl

julia> report(mach).print_tree(3)
Feature 4, Threshold 0.8
L-> 1 : 50/50
R-> Feature 4, Threshold 1.75
    L-> Feature 3, Threshold 4.95
        L->
        R->
    R-> Feature 3, Threshold 4.85
        L->
        R-> 3 : 43/43

To interpret the internal class labelling:

julia> fitted_params(mach).encoding
Dict{CategoricalArrays.CategoricalValue{String, UInt32}, UInt32} with 3 entries:
  "virginica"  => 0x00000003
  "setosa"     => 0x00000001
  "versicolor" => 0x00000002

See also DecisionTree.jl and the unwrapped model type MLJDecisionTreeInterface.DecisionTree.DecisionTreeClassifier.

Instantiating a model

Reference: Getting Started, Loading Model Code

Tree = @load DecisionTreeClassifier pkg=DecisionTree
tree = Tree(min_samples_split=5, max_depth=4)

DecisionTreeClassifier(
  max_depth = 4, 
  min_samples_leaf = 1, 
  min_samples_split = 5, 
  min_purity_increase = 0.0, 
  n_subfeatures = 0, 
  post_prune = false, 
  merge_purity_threshold = 1.0, 
  display_depth = 5, 
  feature_importance = :impurity, 
  rng = Random._GLOBAL_RNG())

tree = (@load DecisionTreeClassifier)()
tree.min_samples_split = 5
tree.max_depth = 4

Evaluating a model

Reference: Evaluating Model Performance

X, y = @load_boston
KNN = @load KNNRegressor
knn = KNN()
evaluate(knn, X, y,
         resampling=CV(nfolds=5),
         measure=[RootMeanSquaredError(), MeanAbsoluteError()])

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────┬───────────┬─────────────┬─────────┬──────────────────
│ measure                │ operation │ measurement │ 1.96*SE │ per_fold        ⋯
├────────────────────────┼───────────┼─────────────┼─────────┼──────────────────
│ RootMeanSquaredError() │ predict   │ 8.77        │ 1.84    │ [8.53, 8.8, 10. ⋯
│ MeanAbsoluteError()    │ predict   │ 6.02        │ 1.26    │ [6.52, 5.7, 7.6 ⋯
└────────────────────────┴───────────┴─────────────┴─────────┴──────────────────
                                                                1 column omitted

Note RootMeanSquaredError() has alias rms and MeanAbsoluteError() has alias mae.

Do measures() to list all losses and scores and their aliases.

Basic fit/evaluate/predict by hand:

Reference: Getting Started, Machines, Evaluating Model Performance, Performance Measures

crabs = load_crabs() |> DataFrames.DataFrame
schema(crabs)

┌───────┬───────────────┬──────────────────────────────────┐
│ names │ scitypes      │ types                            │
├───────┼───────────────┼──────────────────────────────────┤
│ sp    │ Multiclass{2} │ CategoricalValue{String, UInt32} │
│ sex   │ Multiclass{2} │ CategoricalValue{String, UInt32} │
│ index │ Count         │ Int64                            │
│ FL    │ Continuous    │ Float64                          │
│ RW    │ Continuous    │ Float64                          │
│ CL    │ Continuous    │ Float64                          │
│ CW    │ Continuous    │ Float64                          │
│ BD    │ Continuous    │ Float64                          │
└───────┴───────────────┴──────────────────────────────────┘

y, X = unpack(crabs, ==(:sp), !in([:index, :sex]); rng=123)


Tree = @load DecisionTreeClassifier pkg=DecisionTree

DecisionTreeClassifier(
  max_depth = 2, 
  min_samples_leaf = 1, 
  min_samples_split = 2, 
  min_purity_increase = 0.0, 
  n_subfeatures = 0, 
  post_prune = false, 
  merge_purity_threshold = 1.0, 
  display_depth = 5, 
  feature_importance = :impurity, 
  rng = Random._GLOBAL_RNG())

Bind the model and data together in a machine, which will additionally, store the learned parameters (fitresults) when fit:

mach = machine(tree, X, y)

untrained Machine; caches model-specific representations of data
  model: DecisionTreeClassifier(max_depth = 2, …)
  args: 
    1:	Source @391 ⏎ Table{AbstractVector{Continuous}}
    2:	Source @968 ⏎ AbstractVector{Multiclass{2}}

