Merge pull request #29 from JuliaAI/dev

For a 0.2.4 release

Author: ablaom

Project.toml

@@ -1,7 +1,7 @@
 name = "MLJDecisionTreeInterface"
 uuid = "c6f25543-311c-4c74-83dc-3ea6d1015661"
 authors = ["Anthony D. Blaom <[email protected]>"]
-version = "0.2.3"
+version = "0.2.4"
 
 [deps]
 DecisionTree = "7806a523-6efd-50cb-b5f6-3fa6f1930dbb"

src/MLJDecisionTreeInterface.jl

@@ -25,11 +25,9 @@ Base.show(stream::IO, c::TreePrinter) =
 # # DECISION TREE CLASSIFIER
 
 # The following meets the MLJ standard for a `Model` docstring and is
-# created without the use of interpolation so it can be used a
-# template for authors of other MLJ model interfaces. The other
+# created without the use of interpolation so it can be used a # template for authors of other MLJ model interfaces. The other
 # doc-strings, defined later, are generated using the `doc_header`
 # utility to automatically generate the header, another option.
-
 MMI.@mlj_model mutable struct DecisionTreeClassifier <: MMI.Probabilistic
     max_depth::Int               = (-)(1)::(_ ≥ -1)
     min_samples_leaf::Int        = 1::(_ ≥ 0)
@@ -39,6 +37,7 @@ MMI.@mlj_model mutable struct DecisionTreeClassifier <: MMI.Probabilistic
     post_prune::Bool             = false
     merge_purity_threshold::Float64 = 1.0::(_ ≤ 1)
     display_depth::Int           = 5::(_ ≥ 1)
+    feature_importance::Symbol = :impurity::(_ ∈ (:impurity, :split))
     rng::Union{AbstractRNG,Integer} = GLOBAL_RNG
 end
 
@@ -73,8 +72,8 @@ function MMI.fit(m::DecisionTreeClassifier, verbosity::Int, X, y)
     cache  = nothing
     report = (classes_seen=classes_seen,
               print_tree=TreePrinter(tree),
-              features=features)
-
+              features=features,
+              )
     return fitresult, cache, report
 end
 
@@ -107,6 +106,8 @@ function MMI.predict(m::DecisionTreeClassifier, fitresult, Xnew)
     return MMI.UnivariateFinite(classes_seen, scores)
 end
 
+MMI.reports_feature_importances(::Type{<:DecisionTreeClassifier}) = true
+
 
 # # RANDOM FOREST CLASSIFIER
 
@@ -118,13 +119,21 @@ MMI.@mlj_model mutable struct RandomForestClassifier <: MMI.Probabilistic
     n_subfeatures::Int           = (-)(1)::(_ ≥ -1)
     n_trees::Int                 = 10::(_ ≥ 2)
     sampling_fraction::Float64   = 0.7::(0 < _ ≤ 1)
+    feature_importance::Symbol = :impurity::(_ ∈ (:impurity, :split))
     rng::Union{AbstractRNG,Integer} = GLOBAL_RNG
 end
 
 function MMI.fit(m::RandomForestClassifier, verbosity::Int, X, y)
+    schema = Tables.schema(X)
     Xmatrix = MMI.matrix(X)
     yplain  = MMI.int(y)
 
+    if schema === nothing
+        features = [Symbol("x$j") for j in 1:size(Xmatrix, 2)]
+    else
+        features = schema.names |> collect
+    end
+
     classes_seen  = filter(in(unique(y)), MMI.classes(y[1]))
     integers_seen = MMI.int(classes_seen)
 
@@ -138,7 +147,9 @@ function MMI.fit(m::RandomForestClassifier, verbosity::Int, X, y)
                              m.min_purity_increase;
                              rng=m.rng)
     cache  = nothing
-    report = NamedTuple()
+
+    report = (features=features,)
+
     return (forest, classes_seen, integers_seen), cache, report
 end
 
@@ -151,25 +162,38 @@ function MMI.predict(m::RandomForestClassifier, fitresult, Xnew)
     return MMI.UnivariateFinite(classes_seen, scores)
 end
 
+MMI.reports_feature_importances(::Type{<:RandomForestClassifier}) = true
+
 
 # # ADA BOOST STUMP CLASSIFIER
 
 MMI.@mlj_model mutable struct AdaBoostStumpClassifier <: MMI.Probabilistic
     n_iter::Int            = 10::(_ ≥ 1)
+    feature_importance::Symbol = :impurity::(_ ∈ (:impurity, :split))
     rng::Union{AbstractRNG,Integer} = GLOBAL_RNG
 end
 
 function MMI.fit(m::AdaBoostStumpClassifier, verbosity::Int, X, y)
+    schema = Tables.schema(X)
     Xmatrix = MMI.matrix(X)
     yplain  = MMI.int(y)
 
