# Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity

arXiv: https://arxiv.org/abs/2206.11255 · HTML: https://mlsanity.com/paper/2206.11255/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 11 of its 40 references that are in the map.
- First posted on arXiv 17 May 2022.

## Builds on (most cited first, 11 of 11)

- [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)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Bootstrap your own latent: A new approach to self-supervised Learning](https://mlsanity.com/paper/2006.07733/) (2020)
- [Exploring Simple Siamese Representation Learning](https://mlsanity.com/paper/2011.10566/) (2020)
- [Learning deep representations by mutual information estimation and maximization](https://mlsanity.com/paper/1808.06670/) (2018)
- [What Makes for Good Views for Contrastive Learning?](https://mlsanity.com/paper/2005.10243/) (2020)
- [AdCo: Adversarial Contrast for Efficient Learning of Unsupervised Representations from Self-Trained Negative Adversaries](https://mlsanity.com/paper/2011.08435/) (2020)
- [TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks](https://mlsanity.com/paper/2105.03323/) (2021)

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

- [Contrastive learning of T cell receptor representations](https://mlsanity.com/paper/2406.06397/) (2024)
- [A unified cross-attention model for predicting antigen binding specificity to both HLA and TCR molecules](https://mlsanity.com/paper/2405.06653/) (2024)

## Abstract (arXiv)

It has been verified that only a small fraction of the neoantigens presented by MHC class I molecules on the cell surface can elicit T cells. The limitation can be attributed to the binding specificity of T cell receptor (TCR) to peptide-MHC complex (pMHC). Computational prediction of T cell binding to neoantigens is an challenging and unresolved task. In this paper, we propose an attentive-mask contrastive learning model, ATMTCR, for inferring TCR-antigen binding specificity. For each input TCR sequence, we used Transformer encoder to transform it to latent representation, and then masked a proportion of residues guided by attention weights to generate its contrastive view. Pretraining on large-scale TCR CDR3 sequences, we verified that contrastive learning significantly improved the prediction performance of TCR binding to peptide-MHC complex (pMHC). Beyond the detection of important amino acids and their locations in the TCR sequence, our model can also extracted high-order semantic information underlying the TCR-antigen binding specificity. Comparison experiments were conducted on two independent datasets, our method achieved better performance than other existing algorithms. Moreover, we effectively identified important amino acids and their positional preferences through attention weights, which indicated the interpretability of our proposed model.