Merge pull request #964 from JuliaAI/dev

For a 1.2.0 release

Author: ablaom

Project.toml

@@ -1,7 +1,7 @@
 name = "MLJBase"
 uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 authors = ["Anthony D. Blaom <[email protected]>"]
-version = "1.1.2"
+version = "1.2.0"
 
 [deps]
 CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597"

src/composition/learning_networks/nodes.jl

@@ -150,13 +150,19 @@ function _apply(y_plus, input...; kwargs...)
     try
         (y.operation)(mach..., raw_args...)
     catch exception
-        @error "Failed "*
-        "to apply the operation `$(y.operation)` to the machine "*
-        "$(y.machine), which receives it's data arguments from one or more "*
-        "nodes in a learning network. Possibly, one of these nodes "*
-        "is delivering data that is incompatible with the machine's model.\n"*
-        diagnostics(y, input...; kwargs...)
-        throw(exception)
+        diagnostics = MLJBase.diagnostics(y, input...; kwargs...) # defined in sources.jl
+        if !isempty(mach)
+            @error "Failed "*
+                "to apply the operation `$(y.operation)` to the machine "*
+                "$(y.machine), which receives it's data arguments from one or more "*
+                "nodes in a learning network. Possibly, one of these nodes "*
+                "is delivering data that is incompatible "*
+                "with the machine's model.\n"*diagnostics
+        else
+            @error "Failed "*
+                "to apply the operation `$(y.operation)`."*diagnostics
+        end
+        rethrow(exception)
     end
 end
 

src/composition/models/pipelines.jl

@@ -402,15 +402,13 @@ end
 
 # ## Methods to extend a pipeline learning network
 
-# The "front" of a pipeline network, as we grow it, consists of a
-# "predict" and a "transform" node. Once the pipeline is complete
-# (after a series of `extend` operations - see below) the "transform"
-# node is what is used to deliver the output of `transform(pipe)` in
-# the exported model, and the "predict" node is what will be used to
-# deliver the output of `predict(pipe). Both nodes can be changed by
-# `extend` but only the "active" node is propagated.  Initially
-# "transform" is active and "predict" only becomes active when a
-# supervised model is encountered; this change is permanent.
+# The "front" of a pipeline network, as we grow it, consists of a "predict" and a
+# "transform" node. Once the pipeline is complete (after a series of `extend` operations -
+# see below) the "transform" node is what is used to deliver the output of
+# `transform(pipe, ...)` in the exported model, and the "predict" node is what will be
+# used to deliver the output of `predict(pipe, ...). Both nodes can be changed by `extend`
+# but only the "active" node is propagated.  Initially "transform" is active and "predict"
+# only becomes active when a supervised model is encountered; this change is permanent.
 # https://github.com/JuliaAI/MLJClusteringInterface.jl/issues/10
 
 abstract type ActiveNodeOperation end
@@ -587,7 +585,10 @@ end
 # component, only its `abstract_type`. See comment at top of page.
 
 MMI.supports_training_losses(pipe::SupervisedPipeline) =
-    MMI.supports_training_losses(getproperty(pipe, supervised_component_name(pipe)))
+    MMI.supports_training_losses(supervised_component(pipe))
+
+MMI.reports_feature_importances(pipe::SupervisedPipeline) =
+    MMI.reports_feature_importances(supervised_component(pipe))
 
 # This trait cannot be defined at the level of types (see previous comment):
 function MMI.iteration_parameter(pipe::SupervisedPipeline)
@@ -618,3 +619,18 @@ function MMI.training_losses(pipe::SupervisedPipeline, pipe_report)
     report = getproperty(pipe_report, supervised_name)
     return training_losses(supervised, report)
 end
+
+
+# ## Feature importances
+
+function feature_importances(pipe::SupervisedPipeline, fitresult, report)
+    # locate the machine associated with the supervised component:
+    supervised_name = MLJBase.supervised_component_name(pipe)
+    predict_node = fitresult.interface.predict
+    mach = only(MLJBase.machines_given_model(predict_node)[supervised_name])
+
+    # To extract the feature_importances, we can't do `feature_importances(mach)` because
+    # `mach.model` is just a symbol; instead we do:
+    supervised = MLJBase.supervised_component(pipe)
+    return feature_importances(supervised, mach.fitresult, mach.report[:fit])
+end

src/composition/models/transformed_target_model.jl

@@ -237,28 +237,41 @@ const ERR_TT_MISSING_REPORT =
     "Cannot find report for `TransformedTargetModel` atomic model, from which "*
     "to extract training losses. "
 
