Training a Tabnet model from missing-values dataset

Christophe Regouby



Real-life training dataset usually contains missing data. The vast majority of deep-learning networks do not handle missing data and thus either stop or crash when values are missing in the predictors.

But Tabnet use a masking mechanism that we can reuse to cover the missing data in the training set.

As we enter the world of missing-data, we have to question the type of missing-data we deal with. We could have missing data at random (MAR), like for example some transmission errors on a sensor data dataset, or missing not at random (MNAR) when some interactions exists between the missing data and other predictors values for the same sample. The later is a more complex topic to cover, and we will try to investigate it here through the ames dataset.

Missing-data dataset creation

Ames missings understanding

The ames dataset from {modeldata} contains a lot of null values that the human analysis clearly understand as an implicit “missing object” described by that value. We have for example pool surface of 0 square meters means “no pool”, basement surface of 0 square meters means “no basement”, …
Many of those variables can be detected visually by inspecting the distribution of the values like, for example, the Masonry veneer area predictor :

library(tidymodels, quietly = TRUE)
data("ames", package = "modeldata")

ames variable Mas_Vnr_Area histogram showing high occurrence of value zero We know that it will be extremely difficult for a model to capture an internal representation of such distribution, and thus we want to avoid the null values to penalize the model internal representation.

While keeping some room for freedom

Many of those variables come as a pair in the ames dataset, one for the qualitative aspect, the other for the quantitative aspect. We have for example Pool_QC for pool condition, that has a “no_pool” level with Pool_Area=0 in that case.
As human, we have the intuition that knowing if a pool is present is important for the modeling task. So we want the model to get an internal representation of the implicit has_pool=FALSE without having it explicit in the dataset. In order to do so, we have to let the model some freedom to infer the “no_pool” state and thus we should not mutate both variables in the pair Pool_Area=NA and Pool_QC=NA at the same time.

Ames with missing data

Let’s turn those missing objects data explicitly into NAs in an new ames_missing dataset :

A quick and dirty way to achieve this on numerical predictors is to na_if() zeros on any column which name is related to surface and area.
Then, according to the keep room for freedom rule, do it carefully on the matching categorical predictors

col_with_zero_as_na <- ames %>% 
  select(where(is.numeric)) %>% 
  select(matches("_SF|Area|Misc_Val|[Pp]orch$")) %>% 
  summarise_each(min) %>% 
  select_if(~.x==0) %>% 
ames_missing <- ames %>% mutate_at(col_with_zero_as_na, na_if, 0) %>% 
  mutate_at("Alley", na_if, "No_Alley_Access") %>% 
  mutate_at("Fence", na_if, "No_Fence") %>% 
  mutate_at(c("Garage_Cond", "Garage_Finish"), na_if, "No_Garage") %>% 
  mutate_at(c("Bsmt_Exposure", "BsmtFin_Type_1", "BsmtFin_Type_2"), na_if, "No_Basement")


ames missing values visualization showing few variables with more than 90% missingness with a global 13% missing

We can see here that variable are not missing at random, and thus we can expect the model to capture the missingness relation during the pretraining phase.

Note: A better way to achieve proper value mutation to explicit NAs would be to also check if the qualitative column in the pair refers to none or to zero occurrence of the equipment. But this is beyond the scope of this vignette.

Model pretraining

Let’s pretrain one model for each of those dataset, and analyze variable importance that emerge after the unsupervised representation learning step:

Variable importance with raw ames dataset

ames_rec <- recipe(Sale_Price ~ ., data=ames) %>% 

cat_emb_dim <- map_dbl(ames %>% select_if(is.factor), ~log2(nlevels(.x)) %>% round)

ames_pretrain <- tabnet_pretrain(ames_rec, data=ames,  epoch=50, cat_emb_dim = cat_emb_dim,
                            valid_split = 0.2, verbose=TRUE, batch=2930, 
                            early_stopping_patience = 3L, early_stopping_tolerance = 1e-4)
[Epoch 001] Loss: 43.708794 Valid loss: 8066126.500000
[Epoch 002] Loss: 31.463089 Valid loss: 5631984.000000
[Epoch 003] Loss: 23.396217 Valid loss: 3901085.500000
[Epoch 004] Loss: 19.241619 Valid loss: 2947481.750000
[Epoch 005] Loss: 15.032537 Valid loss: 2250338.000000
[Epoch 006] Loss: 12.991020 Valid loss: 1815583.125000
[Epoch 007] Loss: 11.044646 Valid loss: 1533597.875000
[Epoch 008] Loss: 9.114124 Valid loss: 1395840.000000
[Epoch 009] Loss: 8.362211 Valid loss: 1258169.375000
[Epoch 010] Loss: 7.549719 Valid loss: 1064599.500000
[Epoch 011] Loss: 6.808529 Valid loss: 998335.625000
[Epoch 012] Loss: 6.569450 Valid loss: 1047418.500000
[Epoch 013] Loss: 6.606429 Valid loss: 1048583.625000
[Epoch 014] Loss: 6.742617 Valid loss: 993241.312500
[Epoch 015] Loss: 6.806847 Valid loss: 995705.875000
[Epoch 016] Loss: 6.618536 Valid loss: 1026789.625000
[Epoch 017] Loss: 6.593469 Valid loss: 1033726.437500
Early stopping at epoch 017

