# dnaGrinder: a lightweight and high-capacity genomic foundation model

arXiv: https://arxiv.org/abs/2409.15697 · HTML: https://mlsanity.com/paper/2409.15697/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 23 of its 38 references that are in the map.
- First posted on arXiv 24 Sep 2024.

## Builds on (most cited first, 23 of 23)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [ALBERT: A Lite BERT for Self-supervised Learning of Language Representations](https://mlsanity.com/paper/1909.11942/) (2019)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing](https://mlsanity.com/paper/1808.06226/) (2018)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [Language Modeling with Gated Convolutional Networks](https://mlsanity.com/paper/1612.08083/) (2016)
- [How to Fine-Tune BERT for Text Classification?](https://mlsanity.com/paper/1905.05583/) (2019)
- [Effective Long-Context Scaling of Foundation Models](https://mlsanity.com/paper/2309.16039/) (2023)
- [LongNet: Scaling Transformers to 1,000,000,000 Tokens](https://mlsanity.com/paper/2307.02486/) (2023)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [Shortformer: Better Language Modeling using Shorter Inputs](https://mlsanity.com/paper/2012.15832/) (2020)
- [The Stability-Efficiency Dilemma: Investigating Sequence Length Warmup for Training GPT Models](https://mlsanity.com/paper/2108.06084/) (2021)
- [GenBench: A Benchmarking Suite for Systematic Evaluation of Genomic Foundation Models](https://mlsanity.com/paper/2406.01627/) (2024)
- [ChatCell: Facilitating Single-Cell Analysis with Natural Language](https://mlsanity.com/paper/2402.08303/) (2024)

## Built on by (most cited first, 1 of 1)

- [A Deep Learning Pipeline for Epilepsy Genomic Analysis Using GPT-2 XL and NVIDIA H100](https://mlsanity.com/paper/2510.00392/) (2025)

## Abstract (arXiv)

The task of understanding and interpreting the complex information encoded within genomic sequences remains a grand challenge in biological research and clinical applications. In this context, recent advancements in large language model research have led to the development of both encoder-only and decoder-only foundation models designed to decode intricate information in DNA sequences. However, several issues persist, particularly regarding the efficient management of long-range dependencies inherent in genomic sequences, the effective representation of nucleotide variations, and the considerable computational costs associated with large model architectures and extensive pretraining datasets. Current genomic foundation models often face a critical tradeoff: smaller models with mediocre performance versus large models with improved performance. To address these challenges, we introduce dnaGrinder, a unique and efficient genomic foundation model. dnaGrinder excels at managing long-range dependencies within genomic sequences while minimizing computational costs without compromising performance. It achieves results that are not just comparable but often superior to leading DNA models such as Nucleotide Transformer and DNABERT-2. Furthermore, dnaGrinder is designed for easy fine-tuning on workstation-grade GPUs, accommodating input lengths exceeding 17,000 tokens. On a single high-performance GPU, it supports sequences longer than 140,000 tokens, making it a highly efficient and accessible tool for both basic biological research and clinical applications.