Split row indices into training and evaluation rows:

train, test = partition(eachindex(y), 0.7); # 70:30 split

([1, 2, 3, 4, 5, 6, 7, 8, 9, 10  …  131, 132, 133, 134, 135, 136, 137, 138, 139, 140], [141, 142, 143, 144, 145, 146, 147, 148, 149, 150  …  191, 192, 193, 194, 195, 196, 197, 198, 199, 200])

Fit on the train data set and evaluate on the test data set:

fit!(mach, rows=train)
yhat = predict(mach, X[test,:])
mean(LogLoss(tol=1e-4)(yhat, y[test]))

1.0788055664326648

Note LogLoss() has aliases log_loss and cross_entropy.

Run measures() to list all losses and scores and their aliases ("instances").

Predict on the new data set:

Xnew = (FL = rand(3), RW = rand(3), CL = rand(3), CW = rand(3), BD =rand(3))
predict(mach, Xnew)      # a vector of distributions

3-element CategoricalDistributions.UnivariateFiniteVector{Multiclass{2}, String, UInt32, Float64}:
 UnivariateFinite{Multiclass{2}}(B=>0.667, O=>0.333)
 UnivariateFinite{Multiclass{2}}(B=>0.667, O=>0.333)
 UnivariateFinite{Multiclass{2}}(B=>0.667, O=>0.333)

predict_mode(mach, Xnew) # a vector of point-predictions

3-element CategoricalArray{String,1,UInt32}:
 "B"
 "B"
 "B"

More performance evaluation examples

Evaluating model + data directly:

evaluate(tree, X, y,
         resampling=Holdout(fraction_train=0.7, shuffle=true, rng=1234),
         measure=[LogLoss(), Accuracy()])

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────────────┬──────────────┬─────────────┬──────────┐
│ measure                        │ operation    │ measurement │ per_fold │
├────────────────────────────────┼──────────────┼─────────────┼──────────┤
│ LogLoss(                       │ predict      │ 1.12        │ [1.12]   │
│   tol = 2.220446049250313e-16) │              │             │          │
│ Accuracy()                     │ predict_mode │ 0.683       │ [0.683]  │
└────────────────────────────────┴──────────────┴─────────────┴──────────┘

If a machine is already defined, as above:

evaluate!(mach,
          resampling=Holdout(fraction_train=0.7, shuffle=true, rng=1234),
          measure=[LogLoss(), Accuracy()])

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────────────┬──────────────┬─────────────┬──────────┐
│ measure                        │ operation    │ measurement │ per_fold │
├────────────────────────────────┼──────────────┼─────────────┼──────────┤
│ LogLoss(                       │ predict      │ 1.12        │ [1.12]   │
│   tol = 2.220446049250313e-16) │              │             │          │
│ Accuracy()                     │ predict_mode │ 0.683       │ [0.683]  │
└────────────────────────────────┴──────────────┴─────────────┴──────────┘

Using cross-validation:

evaluate!(mach, resampling=CV(nfolds=5, shuffle=true, rng=1234),
          measure=[LogLoss(), Accuracy()])

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────────────┬──────────────┬─────────────┬─────────┬───────
│ measure                        │ operation    │ measurement │ 1.96*SE │ per_ ⋯
├────────────────────────────────┼──────────────┼─────────────┼─────────┼───────
│ LogLoss(                       │ predict      │ 0.748       │ 0.432   │ [0.5 ⋯
│   tol = 2.220446049250313e-16) │              │             │         │      ⋯
│ Accuracy()                     │ predict_mode │ 0.7         │ N/A     │ [0.7 ⋯
└────────────────────────────────┴──────────────┴─────────────┴─────────┴───────
                                                                1 column omitted

With user-specified train/test pairs of row indices:

f1, f2, f3 = 1:13, 14:26, 27:36
pairs = [(f1, vcat(f2, f3)), (f2, vcat(f3, f1)), (f3, vcat(f1, f2))];
evaluate!(mach,
          resampling=pairs,
          measure=[LogLoss(), Accuracy()])