ames_fit model training diagnostic plot

Now we capture the columns with missings, and create a convenience function to color the vip::vip() plot output according to the missingness quality of the column

col_with_missings <- ames_missing %>%
  summarise_all(~sum(>0) %>%
  t %>% enframe(name="Variable") %>% 

vip_color <- function(object, col_has_missing) {
  vip_data <- vip::vip(object)$data %>% arrange(Importance)
  vis_miss_plus <- left_join(vip_data, col_has_missing , by="Variable") %>%
    mutate(Variable=factor(Variable, levels = vip_data$Variable))
  ggplot(vis_miss_plus, aes(x=Variable, y=Importance, fill=has_missing)) +
    geom_col() + coord_flip() + scale_fill_grey()
vip_color(ames_pretrain, col_with_missings)

ames_fit model variable importance plot

We get BsmtFin_Type_1, BsmtFin_SF_1 and Bsmt_Exposure variables in the top ten important variables according to this run of pretraining the model. Those variables has been screened as having few missing values.

Note that this result varies a lot from run to run. The captured result here depends a lot on your initialization conditions.

Variable importance with ames_missing dataset

Let’s pretrain a new model with the same hyperparameter, but now using the ames_missing dataset.
In order to compensate the 13% missingness already present in the ames_missing dataset, we adjust the pretraining_ratio parameter to 0.5 - 0.13 = 0.37

ames_missing_rec <- recipe(Sale_Price ~ ., data=ames_missing) %>% 
ames_missing_pretrain <- tabnet_pretrain(ames_missing_rec, data=ames_missing, epoch=50, 
                                    cat_emb_dim = cat_emb_dim,
                                    valid_split = 0.2, verbose=TRUE, batch=2930, 
                                    early_stopping_patience = 3L, early_stopping_tolerance = 1e-4)
vip_color(ames_missing_pretrain, col_with_missings)
[Epoch 001] Loss: 56.250610 Valid loss: 40321308.000000
[Epoch 002] Loss: 44.254524 Valid loss: 39138240.000000
[Epoch 003] Loss: 33.992207 Valid loss: 38648800.000000
[Epoch 004] Loss: 26.421488 Valid loss: 37445656.000000
[Epoch 005] Loss: 22.290133 Valid loss: 35814052.000000
[Epoch 021] Loss: 10.877335 Valid loss: 20903176.000000
[Epoch 022] Loss: 11.023649 Valid loss: 20772972.000000
[Epoch 023] Loss: 10.819239 Valid loss: 20642806.000000
[Epoch 024] Loss: 10.994371 Valid loss: 20575458.000000
[Epoch 025] Loss: 10.700000 Valid loss: 20449918.000000
[Epoch 026] Loss: 10.902529 Valid loss: 20680102.000000
[Epoch 027] Loss: 10.791571 Valid loss: 20849496.000000
[Epoch 028] Loss: 11.102308 Valid loss: 20995910.000000
Early stopping at epoch 028

ames_missing_pretrain model training diagnostic plot ames_missing_pretrain model variable importance plot

We can see here no variables with high missingness is present in the top 10 important variables. This seems to be a good sign of the model having captured proper interactions between variables.

Model training

Variable importance with raw ames dataset

ames_fit <- tabnet_pretrain(ames_rec, data=ames,  tabnet_model = ames_pretrain, 
                            epoch=50, cat_emb_dim = cat_emb_dim,
                            valid_split = 0.2, verbose=TRUE, batch=2930, 
                            early_stopping_patience = 5L, early_stopping_tolerance = 1e-4)
vip_color(ames_fit, col_with_missings)

ames_fit model training diagnostic plot

ames_fit model training variable importance plot Here again, the model uses two predictors BasmFin_SF_2 and Garage_Finish that have respectively 88 % and 5 % missingness.

Variable importance with ames_missing dataset

ames_missing_fit <- tabnet_pretrain(ames_rec, data=ames_missing,  tabnet_model = ames_missing_pretrain, 
                            epoch=50, cat_emb_dim = cat_emb_dim,
                            valid_split = 0.2, verbose=TRUE, batch=2930, 
                            early_stopping_patience = 5L, early_stopping_tolerance = 1e-4)
vip_color(ames_missing_fit, col_with_missings)

ames_fit model training diagnostic plot

ames_fit model training variable importance plot Here we can see one predictors Garage_Area with 5 % missingness in the top 10.


Even if the models have a huge variability in the variable importance among different training, we have the intuition that model trained with explicit missing data will provide better result than its counterpart trained with zero-imputed variables.

In any case, having the capability to pretrain and fit TabNet models with MAR dataset or MNAR dataset is of high convenience for the real-life use-cases.