# AntigenLM: Structure-Aware DNA Language Modeling for Influenza

arXiv: https://arxiv.org/abs/2602.09067 · HTML: https://mlsanity.com/paper/2602.09067/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 6 of its 51 references that are in the map.
- First posted on arXiv 9 Feb 2026.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [Google's Multilingual Neural Machine Translation System: Enabling Zero-Shot Translation](https://mlsanity.com/paper/1611.04558/) (2016)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [Genomic Language Models: Opportunities and Challenges](https://mlsanity.com/paper/2407.11435/) (2024)
- [VQDNA: Unleashing the Power of Vector Quantization for Multi-Species Genomic Sequence Modeling](https://mlsanity.com/paper/2405.10812/) (2024)

## Abstract (arXiv)

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact, aligned functional units. This structure-aware pretraining enables AntigenLM to capture evolutionary constraints and generalize across tasks. Fine-tuned on time-series hemagglutinin (HA) and neuraminidase (NA) sequences, AntigenLM accurately forecasts future antigenic variants across regions and subtypes, including those unseen during training, outperforming phylogenetic and evolution-based models. It also achieves near-perfect subtype classification. Ablation studies show that disrupting genomic structure through fragmentation or shuffling severely degrades performance, revealing the importance of preserving functional-unit integrity in DNA language modeling. AntigenLM thus provides both a powerful framework for antigen evolution prediction and a general principle for building biologically grounded DNA foundation models.