+    if schema === nothing
+        features = [Symbol("x$j") for j in 1:size(Xmatrix, 2)]
+    else
+        features = schema.names |> collect
+    end
+
+
     classes_seen  = filter(in(unique(y)), MMI.classes(y[1]))
     integers_seen = MMI.int(classes_seen)
 
     stumps, coefs =
         DT.build_adaboost_stumps(yplain, Xmatrix, m.n_iter, rng=m.rng)
     cache  = nothing
-    report = NamedTuple()
+
+    report = (features=features,)
+
     return (stumps, coefs, classes_seen, integers_seen), cache, report
 end
 
@@ -184,6 +208,8 @@ function MMI.predict(m::AdaBoostStumpClassifier, fitresult, Xnew)
     return MMI.UnivariateFinite(classes_seen, scores)
 end
 
+MMI.reports_feature_importances(::Type{<:AdaBoostStumpClassifier}) = true
+
 
 # # DECISION TREE REGRESSOR
 
@@ -195,11 +221,20 @@ MMI.@mlj_model mutable struct DecisionTreeRegressor <: MMI.Deterministic
     n_subfeatures::Int                   = 0::(_ ≥ -1)
     post_prune::Bool                     = false
     merge_purity_threshold::Float64 = 1.0::(0 ≤ _ ≤ 1)
+    feature_importance::Symbol = :impurity::(_ ∈ (:impurity, :split))
     rng::Union{AbstractRNG,Integer} = GLOBAL_RNG
 end
 
 function MMI.fit(m::DecisionTreeRegressor, verbosity::Int, X, y)
+    schema = Tables.schema(X)
     Xmatrix = MMI.matrix(X)
+
+    if schema === nothing
+        features = [Symbol("x$j") for j in 1:size(Xmatrix, 2)]
+    else
+        features = schema.names |> collect
+    end
+
     tree    = DT.build_tree(float(y), Xmatrix,
                             m.n_subfeatures,
                             m.max_depth,
@@ -212,7 +247,9 @@ function MMI.fit(m::DecisionTreeRegressor, verbosity::Int, X, y)
         tree = DT.prune_tree(tree, m.merge_purity_threshold)
     end
     cache  = nothing
-    report = NamedTuple()
+
+    report = (features=features,)
+
     return tree, cache, report
 end
 
@@ -223,6 +260,8 @@ function MMI.predict(::DecisionTreeRegressor, tree, Xnew)
     return DT.apply_tree(tree, Xmatrix)
 end
 
+MMI.reports_feature_importances(::Type{<:DecisionTreeRegressor}) = true
+
 
 # # RANDOM FOREST REGRESSOR
 
@@ -234,11 +273,20 @@ MMI.@mlj_model mutable struct RandomForestRegressor <: MMI.Deterministic
     n_subfeatures::Int           = (-)(1)::(_ ≥ -1)
     n_trees::Int                 = 10::(_ ≥ 2)
     sampling_fraction::Float64   = 0.7::(0 < _ ≤ 1)
+    feature_importance::Symbol = :impurity::(_ ∈ (:impurity, :split))
     rng::Union{AbstractRNG,Integer} = GLOBAL_RNG
 end
 
 function MMI.fit(m::RandomForestRegressor, verbosity::Int, X, y)
+    schema = Tables.schema(X)
     Xmatrix = MMI.matrix(X)
+
+    if schema === nothing
+        features = [Symbol("x$j") for j in 1:size(Xmatrix, 2)]
+    else
+        features = schema.names |> collect
+    end
+
     forest  = DT.build_forest(float(y), Xmatrix,
                               m.n_subfeatures,
                               m.n_trees,
@@ -249,7 +297,8 @@ function MMI.fit(m::RandomForestRegressor, verbosity::Int, X, y)
                               m.min_purity_increase,
                               rng=m.rng)
     cache  = nothing
-    report = NamedTuple()
+    report = (features=features,)
+
     return forest, cache, report
 end
 
@@ -260,6 +309,34 @@ function MMI.predict(::RandomForestRegressor, forest, Xnew)
     return DT.apply_forest(forest, Xmatrix)
 end
 
+MMI.reports_feature_importances(::Type{<:RandomForestRegressor}) = true
+
+
+# # Feature Importances
+
+# get actual arguments needed for importance calculation from various fitresults.
+get_fitresult(m::Union{DecisionTreeClassifier, RandomForestClassifier}, fitresult) = (fitresult[1],)
+get_fitresult(m::Union{DecisionTreeRegressor, RandomForestRegressor}, fitresult) = (fitresult,)
+get_fitresult(m::AdaBoostStumpClassifier, fitresult)= (fitresult[1], fitresult[2])
+
+function MMI.feature_importances(m::Union{DecisionTreeClassifier, RandomForestClassifier, AdaBoostStumpClassifier, DecisionTreeRegressor, RandomForestRegressor}, fitresult, report)
+    # generate feature importances for report
+    if m.feature_importance == :impurity
+        feature_importance_func = DT.impurity_importance
+    elseif m.feature_importance == :split
+        feature_importance_func = DT.split_importance
+    end
+
+    mdl = get_fitresult(m, fitresult)
+    features = report.features
+    fi = feature_importance_func(mdl..., normalize=true)
+    fi_pairs = Pair.(features, fi)
+    # sort descending
+    sort!(fi_pairs, by= x->-x[2])
+
+    return fi_pairs
+end
+
 
 # # METADATA (MODEL TRAITS)
 
@@ -379,6 +456,8 @@ Train the machine using `fit!(mach, rows=...)`.
 
