# BBOmix: A Tabular Benchmark for Hyperparameter Optimization of Unsupervised Biological Representation Learning

arXiv: https://arxiv.org/abs/2606.05139 · HTML: https://mlsanity.com/paper/2606.05139/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 14 of its 50 references that are in the map.
- First posted on arXiv 3 Jun 2026.

## Builds on (most cited first, 14 of 14)

- [Challenging Common Assumptions in the Unsupervised Learning of Disentangled Representations](https://mlsanity.com/paper/1811.12359/) (2018)
- [Regularized Evolution for Image Classifier Architecture Search](https://mlsanity.com/paper/1802.01548/) (2018)
- [Hyperband: A Novel Bandit-Based Approach to Hyperparameter Optimization](https://mlsanity.com/paper/1603.06560/) (2016)
- [BOHB: Robust and Efficient Hyperparameter Optimization at Scale](https://mlsanity.com/paper/1807.01774/) (2018)
- [NAS-Bench-201: Extending the Scope of Reproducible Neural Architecture Search](https://mlsanity.com/paper/2001.00326/) (2020)
- [All Models are Wrong, but Many are Useful: Learning a Variable's Importance by Studying an Entire Class of Prediction Models Simultaneously](https://mlsanity.com/paper/1801.01489/) (2018)
- [Non-stochastic Best Arm Identification and Hyperparameter Optimization](https://mlsanity.com/paper/1502.07943/) (2015)
- [A System for Massively Parallel Hyperparameter Tuning](https://mlsanity.com/paper/1810.05934/) (2018)
- [Hyperparameter Optimization: Foundations, Algorithms, Best Practices and Open Challenges](https://mlsanity.com/paper/2107.05847/) (2021)
- [Tabular Benchmarks for Joint Architecture and Hyperparameter Optimization](https://mlsanity.com/paper/1905.04970/) (2019)
- [Learning search spaces for Bayesian optimization: Another view of hyperparameter transfer learning](https://mlsanity.com/paper/1909.12552/) (2019)
- [TabRepo: A Large Scale Repository of Tabular Model Evaluations and its AutoML Applications](https://mlsanity.com/paper/2311.02971/) (2023)
- [Optimizing Hyperparameters with Conformal Quantile Regression](https://mlsanity.com/paper/2305.03623/) (2023)
- [scSSL-Bench: Benchmarking Self-Supervised Learning for Single-Cell Data](https://mlsanity.com/paper/2506.10031/) (2025)

## Abstract (arXiv)

The rapid advancement of high-throughput sequencing has led to large, high-dimensional omics datasets. Deep unsupervised learning architectures, particularly Autoencoders (AEs), are increasingly used for dimensionality reduction and representation learning in this domain. However, AEs are highly sensitive to architectural choices and hyperparameters, and unsupervised optimization typically relies on reconstruction loss, which may be a poor proxy for downstream utility. Exhaustive hyperparameter optimization (HPO) is computationally expensive, leading researchers to frequently rely on suboptimal default configurations. To democratize access to large-scale unsupervised HPO research, we introduce BBOmix, the first open-source tabular benchmark for unsupervised representation learning on real-world biological data. Our benchmark includes 105,000 evaluations across four AE architectures and seven multi-omics modalities from the TCGA and SCHC datasets. We quantify the correlation between reconstruction loss and downstream task performance and provide an extensive evaluation of state-of-the-art single-fidelity, multi-fidelity, and transfer learning HPO methods, establishing a rigorous baseline for future research in unsupervised biological representation learning.