# Predicting sub-population specific viral evolution

arXiv: https://arxiv.org/abs/2410.21518 · HTML: https://mlsanity.com/paper/2410.21518/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 8 of its 32 references that are in the map.
- First posted on arXiv 28 Oct 2024.

## Builds on (most cited first, 8 of 8)

- [Score-Based Generative Modeling through Stochastic Differential Equations](https://mlsanity.com/paper/2011.13456/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Neural Ordinary Differential Equations](https://mlsanity.com/paper/1806.07366/) (2018)
- [Sequence to Sequence Learning with Neural Networks](https://mlsanity.com/paper/1409.3215/) (2014)
- [A Continuous Time Framework for Discrete Denoising Models](https://mlsanity.com/paper/2205.14987/) (2022)
- [Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design](https://mlsanity.com/paper/2402.04997/) (2024)
- [Self-conditioned Embedding Diffusion for Text Generation](https://mlsanity.com/paper/2211.04236/) (2022)
- [Mobility Based SIR Model For Pandemics -- With Case Study Of COVID-19](https://mlsanity.com/paper/2004.13015/) (2020)

## Abstract (arXiv)

Forecasting the change in the distribution of viral variants is crucial for therapeutic design and disease surveillance. This task poses significant modeling challenges due to the sharp differences in virus distributions across sub-populations (e.g., countries) and their dynamic interactions. Existing machine learning approaches that model the variant distribution as a whole are incapable of making location-specific predictions and ignore transmissions that shape the viral landscape. In this paper, we propose a sub-population specific protein evolution model, which predicts the time-resolved distributions of viral proteins in different locations. The algorithm explicitly models the transmission rates between sub-populations and learns their interdependence from data. The change in protein distributions across all sub-populations is defined through a linear ordinary differential equation (ODE) parametrized by transmission rates. Solving this ODE yields the likelihood of a given protein occurring in particular sub-populations. Multi-year evaluation on both SARS-CoV-2 and influenza A/H3N2 demonstrates that our model outperforms baselines in accurately predicting distributions of viral proteins across continents and countries. We also find that the transmission rates learned from data are consistent with the transmission pathways discovered by retrospective phylogenetic analysis.