Add support for different prediction types

Author: nunosilva800

lib/lightgbm.rb

@@ -3,6 +3,7 @@
 
 # modules
 require_relative "lightgbm/utils"
+require_relative "lightgbm/macros"
 require_relative "lightgbm/booster"
 require_relative "lightgbm/dataset"
 require_relative "lightgbm/version"

lib/lightgbm/booster.rb

@@ -141,8 +141,21 @@ def num_trees
       out.read_int
     end
 
-    # TODO support different prediction types
-    def predict(input, start_iteration: nil, num_iteration: nil, **params)
+
+    # Make prediction for a new dataset.
+    # C-API: LGBM_BoosterPredictForMat.
+    #
+    # @param input [Array, Array<Array,Hash>, Hash{String => Numeric, String}, Daru::DataFrame, Rover::DataFrame] Input data
+    # @param start_iteration [Integer] Start index of the iteration to predict
+    # @param num_iteration [Integer] Number of iteration for prediction, <= 0 means no limit
+    # @param predict_type [Integer] What should be predicted
+    #     - C_API_PREDICT_NORMAL: normal prediction, with transform (if needed);
+    #     - C_API_PREDICT_RAW_SCORE: raw score;
+    #     - C_API_PREDICT_LEAF_INDEX: leaf index;
+    #     - C_API_PREDICT_CONTRIB: feature contributions (SHAP values)
+    # @param **params [Hash] Other parameters for prediction, e.g. early stopping for prediction
+    # @return [Float, Array<Float>] Prediction results
+    def predict(input, start_iteration: nil, num_iteration: nil, predict_type: C_API_PREDICT_NORMAL, **params)
       input =
         if daru?(input)
           input[*cached_feature_name].map_rows(&:to_a)
@@ -170,14 +183,51 @@ def predict(input, start_iteration: nil, num_iteration: nil, **params)
       data.write_array_of_double(flat_input)
 
       out_len = ::FFI::MemoryPointer.new(:int64)
-      out_result = ::FFI::MemoryPointer.new(:double, num_class * input.count)
-      check_result FFI.LGBM_BoosterPredictForMat(handle_pointer, data, 1, input.count, input.first.count, 1, 0, start_iteration, num_iteration, params_str(params), out_len, out_result)
+      case predict_type
+      when C_API_PREDICT_NORMAL, C_API_PREDICT_RAW_SCORE
+        out_result = ::FFI::MemoryPointer.new(:double, num_class * input.count)
+      when C_API_PREDICT_LEAF_INDEX
+        num_predict = num_preds(start_iteration:, num_iteration:, nrow: input.count, predict_type:)
+        out_result = ::FFI::MemoryPointer.new(:double, num_class * input.count * num_predict)
+        singular = false
+      when C_API_PREDICT_CONTRIB
+        out_result = ::FFI::MemoryPointer.new(:double, num_class * input.count * (num_feature + 1))
+        singular = false
+      end
+
+      check_result FFI.LGBM_BoosterPredictForMat(
+        handle_pointer,
+        data,
+        1,
+        input.count,
+        input.first.count,
+        1,
+        predict_type,
+        start_iteration,
+        num_iteration,
+        params_str(params),
+        out_len,
+        out_result
+      )
       out = out_result.read_array_of_double(out_len.read_int64)
       out = out.each_slice(num_class).to_a if num_class > 1
 
       singular ? out.first : out
     end
 
+    def num_preds(start_iteration: 0, num_iteration: best_iteration, nrow: nil, predict_type: C_API_PREDICT_NORMAL)
+      out_len = ::FFI::MemoryPointer.new(:int64)
+      check_result FFI.LGBM_BoosterCalcNumPredict(
+        handle_pointer,
+        nrow,
+        predict_type,
+        start_iteration,
+        num_iteration,
+        out_len
+      )
+      out_len.read_int64
+    end
+
     def save_model(filename, num_iteration: nil, start_iteration: 0)
       num_iteration ||= best_iteration
       feature_importance_type = 0 # TODO add

lib/lightgbm/ffi.rb

@@ -38,6 +38,7 @@ module FFI
     attach_function :LGBM_BoosterLoadModelFromString, %i[string pointer pointer], :int
     attach_function :LGBM_BoosterFree, %i[pointer], :int
     attach_function :LGBM_BoosterAddValidData, %i[pointer pointer], :int
+    attach_function :LGBM_BoosterCalcNumPredict, %i[pointer int int int int pointer], :int
     attach_function :LGBM_BoosterGetNumClasses, %i[pointer pointer], :int
     attach_function :LGBM_BoosterUpdateOneIter, %i[pointer pointer], :int
     attach_function :LGBM_BoosterGetCurrentIteration, %i[pointer pointer], :int

