# epiGPTope: A machine learning-based epitope generator and classifier

arXiv: https://arxiv.org/abs/2509.03351 · HTML: https://mlsanity.com/paper/2509.03351/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 51 references that are in the map.
- First posted on arXiv 3 Sep 2025.

## 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)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [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)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [Sequence to Sequence Learning with Neural Networks](https://mlsanity.com/paper/1409.3215/) (2014)
- [A Comprehensive Survey on Transfer Learning](https://mlsanity.com/paper/1911.02685/) (2019)
- [CompactifAI: Extreme Compression of Large Language Models using Quantum-Inspired Tensor Networks](https://mlsanity.com/paper/2401.14109/) (2024)
- [LLaMAntino: LLaMA 2 Models for Effective Text Generation in Italian Language](https://mlsanity.com/paper/2312.09993/) (2023)

## Abstract (arXiv)

Epitopes are short antigenic peptide sequences which are recognized by antibodies or immune cell receptors. These are central to the development of immunotherapies, vaccines, and diagnostics. However, the rational design of synthetic epitope libraries is challenging due to the large combinatorial sequence space, 20n combinations for linear epitopes of n amino acids, making screening and testing unfeasible, even with high throughput experimental techniques. In this study, we present a large language model, epiGPTope, pre-trained on protein data and specifically fine-tuned on linear epitopes, which for the first time can directly generate novel epitope-like sequences, which are found to possess statistical properties analogous to the ones of known epitopes. This generative approach can be used to prepare libraries of epitope candidate sequences. We further train statistical classifiers to predict whether an epitope sequence is of bacterial or viral origin, thus narrowing the candidate library and increasing the likelihood of identifying specific epitopes. We propose that such combination of generative and predictive models can be of assistance in epitope discovery. The approach uses only primary amino acid sequences of linear epitopes, bypassing the need for a geometric framework or hand-crafted features of the sequences. By developing a method to create biologically feasible sequences, we anticipate faster and more cost-effective generation and screening of synthetic epitopes, with relevant applications in the development of new biotechnologies.