# Example 1: Iris dataset with torch

> 📝 Note
> Since the innsight package relies on the torch package for each method and requires a successful installation of LibTorch and other dependencies (`torch::install_torch()`), no examples can be run in the R vignette for memory reasons. For the executed code chunks we refer to our website.

In this very elementary example, we want to show you the use of the innsight package and its possibilities in the simplest case. For this, we use the Iris dataset, which contains the length and width of the sepals and petals of the three flower species Iris Setosa, Versicolor and Virginica. In total, there are measurements of \(50\) flowers of each type in centimeters.

## Step 0: Train a model

The first step does not necessarily need the innsight package yet, but at this point, it is listed anyway to have a fully working example. In this example, the model is created and trained in torch.

> 📝 Note
> It is also possible to train the torch model using the luz package, which is described in the vignette with the penguin dataset (see `?vignette("Example_2_penguin", package='innsight'`)).

    library(innsight)
    library(torch)

    # Set seeds for reproducibility
    set.seed(42)
    torch_manual_seed(42)

    # Prepare data
    data(iris)
    x <- torch_tensor(as.matrix(iris[, -5]))
    # normalize input to [-1, 1]
    x <- 2 * (x - x$min(1)[[1]]) / (x$max(1)[[1]] - x$min(1)[[1]]) - 1
    y <- torch_tensor(as.integer(iris[, 5]))

    # Define model (`torch::nn_sequential`)
    model <- nn_sequential(
      nn_linear(4, 30),
      nn_relu(),
      nn_dropout(0.3),
      nn_linear(30, 10),
      nn_relu(),
      nn_linear(10, 3),
      nn_softmax(dim = 2)
    )

    # Train model
    optimizer <- optim_adam(model$parameters, lr = 0.001)
    for (t in 1:2500) {
      y_pred <- torch_log(model(x))
      loss <- nnf_nll_loss(y_pred, y)
      if (t %% 250 == 0) {
        cat("Loss: ", as.numeric(loss), "\n")
      }
      optimizer$zero_grad()
      loss$backward()
      optimizer$step()
    }
    #> Loss:  0.1949702
    #> Loss:  0.07439215
    #> Loss:  0.07707331
    #> Loss:  0.04924559
    #> Loss:  0.03550617
    #> Loss:  0.06755876
    #> Loss:  0.04763604
    #> Loss:  0.04390004
    #> Loss:  0.04739835
    #> Loss:  0.05710815

## Step 1: Convert the model

The easiest way to convert a model for the innsight package is just using the model for the `Converter` class without any further arguments (except for torch models, the input dimension is still needed). Thus, the converting part for our trained model is done by:

    # Create the converter object
    converter <- convert(model, input_dim = c(4))
    #> Skipping nn_dropout ...

Since there are no labels for the inputs and outputs stored in the torch model, they were generated automatically by innsight. But you can pass them by yourself using the corresponding arguments. These labels are then also used in the visualizations in step 3. Internally, the dimensions of the input and output labels are also added as checks and errors are thrown if any discrepancies arise.

    # Create `Converter` object (with custom labels)
    converter <- convert(model,
      input_dim = c(4),
      input_names = c("Sepal (length)", "Sepal (width)", "Petal (length)", "Petal (width)"),
      output_names = c("Setosa", "Versicolor", "Virginica")
    )
    #> Skipping nn_dropout ...

In addition, the default `print()` function for R6 classes has been overwritten so that all important properties and contents of the converter object can be displayed in a summarized form:

    converter
    #>
    #> ── Converter (innsight) ────────────────────────────────────────────────────────
    #> Fields:
    #>   • input_dim: (*, 4)
    #>   • output_dim: (*, 3)
    #>   • input_names:
    #>       ─ Feature (4): Sepal (length), Sepal (width), Petal (length), Petal
    #>       (width)
    #>   • output_names:
    #>       ─ Output node/Class (3): Setosa, Versicolor, Virginica
    #>   • model_as_list: not included
    #>   • model (class ConvertedModel):
    #>     1. Dense_Layer: input_dim: (*, 4), output_dim: (*, 30)
    #>     2. Skipping_Layer: input_dim: (*, 30), output_dim: (*, 30)
    #>     3. Dense_Layer: input_dim: (*, 30), output_dim: (*, 10)
    #>     4. Dense_Layer: input_dim: (*, 10), output_dim: (*, 3)
    #>
    #> ────────────────────────────────────────────────────────────────────────────────