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────────────┬──────────────┬─────────────┬─────────┬───────
│ measure                        │ operation    │ measurement │ 1.96*SE │ per_ ⋯
├────────────────────────────────┼──────────────┼─────────────┼─────────┼───────
│ LogLoss(                       │ predict      │ 4.81        │ 0.539   │ [5.1 ⋯
│   tol = 2.220446049250313e-16) │              │             │         │      ⋯
│ Accuracy()                     │ predict_mode │ 0.735       │ N/A     │ [0.6 ⋯
└────────────────────────────────┴──────────────┴─────────────┴─────────┴───────
                                                                1 column omitted

Changing a hyperparameter and re-evaluating:

tree.max_depth = 3
evaluate!(mach,
          resampling=CV(nfolds=5, shuffle=true, rng=1234),
          measure=[LogLoss(), Accuracy()])

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────────────┬──────────────┬─────────────┬─────────┬───────
│ measure                        │ operation    │ measurement │ 1.96*SE │ per_ ⋯
├────────────────────────────────┼──────────────┼─────────────┼─────────┼───────
│ LogLoss(                       │ predict      │ 1.19        │ 0.957   │ [1.2 ⋯
│   tol = 2.220446049250313e-16) │              │             │         │      ⋯
│ Accuracy()                     │ predict_mode │ 0.865       │ N/A     │ [0.8 ⋯
└────────────────────────────────┴──────────────┴─────────────┴─────────┴───────
                                                                1 column omitted

Inspecting training results

Fit an ordinary least square model to some synthetic data:

x1 = rand(100)
x2 = rand(100)

X = (x1=x1, x2=x2)
y = x1 - 2x2 + 0.1*rand(100);

OLS = @load LinearRegressor pkg=GLM
ols = OLS()
mach =  machine(ols, X, y) |> fit!

trained Machine; caches model-specific representations of data
  model: LinearRegressor(fit_intercept = true, …)
  args: 
    1:	Source @660 ⏎ Table{AbstractVector{Continuous}}
    2:	Source @316 ⏎ AbstractVector{Continuous}

Get a named tuple representing the learned parameters, human-readable if appropriate:

fitted_params(mach)

(features = [:x1, :x2],
 coef = [0.9949306940480123, -1.9819634149505425],
 intercept = 0.046342572449619056,)

Get other training-related information:

report(mach)

(stderror = [0.010210239975227405, 0.010366977065819766, 0.008282814909063478],
 dof_residual = 97.0,
 vcov = [0.00010424900035173173 2.2487590405552644e-6 -5.497572311209681e-5; 2.2487590405552644e-6 0.00010747421348323301 -5.869932130705701e-5; -5.497572311209681e-5 -5.869932130705701e-5 6.860502281780424e-5],
 deviance = 0.08557434103059575,
 coef_table = ──────────────────────────────────────────────────────────────────────────────
                  Coef.  Std. Error        t  Pr(>|t|)   Lower 95%   Upper 95%
──────────────────────────────────────────────────────────────────────────────
x1            0.994931   0.0102102     97.44    <1e-97   0.974666    1.0152
x2           -1.98196    0.010367    -191.18    <1e-99  -2.00254    -1.96139
(Intercept)   0.0463426  0.00828281     5.60    <1e-06   0.0299035   0.0627817
──────────────────────────────────────────────────────────────────────────────,)

Basic fit/transform for unsupervised models

Load data:

X, y = @load_iris
train, test = partition(eachindex(y), 0.97, shuffle=true, rng=123)

([125, 100, 130, 9, 70, 148, 39, 64, 6, 107  …  110, 59, 139, 21, 112, 144, 140, 72, 109, 41], [106, 147, 47, 5])

Instantiate and fit the model/machine:

PCA = @load PCA
pca = PCA(maxoutdim=2)
mach = machine(pca, X)
fit!(mach, rows=train)

trained Machine; caches model-specific representations of data
  model: PCA(maxoutdim = 2, …)
  args: 
    1:	Source @963 ⏎ Table{AbstractVector{Continuous}}

Transform selected data bound to the machine:

transform(mach, rows=test);

(x1 = [-3.394282685448322, -1.5219827578765053, 2.53824745518522, 2.7299639893931382],
 x2 = [0.547245022374522, -0.36842368617126425, 0.5199299511335688, 0.3448466122232349],)

Transform new data:

Xnew = (sepal_length=rand(3), sepal_width=rand(3),
        petal_length=rand(3), petal_width=rand(3));
transform(mach, Xnew)

(x1 = [4.377312629490492, 4.8806810394534725, 5.018807609251294],
 x2 = [-4.342986983612582, -4.364759615256477, -4.433934976460561],)

Inverting learned transformations

y = rand(100);
stand = Standardizer()
mach = machine(stand, y)
fit!(mach)
z = transform(mach, y);
@assert inverse_transform(mach, z) ≈ y # true

[ Info: Training machine(Standardizer(features = Symbol[], …), …).