-function training_losses(composite::SomeTT, tt_report)
+function MMI.training_losses(composite::SomeTT, tt_report)
     hasproperty(tt_report, :model) || throw(ERR_TT_MISSING_REPORT)
     atomic_report = getproperty(tt_report, :model)
     return training_losses(composite.model, atomic_report)
 end
 
 
+# # FEATURE IMPORTANCES
+
+function MMI.feature_importances(composite::SomeTT, fitresult, report)
+    # locate the machine associated with the supervised component:
+    predict_node = fitresult.interface.predict
+    mach = only(MLJBase.machines_given_model(predict_node)[:model])
+
+    # To extract the feature_importances, we can't do `feature_importances(mach)` because
+    # `mach.model` is just a symbol; instead we do:
+    return feature_importances(composite.model, mach.fitresult, mach.report[:fit])
+end
+
+
 ## MODEL TRAITS
 
 MMI.package_name(::Type{<:SomeTT}) = "MLJBase"
 MMI.package_license(::Type{<:SomeTT}) = "MIT"
 MMI.package_uuid(::Type{<:SomeTT}) = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 MMI.is_wrapper(::Type{<:SomeTT}) = true
-MMI.package_url(::Type{<:SomeTT}) =
-    "https://github.com/JuliaAI/MLJBase.jl"
+MMI.package_url(::Type{<:SomeTT}) = "https://github.com/JuliaAI/MLJBase.jl"
 
 for New in TT_TYPE_EXS
     quote
         MMI.iteration_parameter(::Type{<:$New{M}}) where M =
             MLJBase.prepend(:model, iteration_parameter(M))
     end |> eval
-    for trait in [:input_scitype,
+    for trait in [
+        :input_scitype,
         :output_scitype,
         :target_scitype,
         :fit_data_scitype,
@@ -270,8 +283,10 @@ for New in TT_TYPE_EXS
         :supports_class_weights,
         :supports_online,
         :supports_training_losses,
+        :reports_feature_importances,
         :is_supervised,
-        :prediction_type]
+        :prediction_type
+        ]
         quote
             MMI.$trait(::Type{<:$New{M}}) where M = MMI.$trait(M)
         end |> eval

src/machines.jl

@@ -808,10 +808,6 @@ julia> fitted_params(mach).logistic_classifier
  intercept = 0.0883301599726305,)
 ```
 
-Additional keys, `machines` and `fitted_params_given_machine`, give a
-list of *all* machines in the underlying network, and a dictionary of
-fitted parameters keyed on those machines.
-
 See also [`report`](@ref)
 
 """
@@ -852,10 +848,6 @@ julia> report(mach).linear_binary_classifier
 
 ```
 
-Additional keys, `machines` and `report_given_machine`, give a
-list of *all* machines in the underlying network, and a dictionary of
-reports keyed on those machines.
-
 See also [`fitted_params`](@ref)
 
 """

src/sources.jl

@@ -85,10 +85,21 @@ function diagnostics(X::AbstractNode, input...; kwargs...)
     _sources = sources(X)
     scitypes = scitype.(raw_args)
     mach = X.machine
-    model = mach.model
-    _input = input_scitype(model)
-    _target = target_scitype(model)
-    _output = output_scitype(model)
+
+    table0 = if !isnothing(mach)
+        model = mach.model
+        _input = input_scitype(model)
+        _target = target_scitype(model)
+        _output = output_scitype(model)
+        """
+        Model ($model):
+        input_scitype = $_input
+        target_scitype =$_target
+        output_scitype =$_output
+        """
+    else
+        ""
+    end
 
     table1 = "Incoming data:\n"*
     "arg of $(X.operation)\tscitype\n"*
@@ -97,11 +108,7 @@ function diagnostics(X::AbstractNode, input...; kwargs...)
 
     table2 =  diagnostic_table_sources(X)
     return """
-    Model ($model):
-    input_scitype = $_input
-    target_scitype =$_target
-    output_scitype =$_output
-
+    $table0
     $table1
     $table2"""
 end

test/_models/DecisionTree.jl

@@ -2,7 +2,7 @@ export DecisionTreeClassifier, DecisionTreeRegressor
 
 import MLJBase
 import MLJBase: @mlj_model, metadata_pkg, metadata_model
-
+import MLJBase.Tables
 using ScientificTypes
 
 using CategoricalArrays
@@ -98,8 +98,11 @@ function MLJBase.fit(model::DecisionTreeClassifier, verbosity::Int, X, y)
     #> empty values):
 
     cache = nothing
-    report = (classes_seen=classes_seen,
-              print_tree=TreePrinter(tree))
+    report = (
+        classes_seen=classes_seen,
+        print_tree=TreePrinter(tree),
+        features=Tables.columnnames(Tables.columns(X)) |> collect,
+    )
 
     return fitresult, cache, report
 end
@@ -137,6 +140,17 @@ function MLJBase.predict(model::DecisionTreeClassifier
             for i in 1:size(y_probabilities, 1)]
 end
 