## Step 2: Apply methods

Now we can apply the implemented methods to our trained model. Although these methods are different, they are called the same way in innsight. Essential arguments are the converter object (`converter`) and the data (`data`) to which the method is to be applied. In addition to the necessary and method-specific arguments, the following other arguments can be set for each (local) method:

- `channels_first`: There are, basically, two data formats for image and signal data, having the channels at the last position or directly after the batch axis. To be able to handle both formats, the format of the passed data can be specified with this argument. In this example, it is unused because we have tabular data.

- `output_idx`: These indices specify the output nodes (or classes) for which the method is to be applied. By default, the result for the first ten classes is calculated for efficiency reasons. However, if you want to examine several specific classes simultaneously, you must specify the corresponding indices with this argument.

- `ignore_last_act`: Often it makes more sense to ignore the last activation function to get better results. This is especially true for classification problems with softmax or sigmoid as the last activation.

For all possible and more detailed information on the arguments, see the detailed explanation. In the following, we apply our trained model to different methods provided in the package:

- Gradient without last activation

      grad_no_softmax <- run_grad(converter, x, ignore_last_act = TRUE)

- Gradient with last activation

      grad_softmax <- run_grad(converter, x, ignore_last_act = FALSE)

- LRP with \(\varepsilon\)-rule (\(\varepsilon = 0.01\))

  We can also set the method-specific arguments, such as the LRP rule and its associated parameter:

      lrp_eps <- run_lrp(converter, x, rule_name = "epsilon", rule_param = 0.01)

- DeepLift with mean as reference value

      x_ref <- x$mean(1, keepdim = TRUE) # ref value needs the shape (1,4)
      deeplift_mean <- run_deeplift(converter, x, x_ref = x_ref)

Similar to the instances of the `Converter` class, the default `print()` function for R6 classes was also overridden for each method so that all important contents of the corresponding method are displayed:

    deeplift_mean
    #>
    #> ── Method DeepLift (innsight) ──────────────────────────────────────────────────
    #> Fields (method-specific):
    #>   • rule_name: 'rescale'
    #>   • winner_takes_all: TRUE
    #>   • x_ref: mean: -0.102613838389516 (q1: -0.124814866110682, q3:
    #>   -0.0791879296302795)
    #> Fields (other):
    #>   • output_idx: 1, 2, 3 (→ corresponding labels: 'Setosa', 'Versicolor',
    #>   'Virginica')
    #>   • ignore_last_act: TRUE
    #>   • channels_first: TRUE
    #>   • dtype: 'float'
    #>
    #> ── Result (result) ──
    #>
    #>   ─ Shape: (150, 4, 3)
    #>   ─ Range: min: -6.85093, median: -0.060229, max: 10.6358
    #>   ─ Number of NaN values: 0
    #>
    #> ────────────────────────────────────────────────────────────────────────────────

Afterward, the results can be retrieved either with the class method `method$get_result()` or the equivalent S3 function `get_result()`. With the argument `type`, it is also possible to select whether the results are returned as `array`, `data.frame` or `torch_tensor`:

    # Get result as a `data.frame` using the class method
    head(grad_no_softmax$get_result(type = "data.frame"), 5)
    #>     data model_input model_output        feature output_node       value      pred
    #> 1 data_1     Input_1     Output_1 Sepal (length)      Setosa  0.00574851 0.9999999
    #> 2 data_2     Input_1     Output_1 Sepal (length)      Setosa -0.11795358 0.9999995
    #> 3 data_3     Input_1     Output_1 Sepal (length)      Setosa  0.00574851 0.9999999
    #> 4 data_4     Input_1     Output_1 Sepal (length)      Setosa -0.11795358 0.9999996
    #> 5 data_5     Input_1     Output_1 Sepal (length)      Setosa  0.00574851 1.0000000
    #>   decomp_sum decomp_goal input_dimension
    #> 1  -8.772927    11.77154               1
    #> 2  -8.811043    10.56666               1
    #> 3  -8.772927    11.26146               1
    #> 4  -8.811043    10.64038               1
    #> 5  -8.772927    12.00486               1

