# Self-Distillation Improves DNA Sequence Inference

arXiv: https://arxiv.org/abs/2405.08538 · HTML: https://mlsanity.com/paper/2405.08538/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Knowledge distillation for LLMs, one of 12 directions in Knowledge distillation.
- Builds on 19 of its 34 references that are in the map.
- First posted on arXiv 14 May 2024.

## Placed in

- Knowledge distillation / [Knowledge distillation for LLMs](https://mlsanity.com/distill/knowledge-distillation-for-llms/)

## Builds on (most cited first, 19 of 19)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Distilling the Knowledge in a Neural Network](https://mlsanity.com/paper/1503.02531/) (2015)
- [DINOv2: Learning Robust Visual Features without Supervision](https://mlsanity.com/paper/2304.07193/) (2023)
- [Emerging Properties in Self-Supervised Vision Transformers](https://mlsanity.com/paper/2104.14294/) (2021)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [Unsupervised Learning of Visual Features by Contrasting Cluster Assignments](https://mlsanity.com/paper/2006.09882/) (2020)
- [Improved Baselines with Momentum Contrastive Learning](https://mlsanity.com/paper/2003.04297/) (2020)
- [iBOT: Image BERT Pre-Training with Online Tokenizer](https://mlsanity.com/paper/2111.07832/) (2021)
- [Contrastive Representation Distillation](https://mlsanity.com/paper/1910.10699/) (2019)
- [Hyena Hierarchy: Towards Larger Convolutional Language Models](https://mlsanity.com/paper/2302.10866/) (2023)
- [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)
- [Contrastive Learning of Musical Representations](https://mlsanity.com/paper/2103.09410/) (2021)
- [Sequence-to-Sequence Contrastive Learning for Text Recognition](https://mlsanity.com/paper/2012.10873/) (2020)
- [ChordMixer: A Scalable Neural Attention Model for Sequences with Different Lengths](https://mlsanity.com/paper/2206.05852/) (2022)
- [Paramixer: Parameterizing Mixing Links in Sparse Factors Works Better than Dot-Product Self-Attention](https://mlsanity.com/paper/2204.10670/) (2022)

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

- [Agentomics-ML: Autonomous Machine Learning Experimentation Agent for Genomic and Transcriptomic Data](https://mlsanity.com/paper/2506.05542/) (2025)

## Abstract (arXiv)

Self-supervised pretraining (SSP) has been recognized as a method to enhance prediction accuracy in various downstream tasks. However, its efficacy for DNA sequences remains somewhat constrained. This limitation stems primarily from the fact that most existing SSP approaches in genomics focus on masked language modeling of individual sequences, neglecting the crucial aspect of encoding statistics across multiple sequences. To overcome this challenge, we introduce an innovative deep neural network model, which incorporates collaborative learning between a `student' and a `teacher' subnetwork. In this model, the student subnetwork employs masked learning on nucleotides and progressively adapts its parameters to the teacher subnetwork through an exponential moving average approach. Concurrently, both subnetworks engage in contrastive learning, deriving insights from two augmented representations of the input sequences. This self-distillation process enables our model to effectively assimilate both contextual information from individual sequences and distributional data across the sequence population. We validated our approach with preliminary pretraining using the human reference genome, followed by applying it to 20 downstream inference tasks. The empirical results from these experiments demonstrate that our novel method significantly boosts inference performance across the majority of these tasks. Our code is available at https://github.com/wiedersehne/FinDNA.