Epitope Prediction

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1 paper in the last four weeks, with none the four weeks before. 0.0% of all new papers.

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Explainability from Training with Applications to TCR-Epitope Prediction
Sep 28, 2026Jiarui Li, Zixiang Yin, Samuel Landry +2Epitope Prediction Explainability
Department of Computer Science, Tulane University · Department of Biochemistry and Molecular Biology, Tulane University School of Medicine
EpiBench: Can LLMs Understand Epitopes for Antibody Drug Discovery?
Aug 6, 2026Zirui Wang, Jiaqi Wang, Qinghan Wang +4Epitope Prediction Antibody
1Valhalla Technology · 2Zhejiang University
Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction
Aug 2, 2026Chuanliu Fan, Nan Yu, Junjie Wu +1Epitope Prediction Rotary Position Embedding
School of Computer Science and Technology, Soochow University · Institute of Artificial Intelligence, Soochow University
Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design
Jul 22, 2026Xiaoliang Shi, Zichen Wang, Runze Ma +2Antibody Epitope Prediction
Shanghai Jiao Tong University
ABOPD: Antibody CDR Design via On-Policy Distillation
Jul 21, 2026Zhuo Yang, Jiaying He, Jiaqing Xie +5Antibody Protein Design
Shanghai Innovation Institute · Southeast University · Zhejiang University +4
Structure-Regularized Interpretable TCR-Epitope Prediction
Jun 29, 2026Jiarui Li, Zixiang Yin, Yunbei Zhang +4Epitope Prediction Interpretability
Department of Computer Science, Tulane University · Department of Biochemistry and Molecular Biology, Tulane University School of Medicine
Transformer-Based Active Learning for Data-Efficient Vaccine Epitope Selection in PRRS
Jun 27, 2026Aspen Erlandsson Brisebois, Zahed Khatooni, Connor Burbridge +5Epitope Prediction Pool-Based Active Learning
Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada · Engineering Science, Faculty of Applied Science, University of Toronto, Toronto, ON, Canada · Department of Mathematics and Statistics, University of Saskatchewan, Saskatoon, SK, Canada +4
Exploring the Effects of Entanglement on Quantum Machine Learning of Pathogen Epitope-Receptor Binding
Jun 27, 2026Aspen Erlandsson Brisebois, Luis Pablo Gonzalez Dominguez, Shivansi Prajapati +8Quantum Machine Learning Epitope Prediction
Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada · Engineering Science, Faculty of Applied Science, University of Toronto, Toronto, ON, Canada · Department of Mathematics and Statistics, University of Saskatchewan, Saskatoon, SK, Canada +5
Deciphering Fingerprints of 3D Molecular Surfaces for Accurate Epitope Prediction
Jun 22, 2026Fang Wu, Weihao Xuan, Jure Leskovec +2Epitope Prediction Molecular Property Prediction
Stanford University Palo Alto, USA · The University of Tokyo Tokyo, Japan · Amazon AWS Palo Alto, USA
Residue-Level Attributions in Protein Language Models Do Not Recover Allergen Epitopes
Jun 20, 2026Jianzhou Yao, Anxiong Song, Katja Baerenfaller +1Epitope Prediction Antimicrobial Peptide
Swiss Institute of Allergy and Asthma Research, Davos, Switzerland · ETH Zurich, Zurich, Switzerland · Swiss Institute of Bioinformatics, Lausanne, Switzerland
New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models
Jun 3, 2026Yiming Liao, Yiheng Li, Ning Jiang +2Epitope Prediction Benchmark Datasets
Trustworthy and Intelligent Computing Lab (TAIC), Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, Maryland 21250, USA · Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA · Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA +5
EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning
Jun 2, 2026Mansoor Ahmed, Huirong Chai, Haoxin Wang +2Epitope Prediction Antibody
Georgia State University, Atlanta, GA, USA · Georgia Institute of Technology, Atlanta, GA, USA
EvoStruct: Bridging Evolutionary and Structural Priors for Antibody CDR Design via Protein Language Model Adaptation
May 20, 2026Mansoor Ahmed, Sujin Lee, Umar Khayaz +1Antibody Epitope Prediction
Georgia State University, Atlanta, USA · Georgia Institute of Technology, Atlanta, USA

Sep 28, 2026, cs.LGJ/K move · Enter open · S save

Explainability from Training with Applications to TCR-Epitope Prediction

Jiarui Li, Zixiang Yin, Samuel Landry, Zhengming Ding+1

Department of Computer Science, Tulane University · Department of Biochemistry and Molecular Biology, Tulane University School of Medicine

Epitope Prediction Explainability

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Deep learning models have achieved strong performance in artificial intelligence for science, yet their black-box nature limits our understanding of how they learn scientific tasks. Existing methods for interpretability provide limited insight into how models organize evidence and evolve during learning. We introduce explainability from training (EFT), a model-agnostic paradigm that traces model interpretation during training to explain why models rely on specific features and how they organize these features as predictive evidence. We apply EFT to four state-of-the-art T cell receptor (TCR)-epitope prediction models, TCR-SRIM, TULIP, MixTCRpred, and NetTCR-2.2, spanning post-hoc and interpret-by-design approaches as well as transformers and CNNs. To investigate how structural information affects model explanations, we introduce a benchmark, TCR-XAI2, containing 388 unique experimentally resolved TCR-epitope structures, complemented by structures predicted using AlphaFold3, Boltz-2, TCRModel2, tFold-TCR, and OpenFold3. Using EFT with TCR-XAI2, we demonstrate that (1) CNN and transformer models exhibit distinct learning trajectories; (2) TCR

α

and

β

evidence can conflict during learning, limiting the benefits of jointly modeling both chains, while MHC information mitigates this; and (3) real versus predicted structural data for TCR-epitope prediction exhibits distinct TCR and peptide feature preferences as well as differing trajectories of model certainty.

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