    # Get result as `array` (default) using the generic S3 function
    str(get_result(grad_no_softmax))
    #>  num [1:150, 1:4, 1:3] 0.00575 -0.11795 0.00575 -0.11795 0.00575 ...
    #>  - attr(*, "dimnames")=List of 3
    #>   ..$ : NULL
    #>   ..$ : chr [1:4] "Sepal (length)" "Sepal (width)" "Petal (length)" "Petal (width)"
    #>   ..$ : chr [1:3] "Setosa" "Versicolor" "Virginica"

## Step 3: Visualization

The package innsight provides two ways to visualize the results of a method, namely as `innsight_ggplot2` or `innsight_plotly` object. Both are S4 classes to combine multiple plots nicely and to be able to make visual modifications or adjustments to the selection of plots even after the object has been created. The first class is based on ggplot2 and behaves partly like an ordinary ggplot2 object. Whereas the other one is based on the plotly package and creates an interactive graph with more detailed information about each variable. For more information on the S4 classes `innsight_ggplot` and `innsight_plotly` see the in-depth vignette or the respective R documentation (`?innsight_ggplot2` or `?innsight_plotly`).

For each of these classes and thus, of course, also for each method, there are two plot functions:

- `plot()` shows only individual data points and
- `plot_global()` visualizes summaries of multiple data points using summary statistics (you can also use the alias `boxplot()` for tabular and signal data).

#### Plot individual results

The function `plot()` is implemented for each of the available methods. You can select your desired data points and output nodes/classes with the `data_idx` and `output_idx` arguments, respectively. To switch between a ggplot2 and plotly based plot, you can use the logical `as_plotly` parameter, but this requires a successful installation of the plotly package.

> 📝 Note
> Of course, only results of output nodes/classes to which the method has been applied can be plotted, i.e., the indices in the `output_idx` argument must be a subset of the argument with the same name when calling the method in Step 2.

##### ggplot2-based plot

Despite being an object of the class `innsight_ggplot2`, it can be treated like a normal ggplot2 object, i.e., geoms, scales and themes can be added and modified.

    # Show data point 1 and 111 for output node 1 (Setosa) and 2 (Versicolor)
    plot(grad_no_softmax, data_idx = c(1, 111), output_idx = c(1, 2)) +
      ggplot2::theme_bw()

##### plotly-based plot

    # Show data point 1 for output node 1 (Setosa) and 2 (Versicolor)
    plot(deeplift_mean, data_idx = 1, output_idx = c(1, 2), as_plotly = TRUE)

#### Plot summarized results

The S3 function `plot_global()` (or `boxplot()` for tabular and signal data) is implemented for each of the available local methods. You can select your desired data points (default is `'all'`) and output nodes/classes with the `data_idx` and `output_idx` arguments, respectively. To switch between a ggplot2 and plotly based plot, you can use the logical `as_plotly` parameter, but this requires a successful installation of the plotly package. In addition, you can use `ref_data_idx` to select a single data point that will be visualized in red as a reference value, and `preprocess_FUN` to select a function that will be applied to all relevances in advance (e.g., the absolute value).

> 📝 Note
> Of course, only results of output nodes/classes to which the method has been applied can be plotted, i.e., the indices in the `output_idx` argument must be subset of the argument with the same name when calling the method in Step 2.

##### ggplot2-based plot

Despite being an object of the class `innsight_ggplot2`, it can be treated like a normal ggplot2 object, i.e. geoms, scales and themes can be added and modified.

    # Summarized results for output node 1 (Setosa) and 2 (Versicolor) and
    # reference value of index 3
    boxplot(grad_no_softmax, output_idx = c(1, 2), ref_data_idx = 3, preprocess_FUN = abs) +
      ggplot2::theme_bw()

##### plotly-based plot

    # Show boxplot only for instances of class setosa for output node 1 (Setosa)
    # and 2 (Versicolor)
    boxplot(lrp_eps, data_idx = 1:50, output_idx = c(1, 2), as_plotly = TRUE)