Protein Representation Learning

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Overview

Protein representation learning studies how to encode amino-acid sequences and three-dimensional structures so models can compare proteins and predict properties such as function, folding, interactions, and mutation effects. Common approaches include protein language models trained with masked-token prediction, geometric and graph encoders of residue contacts, structure-aware masking, and contrastive learning that aligns sequence with structure or function. These representations are tested on tasks such as remote homology, protein fitness, structure prediction, and binding, using both pooled protein embeddings and residue-level features. A central challenge is making representations transferable across proteins and data splits: larger pretrained models can help, but useful information varies by task and layer, and structural or evolutionary features may offer gains with less data or computation.

Latest papers

CardsList

69 papers12 papers in the last four weeks, up 100% on the four weeks before. 0.1% of all new papers.

  1. Structure, Not Sequence: Tracking and Validating Folding Mechanisms in ESMFold's Trunk with Sparse Autoencoders

    Oct 26, 2026Bohan Liu, Xiaohan Fan, Wenqian Ye +1Protein Structure PredictionNeural Network Interpretability

    University of Virginia Charlottesville VA 22903, USA

  2. Trion-1: Unifying Language, Protein Sequence, and Structure with Diffusion Language Models

    Oct 22, 2026Tianyu Lu, Kaicheng Yang, Jiangtao Feng +7Protein Language ModelsProtein Structure Generation

  3. Escaping the Phylogenetic Trap: Persistent Homology Enables Cross-Species Ion Channel Classification via Multimodal Graph Neural Networks

    Oct 21, 2026Arezoo Bybordi, Favour Achimba, Mariam Gelashvili +4OOD GeneralizationProtein Representation Learning

    The Graduate Center, City University of New York · Hunter College, City University of New York · Tandon School of Engineering, New York University +3

  4. Ensemble-Aware Structural Encoding (EASE): Conditioning Protein Encoders on Peptide Conformational Ensembles

    Oct 20, 2026Ruoyao Zhang, Hongxuan Li, Jie Peng +1Protein Representation LearningMolecular Property Prediction

    University of Waterloo · University of North Carolina at Chapel Hill

  5. EMBER: Predicting TCR--pMHC Binding Without a Docked Complex

    Oct 19, 2026Lin Ha, Chen Zhou, Haozheng Luo +3Protein-Protein Interaction PredictionProtein Representation Learning

    Northwestern University

  6. ProTok: Unified Protein Tokenization via Modular Multi-Codebook Quantization

    Oct 13, 2026Romain Hardy, Xiaoman Zhang, Pranav RajpurkarProtein Representation LearningProtein Language Models

    Department of Biomedical Informatics, Harvard Medical School

  7. Blending experimental electron density information to protein-ligand interaction

    Oct 10, 2026Seonghyun Park, Shuan Chen, Jun Jin Choong +6Molecular Representation LearningRepresentation Learning

    KAIST · SB Intuitions

  8. PIT-GCL: Protein Interaction using Topological Graph Contrastive Learning

    Oct 4, 2026Jae Won Choi, Ryoonki Hong, Alan Liang +5Protein-Protein Interaction PredictionProtein Representation Learning

    Department of Computer Science, University of Southern California

  9. Learning Latent Protein Languages for Autoregressive Generation

    Oct 2, 2026Mahdi Pourmirzaei, Farzaneh Esmaili, Amir Ziashahabi +2Protein Structure GenerationProtein Language Models

    University of Missouri · University of Southern California · Independent Researcher

  10. StabilityArc: Decoding Protein Sequence Embeddings into Generalizable Stability Landscapes

    Sep 30, 2026Aaron L. Feller, Andrew D. Ellington, Claus O. WilkeTransfer LearningMolecular Property Prediction

    The University of Texas at Austin, Interdisciplinary Life Sciences · The University of Texas at Austin, Integrative Biology

  11. ORBIT-FMIB: Tracking Order-Resolved Epistatic Information Through ESM-2

    Sep 30, 2026Maryam Rahimimovassagh, Ivan Garibay, Niloofar YousefiProtein Language ModelsProtein Representation Learning

    University of Central Florida

  12. LEMON-ZEST: Evolution-Informed Tokenization for Efficient Protein Language Modeling

    Sep 29, 2026Biswajit Banerjee, Claudia Alvarez Carreno, Anton S. PetrovProtein Language ModelsProtein Representation Learning

    Georgia Institute of Technology · University College London

  13. From Surfaces to Volumes: Registered Geometry for Protein Representation Learning

    Sep 28, 2026Siyuan Chen, Cai Zhou, Jinrui Zhang +8Protein-Protein Interaction Prediction3D Representation Learning

    University of British Columbia · Massachusetts Institute of Technology · Carnegie Mellon University +2

  14. Flow-Matching-Based Protein Structure Tokenizer Made Efficient and Easy

    Sep 27, 2026Zhe Zhang, Yikai Zhang, Jiangtao Feng +3Protein Representation LearningDiscrete Flow Matching

    Institute for AI Industry Research (AIR), Tsinghua University · Department of Computer Science and Technology, Tsinghua University · Fudan University

  15. MT-ProtBERT: Multi-task Learning ProtBERT for Intrinsically Disordered Proteins Classification with Scarce Data

    Sep 21, 2026Jian Sun, Kingshuk Ghosh, Lilianna Houston +1Protein Language ModelsMulti-Task Learning

