Nothing
context('Test prediction of feature interactions')
require(xgboost)
set.seed(123)
n_threads <- 2
test_that("predict feature interactions works", {
# simulate some binary data and a linear outcome with an interaction term
N <- 1000
P <- 5
X <- matrix(rbinom(N * P, 1, 0.5), ncol = P, dimnames = list(NULL, letters[1:P]))
# center the data (as contributions are computed WRT feature means)
X <- scale(X, scale = FALSE)
# outcome without any interactions, without any noise:
f <- function(x) 2 * x[, 1] - 3 * x[, 2]
# outcome with interactions, without noise:
f_int <- function(x) f(x) + 2 * x[, 2] * x[, 3]
# outcome with interactions, with noise:
#f_int_noise <- function(x) f_int(x) + rnorm(N, 0, 0.3)
y <- f_int(X)
dm <- xgb.DMatrix(X, label = y, nthread = n_threads)
param <- list(
eta = 0.1, max_depth = 4, base_score = mean(y), lambda = 0, nthread = n_threads
)
b <- xgb.train(param, dm, 100)
pred <- predict(b, dm, outputmargin = TRUE)
# SHAP contributions:
cont <- predict(b, dm, predcontrib = TRUE)
expect_equal(dim(cont), c(N, P + 1))
# make sure for each row they add up to marginal predictions
expect_lt(max(abs(rowSums(cont) - pred)), 0.001)
# Hand-construct the 'ground truth' feature contributions:
gt_cont <- cbind(
2. * X[, 1],
-3. * X[, 2] + 1. * X[, 2] * X[, 3], # attribute a HALF of the interaction term to feature #2
1. * X[, 2] * X[, 3] # and another HALF of the interaction term to feature #3
)
gt_cont <- cbind(gt_cont, matrix(0, nrow = N, ncol = P + 1 - 3))
# These should be relatively close:
expect_lt(max(abs(cont - gt_cont)), 0.05)
# SHAP interaction contributions:
intr <- predict(b, dm, predinteraction = TRUE)
expect_equal(dim(intr), c(N, P + 1, P + 1))
# check assigned colnames
cn <- c(letters[1:P], "BIAS")
expect_equal(dimnames(intr), list(NULL, cn, cn))
# check the symmetry
expect_lt(max(abs(aperm(intr, c(1, 3, 2)) - intr)), 0.00001)
# sums WRT columns must be close to feature contributions
expect_lt(max(abs(apply(intr, c(1, 2), sum) - cont)), 0.00001)
# diagonal terms for features 3,4,5 must be close to zero
expect_lt(Reduce(max, sapply(3:P, function(i) max(abs(intr[, i, i])))), 0.05)
# BIAS must have no interactions
expect_lt(max(abs(intr[, 1:P, P + 1])), 0.00001)
# interactions other than 2 x 3 must be close to zero
intr23 <- intr
intr23[, 2, 3] <- 0
expect_lt(
Reduce(max, sapply(1:P, function(i) max(abs(intr23[, i, (i + 1):(P + 1)])))),
0.05
)
# Construct the 'ground truth' contributions of interactions directly from the linear terms:
gt_intr <- array(0, c(N, P + 1, P + 1))
gt_intr[, 2, 3] <- 1. * X[, 2] * X[, 3] # attribute a HALF of the interaction term to each symmetric element
gt_intr[, 3, 2] <- gt_intr[, 2, 3]
# merge-in the diagonal based on 'ground truth' feature contributions
intr_diag <- gt_cont - apply(gt_intr, c(1, 2), sum)
for (j in seq_len(P)) {
gt_intr[, j, j] <- intr_diag[, j]
}
# These should be relatively close:
expect_lt(max(abs(intr - gt_intr)), 0.1)
})
test_that("SHAP contribution values are not NAN", {
d <- data.frame(
x1 = c(-2.3, 1.4, 5.9, 2, 2.5, 0.3, -3.6, -0.2, 0.5, -2.8, -4.6, 3.3, -1.2,
-1.1, -2.3, 0.4, -1.5, -0.2, -1, 3.7),
x2 = c(291.179171, 269.198331, 289.942097, 283.191669, 269.673332,
294.158346, 287.255835, 291.530838, 285.899586, 269.290833,
268.649586, 291.530841, 280.074593, 269.484168, 293.94042,
294.327506, 296.20709, 295.441669, 283.16792, 270.227085),
y = c(9, 15, 5.7, 9.2, 22.4, 5, 9, 3.2, 7.2, 13.1, 7.8, 16.9, 6.5, 22.1,
5.3, 10.4, 11.1, 13.9, 11, 20.5),
fold = c(2, 2, 2, 1, 2, 2, 1, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2))
ivs <- c("x1", "x2")
fit <- xgboost(
verbose = 0,
params = list(
objective = "reg:squarederror",
eval_metric = "rmse",
nthread = n_threads
),
data = as.matrix(subset(d, fold == 2)[, ivs]),
label = subset(d, fold == 2)$y,
nrounds = 3
)
shaps <- as.data.frame(predict(fit,
newdata = as.matrix(subset(d, fold == 1)[, ivs]),
predcontrib = TRUE))
result <- cbind(shaps, sum = rowSums(shaps), pred = predict(fit,
newdata = as.matrix(subset(d, fold == 1)[, ivs])))
expect_true(identical(TRUE, all.equal(result$sum, result$pred, tol = 1e-6)))
})
test_that("multiclass feature interactions work", {
dm <- xgb.DMatrix(
as.matrix(iris[, -5]), label = as.numeric(iris$Species) - 1, nthread = n_threads
)
param <- list(
eta = 0.1, max_depth = 4, objective = 'multi:softprob', num_class = 3, nthread = n_threads
)
b <- xgb.train(param, dm, 40)
pred <- t(
array(
data = predict(b, dm, outputmargin = TRUE),
dim = c(3, 150)
)
)
# SHAP contributions:
cont <- predict(b, dm, predcontrib = TRUE)
expect_length(cont, 3)
# rewrap them as a 3d array
cont <- array(
data = unlist(cont),
dim = c(150, 5, 3)
)
# make sure for each row they add up to marginal predictions
expect_lt(max(abs(apply(cont, c(1, 3), sum) - pred)), 0.001)
# SHAP interaction contributions:
intr <- predict(b, dm, predinteraction = TRUE)
expect_length(intr, 3)
# rewrap them as a 4d array
intr <- aperm(
a = array(
data = unlist(intr),
dim = c(150, 5, 5, 3)
),
perm = c(4, 1, 2, 3) # [grp, row, col, col]
)
# check the symmetry
expect_lt(max(abs(aperm(intr, c(1, 2, 4, 3)) - intr)), 0.00001)
# sums WRT columns must be close to feature contributions
expect_lt(max(abs(apply(intr, c(1, 2, 3), sum) - aperm(cont, c(3, 1, 2)))), 0.00001)
})
test_that("SHAP single sample works", {
train <- agaricus.train
test <- agaricus.test
booster <- xgboost(
data = train$data,
label = train$label,
max_depth = 2,
nrounds = 4,
objective = "binary:logistic",
nthread = n_threads
)
predt <- predict(
booster,
newdata = train$data[1, , drop = FALSE], predcontrib = TRUE
)
expect_equal(dim(predt), c(1, dim(train$data)[2] + 1))
predt <- predict(
booster,
newdata = train$data[1, , drop = FALSE], predinteraction = TRUE
)
expect_equal(dim(predt), c(1, dim(train$data)[2] + 1, dim(train$data)[2] + 1))
})
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