modelStudio(), explainer_mlr3() and NAs

[andreassot10]

Hi,

There's a glitch with modelStudio when using mlr3 pipelines with data with missing values.

It looks like modelStudio() doesn't know how to impute missing data before crunching the numbers, even when the user has incorporated a pipe operator for missing values in the mlr3 pipeline. In fact, modelStudio() does not even recognize mlr3 learners if their class is other than [1] "LearnerClassifRanger" "LearnerClassif" "Learner" "R6" (e.g. try class(learner) for a Random Forest learner). If you have a pipeline, whose class is [1] "GraphLearner" "Learner" "R6", modelStudio() doesn't know how to handle it.

Package DALExtra's explainer_mlr3() suffers from the same issue, although this can be dealt with by providing custom functions for arguments predict_function and residual_function.

Below is an example of a pipeline that imputes missing data and then balances classes. Note that it works fine when there are no missing data, but returns an error otherwise.

Example 1: no missing data

library(tidyverse)
library(data.table)
library(tidymodels)
library(paradox)
library(mlr3) # NOTE: install mlr3 packages from GitHub, not CRAN, as they differ in a few things, e.g. with GitHub you tune the pipeline with $optimize() but with CRAN with $tune()
library(mlr3filters)
library(mlr3learners)
library(mlr3misc)
library(mlr3pipelines)
library(mlr3tuning)
library(DALEXtra)
library(modelStudio)

# Load task and make smaller so code runs faster
task <- tsk('sonar')
task$select(paste0('V', 1:10))

# Ratio values for class-balancing pipe operators
class_counts <- table(task$truth())
upsample_ratio <- class_counts[class_counts == max(class_counts)] / 
  class_counts[class_counts == min(class_counts)]
downsample_ratio <- 1 / upsample_ratio

# Pipe operators for class-balancing
# 1. Enrich minority class by factor 'ratio'
po_over <- po("classbalancing", id = "up", adjust = "minor", 
  reference = "minor", shuffle = FALSE, ratio = upsample_ratio)

# 2. Reduce majority class by factor '1/ratio'
po_under <- po("classbalancing", id = "down", adjust = "major", 
  reference = "major", shuffle = FALSE, ratio = downsample_ratio)

# Handle missing values
features_with_nas <- sort(task$missings() / task$nrow, decreasing = TRUE)
features_with_nas <- features_with_nas[features_with_nas != 0]

# Imputes values based on histogram
hist_imp <- po("imputehist", param_vals = 
  list(affect_columns = selector_name(names(features_with_nas))))

# Add an indicator column for each feature with missing values
# One-hot encode these new categorical columns, and then remove the categorical versions of them
miss_ind <- po("missind") %>>% 
  po("encode") %>>%
  po("select", 
     selector = selector_invert(selector_type("factor")), 
     id = 'dummy_encoding')

impute_data <- po("copy", 2) %>>%
  gunion(list(hist_imp, miss_ind)) %>>%
  po("featureunion")

impute_data$plot() # This is the Graph we'll add to the pipeline
impute_data$plot(html = TRUE)

# Random Forest learner with up- and down-balancing
rf <- lrn("classif.ranger", predict_type = "prob")

rf_up <- GraphLearner$new(
  po_over %>>%
    po('learner', rf, id = 'rf'),
  predict_type = 'prob'
)

rf_down <- GraphLearner$new(
  po_under %>>%
    po('learner', rf, id = 'rf'),
  predict_type = 'prob')

# All learners (Random Forest with up- and down-balancing)
learners <- list(
  rf_up,
  rf_down
)
names(learners) <- sapply(learners, function(x) x$id)

# Our pipeline
graph <- 
  impute_data %>>%
  po("branch", names(learners)) %>>% 
  gunion(unname(learners)) %>>%
  po("unbranch")

graph$plot() # Plot pipeline
graph$plot(html = TRUE) # Plot pipeline

pipe <- GraphLearner$new(graph) # Convert pipeline to learner
pipe$predict_type <- 'prob' # We want to predict probabilities and not classes.

param_set <- ParamSetCollection$new(list(
  ParamSet$new(list(pipe$param_set$params$branch.selection$clone()))
))

# Set up tuning instance
instance <- TuningInstance$new(
  task = task,
  learner = pipe,
  resampling = rsmp('cv', folds = 2),
  measures = msr('classif.bbrier'),
  param_set,
  terminator = term("evals", n_evals = 3), 
  store_models = TRUE)
tuner <- TunerRandomSearch$new()

# Tune pipe learner to find best-performing branch
tuner$optimize(instance)

# Take a look at the results
instance$result
print(instance$result$tune_x$branch.selection) # Best model

# Train pipeline
pipe$train(task)

################################################################################################
# DALEXextra and modelStudio stuff
################################################################################################