Nested hyperparameter tuning

Reference: Tuning Models

Define a model with nested hyperparameters:

Tree = @load DecisionTreeClassifier pkg=DecisionTree
tree = Tree()
forest = EnsembleModel(model=tree, n=300)

ProbabilisticEnsembleModel(
  model = DecisionTreeClassifier(
        max_depth = -1, 
        min_samples_leaf = 1, 
        min_samples_split = 2, 
        min_purity_increase = 0.0, 
        n_subfeatures = 0, 
        post_prune = false, 
        merge_purity_threshold = 1.0, 
        display_depth = 5, 
        feature_importance = :impurity, 
        rng = Random._GLOBAL_RNG()), 
  atomic_weights = Float64[], 
  bagging_fraction = 0.8, 
  rng = Random._GLOBAL_RNG(), 
  n = 300, 
  acceleration = CPU1{Nothing}(nothing), 
  out_of_bag_measure = Any[])

Define ranges for hyperparameters to be tuned:

r1 = range(forest, :bagging_fraction, lower=0.5, upper=1.0, scale=:log10)

NumericRange(0.5 ≤ bagging_fraction ≤ 1.0; origin=0.75, unit=0.25; on log10 scale)

r2 = range(forest, :(model.n_subfeatures), lower=1, upper=4) # nested

NumericRange(1 ≤ model.n_subfeatures ≤ 4; origin=2.5, unit=1.5)

Wrap the model in a tuning strategy:

tuned_forest = TunedModel(model=forest,
                          tuning=Grid(resolution=12),
                          resampling=CV(nfolds=6),
                          ranges=[r1, r2],
                          measure=BrierLoss())

ProbabilisticTunedModel(
  model = ProbabilisticEnsembleModel(
        model = DecisionTreeClassifier(max_depth = -1, …), 
        atomic_weights = Float64[], 
        bagging_fraction = 0.8, 
        rng = Random._GLOBAL_RNG(), 
        n = 300, 
        acceleration = CPU1{Nothing}(nothing), 
        out_of_bag_measure = Any[]), 
  tuning = Grid(
        goal = nothing, 
        resolution = 12, 
        shuffle = true, 
        rng = Random._GLOBAL_RNG()), 
  resampling = CV(
        nfolds = 6, 
        shuffle = false, 
        rng = Random._GLOBAL_RNG()), 
  measure = BrierLoss(), 
  weights = nothing, 
  class_weights = nothing, 
  operation = nothing, 
  range = MLJBase.NumericRange{T, MLJBase.Bounded, Symbol} where T[NumericRange(0.5 ≤ bagging_fraction ≤ 1.0; origin=0.75, unit=0.25; on log10 scale), NumericRange(1 ≤ model.n_subfeatures ≤ 4; origin=2.5, unit=1.5)], 
  selection_heuristic = MLJTuning.NaiveSelection(nothing), 
  train_best = true, 
  repeats = 1, 
  n = nothing, 
  acceleration = CPU1{Nothing}(nothing), 
  acceleration_resampling = CPU1{Nothing}(nothing), 
  check_measure = true, 
  cache = true)

Bound the wrapped model to data:

mach = machine(tuned_forest, X, y)

untrained Machine; does not cache data
  model: ProbabilisticTunedModel(model = ProbabilisticEnsembleModel(model = DecisionTreeClassifier(max_depth = -1, …), …), …)
  args: 
    1:	Source @096 ⏎ Table{AbstractVector{Continuous}}
    2:	Source @126 ⏎ AbstractVector{Multiclass{3}}

Fitting the resultant machine optimizes the hyperparameters specified in range, using the specified tuning and resampling strategies and performance measure (possibly a vector of measures), and retrains on all data bound to the machine:

fit!(mach)

trained Machine; does not cache data
  model: ProbabilisticTunedModel(model = ProbabilisticEnsembleModel(model = DecisionTreeClassifier(max_depth = -1, …), …), …)
  args: 
    1:	Source @096 ⏎ Table{AbstractVector{Continuous}}
    2:	Source @126 ⏎ AbstractVector{Multiclass{3}}

