# Rethinking Genomic Modeling Through Optical Character Recognition

arXiv: https://arxiv.org/abs/2602.02014 · HTML: https://mlsanity.com/paper/2602.02014/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 20 of its 52 references that are in the map.
- First posted on arXiv 2 Feb 2026.

## Builds on (most cited first, 20 of 20)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [DeepSeek-V2: A Strong, Economical, and Efficient Mixture-of-Experts Language Model](https://mlsanity.com/paper/2405.04434/) (2024)
- [LayoutLM: Pre-training of Text and Layout for Document Image Understanding](https://mlsanity.com/paper/1912.13318/) (2019)
- [LayoutLMv3: Pre-training for Document AI with Unified Text and Image Masking](https://mlsanity.com/paper/2204.08387/) (2022)
- [OCR-free Document Understanding Transformer](https://mlsanity.com/paper/2111.15664/) (2021)
- [Pix2Struct: Screenshot Parsing as Pretraining for Visual Language Understanding](https://mlsanity.com/paper/2210.03347/) (2022)
- [Nougat: Neural Optical Understanding for Academic Documents](https://mlsanity.com/paper/2308.13418/) (2023)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [DeepSeek-OCR: Contexts Optical Compression](https://mlsanity.com/paper/2510.18234/) (2025)
- [MEGABYTE: Predicting Million-byte Sequences with Multiscale Transformers](https://mlsanity.com/paper/2305.07185/) (2023)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)
- [LayoutLLM: Layout Instruction Tuning with Large Language Models for Document Understanding](https://mlsanity.com/paper/2404.05225/) (2024)
- [Dolphin: Document Image Parsing via Heterogeneous Anchor Prompting](https://mlsanity.com/paper/2505.14059/) (2025)
- [Glyph: Scaling Context Windows via Visual-Text Compression](https://mlsanity.com/paper/2510.17800/) (2025)
- [BEND: Benchmarking DNA Language Models on biologically meaningful tasks](https://mlsanity.com/paper/2311.12570/) (2023)
- [GENERator: A Long-Context Generative Genomic Foundation Model](https://mlsanity.com/paper/2502.07272/) (2025)
- [HunyuanOCR Technical Report](https://mlsanity.com/paper/2511.19575/) (2025)
- [JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model](https://mlsanity.com/paper/2505.17257/) (2025)

## Abstract (arXiv)

Recent genomic foundation models largely adopt large language model architectures that treat DNA as a one-dimensional token sequence. However, exhaustive sequential reading is structurally misaligned with sparse and discontinuous genomic semantics, leading to wasted computation on low-information background and preventing understanding-driven compression for long contexts. Here, we present OpticalDNA, a vision-based framework that reframes genomic modeling as Optical Character Recognition (OCR)-style document understanding. OpticalDNA renders DNA into structured visual layouts and trains an OCR-capable vision--language model with a visual DNA encoder and a document decoder, where the encoder produces compact, reconstructible visual tokens for high-fidelity compression. Building on this representation, OpticalDNA defines prompt-conditioned objectives over core genomic primitives-reading, region grounding, subsequence retrieval, and masked span completion-thereby learning layout-aware DNA representations that retain fine-grained genomic information under a reduced effective token budget. Across diverse genomic benchmarks, OpticalDNA consistently outperforms recent baselines; on sequences up to 450k bases, it achieves the best overall performance with nearly 20× fewer effective tokens, and surpasses models with up to 985× more activated parameters while tuning only 256k trainable parameters.