# Deep Generative Models for Discrete Genotype Simulation

arXiv: https://arxiv.org/abs/2508.09212 · HTML: https://mlsanity.com/paper/2508.09212/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 13 of its 61 references that are in the map.
- First posted on arXiv 11 Aug 2025.

## Builds on (most cited first, 13 of 13)

- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Very Deep Convolutional Networks for Large-Scale Image Recognition](https://mlsanity.com/paper/1409.1556/) (2014)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [Improved Training of Wasserstein GANs](https://mlsanity.com/paper/1704.00028/) (2017)
- [Conditional Generative Adversarial Nets](https://mlsanity.com/paper/1411.1784/) (2014)
- [An Introduction to Variational Autoencoders](https://mlsanity.com/paper/1906.02691/) (2019)
- [Improved Precision and Recall Metric for Assessing Generative Models](https://mlsanity.com/paper/1904.06991/) (2019)
- [Seeing What a GAN Cannot Generate](https://mlsanity.com/paper/1910.11626/) (2019)
- [GANS for Sequences of Discrete Elements with the Gumbel-softmax Distribution](https://mlsanity.com/paper/1611.04051/) (2016)
- [Alleviating Matthew Effect of Offline Reinforcement Learning in Interactive Recommendation](https://mlsanity.com/paper/2307.04571/) (2023)
- [Latent Diffusion Model for DNA Sequence Generation](https://mlsanity.com/paper/2310.06150/) (2023)
- [Class-Conditional VAE-GAN for Local-Ancestry Simulation](https://mlsanity.com/paper/1911.13220/) (2019)

## Abstract (arXiv)

Deep generative models open new avenues for simulating realistic genomic data while preserving privacy and addressing data accessibility constraints. While previous studies have primarily focused on generating gene expression or haplotype data, this study explores generating genotype data in both unconditioned and phenotype-conditioned settings, which is inherently more challenging due to the discrete nature of genotype data. In this work, we developed and evaluated commonly used generative models, including Variational Autoencoders (VAEs), Diffusion Models, and Generative Adversarial Networks (GANs), and proposed adaptation tailored to discrete genotype data. We conducted extensive experiments on large-scale datasets, including all chromosomes from cow and multiple chromosomes from human. Model performance was assessed using a well-established set of metrics drawn from both deep learning and quantitative genetics literature. Our results show that these models can effectively capture genetic patterns and preserve genotype-phenotype association. Our findings provide a comprehensive comparison of these models and offer practical guidelines for future research in genotype simulation. We have made our code publicly available at https://github.com/SihanXXX/DiscreteGenoGen.