# BeeTLe: An Imbalance-Aware Deep Sequence Model for Linear B-Cell Epitope Prediction and Classification with Logit-Adjusted Losses

arXiv: https://arxiv.org/abs/2309.02071 · HTML: https://mlsanity.com/paper/2309.02071/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 19 of its 55 references that are in the map.
- First posted on arXiv 5 Sep 2023.

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

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Deep Residual Learning for Image Recognition](https://mlsanity.com/paper/1512.03385/) (2015)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift](https://mlsanity.com/paper/1502.03167/) (2015)
- [Layer Normalization](https://mlsanity.com/paper/1607.06450/) (2016)
- [XGBoost: A Scalable Tree Boosting System](https://mlsanity.com/paper/1603.02754/) (2016)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour](https://mlsanity.com/paper/1706.02677/) (2017)
- [Class-Balanced Loss Based on Effective Number of Samples](https://mlsanity.com/paper/1901.05555/) (2019)
- [On the Convergence of Adam and Beyond](https://mlsanity.com/paper/1904.09237/) (2019)
- [Decoupling Representation and Classifier for Long-Tailed Recognition](https://mlsanity.com/paper/1910.09217/) (2019)
- [Long-tail learning via logit adjustment](https://mlsanity.com/paper/2007.07314/) (2020)
- [Generating Sequences With Recurrent Neural Networks](https://mlsanity.com/paper/1308.0850/) (2013)
- [Long Short-Term Memory-Networks for Machine Reading](https://mlsanity.com/paper/1601.06733/) (2016)
- [Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity](https://mlsanity.com/paper/2107.10670/) (2021)
- [Modern Hopfield Networks and Attention for Immune Repertoire Classification](https://mlsanity.com/paper/2007.13505/) (2020)

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

- [A Survey on Graph Neural Networks for Fraud Detection in Ride Hailing Platforms](https://mlsanity.com/paper/2512.23777/) (2025)

## Abstract (arXiv)

The process of identifying and characterizing B-cell epitopes, which are the portions of antigens recognized by antibodies, is important for our understanding of the immune system, and for many applications including vaccine development, therapeutics, and diagnostics. Computational epitope prediction is challenging yet rewarding as it significantly reduces the time and cost of laboratory work. Most of the existing tools do not have satisfactory performance and only discriminate epitopes from non-epitopes. This paper presents a new deep learning-based multi-task framework for linear B-cell epitope prediction as well as antibody type-specific epitope classification. Specifically, a sequenced-based neural network model using recurrent layers and Transformer blocks is developed. We propose an amino acid encoding method based on eigen decomposition to help the model learn the representations of epitopes. We introduce modifications to standard cross-entropy loss functions by extending a logit adjustment technique to cope with the class imbalance. Experimental results on data curated from the largest public epitope database demonstrate the validity of the proposed methods and the superior performance compared to competing ones.