mlr3keras

An extension for mlr3 to enable using various keras models as learners.

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Status

mlr3keras is in very early stages, and currently under development. Functionality is therefore experimental and we do not guarantee correctness, safety or stability. It builds on top of the (awesome) R packages reticulate, tensorflow and keras. Comments, discussion and issues/bug reports and PR’s are highly appreciated.

If you want to contribute, please propose / discuss adding functionality in an issue in order to avoid unnecessary or duplicate work.

Installation:

# Install from GitHub
remotes::install_github("mlr-org/mlr3keras")

Troubleshooting:

If you encounter problems using the correct python versions, see here.

mlr3keras is currently tested and works using the python packages keras (2.4) and tensorflow (2.3.1).

Setting up mlr3keras with anaconda

One possible workflow for working with mlr3keras is described below. While (1.) and (2.) are one-time setup steps, (3.) now has to be called everytime mlr3keras is loaded.

Note from the author: The workflow described below is something that works for me personally, as I have to switch between versions and projects often. It is described for the user, as I personally find it useful. It assumes, the R packages keras, tensorflow and reticulate are installed. In order to load mlr3keras I now have to execute an additional one additional line (see 3.), but version management is heavily simplified. Note, that this seems to work on Linux but has not been extensively tested on other systems.

  1. Install Miniconda (if not already installed)
# Execute and restart R afterwards
reticulate::install_miniconda()

NOTE: It might make sense, to set the RETICULATE_PYTHON environment variable to your miniconda / Anaconda installation path as explained here.

  1. Install a mlr3keras conda environment together with keras and tensorflow 
# Execute and restart R afterwards
reticulate::conda_create(
  envname = "mlr3keras",
  packages = c("pandas", "python=3.8")
)
keras::install_keras("conda", tensorflow="2.3.1", envname="mlr3keras")
  1. Loading the mlr3keras package
reticulate::use_condaenv("mlr3keras")
library(mlr3keras)
  1. Installing a new package
conda_install("mlr3keras", packages = "tabnet", pip = TRUE)

Usage

mlr3keras currently exposes three Learners for regression and classification respectively.

Learner Details Reference
regr/classif.keras A generic wrapper that allows to supply a custom keras architecture as a hyperparameter. –
regr/classif.kerasFF A fully-connected feed-forward Neural Network with entity embeddings Guo et al. (2016) Entity Embeddings for Categorical Variables
regr/classif.tabNet An implementation of TabNet Sercan, A. and Pfister, T. (2019): TabNet
regr/classif.smlp Shaped MLP inspired by Configuration Space 1* Zimmer, L. et al. (2020): Auto PyTorch Tabular
regr/classif.smlp2 Shaped MLP inspired by Configuration Space 2* Zimmer, L. et al. (2020): Auto PyTorch Tabular
regr/classif.deep_wide Deep and Wide Architecture inspired by Ericson et al., 2020 AutoGluon-Tabular: Robust and Accurate AutoML for Structured Data
classif.kerascnn Various CNN Applications via Transfer-learning Uses keras::application_XXX (e.g. mobilenet)
  • with some slight changes, namely no Shake-Shake, Shake-Drop, Mixup Training. and added Entity Embeddings for categorical variables.

Learners can be used for training and prediction as follows:

  library("mlr3")
  # Instantiate Learner
  lrn = LearnerClassifKerasFF$new()

  # Set Learner Hyperparams
  lrn$param_set$values$epochs = 50
  lrn$param_set$values$layer_units = 12

  # Train and Predict
  lrn$train(tsk("iris"))
  lrn$predict(tsk("iris"))

The vignette has some examples on how to use some of the functionality introduces in mlr3keras.

Design

This package’s purpose for now is to understand the design-decisions required to make keras  tensorflow work with mlr3 and flexible enough for users.

Several design decisions are not made yet, so input is highly appreciated.

Current Design and Scope

Design

The goal of the project is to expose keras models as mlr3 learners. A keras model in this context should be understood as the combination of

  • model architecture:

    keras_model_sequential() %>%
... %>%
layer_activation(...)

  • training procedure:

    model$compile(...)
model$fit(...)

  • All hyperparameters that control the steps:

    • architecture hyperparams (dropout, neurons / filters, activation functions, …)
    • optimizer choice and hyperparams (learning rate, …)
    • fit hyperparams (epochs, callbacks, …)

Some important caveats:

  • Architectures are often data-dependent, e.g. require correct number of input / output neurons. As a result, in mlr3keras, the architecture is a function of the incoming training data. In mlr3keras, this is abstracted via KerasArchitecture: See KerasArchitectureFF for an example. This Architecture is initialized with a build_arch_fun which given the task and a set of hyperparameters constructs & compiles the architecture.

  • Depending on the architecture, different data-formats are required for x (features) and y (target) (e.g. a matrix for a feed-forward NN, a list of features if we use embeddings, …) To accomodate this, each architecture comes with an x_transform and a y_transform method, which are called on the features and target respectively before passing those on to fit(...).

Scope The current scope for mlr3keras is to support deep learning on different kinds of tabular data. In the future, we aim to extend this to other data modalities, but as of yet, work on this has not started.

In an initial version, we aim to support two types of models:

  • Pre-defined architectures: In many cases, we just want to try out and tune architectures that have already been successfully used in other contexts (LeNet, ResNet, TabNet). We aim to implement / make those accessible for simplified tuning and fast iteration. Example: LearnerClassifTabNet$new().

  • Fully custom architectures: Some operations require completely new architectures. We aim to allow users to supply custom architectures and tune hyperparameters of those. This can be done via KerasArchitectureCustom by providing a function that builds the model given a Task and a set of hyperparameters.

All architectures can be parametrized and tuned using the mlr3tuning library.

Open Issues:

  • Custom Optimizers / Losses / Activations
    • As keras and it’s ecosystem is constantly growing, the interface needs to be flexible and highly adaptable. We try to solve this using a reflections mechanism: keras_reflections that stores possible values for exchangable parts of an architecture. New methods can now be added by adding to the respective reflection.
  • More data types:
    • Currently mlr3 does not support features such as images / audio / …, therefore mlr3keras is not yet applicable for image classification and other related tasks. We aim to make this possible in the future! A minor road block here is to find a way to not read images to memory in R but directly load from disk to avoid additional overhead.
    • It is unclear how efficient data preprocessing for images etc. can be paired with mlr3pipelines, yet we hope this can be solved at some point in the future.
  • More task types:
    • Currently mlr3 focusses heavily on standard classification and regression. Many Deep Learning tasks require slight extensions (image annotation, bounding boxes, object detection, … ) of those existing data containers (Task, Prediction, …).

Installation

remotes::install_github("mlr-org/mlr3keras")

Resources