# SNP2Vec: Scalable Self-Supervised Pre-Training for Genome-Wide Association Study

arXiv: https://arxiv.org/abs/2204.06699 · HTML: https://mlsanity.com/paper/2204.06699/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 57 references that are in the map.
- First posted on arXiv 14 Apr 2022.

## 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)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [BART: Denoising Sequence-to-Sequence Pre-training for Natural Language Generation, Translation, and Comprehension](https://mlsanity.com/paper/1910.13461/) (2019)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [Neural Machine Translation of Rare Words with Subword Units](https://mlsanity.com/paper/1508.07909/) (2015)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing](https://mlsanity.com/paper/1808.06226/) (2018)
- [Big Bird: Transformers for Longer Sequences](https://mlsanity.com/paper/2007.14062/) (2020)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [Aligning Books and Movies: Towards Story-like Visual Explanations by Watching Movies and Reading Books](https://mlsanity.com/paper/1506.06724/) (2015)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [ProGen: Language Modeling for Protein Generation](https://mlsanity.com/paper/2004.03497/) (2020)
- [IndoNLU: Benchmark and Resources for Evaluating Indonesian Natural Language Understanding](https://mlsanity.com/paper/2009.05387/) (2020)
- [Are Multilingual Models Effective in Code-Switching?](https://mlsanity.com/paper/2103.13309/) (2021)
- [AdaptSum: Towards Low-Resource Domain Adaptation for Abstractive Summarization](https://mlsanity.com/paper/2103.11332/) (2021)

## Built on by (most cited first, 5 of 5)

- [High-Dimension Human Value Representation in Large Language Models](https://mlsanity.com/paper/2404.07900/) (2024)
- [CLIBD: Bridging Vision and Genomics for Biodiversity Monitoring at Scale](https://mlsanity.com/paper/2405.17537/) (2024)
- [BMFM-DNA: A SNP-aware DNA foundation model to capture variant effects](https://mlsanity.com/paper/2507.05265/) (2025)
- [Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis](https://mlsanity.com/paper/2507.09378/) (2025)
- [HEMERA: A Human-Explainable Transformer Model for Estimating Lung Cancer Risk using GWAS Data](https://mlsanity.com/paper/2510.07477/) (2025)

## Abstract (arXiv)

Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they focus only on understanding haploid sequences, which hinders their applicability towards understanding genetic variations, also known as single nucleotide polymorphisms (SNPs), which is crucial for genome-wide association study. In this paper, we introduce SNP2Vec, a scalable self-supervised pre-training approach for understanding SNP. We apply SNP2Vec to perform long-sequence genomics modeling, and we evaluate the effectiveness of our approach on predicting Alzheimer's disease risk in a Chinese cohort. Our approach significantly outperforms existing polygenic risk score methods and all other baselines, including the model that is trained entirely with haploid sequences. We release our code and dataset on https://github.com/HLTCHKUST/snp2vec.