# First create custom functions for predictions and residuals
# We need custom functions because explain_mlr3() doesn't recognize the Graph Learner class of mlr3
predict_function_custom <- function(model, data) {
  pr <- model$
    predict_newdata(data)$
    data$
    prob[, 1]
  
  return(pr)
}

residual_function_custom <- function(model, data, y) {
  pr <- model$
    predict_newdata(data)
  
  y_hat <- pr$
    data$
    prob[, 1]
  
  return(as.integer(y == 0) - y_hat)
}

# Run explainer- works fine with cthe above functions
explainer <- explain_mlr3(model = pipe,
  data = task$data()[, -1],
  y = as.integer(task$data()[, 1] == 'M'),
  predict_function = predict_function_custom,
  residual_function = residual_function_custom,
  label = "mlr3")

# HOWEVER: we have a classification task, but explainer thinks it's regression!
explainer$model_info

# Let's run modelStudio. You'll need to wait for a while
modelStudio(
  explainer, 
  new_observation = task$data()[6, -1]
)

# Ignore warning about data format. Argument `new_observation` is a `data.table`, so its class is `[1] "data.table" "data.frame"`, 
# which is essentially a data frame. so the class has two elements, but the condition only looks at the first one.

Working just fine.

Example 2: missing data

library(tidyverse)
library(data.table)
library(tidymodels)
library(paradox)
library(mlr3)
library(mlr3filters)
library(mlr3learners)
library(mlr3misc)
library(mlr3pipelines)
library(mlr3tuning)
library(DALEXtra)
library(modelStudio)

# Load task and make smaller so code runs faster
task <- tsk('sonar')
task$select(paste0('V', 1:10))

# Create some missing data
data <- task$data()
data$V1[1:5] <- NA
task <- TaskClassif$new(data, id = 'sonar', target = 'Class')

# Ratio values for class-balancing pipe operators
class_counts <- table(task$truth())
upsample_ratio <- class_counts[class_counts == max(class_counts)] / 
  class_counts[class_counts == min(class_counts)]
downsample_ratio <- 1 / upsample_ratio

# Pipe operators for class-balancing
# 1. Enrich minority class by factor 'ratio'
po_over <- po("classbalancing", id = "up", adjust = "minor", 
  reference = "minor", shuffle = FALSE, ratio = upsample_ratio)

# 2. Reduce majority class by factor '1/ratio'
po_under <- po("classbalancing", id = "down", adjust = "major", 
  reference = "major", shuffle = FALSE, ratio = downsample_ratio)

# Handle missing values
features_with_nas <- sort(task$missings() / task$nrow, decreasing = TRUE)
features_with_nas <- features_with_nas[features_with_nas != 0]

# Imputes values based on histogram
hist_imp <- po("imputehist", param_vals = 
  list(affect_columns = selector_name(names(features_with_nas))))

# Add an indicator column for each feature with missing values
# One-hot encode these new categorical columns, and then remove the categorical versions of them
miss_ind <- po("missind") %>>% 
  po("encode") %>>%
  po("select", 
     selector = selector_invert(selector_type("factor")), 
     id = 'dummy_encoding')

impute_data <- po("copy", 2) %>>%
  gunion(list(hist_imp, miss_ind)) %>>%
  po("featureunion")

impute_data$plot() # This is the Graph we'll add to the pipeline
impute_data$plot(html = TRUE)

# Random Forest learner with up- and down-balancing
rf <- lrn("classif.ranger", predict_type = "prob")

rf_up <- GraphLearner$new(
  po_over %>>%
    po('learner', rf, id = 'rf'),
  predict_type = 'prob'
)

rf_down <- GraphLearner$new(
  po_under %>>%
    po('learner', rf, id = 'rf'),
  predict_type = 'prob')

# All learners (Random Forest with up- and down-balancing)
learners <- list(
  rf_up,
  rf_down
)
names(learners) <- sapply(learners, function(x) x$id)

# Our pipeline
graph <- 
  impute_data %>>%
  po("branch", names(learners)) %>>% 
  gunion(unname(learners)) %>>%
  po("unbranch")

graph$plot() # Plot pipeline
graph$plot(html = TRUE) # Plot pipeline

pipe <- GraphLearner$new(graph) # Convert pipeline to learner
pipe$predict_type <- 'prob' # We want to predict probabilities and not classes.

param_set <- ParamSetCollection$new(list(
  ParamSet$new(list(pipe$param_set$params$branch.selection$clone()))
))

# Set up tuning instance
instance <- TuningInstance$new(
  task = task,
  learner = pipe,
  resampling = rsmp('cv', folds = 2),
  measures = msr('classif.bbrier'),
  param_set,
  terminator = term("evals", n_evals = 3), 
  store_models = TRUE)
tuner <- TunerRandomSearch$new()

# Tune pipe learner to find best-performing branch
tuner$optimize(instance)

# Take a look at the results
instance$result
print(instance$result$tune_x$branch.selection) # Best model

# Train pipeline
pipe$train(task)

################################################################################################
# DALEXextra and modelStudio stuff
################################################################################################