 - `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
 
 
@@ -512,6 +591,8 @@ Train the machine with `fit!(mach, rows=...)`.
 
 - `sampling_fraction=0.7`  fraction of samples to train each tree on
 
+- `feature_importance`:    method to use for computing feature importances. One of `(:impurity, :split)`
+
 - `rng=Random.GLOBAL_RNG`: random number generator or seed
 
 
@@ -587,6 +668,9 @@ Train the machine with `fit!(mach, rows=...)`.
 
 - `n_iter=10`:   number of iterations of AdaBoost
 
+- `feature_importance`: method to use for computing feature importances. One of `(:impurity,
+  :split)`
+
 - `rng=Random.GLOBAL_RNG`: random number generator or seed
 
 # Operations
@@ -678,6 +762,8 @@ Train the machine with `fit!(mach, rows=...)`.
 - `merge_purity_threshold=1.0`: (post-pruning) merge leaves having
                            combined purity `>= merge_purity_threshold`
 
+- `feature_importance`:    method to use for computing feature importances. One of `(:impurity, :split)`
+
 - `rng=Random.GLOBAL_RNG`: random number generator or seed
 
 
@@ -760,6 +846,8 @@ Train the machine with `fit!(mach, rows=...)`.
 
 - `sampling_fraction=0.7`  fraction of samples to train each tree on
 
+- `feature_importance`:    method to use for computing feature importances. One of `(:impurity, :split)`
+
 - `rng=Random.GLOBAL_RNG`: random number generator or seed
 
 

test/runtests.jl

@@ -45,6 +45,7 @@ yyhat = predict_mode(baretree, fitresult, MLJBase.selectrows(X, 1:3))
 @test Set(report.classes_seen) == Set(levels(y))
 @test report.print_tree(2) === nothing # :-(
 @test report.features == [:sepal_length, :sepal_width, :petal_length, :petal_width]
+
 fp = fitted_params(baretree, fitresult)
 @test Set([:tree, :encoding, :features]) == Set(keys(fp))
 @test fp.features == report.features
@@ -155,3 +156,81 @@ end
         @test reproducibility(model, X, y, loss)
     end
 end
+
+
+@testset "feature importance defined" begin
+    for model ∈ [
+        DecisionTreeClassifier(),
+        RandomForestClassifier(),
+        AdaBoostStumpClassifier(),
+        DecisionTreeRegressor(),
+        RandomForestRegressor(),
+        ]
+
+        @test reports_feature_importances(model) == true
+    end
+end
+
+
+
+@testset "impurity importance" begin
+
+    X, y = MLJBase.make_blobs(100, 3; rng=stable_rng())
+
+    for model ∈ [
+        DecisionTreeClassifier(),
+        RandomForestClassifier(),
+        AdaBoostStumpClassifier(),
+        ]
+        m = machine(model, X, y)
+        fit!(m)
+        rpt = MLJBase.report(m)
+        fi = MLJBase.feature_importances(model, m.fitresult, rpt)
+        @test size(fi,1) == 3
+    end
+
+
+    X, y = make_regression(100,3; rng=stable_rng());
+    for model in [
+        DecisionTreeRegressor(),
+        RandomForestRegressor(),
+        ]
+        m = machine(model, X, y)
+        fit!(m)
+        rpt = MLJBase.report(m)
+        fi = MLJBase.feature_importances(model, m.fitresult, rpt)
+        @test size(fi,1) == 3
+    end
+end
+
+
+@testset "split importance" begin
+    X, y = MLJBase.make_blobs(100, 3; rng=stable_rng())
+
+    for model ∈ [
+        DecisionTreeClassifier(feature_importance=:split),
+        RandomForestClassifier(feature_importance=:split),
+        AdaBoostStumpClassifier(feature_importance=:split),
+        ]
+        m = machine(model, X, y)
+        fit!(m)
+        rpt = MLJBase.report(m)
+        fi = MLJBase.feature_importances(model, m.fitresult, rpt)
+        @test size(fi,1) == 3
+    end
+
+
+    X, y = make_regression(100,3; rng=stable_rng());
+    for model in [
+        DecisionTreeRegressor(feature_importance=:split),
+        RandomForestRegressor(feature_importance=:split),
+        ]
+        m = machine(model, X, y)
+        fit!(m)
+        rpt = MLJBase.report(m)
+        fi = MLJBase.feature_importances(model, m.fitresult, rpt)
+        @test size(fi,1) == 3
+    end
+end
+
+