Inspecting the optimal model:

F = fitted_params(mach)

(best_model = ProbabilisticEnsembleModel(model = DecisionTreeClassifier(max_depth = -1, …), …),
 best_fitted_params = (fitresult = WrappedEnsemble(atom = DecisionTreeClassifier(max_depth = -1, …), …),),)

F.best_model

ProbabilisticEnsembleModel(
  model = DecisionTreeClassifier(
        max_depth = -1, 
        min_samples_leaf = 1, 
        min_samples_split = 2, 
        min_purity_increase = 0.0, 
        n_subfeatures = 3, 
        post_prune = false, 
        merge_purity_threshold = 1.0, 
        display_depth = 5, 
        feature_importance = :impurity, 
        rng = Random._GLOBAL_RNG()), 
  atomic_weights = Float64[], 
  bagging_fraction = 0.5, 
  rng = Random._GLOBAL_RNG(), 
  n = 300, 
  acceleration = CPU1{Nothing}(nothing), 
  out_of_bag_measure = Any[])

Inspecting details of tuning procedure:

r = report(mach);
keys(r)

(:best_model, :best_history_entry, :history, :best_report, :plotting)

r.history[[1,end]]

2-element Vector{NamedTuple{(:model, :measure, :measurement, :per_fold), Tuple{MLJEnsembles.ProbabilisticEnsembleModel{MLJDecisionTreeInterface.DecisionTreeClassifier}, Vector{BrierLoss}, Vector{Float64}, Vector{Vector{Float64}}}}}:
 (model = ProbabilisticEnsembleModel(model = DecisionTreeClassifier(max_depth = -1, …), …), measure = [BrierLoss()], measurement = [0.12180079115226344], per_fold = [[0.024923555555555695, 0.00667466666666682, 0.19803022222222236, 0.15237267283950606, 0.1639654074074074, 0.18483822222222238]])
 (model = ProbabilisticEnsembleModel(model = DecisionTreeClassifier(max_depth = -1, …), …), measure = [BrierLoss()], measurement = [0.1097899259259257], per_fold = [[-0.0, -0.0, 0.14789955555555537, 0.15325333333333283, 0.14361244444444407, 0.213974222222222]])

Visualizing these results:

using Plots
plot(mach)

Predicting on new data using the optimized model:

predict(mach, Xnew)

3-element CategoricalDistributions.UnivariateFiniteVector{Multiclass{3}, String, UInt32, Float64}:
 UnivariateFinite{Multiclass{3}}(setosa=>1.0, versicolor=>0.0, virginica=>0.0)
 UnivariateFinite{Multiclass{3}}(setosa=>1.0, versicolor=>0.0, virginica=>0.0)
 UnivariateFinite{Multiclass{3}}(setosa=>0.513, versicolor=>0.443, virginica=>0.0433)

Constructing linear pipelines

Reference: Composing Models

Constructing a linear (unbranching) pipeline with a learned target transformation/inverse transformation:

X, y = @load_reduced_ames
KNN = @load KNNRegressor
knn_with_target = TransformedTargetModel(model=KNN(K=3), target=Standardizer())
pipe = (X -> coerce(X, :age=>Continuous)) |> OneHotEncoder() |> knn_with_target

DeterministicPipeline(
  f = Main.var"ex-workflows".var"#15#16"(), 
  one_hot_encoder = OneHotEncoder(
        features = Symbol[], 
        drop_last = false, 
        ordered_factor = true, 
        ignore = false), 
  transformed_target_model_deterministic = TransformedTargetModelDeterministic(
        model = KNNRegressor(K = 3, …), 
        transformer = Standardizer(features = Symbol[], …), 
        inverse = nothing, 
        cache = true), 
  cache = true)

Evaluating the pipeline (just as you would any other model):

pipe.one_hot_encoder.drop_last = true
evaluate(pipe, X, y, resampling=Holdout(), measure=RootMeanSquaredError(), verbosity=2)

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────┬───────────┬─────────────┬───────────┐
│ measure                │ operation │ measurement │ per_fold  │
├────────────────────────┼───────────┼─────────────┼───────────┤
│ RootMeanSquaredError() │ predict   │ 51200.0     │ [51200.0] │
└────────────────────────┴───────────┴─────────────┴───────────┘

