In giuseppec/featureImportance: Model-agnostic feature importance with the mlr package

knitr::opts_chunk$set(echo = TRUE)

Introduction

In this short tutorial, we provide the code that reproduces the results of the application section of our article entitled "Visualizing the Feature Importance for Black Box Models". We used batchtools to run our experiments. The files application_pi_simulation.R, application_shapley_simulation.R and application_importance_realdata.R contain the batchtools code to reproduce the expermients and can be found in this directory. The directory also includes the results of both files in an .Rds file which is used in the code below to produce the figures and tables.

Load Packages

# load required packages
library(data.table)
library(ggplot2)
library(gridExtra)
library(ggExtra)
library(xtable)
library(knitr)
library(featureImportance)
source("helper/functions.R")

Simulation

PI and ICI Plots

res = readRDS("application_pi_simulation.Rds")

imp.global = rbindlist(lapply(res, function(x) {
  getImpTable(x, sort = FALSE)
}))

# compute conditional PFI based on feature V3 = 0
imp0 = rbindlist(lapply(res, function(x) {
  use0 = x[features == "V3" & feature.value == 0, unique(replace.id)]
  getImpTable(x, obs.id = use0, sort = FALSE)
}))

# compute conditional PFI based on feature V3 = 1
imp1 = rbindlist(lapply(res, function(x) {
  use1 = x[features == "V3" & feature.value == 1, unique(replace.id)]
  getImpTable(x, obs.id = use1, sort = FALSE)
}))

tab = rbind(
  imp.global[, lapply(.SD, pasteMeanSd)],
  imp0[, lapply(.SD, pasteMeanSd)],
  imp1[, lapply(.SD, pasteMeanSd)]
)
kable(tab)

pfi = res[[1]]

# Get index of observations for V3 = 0 and V3 = 1
use0 = pfi[features == "V3" & feature.value == 0, unique(replace.id)]
use1 = pfi[features == "V3" & feature.value == 1, unique(replace.id)]

vars = c("V1", "V2")
pi = lapply(vars, function(var) {
  pi.cond = conditionalPFI(pfi, var, use0, use1, group.var = "V3")
  ici = subset(pfi, features == var)
  ici[, V3 := as.factor(as.numeric(row.id %in% use1))]
  ind = gsub("[[:alpha:]]", "", var)

  plotImportance(pfi, feat = var, mid = "mse", hline = FALSE) +
    geom_line(data = pi.cond, aes(color = V3)) +
    geom_point(data = pi.cond, aes(color = V3)) +
    labs(x = bquote(X[.(ind)]), color = bquote(X[3])) +
    ylim(c(-10, 300))
})
marrangeGrob(pi, nrow = 1, ncol = 2)

Shapley Feature Importance

res = readRDS("application_shapley_simulation.Rds")
# use shorter learner name
res[, learner := factor(gsub("regr.", "", learner))]
# compute ratio of the importance values w.r.t feature "V3"
res[, ratio := mse/mse[feature == "V3"], by = c("method", "learner", "repl")]

### Plot simulation results of all 500 repititions
shap = subset(res, method %in% c("pfi.diff", "pfi.ratio", "shapley") & feature != "V3")
new.names = setNames(expression(X[1]/X[3], X[2]/X[3]), c("V1", "V2"))

pp = ggplot(data = shap, aes(x = feature, y = ratio)) + 
  geom_boxplot(aes(fill = method), lwd = 0.2, outlier.size = 0.8) + 
  facet_grid(. ~ learner, scales = "free") +
  scale_fill_grey(labels = c("PFI (Diff.)", "PFI (Ratio)", "SFIMP"), start = 0.4, end = 0.9) +
  scale_x_discrete(labels = new.names) +
  labs(title = "(b) Simulation with 500 repetitions", 
    x = "Features involved to compute the ratio", y = "Value of the ratio")

### Plot example of an individual repetition (2nd replication)
shap2 = subset(res, repl == 2 & method %in% c("shapley", "geP"))
# reorder features for plotting
feat.order = c("V3", "V2", "V1", "geP")
shap2$feature = factor(shap2$feature, levels = feat.order)
# change sign
shap2[, mse := round(ifelse(method == "geP", mse, -mse), 2)]
# add column containing proportion of explained importance
shap2[, perc := ifelse(feature == "geP", NA, mse/sum(mse[feature != "geP"])), by = "learner"]
# add column containing drop in MSE + proportion of explained importance
shap2[, lab := ifelse(feature == "geP", mse, paste0(mse, " (", round(perc*100, 0), "%)"))]

col = c(gray.colors(3, start = 0.4, end = 0.9), hcl(h = 195, l = 65, c = 100))
col = setNames(col, feat.order)
legend = c("V1" = bquote(phi[1]), "V2" = bquote(phi[2]), 
  "V3" = bquote(phi[3]), "geP" = bquote(widehat(GE)[P]))

pp2 = ggplot(shap2, aes(x = learner, y = mse, fill = feature)) + 
  geom_bar(stat = "identity", colour = "white", pos = "stack") + 
  geom_text(aes(label = lab), position = position_stack(vjust = 0.5), size = 3) + 
  coord_flip() + 
  scale_fill_manual(values = col, name = " performance \n explained by", labels = legend) +
  labs(title = "(a) Comparing the model performance and SFIMP values across different models", 
    x = "", y = "performance (MSE)")

grid.arrange(pp2, pp, heights = c(3, 5))

Application on Real Data

Produce Table

pfi = readRDS("application_importance_realdata.Rds")

# get index for LSTAT <= 10 in order to keep those observations
pi.ind = unique(pfi[features == "LSTAT" & feature.value <= 10, replace.id])
# compute integral of each ICI curve and select observations with positive ICI integral
ici = subset(pfi, features == "LSTAT")
ici.area = ici[, lapply(.SD, mean, na.rm = TRUE), .SDcols = "mse", by = "row.id"]
ici.ind = which(ici.area$mse > 0)

# produce table
imp = getImpTable(pfi)
imp.pi = getImpTable(pfi, pi.ind)
imp.ici = getImpTable(pfi, ici.ind)
kable(rbind(imp, imp.pi, imp.ici))

Produce PI and ICI plots

features = c("LSTAT", "RM")

pp = lapply(features, function(feat) {
  ici = subset(pfi, features == feat)
  ici.area = ici[, lapply(.SD, mean, na.rm = TRUE), .SDcols = "mse", by = "row.id"]
  ind = c(which.min(ici.area$mse), which.max(ici.area$mse))
  ici.obs = subset(ici, row.id %in% ici.area$row.id[ind])

  # PI plot
  pi.plot = plotImportance(pfi, feat, "mse") + theme(legend.position = "none")

  # ICI plot
  ici.plot = plotImportance(pfi, feat, "mse", individual = TRUE, grid.points = FALSE, hline = FALSE) +
    geom_line(data = ici.obs, aes(color = factor(row.id), group = row.id)) +
    theme(legend.position = "none")

  list(ggMarginal(pi.plot, type = "histogram", fill = "transparent", margins = "x"), ici.plot)
})
pp = unlist(pp, recursive = FALSE)
marrangeGrob(pp, nrow = 2, ncol = 2)

giuseppec/featureImportance documentation built on June 1, 2021, 11:04 a.m.