    Department of Computer Science, Ritchie School of Engineering and Computer Science, University of Denver, 2155 E Wesley Ave, Denver, CO 80210 · Department of Surgery, David Geffen School of Medicine at the University of California, Los Angeles, 10833 Le Conte Ave, Los Angeles, CA 90095 · Department of Physics and Astronomy, at the University of Denver, CO 80210 +1

  16. The microscope is the mask: privileged views and labels from a cryo-ET forward model

    Sep 3, 2026Bogdan Toader, Kiarash Jamali, Tanmay A. M. Bharat +1Protein Representation LearningCryo-Electron Microscopy

    MRC Laboratory of Molecular Biology Cambridge, UK

  17. Chemical and geometric representation fidelity improves drug--target affinity prediction

    Sep 2, 2026Yixiao Li, Yining Qian, Yefan Chen +5Privacy-Preserving Representation LearningProtein-Ligand Binding Affinity Prediction

    College of Information Science and Engineering, Northeastern University, Shenyang 110819, China · School of Computer and Communication Engineering, Northeastern University at Qinhuangdao, Qinhuangdao 066004, China · School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China +1

  18. Learning Task-Specific Antibody Representations via Function-Aware Masking

    Sep 1, 2026Ayan Goel, Thomas A. Walton, Amirali AghazadehMasked Language ModelingProtein Language Models

    School of Computer Science, Georgia Institute of Technology · School of Electrical and Computer Engineering, Georgia Institute of Technology

  19. Benchmarking Peptide-Protein Affinity Prediction Across Peptide and Target Shifts

    Aug 31, 2026Jiaxin Tian, Darren An, Jun LiProtein-Ligand Binding Affinity PredictionOOD Generalization

    College of Biology, Hunan University, Changsha, Hunan, China · 2Lingang Laboratory, Shanghai, China

  20. Hyper-Fold: Exploring the Expressive Limit of Sequence-Geometry Learning for Proteins via Hypergraph Modeling

    Aug 29, 2026Yifan Feng, Guanjie Cheng, Shihui Ying +2Protein Function PredictionHypergraph Neural Networks

    1{School of Software, BNRist, THUIBCS}, Tsinghua University, Beijing 100084, China · School of Software Technology, Zhejiang University, Ningbo 315100, China · 3Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai 200072, China +1

  21. Interpreting Protein Language Model Embeddings via Orthogonal Projection for Protein Fitness Prediction

    Aug 26, 2026Paulo Yanez Sarmiento, Pia Francesca Rissom, Manuel Pfeuffer +6Protein Language ModelsProtein Representation Learning

    Hasso Plattner Institute, University of Potsdam · Bioinformatics and Machine Learning, Broad Institute of MIT and Harvard · School of Business and Economics, Humboldt University of Berlin +1

  22. Beyond Tokens: Probing Higher-Order Epistasis in Learned Protein Representations

    Aug 24, 2026Maryam Rahimimovassagh, Ivan Garibay, Niloofar YousefiProtein Representation LearningProtein Fitness Prediction

    University of Central Florida

  23. Protein Structure Prediction: From Evolutionary Constraints to Generative Modeling

    Aug 17, 2026Wengan He, Yongsheng Luo, Lihong Jiang +2Protein Structure PredictionProtein Representation Learning

    Zhuhai College of Science and Technology, Zhuhai, China · Zhuhai UNO Technology Co., Ltd., Zhuhai, China

  24. Task- and dataset-specific information in protein language models

    Aug 12, 2026Roman Joeres, Ilya Senatorov, Anastasia Kolchina +2Protein Language ModelsProtein Representation Learning

    Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland, 66123 Saarbruecken, Germany · Center for Bioinformatics, Saarland University, 66123 Saarbruecken, Germany · Saarland Informatics Campus, Saarland University, 66123 Saarbruecken, Germany +2

  25. Probing and steering biology across Boltz-1s trunk-diffusion boundary

    Aug 11, 2026Piotr Jedryszek, Tongmeng Xie, Adam Winnifrith +5Protein Structure PredictionActivation Steering

    Department of Biology, University of Oxford, Oxford, UK · Evolvere Biosciences, London, UK · Independent Researcher +4

  26. Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction

    Aug 2, 2026Chuanliu Fan, Nan Yu, Junjie Wu +1Rotary Positional EmbeddingsPositional Encoding

    School of Computer Science and Technology, Soochow University · Institute of Artificial Intelligence, Soochow University

  27. LC-SEPLM: long-range contact-supervised adaptation for sequence-only protein representation learning

    Jul 24, 2026Chen Wang, Boming Kang, Qinghua CuiProtein Language ModelsProtein Representation Learning

    School of Electrical and Electronic Engineering, Hubei University of Technology, Hubei, China · Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing, 100191, China. · School of Sports Medicine, Wuhan Institute of Physical Education, No. 461 Luoyu Rd. Wuchang District, Wuhan 430079, Hubei Province, China

  28. Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design

    Jul 22, 2026Xiaoliang Shi, Zichen Wang, Runze Ma +2Multimodal PretrainingProtein Design

    Shanghai Jiao Tong University

  29. Neural spectroscopy of AlphaFold2 reveals encoded protein conformational landscapes

    Jul 17, 2026Kaustav MehtaProtein Structure PredictionNeural Network Interpretability

    Independent researcher, India

  30. Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning

    Jul 8, 2026Chen Tang, Yizhou Wang, Jianyu Wu +26Scientific ReasoningMaterials Property Prediction

    Shanghai Artificial Intelligence Laboratory, China. · The Chinese University of Hong Kong, Hong Kong. · Shanghai Jiao Tong University, China. +8