# PETRA: Pretrained Evolutionary Transformer for SARS-CoV-2 Mutation Prediction

arXiv: https://arxiv.org/abs/2511.03976 · HTML: https://mlsanity.com/paper/2511.03976/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 38 references that are in the map.
- First posted on arXiv 6 Nov 2025.

## Builds on (most cited first, 6 of 6)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Megatron-LM: Training Multi-Billion Parameter Language Models Using Model Parallelism](https://mlsanity.com/paper/1909.08053/) (2019)

## Abstract (arXiv)

Since its emergence, SARS-CoV-2 has demonstrated a rapid and unpredictable evolutionary trajectory, characterized by the continual emergence of immune-evasive variants. This poses persistent challenges to public health and vaccine development. While large-scale generative pre-trained transformers (GPTs) have revolutionized the modeling of sequential data, their direct applications to noisy viral genomic sequences are limited. In this paper, we introduce PETRA(Pretrained Evolutionary TRAnsformer), a novel transformer approach based on evolutionary trajectories derived from phylogenetic trees rather than raw RNA sequences. This method effectively mitigates sequencing noise and captures the hierarchical structure of viral evolution. With a weighted training framework to address substantial geographical and temporal imbalances in global sequence data, PETRA excels in predicting future SARS-CoV-2 mutations, achieving a weighted recall@1 of 9.45% for nucleotide mutations and 17.10% for spike amino-acid mutations, compared to 0.49% and 6.64% respectively for the best baseline. PETRA also demonstrates its ability to aid in the real-time mutation prediction of major clades like 24F(XEC) and 25A(LP.8.1). The code is open sourced on https://github.com/xz-keg/PETra