+MLJBase.reports_feature_importances(::Type{<:DecisionTreeClassifier}) = true
+
+function MMI.feature_importances(m::DecisionTreeClassifier, fitresult, report)
+    features = report.features
+    fi = DecisionTree.impurity_importance(first(fitresult), normalize=true)
+    fi_pairs = Pair.(features, fi)
+    # sort descending
+    sort!(fi_pairs, by= x->-x[2])
+
+    return fi_pairs
+end
 
 ## REGRESSOR
 

test/composition/models/network_composite.jl

@@ -48,7 +48,7 @@ end
 MLJBase.reporting_operations(::Type{<:ReportingScaler}) = (:transform, )
 
 MLJBase.transform(model::ReportingScaler, _, X) = (
-    model.alpha*Tables.matrix(X),
+    Tables.table(model.alpha*Tables.matrix(X)),
     (; nrows = size(MLJBase.matrix(X))[1]),
 )
 
@@ -143,7 +143,7 @@ composite = WatermelonComposite(
         Set([:scaler, :clusterer, :classifier1, :training_loss, :len])
     @test fitr.scaler == (nrows=10,)
     @test fitr.clusterer == (labels=['A', 'B', 'C'],)
-    @test Set(keys(fitr.classifier1)) == Set([:classes_seen, :print_tree])
+    @test Set(keys(fitr.classifier1)) == Set([:classes_seen, :print_tree, :features])
     @test fitr.training_loss isa Real
     @test fitr.len == 10
 
@@ -164,7 +164,7 @@ composite = WatermelonComposite(
         Set([:scaler, :clusterer, :classifier1, :finalizer])
     @test predictr.scaler == (nrows=5,)
     @test predictr.clusterer == (labels=['A', 'B', 'C'],)
-    @test Set(keys(predictr.classifier1)) == Set([:classes_seen, :print_tree])
+    @test Set(keys(predictr.classifier1)) == Set([:classes_seen, :print_tree, :features])
     @test predictr.finalizer == (nrows=5,)
 
     o, predictr = predict(composite, f, selectrows(X, 1:2))
@@ -174,7 +174,7 @@ composite = WatermelonComposite(
         Set([:scaler, :clusterer, :classifier1, :finalizer])
     @test predictr.scaler == (nrows=2,)    # <----------- different
     @test predictr.clusterer == (labels=['A', 'B', 'C'],)
-    @test Set(keys(predictr.classifier1)) == Set([:classes_seen, :print_tree])
+    @test Set(keys(predictr.classifier1)) == Set([:classes_seen, :print_tree, :features])
     @test predictr.finalizer == (nrows=2,) # <---------- different
 
     r = MMI.report(composite, Dict(:fit => fitr, :predict=> predictr))

test/composition/models/pipelines.jl

@@ -690,6 +690,16 @@ end
     rm(filename)
 end
 
+@testset "feature importances" begin
+    # the DecisionTreeClassifier in /test/_models/ supports feature importances.
+    pipe = Standardizer |> DecisionTreeClassifier()
+    @test reports_feature_importances(pipe)
+    X, y = @load_iris
+    fitresult, _, report = MLJBase.fit(pipe, 0, X, y)
+    features = first.(feature_importances(pipe, fitresult, report))
+    @test Set(features) == Set(keys(X))
+end
+
 end # module
 
 true

test/composition/models/transformed_target_model.jl

@@ -177,5 +177,14 @@ y = rand(5)
     @test training_losses(mach) == ones(5)
 end
 
+@testset "feature_importances" begin
+    X, y = @load_iris
+    atom = DecisionTreeClassifier()
+    model = TransformedTargetModel(atom, transformer=identity, inverse=identity)
+    @test reports_feature_importances(model)
+    fitresult, _, rpt = MMI.fit(model, 0, X, y)
+    @test Set(first.(feature_importances(model, fitresult, rpt))) == Set(keys(X))
+end
+
 end
 true