# First create custom functions for predictions and residuals
# We need custom functions because explain_mlr3() doesn't recognize the Graph Learner class of mlr3
predict_function_custom <- function(model, data) {
  pr <- model$
    predict_newdata(data)$
    data$
    prob[, 1]
  
  return(pr)
}

residual_function_custom <- function(model, data, y) {
  pr <- model$
    predict_newdata(data)
  
  y_hat <- pr$
    data$
    prob[, 1]
  
  return(as.integer(y == 0) - y_hat)
}

# Run explainer- works fine with cthe above functions
explainer <- explain_mlr3(model = pipe,
  data = task$data()[, -1],
  y = as.integer(task$data()[, 1] == 'M'),
  predict_function = predict_function_custom,
  residual_function = residual_function_custom,
  label = "mlr3")

# HOWEVER: we have a classification task, but explainer thinks it's regression!
explainer$model_info

# Let's run modelStudio. You'll need to wait for a while
modelStudio(
  explainer, 
  new_observation = task$data()[6, -1]
)

# Ignore warning about data format. Argument `new_observation` is a `data.table`, so its class is `[1] "data.table" "data.frame"`, 
# which is essentially a data frame. so the class has two elements, but the condition only looks at the first one.

We get errors and no plot:

Calculating ... 
  Calculating ingredients::feature_importance 
  Calculating ingredients::partial_dependence (numerical) 
  Calculating ingredients::accumulated_dependence (numerical) 
    Elapsed time: 00:01:01 ETA...Error in seq.default(min(x[, name]), max(x[, name]), length.out = nbins) : 
  'from' must be a finite number
In addition: Warning messages:
1: In value[[3L]](cond) : 
Error occurred in ingredients::partial_dependence (numerical) function: missing values and NaN's not allowed if 'na.rm' is FALSE
2: In value[[3L]](cond) : 
Error occurred in ingredients::accumulated_dependence (numerical) function: missing values and NaN's not allowed if 'na.rm' is FALSE

Is there a way to pass imputed data from explainer_mlr3() to modelStudio() just like you can pass predictions and residuals with arguments predict_function and residual_function respectively? Any chances of implementing this please?

Thanks

[hbaniecki]

Hi,
Thanks for this extensive example. My take on this:

1. The data.table/new_observation warning is fixed in the GitHub version (soon on CRAN)
2. modelStudio relies on DALEXtra::explain_mlr3() to choose a proper predict_function - the function for GraphLearner class is missing and we can add it to the next release
3. DALEX::model_profile(explainer) and DALEX::predict_profile(explainer, data[1,]) explanations won't work if the data argument has missing values - the same occurs in modelStudio calculations - pipeline won't fix this issue because some operations are made on data which contains NA (always was the case)

I can tell that (2) is within reach, while (3) needs more thought process. If you have more issues don't hesitate.

[andreassot10]

Hi,
Thanks for this extensive example. My take on this:

1. The `data.table/new_observation` warning is fixed in the GitHub version (soon on CRAN)

2. `modelStudio` relies on `DALEXtra::explain_mlr3()` to choose a proper `predict_function` - the function for `GraphLearner` class is missing and we can add it to the next release

3. `DALEX::model_profile(explainer)` and `DALEX::predict_profile(explainer, data[1,])` explanations won't work if the `data` argument has missing values - the same occurs in `modelStudio` calculations - pipeline won't fix this issue because some operations are made on `data` which contains `NA` (always was the case)

I can tell that (2) is within reach, while (3) needs more thought process. If you have more issues don't hesitate.

Hi,

Many thanks for the quick response. Great to hear 1 has been dealt with and 2 is within reach. Point 3 is indeed a tricky one. For the time being, my intention is to hard-code the chunks of code in DALEX::model_profile(explainer) and DALEX::predict_profile(explainer, data[1,]) that cause the glitches (e.g. supply the imputed data directly). A proper solution from your side on the long term would be welcomed. Good luck!

[maksymiuks]

Hi,

Thank You @andreassot10 for an extensive example. Right now explain_mlr3 supports GraphLearner objects. You can check it downloading the package from github. In case of any problems feel free to raise an issue!

[andreassot10]

Hi,

Thank You @andreassot10 for an extensive example. Right now explain_mlr3 supports GraphLearner objects. You can check it downloading the package from github. In case of any problems feel free to raise an issue!

That's amazing, thanks!

[hbaniecki]

TODO: add na.rm in

modelStudio/R/prepare.R

Line 601 in 867e12a

variable_splits <- seq(min(x[,name]), max(x[,name]), length.out = nbins)

and more

[Tato14]

Hi,

I opened an issue on mlr3 github with a similar problem. I cannot solve the issue using the predict_function_custom and residual_function_custom from @andreassot10.

Thanks

[hbaniecki]

Hi @Tato14,
trying to run your example, what package is %>>% from?

[Tato14]

Hi @hbaniecki, should be from mlr3pipelines (page 195)

[hbaniecki]

@Tato14 sure it works, but now I have another problem: Error in isTRUE(lhs) : object 'task' not found. Could you please check the example to run as intended?

[Tato14]

@hbaniecki I apologise for the inconvenience. I add the missing variables in the code. Now it should work properly.
Thanks