---
title: "BioMoR Autoencoder and Embeddings"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{BioMoR Autoencoder and Embeddings}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
library(BioMoR)
set.seed(99)
```

This vignette illustrates the intended role of autoencoders within **BioMoR**.

Currently, the autoencoder functionality is implemented as a lightweight stub
that returns placeholder embeddings. This allows users to experiment with the
high-level pipeline without requiring heavy deep-learning dependencies.

```{r, eval=FALSE}
# Example: training a stub autoencoder and obtaining embeddings

data(iris)
feature_cols <- c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width")

ae <- train_autoencoder(iris, feature_cols = feature_cols, epochs = 10)
emb <- get_embeddings(ae, iris, feature_cols = feature_cols)

str(emb)
```
