3   Create your own Dataset

Unless the data you’re working with comes with some package in the torch ecosystem, you’ll need to wrap in a Dataset.

torch Dataset objects

A Dataset is an R6 object that knows how to iterate over data. This is because it acts as supplier to a DataLoader , who will ask it to return some number of items.

(How many? That is dependent on the batch size – but batch sizes are handled by DataLoaders, so it needn’t be concerned about that. All it has to know is what to do when asked for, e.g., item no. 7.)

While a Dataset may have any number of methods – each responsible for some aspect of pre-processing logic, for example – just three methods are required:

  • initialize() , to pre-process and store the data;

  • .getitem(i), to pick the item at position i, and

  • .length(), to indicate to the DataLoader how many items it has.

Let’s see an example.

Penguins

penguins is a very nice dataset that lives in the palmerpenguins package.

library(dplyr)
library(palmerpenguins)

penguins %>% glimpse()
Rows: 344
Columns: 8
$ species           <fct> Adelie, Adelie, Adelie, Adelie, Adelie, Adelie…
$ island            <fct> Torgersen, Torgersen, Torgersen, Torgersen…
$ bill_length_mm    <dbl> 39.1, 39.5, 40.3, NA, 36.7, 39.3, 38.9, 39.2,…
$ bill_depth_mm     <dbl> 18.7, 17.4, 18.0, NA, 19.3, 20.6, 17.8, 19.6,…
$ flipper_length_mm <int> 181, 186, 195, NA, 193, 190, 181, 195, 193,…
$ body_mass_g       <int> 3750, 3800, 3250, NA, 3450, 3650, 3625, 4675…
$ sex               <fct> male, female, female, NA, female, male, female…
$ year              <int> 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007…

There are three species, and we’ll infer them making use of all available information: “biometrics” like bill_length_mm, geographic indicators like the island the penguins inhabit, and more.

Predictors are of two different types, categorical and continuous.

Continuous features, of R type double, may be fed to torch without further ado. We just directly use them to initialize a torch tensor, which will be of type Float:

library(torch)
torch_tensor(1)
torch_tensor
 1
[ CPUFloatType{1} ]

It’s different with categorical data though. Firstly, torch needs all data to be in numerical form, so vectors of type character need to become factors – which can then be treated as numeric via level extraction. In the penguins dataset, island, sex , as well as the target column, species, are factors already. So can we just do an as.numeric() and that’s it?

Not quite: We also need to reflect on the semantic side of things.

Categorical data in deep learning

If we just replace islands Biscoe, Dream, and Torgersen by numbers 1, 2, and 3, we present them to the network as interval data, which of course they’re not.

We have two options: transform them to one-hot vectors, where e.g. Biscoe would be 0,0,1, Dream 0,1,0, and Torgersen, 1,0,0, or leave them as they are, but have the network map each discrete value to a multidimensional, continuous representation. The latter is called embedding, and it often helps networks make sense of discrete data.

Embedding modules expect their inputs to be of type Long. A tensor created from an R value will have the correct type if we make sure it’s an integer:

torch_tensor(as.integer(as.numeric(as.factor("one"))))
torch_tensor
 1
[ CPULongType{1} ]

Now, let’s create a dataset for penguins.

A dataset for penguins

In initialize(), we convert the data as planned and store them for later delivery. Like the categorical input features, species, the target, is discrete, and thus, converted to torch Long.

penguins_dataset <- dataset(
  
  name = "penguins_dataset",
  
  initialize = function(df) {
    
    df <- na.omit(df) 
    
    # continuous input data (x_cont)   
    x_cont <- df[ , c("bill_length_mm", "bill_depth_mm", "flipper_length_mm", "body_mass_g", "year")] %>%
      as.matrix()
    self$x_cont <- torch_tensor(x_cont)
    
    # categorical input data (x_cat)
    x_cat <- df[ , c("island", "sex")]
    x_cat$island <- as.integer(x_cat$island)
    x_cat$sex <- as.integer(x_cat$sex)
    self$x_cat <- as.matrix(x_cat) %>% torch_tensor()

    # target data (y)
    species <- as.integer(df$species)
    self$y <- torch_tensor(species)
    
  },
  
  .getitem = function(i) {
     list(x_cont = self$x_cont[i, ], x_cat = self$x_cat[i, ], y = self$y[i])
    
  },
  
  .length = function() {
    self$y$size()[[1]]
  }
 
)

Unlike initialize, .getitem(i) and .length() are just one-liners.

Let’s see if this behaves like we want it to. We randomly split the data into training and validation sets and query their respective lengths:

train_indices <- sample(1:nrow(penguins), 250)

train_ds <- penguins_dataset(penguins[train_indices, ])
valid_ds <- penguins_dataset(penguins[setdiff(1:nrow(penguins), train_indices), ])

length(train_ds)
length(valid_ds)
[1] 242
[1] 91

We can index into Datasets in an R-like way:

train_ds[1]
$x_cont
torch_tensor
   45.2000
   16.4000
  223.0000
 5950.0000
 2008.0000
[ CPUFloatType{5} ]

$x_cat
torch_tensor
 1
 2
[ CPULongType{2} ]

$y
torch_tensor
3
[ CPULongType{} ]

From here on, everything proceeds like in the first tutorial: We use the Datasets to instantiate DataLoaders…

train_dl <- train_ds %>% dataloader(batch_size = 16, shuffle = TRUE)

valid_dl <- valid_ds %>% dataloader(batch_size = 16, shuffle = FALSE)

… and then, create and train the network. The network will look pretty different now though: most notably, you’ll see embeddings at work.

