# Compressed representation of brain genetic transcription

arXiv: https://arxiv.org/abs/2310.16113 · HTML: https://mlsanity.com/paper/2310.16113/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 10 of its 65 references that are in the map.
- First posted on arXiv 24 Oct 2023.

## Builds on (most cited first, 10 of 10)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Fast and Accurate Deep Network Learning by Exponential Linear Units (ELUs)](https://mlsanity.com/paper/1511.07289/) (2015)
- [NVAE: A Deep Hierarchical Variational Autoencoder](https://mlsanity.com/paper/2007.03898/) (2020)
- [Adversarial Variational Bayes: Unifying Variational Autoencoders and Generative Adversarial Networks](https://mlsanity.com/paper/1701.04722/) (2017)
- [NIMFA: A Python Library for Nonnegative Matrix Factorization](https://mlsanity.com/paper/1808.01743/) (2018)
- [AVAE: Adversarial Variational Auto Encoder](https://mlsanity.com/paper/2012.11551/) (2020)
- [Brain tumour genetic network signatures of survival](https://mlsanity.com/paper/2301.06111/) (2023)

## Abstract (arXiv)

The architecture of the brain is too complex to be intuitively surveyable without the use of compressed representations that project its variation into a compact, navigable space. The task is especially challenging with high-dimensional data, such as gene expression, where the joint complexity of anatomical and transcriptional patterns demands maximum compression. Established practice is to use standard principal component analysis (PCA), whose computational felicity is offset by limited expressivity, especially at great compression ratios. Employing whole-brain, voxel-wise Allen Brain Atlas transcription data, here we systematically compare compressed representations based on the most widely supported linear and non-linear methods-PCA, kernel PCA, non-negative matrix factorization (NMF), t-stochastic neighbour embedding (t-SNE), uniform manifold approximation and projection (UMAP), and deep auto-encoding-quantifying reconstruction fidelity, anatomical coherence, and predictive utility with respect to signalling, microstructural, and metabolic targets. We show that deep auto-encoders yield superior representations across all metrics of performance and target domains, supporting their use as the reference standard for representing transcription patterns in the human brain.