ShapML.jl

A Julia package for interpretable machine learning with stochastic Shapley values
Author nredell
Popularity
28 Stars
Updated Last
1 Year Ago
Started In
January 2020

Build Status Codecov

ShapML ShapML logo

The purpose of ShapML is to compute stochastic feature-level Shapley values which can be used to (a) interpret and/or (b) assess the fairness of any machine learning model. Shapley values are an intuitive and theoretically sound model-agnostic diagnostic tool to understand both global feature importance across all instances in a data set and instance/row-level local feature importance in black-box machine learning models.

This package implements the algorithm described in Štrumbelj and Kononenko's (2014) sampling-based Shapley approximation algorithm to compute the stochastic Shapley values for a given instance and model feature.

  • Flexibility:

    • Shapley values can be estimated for any machine learning model using a simple user-defined predict() wrapper function.
  • Speed:

    • The speed advantage of ShapML comes in the form of giving the user the ability to select 1 or more target features of interest and avoid having to compute Shapley values for all model features (i.e., a subset of target features from a trained model will return the same feature-level Shapley values as the full model with all features). This is especially useful in high-dimensional models as the computation of a Shapley value is exponential in the number of features.

Install

using Pkg
Pkg.add("ShapML")
  • Development
using Pkg
Pkg.add(PackageSpec(url = "https://github.com/nredell/ShapML.jl"))

Documentation and Vignettes

Examples

Random Forest regression model - Non-parallel

  • We'll explain the impact of 13 features from the Boston Housing dataset on the predicted outcome MedV--or the median value of owner-occupied homes in $1000's--using predictions from a trained Random Forest regression model and stochastic Shapley values.

  • We'll explain a subset of 300 instances and then assess global feature importance by aggregating the unique feature importances for each of these instances.

using ShapML
using RDatasets
using DataFrames
using MLJ  # Machine learning
using Gadfly  # Plotting

# Load data.
boston = RDatasets.dataset("MASS", "Boston")
#------------------------------------------------------------------------------
# Train a machine learning model; currently limited to single outcome regression and binary classification.
outcome_name = "MedV"

# Data prep.
y, X = MLJ.unpack(boston, ==(Symbol(outcome_name)), colname -> true)

# Instantiate an ML model; choose any single-outcome ML model from any package.
random_forest = @load RandomForestRegressor pkg = "DecisionTree"
model = MLJ.machine(random_forest, X, y)

# Train the model.
fit!(model)

# Create a wrapper function that takes the following positional arguments: (1) a
# trained ML model from any Julia package, (2) a DataFrame of model features. The
# function should return a 1-column DataFrame of predictions--column names do not matter.
function predict_function(model, data)
  data_pred = DataFrame(y_pred = predict(model, data))
  return data_pred
end
#------------------------------------------------------------------------------
# ShapML setup.
explain = copy(boston[1:300, :]) # Compute Shapley feature-level predictions for 300 instances.
explain = select(explain, Not(Symbol(outcome_name)))  # Remove the outcome column.

reference = copy(boston)  # An optional reference population to compute the baseline prediction.
reference = select(reference, Not(Symbol(outcome_name)))

sample_size = 60  # Number of Monte Carlo samples.
#------------------------------------------------------------------------------
# Compute stochastic Shapley values.
data_shap = ShapML.shap(explain = explain,
                        reference = reference,
                        model = model,
                        predict_function = predict_function,
                        sample_size = sample_size,
                        seed = 1
                        )

show(data_shap, allcols = true)

shap_output

  • Now we'll create several plots that summarize the Shapley results for our Random Forest model. These plots will eventually be refined and incorporated into ShapML.

