# Evaluation of Coding Schemes for Transformer-based Gene Sequence Modeling

arXiv: https://arxiv.org/abs/2507.15087 · HTML: https://mlsanity.com/paper/2507.15087/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 18 of its 39 references that are in the map.
- First posted on arXiv 20 Jul 2025.

## Builds on (most cited first, 18 of 18)

- [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)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [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)
- [DeBERTa: Decoding-enhanced BERT with Disentangled Attention](https://mlsanity.com/paper/2006.03654/) (2020)
- [Transformer-XL: Attentive Language Models Beyond a Fixed-Length Context](https://mlsanity.com/paper/1901.02860/) (2019)
- [Reformer: The Efficient Transformer](https://mlsanity.com/paper/2001.04451/) (2020)
- [Train Short, Test Long: Attention with Linear Biases Enables Input Length Extrapolation](https://mlsanity.com/paper/2108.12409/) (2021)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (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)
- [Relative Positional Encoding for Transformers with Linear Complexity](https://mlsanity.com/paper/2105.08399/) (2021)
- [GENERator: A Long-Context Generative Genomic Foundation Model](https://mlsanity.com/paper/2502.07272/) (2025)
- [DNAZEN: Enhanced Gene Sequence Representations via Mixed Granularities of Coding Units](https://mlsanity.com/paper/2505.02206/) (2025)

## Abstract (arXiv)

Currently, many studies view DNA sequences as a special type of language and utilize Transformers to model them. These studies use fixed-length k-mer segmentation and BPE subword tokenization but lack a systematic evaluation to determine which is superior. We compare k-mer segmentation with k=1,3,4,5,6, a 4,096-token BPE vocabulary, and three positional encoding methods-sinusoidal, AliBi, and RoPE. Each configuration is trained from scratch in 3, 6, 12, and 24-layer Transformer encoders and evaluated on GUE benchmark dataset. In general, BPE delivers higher and more stable performance across tasks by compressing frequent motifs into variable-length tokens, reducing sequence length, and improving model generalization. RoPE excels at capturing periodic motifs and extrapolating to long sequences, while AliBi also performs well on tasks driven by local dependencies. In terms of depth, we observe significant gains when increasing layers from 3 to 12, with only marginal improvements or slight overfitting at 24 layers. This study provides practical guidance for designing tokenization and positional encoding in DNA Transformer models.