# EvoVGM: a Deep Variational Generative Model for Evolutionary Parameter Estimation

arXiv: https://arxiv.org/abs/2205.13034 · HTML: https://mlsanity.com/paper/2205.13034/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 38 references that are in the map.
- First posted on arXiv 25 May 2022.

## Builds on (most cited first, 5 of 5)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Variational Inference: A Review for Statisticians](https://mlsanity.com/paper/1601.00670/) (2016)
- [Improved Variational Bayesian Phylogenetic Inference with Normalizing Flows](https://mlsanity.com/paper/2012.00459/) (2020)
- [Variational auto-encoding of protein sequences](https://mlsanity.com/paper/1712.03346/) (2017)

## Abstract (arXiv)

Most evolutionary-oriented deep generative models do not explicitly consider the underlying evolutionary dynamics of biological sequences as it is performed within the Bayesian phylogenetic inference framework. In this study, we propose a method for a deep variational Bayesian generative model (EvoVGM) that jointly approximates the true posterior of local evolutionary parameters and generates sequence alignments. Moreover, it is instantiated and tuned for continuous-time Markov chain substitution models such as JC69, K80 and GTR. We train the model via a low-variance stochastic estimator and a gradient ascent algorithm. Here, we analyze the consistency and effectiveness of EvoVGM on synthetic sequence alignments simulated with several evolutionary scenarios and different sizes. Finally, we highlight the robustness of a fine-tuned EvoVGM model using a sequence alignment of gene S of coronaviruses.