Protein Language Models

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Overview

Protein language models treat amino-acid sequences as languages, learning representations through objectives such as masked-residue prediction and autoregressive sequence generation. Researchers use these representations for tasks including remote homology, structure and function prediction, and mutation-effect scoring, evaluating them on benchmarks such as SCOPe, FLIP, and ProteinGym; fine-tuning, contrastive learning, and evolutionary or structural signals can further adapt the models. Generative approaches, including diffusion and reinforcement learning, aim to design proteins with desired properties, sometimes conditioning on structures, ligands, or natural-language instructions. A central challenge is balancing scale with efficiency and biological grounding: benchmark gains do not always transfer to new families or experiments, and predicted plausibility, interpretability, and safety require careful validation.

Latest papers

CardsList

69 papers13 papers in the last four weeks, up 117% on the four weeks before. 0.1% of all new papers.

  1. 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

  2. recAMPLIFY: Large-Scale Pretraining of Recursive Protein Language Models

    Oct 19, 2026Saurav Jha, Qianli Liao, Robert Vernon +2Protein Language ModelsRecursive Language Models

    Mila – Quebec AI Institute · Polytechnique Montréal · Center for Brains, Minds, and Machines +4

  3. The Effectiveness and Durability of Pretraining Data Filtering in Protein Language Models

    Oct 19, 2026Aaron Maiwald, Roderick McNeill, Jaeyoung Lee +9Training Data CurationProtein Language Models

    Department of Statistics, University of Oxford · SecureBio · UK AI Security Institute +3

  4. Poisoning the corpora of protein design systems during pre-training and retrieval

    Oct 15, 2026Charalampos Koilakos, Kimon-Antonios Provatas, Michail Patsakis +3Data Poisoning AttacksRAG Poisoning Attacks

    Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, TX, USA. · Department of Computer Science, The University of Texas at Austin · Institute for Fundamental Biomedical Research, BSRC “Alexander Fleming,”16672 Vari, Greece +1

  5. ProtModernBERT: Compute-Efficient Protein Language Modeling

    Oct 14, 2026Alberto Martínez, Natalia Flechas Manrique, Llorenç Espinosa-Portalés +1Protein Language ModelsEfficient Language Model Training

    Multiverse Computing, Parque Científico y Tecnológico de Gipuzkoa, Paseo de Miramón 170, 20014 Donostia-San Sebastián, Spain. · Multiverse Computing, 7 rue de la Croix Martre, 91120 Palaiseau, Paris, France

  6. InstructPro2: Natural Language and Biological Grounding Guided De Novo Protein Design

    Oct 14, 2026Charles Novak, Zhenqiao Song, Chuan Li +2Protein DesignProtein Language Models

    Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA · Language Technologies Institute, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA · Lambda Inc, San Francisco, CA 94105, USA

  7. 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

  8. Linear Fitness Subspace in Protein Language Models Enables Sample-Efficient Directed Evolution

    Oct 6, 2026SiYuan Ma, Canran Xiao, Zikai Xiao +5Protein Fitness PredictionProtein Language Models

    College of Computing and Data Science, Nanyang Technological University, Singapore · Sun Yat-sen University, China · Zhejiang University, China +4

  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. 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

  11. Analysis of Quantized and Efficiently Adapted Protein Language Models

    Sep 30, 2026Ilan Yaniv Zeisler, Sebastian Clancy, Pouriya Bayat +8Protein Language ModelsQuantization-Aware LoRA

    Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada. · Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada. · Department of Computer Science, University of Toronto, Toronto, Ontario, Canada. +2

  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. A General Harness for Protein Foundation Model Fitness Prediction

    Sep 28, 2026Yang Tan, Qijia Tian, Gangyu Sun +5Protein Fitness PredictionProtein Language Models

    Shanghai Jiao Tong University · Shanghai Innovation Institute · Shanghai Artificial Intelligence Laboratory

  14. PFArena: Benchmarking Language Models for Protein Modification

    Sep 24, 2026Yawen Ouyang, Xinbo Zhang, Ziyuan Ma +15Protein Fitness PredictionProtein Language Models

    Shanghai Artificial Intelligence Laboratory · Generative Symbolic Intelligence Lab (GenSI), Tsinghua University · Institute for AI Industry Research (AIR), Tsinghua University +1