  • Global feature importance

    • Because Shapley values represent deviations from the average or baseline prediction, plotting their average absolute value for each feature gives a sense of the magnitude with which they affect model predictions across all explained instances.
data_plot = DataFrames.by(data_shap, [:feature_name],
                          mean_effect = [:shap_effect] => x -> mean(abs.(x.shap_effect)))

data_plot = sort(data_plot, order(:mean_effect, rev = true))

baseline = round(data_shap.intercept[1], digits = 1)

p = plot(data_plot, y = :feature_name, x = :mean_effect, Coord.cartesian(yflip = true),
         Scale.y_discrete, Geom.bar(position = :dodge, orientation = :horizontal),
         Theme(bar_spacing = 1mm),
         Guide.xlabel("|Shapley effect| (baseline = $baseline)"), Guide.ylabel(nothing),
         Guide.title("Feature Importance - Mean Absolute Shapley Value"))
p

feature_importance

  • Global feature effects
    • The plot below shows how changing the value of the Rm feature--the most influential feature overall--affects model predictions (holding the other features constant). Each point represents 1 of our 300 explained instances. The black line is a loess line of best fit to summarize the effect.
data_plot = data_shap[data_shap.feature_name .== "Rm", :]  # Selecting 1 feature for ease of plotting.

baseline = round(data_shap.intercept[1], digits = 1)

p_points = layer(data_plot, x = :feature_value, y = :shap_effect, Geom.point())
p_line = layer(data_plot, x = :feature_value, y = :shap_effect, Geom.smooth(method = :loess, smoothing = 0.5),
               style(line_width = 0.75mm,), Theme(default_color = "black"))
p = plot(p_line, p_points, Guide.xlabel("Feature value"), Guide.ylabel("Shapley effect (baseline = $baseline)"),
         Guide.title("Feature Effect - $(data_plot.feature_name[1])"))
p

feature_effects


Random Forest regression model - Parallel

  • We'll explain the same dataset with the same model, but this time we'll compute the Shapley values in parallel across cores using the built-in distributed computing in ShapML which implements Distributed.pmap() internally.

  • The stochastic Shapley values will be computed in parallel over 6 cores on the same machine.

  • With the same seed set, non-parallel and parallel computation will return the same results.

using Distributed
addprocs(6)  # 6 cores.
  • The @everywhere block of code will load the relevant packages on each core. If you use another ML package, you would swap it in for using MLJ.
@everywhere begin
  using ShapML
  using DataFrames
  using MLJ
end
using RDatasets

# Load data.
boston = RDatasets.dataset("MASS", "Boston")
#------------------------------------------------------------------------------
# Train a machine learning model; currently limited to single outcome regression and binary classification.
outcome_name = "MedV"

# Data prep.
y, X = MLJ.unpack(boston, ==(Symbol(outcome_name)), colname -> true)

# Instantiate an ML model; choose any single-outcome ML model from any package.
random_forest = @load RandomForestRegressor pkg = "DecisionTree"
model = MLJ.machine(random_forest, X, y)

# Train the model.
fit!(model)
  • @everywhere is needed to properly initialize the predict() wrapper function.
# Create a wrapper function that takes the following positional arguments: (1) a
# trained ML model from any Julia package, (2) a DataFrame of model features. The
# function should return a 1-column DataFrame of predictions--column names do not matter.
@everywhere function predict_function(model, data)
  data_pred = DataFrame(y_pred = predict(model, data))
  return data_pred
end
  • Notice that we've set ShapML.shap(parallel = :samples) to perform the computation in parallel across our 60 Monte Carlo samples.
# ShapML setup.
explain = copy(boston[1:300, :]) # Compute Shapley feature-level predictions for 300 instances.
explain = select(explain, Not(Symbol(outcome_name)))  # Remove the outcome column.

reference = copy(boston)  # An optional reference population to compute the baseline prediction.
reference = select(reference, Not(Symbol(outcome_name)))

sample_size = 60  # Number of Monte Carlo samples.
#------------------------------------------------------------------------------
# Compute stochastic Shapley values.
data_shap = ShapML.shap(explain = explain,
                        reference = reference,
                        model = model,
                        predict_function = predict_function,
                        sample_size = sample_size,
                        parallel = :samples,  # Parallel computation over "sample_size".
                        seed = 1
                        )

show(data_shap, allcols = true)

shap_output