Inspecting the learned parameters in a pipeline:

mach = machine(pipe, X, y) |> fit!
F = fitted_params(mach)
F.transformed_target_model_deterministic.model

(tree = NearestNeighbors.KDTree{StaticArraysCore.SVector{56, Float64}, Distances.Euclidean, Float64}
  Number of points: 1456
  Dimensions: 56
  Metric: Distances.Euclidean(0.0)
  Reordered: true,)

Constructing a linear (unbranching) pipeline with a static (unlearned) target transformation/inverse transformation:

Tree = @load DecisionTreeRegressor pkg=DecisionTree verbosity=0
tree_with_target = TransformedTargetModel(model=Tree(),
                                          target=y -> log.(y),
                                          inverse = z -> exp.(z))
pipe2 = (X -> coerce(X, :age=>Continuous)) |> OneHotEncoder() |> tree_with_target;

┌ Warning: `TransformedTargetModel(target=...)` is deprecated in favor of `TransformedTargetModel(transformer=...)`.
│   caller = ip:0x0
└ @ Core :-1

Creating a homogeneous ensemble of models

Reference: Homogeneous Ensembles

X, y = @load_iris
Tree = @load DecisionTreeClassifier pkg=DecisionTree
tree = Tree()
forest = EnsembleModel(model=tree, bagging_fraction=0.8, n=300)
mach = machine(forest, X, y)
evaluate!(mach, measure=LogLoss())

PerformanceEvaluation object with these fields:
  measure, operation, measurement, per_fold,
  per_observation, fitted_params_per_fold,
  report_per_fold, train_test_rows
Extract:
┌────────────────────────────────┬───────────┬─────────────┬─────────┬──────────
│ measure                        │ operation │ measurement │ 1.96*SE │ per_fol ⋯
├────────────────────────────────┼───────────┼─────────────┼─────────┼──────────
│ LogLoss(                       │ predict   │ 0.438       │ 0.55    │ [3.89e- ⋯
│   tol = 2.220446049250313e-16) │           │             │         │         ⋯
└────────────────────────────────┴───────────┴─────────────┴─────────┴──────────
                                                                1 column omitted

Performance curves

Generate a plot of performance, as a function of some hyperparameter (building on the preceding example)

Single performance curve:

r = range(forest, :n, lower=1, upper=1000, scale=:log10)
curve = learning_curve(mach,
                       range=r,
                       resampling=Holdout(),
                       resolution=50,
                       measure=LogLoss(),
                       verbosity=0)

(parameter_name = "n",
 parameter_scale = :log10,
 parameter_values = [1, 2, 3, 4, 5, 6, 7, 8, 10, 11  …  281, 324, 373, 429, 494, 569, 655, 754, 869, 1000],
 measurements = [8.009700753137142, 4.081866729964122, 4.126918408642807, 4.1588830833596715, 1.89797993734079, 1.9441536088511273, 1.972775140086068, 1.9912665556678937, 2.0302224210156234, 2.0499468414779676  …  1.2689398399050775, 1.2756668067663597, 1.268507940360816, 1.2631446097729992, 1.2632518420420762, 1.2649323533055645, 1.261947637742257, 1.2623656952649547, 1.2596284180668724, 1.2521481588785621],)

using Plots
plot(curve.parameter_values, curve.measurements, xlab=curve.parameter_name, xscale=curve.parameter_scale)

Multiple curves:

curve = learning_curve(mach,
                       range=r,
                       resampling=Holdout(),
                       measure=LogLoss(),
                       resolution=50,
                       rng_name=:rng,
                       rngs=4,
                       verbosity=0)

(parameter_name = "n",
 parameter_scale = :log10,
 parameter_values = [1, 2, 3, 4, 5, 6, 7, 8, 10, 11  …  281, 324, 373, 429, 494, 569, 655, 754, 869, 1000],
 measurements = [4.004850376568572 9.611640903764572 15.218431430960573 9.611640903764572; 4.004850376568572 9.611640903764572 15.218431430960573 8.040507294495363; … ; 1.2053272700409534 1.232760548689883 1.2644971143185944 1.2732955730443574; 1.2108933396684327 1.2321376994018858 1.2667473799197961 1.2716130177418612],)

plot(curve.parameter_values, curve.measurements,
xlab=curve.parameter_name, xscale=curve.parameter_scale)