# Efficient HLA imputation from sequential SNPs data by Transformer

arXiv: https://arxiv.org/abs/2211.06430 · HTML: https://mlsanity.com/paper/2211.06430/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 8 of its 41 references that are in the map.
- First posted on arXiv 11 Nov 2022.

## Builds on (most cited first, 8 of 8)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation](https://mlsanity.com/paper/1406.1078/) (2014)
- [Towards a Human-like Open-Domain Chatbot](https://mlsanity.com/paper/2001.09977/) (2020)
- [Image Classification with Consistent Supporting Evidence](https://mlsanity.com/paper/2111.07048/) (2021)

## Built on by (most cited first, 2 of 2)

- [Tractable Transformers for Flexible Conditional Generation](https://mlsanity.com/paper/2502.07616/) (2025)
- [FastImpute: A Baseline for Open-source, Reference-Free Genotype Imputation Methods -- A Case Study in PRS313](https://mlsanity.com/paper/2407.09355/) (2024)

## Abstract (arXiv)

Human leukocyte antigen (HLA) genes are associated with a variety of diseases, however direct typing of HLA is time and cost consuming. Thus various imputation methods using sequential SNPs data have been proposed based on statistical or deep learning models, e.g. CNN-based model, named DEEP*HLA. However, imputation efficiency is not sufficient for in frequent alleles and a large size of reference panel is required. Here, we developed a Transformer-based model to impute HLA alleles, named "HLA Reliable IMputatioN by Transformer (HLARIMNT)" to take advantage of sequential nature of SNPs data. We validated the performance of HLARIMNT using two different reference panels; Pan-Asian reference panel (n = 530) and Type 1 Diabetes Genetics Consortium (T1DGC) reference panel (n = 5,225), as well as the mixture of those two panels (n = 1,060). HLARIMNT achieved higher accuracy than DEEP*HLA by several indices, especially for infrequent alleles. We also varied the size of data used for training, and HLARIMNT imputed more accurately among any size of training data. These results suggest that Transformer-based model may impute efficiently not only HLA types but also any other gene types from sequential SNPs data.