Classifying penguins – the network

We just heard that embedding layers work with a datatype that’s different from most other neural network layers. It is therefore convenient to have them work in a space of their own, that is, put them into a dedicated container.

Here we define a specialized module that has one embedding layer for every categorical feature. It gets passed the cardinalities of the respective features, and creates an nn_embedding() for each of them.

When called, it iterates over its submodules, lets them do their work, and returns the concatenated output.

embedding_module <- nn_module(
  
  initialize = function(cardinalities) {
    
    self$embeddings = nn_module_list(lapply(cardinalities, function(x) nn_embedding(num_embeddings = x, embedding_dim = ceiling(x/2))))
    
  },
  
  forward = function(x) {
    
    embedded <- vector(mode = "list", length = length(self$embeddings))
    for (i in 1:length(self$embeddings)) {
      embedded[[i]] <- self$embeddings[[i]](x[ , i])
    }
    
    torch_cat(embedded, dim = 2)
  }
)

The top-level module has three submodules: said embedding_module and two linear layers.

The first linear layer takes the output from embedding_module , computes an affine transformation as it sees fit, and passes its result to the output layer. output then has three units, one for every possible target class.

The activation function we apply to the raw aggregation, nnf_log_softmax(), composes two operations: the popular-in-deep-learning softmax normalization and taking the logarithm. Like that, we end up with the format expected by nnf_nll_loss(), the loss function that computes the negative log likelihood (NLL) loss between inputs and targets.

net <- nn_module(
  "penguin_net",

  initialize = function(cardinalities,
                        n_cont,
                        fc_dim,
                        output_dim) {
    
    self$embedder <- embedding_module(cardinalities)
    self$fc1 <- nn_linear(sum(purrr::map(cardinalities, function(x) ceiling(x/2)) %>% unlist()) + n_cont, fc_dim)
    self$output <- nn_linear(fc_dim, output_dim)
    
  },

  forward = function(x_cont, x_cat) {
    
    embedded <- self$embedder(x_cat)
    
    all <- torch_cat(list(embedded, x_cont$to(dtype = torch_float())), dim = 2)
    
    all %>% self$fc1() %>%
      nnf_relu() %>%
      self$output() %>%
      nnf_log_softmax(dim = 2)
    
  }
)

Let’s instantiate the top-level module:

model <- net(
  cardinalities = c(length(levels(penguins$island)), length(levels(penguins$sex))),
  n_cont = 5,
  fc_dim = 32,
  output_dim = 3
)

And we’re ready for training!

Model training

optimizer <- optim_adam(model$parameters, lr = 0.01)

for (epoch in 1:20) {

  model$train()
  train_losses <- c()  

  for (b in enumerate(train_dl)) {
    
    optimizer$zero_grad()
    output <- model(b$x_cont, b$x_cat)
    loss <- nnf_nll_loss(output, b$y)
    
    loss$backward()
    optimizer$step()
    
    train_losses <- c(train_losses, loss$item())
    
  }

  model$eval()
  valid_losses <- c()

  for (b in enumerate(valid_dl)) {
    
    output <- model(b$x_cont, b$x_cat)
    loss <- nnf_nll_loss(output, b$y)
    valid_losses <- c(valid_losses, loss$item())
    
  }

  cat(sprintf("Loss at epoch %d: training: %3.3f, validation: %3.3f\n", epoch, mean(train_losses), mean(valid_losses)))
}
Loss at epoch 1: training: 34.962, validation: 4.354
Loss at epoch 2: training: 8.207, validation: 14.512
Loss at epoch 3: training: 7.804, validation: 2.820
Loss at epoch 4: training: 5.998, validation: 8.525
Loss at epoch 5: training: 8.293, validation: 5.594
Loss at epoch 6: training: 6.375, validation: 4.540
Loss at epoch 7: training: 7.478, validation: 2.120
Loss at epoch 8: training: 3.470, validation: 3.508
Loss at epoch 9: training: 12.155, validation: 4.266
Loss at epoch 10: training: 10.168, validation: 4.285
Loss at epoch 11: training: 5.963, validation: 1.888
Loss at epoch 12: training: 3.035, validation: 2.454
Loss at epoch 13: training: 1.993, validation: 1.185
Loss at epoch 14: training: 2.454, validation: 2.200
Loss at epoch 15: training: 1.641, validation: 0.588
Loss at epoch 16: training: 0.996, validation: 1.959
Loss at epoch 17: training: 0.912, validation: 0.674
Loss at epoch 18: training: 1.517, validation: 0.487
Loss at epoch 19: training: 1.569, validation: 1.202
Loss at epoch 20: training: 0.735, validation: 1.313`