  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. MI-PEFT: Mixture-of-Experts Integrated Parameter-Efficient Fine-Tuning Protein Language Models Improves Acidophilic Proteins Classification

    Sep 7, 2026Honghan ShenMixture of ExpertsProtein Language Models

    University of Wisconsin–Madison, Madison, WI 53706, USA

  17. ProtLingo: Efficient Protein Language Modeling via Conditional Memory and Expert Routing

    Sep 4, 2026Mingrui Li, Sixian Shen, Minzhang Li +4Mixture-of-Experts Language ModelsProtein Fitness Prediction

    ShanghaiTech University

  18. SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding

    Sep 1, 2026Handong Wang, Jiaxin Qi, Baisheng Lai +1Protein Language ModelsProtein Design

    Computer Network Information Center, Chinese Academy of Sciences · University of Chinese Academy of Sciences

  19. 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

  20. Interpreting Latent Protein Language Model Features with Geometric Annotations

    Aug 26, 2026Siddharth Setlur, Djordje Mihajlovic, Darrick LeeMechanistic InterpretabilityProtein Language Models

    School of Mathematics University of Edinburgh, UK

  21. Unlocking Multimodal Protein Language Models at Inference Time

    Aug 26, 2026Yi Zhou, Qipeng Wang, Yunqing Liu +3Inference-Time SearchProtein Language Models

    The Hong Kong Polytechnic University · The Hong Kong University of Science and Technology (Guangzhou)

  22. 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

  23. Off-Manifold Collapse in Guided Protein Language Models

    Aug 19, 2026Shuibai Zhang, Xinchi Liu, Fred Zhangzhi Peng +4Protein Language ModelsLarge Language Model-Guided Optimization

    University of Wisconsin–Madison · Duke University · Cornell University

  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. 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

  26. Two-Stage Fine-Tuning for Protein Sequence Generation with Targeted Amino-Acid Composition

    Jun 26, 2026Violeta Basten-Romero, Rubén Muñoz-Tafalla, Anna María Díaz-Rovira +3Protein Language ModelsProtein Design

    Barcelona Supercomputing Center (BSC), Plaça d’Eusebi Güell, 1-3, 08034, Barcelona, Spain · Department of Bioinformatics, School of Mathematics and Statistics (FME), Universitat Politècnica de Catalunya - BarcelonaTech (UPC), 08034 Barcelona, Spain · Nostrum Biodiscovery S.L., Av. Josep Tarradellas, 8-10, 3-2, 08029, Barcelona, Spain +1

  27. Residue-Level Attributions in Protein Language Models Do Not Recover Allergen Epitopes

    Jun 20, 2026Jianzhou Yao, Anxiong Song, Katja Baerenfaller +1Gradient-Based AttributionProtein Language Models

    Swiss Institute of Allergy and Asthma Research, Davos, Switzerland · ETH Zurich, Zurich, Switzerland · Swiss Institute of Bioinformatics, Lausanne, Switzerland

  28. BioMatrix: Towards a Comprehensive Biological Foundation Model Spanning the Modality Matrix of Sequences, Structures, and Language

    Jun 20, 2026Qizhi Pei, Zhimeng Zhou, Yi Duan +9Multimodal UnderstandingMultimodal Pretraining

    1Gaoling School of Artificial Intelligence, Renmin University of China, 2OpenDataLab, Shanghai Artificial Intelligence Laboratory · 3Zhejiang University, 4Shanghai Innovation Institute · 2OpenDataLab, Shanghai Artificial Intelligence Laboratory, 3Zhejiang University, 4Shanghai Innovation Institute +5

  29. Protein contacts are already in the attention: a single-forward-pass alternative to the Categorical Jacobian

    Jun 20, 2026Rome ThorstensonProtein Structure PredictionAttention Head Analysis

    Independent Researcher

  30. Be Your Own Teacher: Steering Protein Language Models via Unsupervised Reward Optimization

    Jun 17, 2026Lanqing Li, Shentong Mo, Yang Yu +1RL for Language ModelsReinforcement Learning

    The Chinese University of Hong Kong · MBZUAI · Hong Kong University of Science and Technology