lib/lightgbm/macros.rb

@@ -0,0 +1,7 @@
+module LightGBM
+  # Macro definition of prediction type in C API of LightGBM
+  C_API_PREDICT_NORMAL = 0
+  C_API_PREDICT_RAW_SCORE = 1
+  C_API_PREDICT_LEAF_INDEX = 2
+  C_API_PREDICT_CONTRIB = 3
+end

test/booster_test.rb

@@ -1,7 +1,7 @@
 require_relative "test_helper"
 
 class BoosterTest < Minitest::Test
-  def test_model_file
+  def test_predict
     x_test = [[3.7, 1.2, 7.2, 9.0], [7.5, 0.5, 7.9, 0.0]]
     booster = LightGBM::Booster.new(model_file: "test/support/model.txt")
     y_pred = booster.predict(x_test)
@@ -23,21 +23,6 @@ def test_model_from_string
     assert_elements_in_delta [0.9823112229173586, 0.9583143724610858], y_pred.first(2)
   end
 
-  def test_feature_importance
-    assert_equal [280, 285, 335, 148], booster.feature_importance
-  end
-
-  def test_feature_name
-    assert_equal ["x0", "x1", "x2", "x3"], booster.feature_name
-  end
-
-  def test_feature_importance_bad_importance_type
-    error = assert_raises(LightGBM::Error) do
-      booster.feature_importance(importance_type: "bad")
-    end
-    assert_includes error.message, "Unknown importance type"
-  end
-
   def test_predict_hash
     pred = booster.predict({x0: 3.7, x1: 1.2, x2: 7.2, x3: 9.0})
     assert_in_delta 0.9823112229173586, pred
@@ -88,6 +73,68 @@ def test_predict_rover
     end
   end
 
+  def test_predict_type_leaf_index
+    x_test = [[3.7, 1.2, 7.2, 9.0], [7.5, 0.5, 7.9, 0.0]]
+    leaf_indexes = booster.predict(x_test, predict_type: LightGBM::C_API_PREDICT_LEAF_INDEX)
+    assert_equal 200, leaf_indexes.count
+    assert_equal 9.0, leaf_indexes.first
+    assert_equal 7.0, leaf_indexes.last
+
+    x_test = [3.7, 1.2, 7.2, 9.0]
+    leaf_indexes = booster.predict(x_test, predict_type: LightGBM::C_API_PREDICT_LEAF_INDEX)
+    assert_equal 100, leaf_indexes.count
+    assert_equal 9.0, leaf_indexes.first
+    assert_equal 10.0, leaf_indexes.last
+  end
+
+  def test_predict_type_contrib
+    x_test = [[3.7, 1.2, 7.2, 9.0], [7.5, 0.5, 7.9, 0.0]]
+    results = booster.predict(x_test, predict_type: LightGBM::C_API_PREDICT_CONTRIB)
+    assert_equal 10, results.count
+
+    # split results on num_features + 1
+    predictions = results.each_slice(5).to_a
+    shap_values_1 = predictions.first[0..-2]
+    ypred_1 = predictions.first[-1]
+    assert_elements_in_delta [
+      -0.0733949225678886, -0.24289592050101766, 0.24183795683166504, 0.063430775771174
+    ], shap_values_1
+    assert_in_delta (0.9933333333834246), ypred_1
+
+    shap_values_2 = predictions.last[0..-2]
+    ypred_2 = predictions.last[-1]
+    assert_elements_in_delta [
+      0.1094902954684793, -0.2810485083947154, 0.26691627597706397, -0.13037702397316747
+    ], shap_values_2
+    assert_in_delta (0.9933333333834246), ypred_2
+
+    # single row
+    x_test = [3.7, 1.2, 7.2, 9.0]
+    results = booster.predict(x_test, predict_type: LightGBM::C_API_PREDICT_CONTRIB)
+    assert_equal 5, results.count
+    shap_values = results[0..-2]
+    ypred = results[-1]
+    assert_elements_in_delta [
+      -0.0733949225678886, -0.24289592050101766, 0.24183795683166504, 0.063430775771174
+    ], shap_values
+    assert_in_delta (0.9933333333834246), ypred
+  end
+
+  def test_feature_importance
+    assert_equal [280, 285, 335, 148], booster.feature_importance
+  end
+
+  def test_feature_name
+    assert_equal ["x0", "x1", "x2", "x3"], booster.feature_name
+  end
+
+  def test_feature_importance_bad_importance_type
+    error = assert_raises(LightGBM::Error) do
+      booster.feature_importance(importance_type: "bad")
+    end
+    assert_includes error.message, "Unknown importance type"
+  end
+
   def test_model_to_string
     assert booster.model_to_string
   end