I am working on a Machine Learning model. One of the requests is to explain the models 'decisions' to the business. Therefore I am using Shapley Values (Game Theory).

I found an interesting example on the internet (https://cran.r-project.org/web/packages/iml/vignettes/intro.html), how we can Explain a Single prediction with Shapley (see code in R below). But this is only explaining one single prediction.

My questions:

  1. Is it possible to create one explanation for a whole data frame, instead of for just one single row? (for example: having the plot for the whole (test) data frame, instead of only one row).
  2. If yes, is it academically legit and how can I do that in R?

More information about Shapley values in R (https://www.rdocumentation.org/packages/iml/versions/0.9.0/topics/Shapley)

Thanks in advance!


#Example Shapley

data("Boston", package  = "MASS")

data("Boston", package  = "MASS")
rf = randomForest(medv ~ ., data = Boston, ntree = 50)

# We create a Predictor object, that holds the model and the data. 
# The iml package uses R6 classes: New objects can be created by calling Predictor$new()
X = Boston[which(names(Boston) != "medv")]
predictor = Predictor$new(rf, data = X, y = Boston$medv)

# Feature Importance
## Shifting each future, and measring how much the performance drops ## 
imp = FeatureImp$new(predictor, loss = "mae")

# Shapley value. Assume that for 1 data point, the feature values play a game together, in which 
# they get the prediction as payout. Tells us how fairly distibute the payout among the feature values. 
shapley = Shapley$new(predictor, x.interest = X[1,])

# Reuse the object to explain other data points 
shapley$explain(x.interest = X[2,])

# Results in data.frame form can be extracted like this: 
results = shapley$results

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The function itself isn't vectorized, but you can loop through your data explaining one instance at a time and then concatenate the instance-level lists into one data.frame.

Below is R code that should work with your example (~3 min run time on a 16GB RAM laptop).

# Loop through the samples, explaining one instance at a time.
shap_values <- vector("list", nrow(X))  # initialize the results list.
  for (i in seq_along(shap_values)) {
    shap_values[[i]] <- iml::Shapley$new(predictor, x.interest = X[i, ],
                                         sample.size = 30)$results
    shap_values[[i]]$sample_num <- i  # identifier to track our instances.
  data_shap_values <- dplyr::bind_rows(shap_values)  # collapse the list.

Is this approach legit? I can't think of a reason why it wouldn't be. I've seen Shapley value plots similar to partial dependence plots used in a variety of contexts. In addition to the awesome package iml, check out DALEX and--shameless plug--my package shapFlex (the overview vignette has plots) for this and other uses of Shapley values.

  • $\begingroup$ Thanks! The result is then 1 data frame with all the Shapely values (data_shap_values).But can you help me to explain all the features for the whole data frame? Take the mean per feature, or the median? And, in addition: can we plot the whole data_shap_values data frame? Thanks!! $\endgroup$ – R overflow Jun 25 at 8:38
  • 1
    $\begingroup$ Correct. The shap Python package has some interesting plots. If you're looking for global feature importance across all features in the dataset, taking the mean absolute value makes sense (absolute value because Shapley values are +/- deviations from the average prediction). And a simple bar chart of these values makes for a nice summary. Plotting the whole data frame? I'd go with a cluster analysis of the Shapley values. I haven't come across a paper that shows how well this approach recovers ground-truth clusters, but I bet it's fairly truthy. $\endgroup$ – nredell Jun 27 at 21:46
  • $\begingroup$ That sounds good @nredell! To be sure: 'I'd go with a cluster analysis of the Shapley values'. You mean for example, cluster the values from a range (1-5, 5-10, 10-20 etc.), look at the mean absolute values of all the variables in that range, and then make a plot to see the impact? Really Appreciate your help!! $\endgroup$ – R overflow Jun 28 at 6:13
  • $\begingroup$ Small note: Mean Absolute Value will actually be a bad idea I guess, because you will lose the (positive/negative) effect of the shapley value, or am i totally wrong here? $\endgroup$ – R overflow Jun 28 at 11:18
  • $\begingroup$ The cluster suggestion may add more confusion than it's worth. At that link for shap above, check out the plot produced with shap.summary_plot(shap_values, X, plot_type="bar") and the plot above it. The bar plot is a summary of the plot immediately above it. Absolute values are good if you're trying to make a case about the strength of an effect but not it's direction. $\endgroup$ – nredell Jun 28 at 22:30

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