Revisiting Reconstruction Likelihood: Variational Autoencoders for Biological and Biomedical Data Clustering

Background and ObjectiveVariational Autoencoders (VAEs) offer a powerful framework for unsupervised anomaly detection and data clustering, often surpassing traditional methods. A core strength of VAEs lies in their ability to model data distributions probabilistically, enabling robust identification of anomalies and clusters through reconstruction likelihood -- a stochastic metric providing a principled alternative to deterministic error scores. MethodsWe investigated how different VAE architectures, combining reconstruction likelihood with a learnable or data-driven prior, performed in a clustering task on a toy dataset such as MNIST. Results were verified using dimensionality reduction techniques like t-distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP), alongside clustering algorithms such as k-means and Hierarchical Density-Based Spatial Clustering of Applications with Noise (HDBSCAN). ResultsThe VAEs encoder inherently maps data points into a latent space exhibiting discernible cluster structure, as evidenced by alignment with ground truth labels. While dimensionality reduction techniques (both t-SNE and UMAP) facilitated the application of clustering algorithms (k-means and HDBSCAN), these methods were primarily used to visualize and interpret the latent space organization. ConclusionsThis study demonstrates that VAEs effectively cluster data by implicitly encoding assignments in their latent representations. Determining cluster membership from encoder output, combined with reconstruction likelihood using semantic features, offers a principled approach for identifying typical samples and anomalies. Future research should focus on leveraging this inherent clustering capability of VAEs to enhance interpretability and facilitate clinical application.