Protein Language Models

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7 papers in the last four weeks, up 133% on the four weeks before. 0.1% of all new papers.

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Linear Fitness Subspace in Protein Language Models Enables Sample-Efficient Directed Evolution
Oct 6, 2026SiYuan Ma, Canran Xiao, Zikai Xiao +5Protein Fitness Prediction Protein Language Models
College of Computing and Data Science, Nanyang Technological University, Singapore · Sun Yat-sen University, China · Zhejiang University, China +4
ORBIT-FMIB: Tracking Order-Resolved Epistatic Information Through ESM-2
Sep 30, 2026Maryam Rahimimovassagh, Ivan Garibay, Niloofar YousefiProtein Language Models Protein Representation Learning
University of Central Florida
Analysis of Quantized and Efficiently Adapted Protein Language Models
Sep 30, 2026Ilan Yaniv Zeisler, Sebastian Clancy, Pouriya Bayat +8Protein Language Models Quantization-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
A General Harness for Protein Foundation Model Fitness Prediction
Sep 28, 2026Yang Tan, Qijia Tian, Gangyu Sun +5Protein Fitness Prediction Protein Language Models
Shanghai Jiao Tong University · Shanghai Innovation Institute · Shanghai Artificial Intelligence Laboratory
PFArena: Benchmarking Language Models for Protein Modification
Sep 24, 2026Yawen Ouyang, Xinbo Zhang, Ziyuan Ma +15Protein Fitness Prediction Protein Language Models
Shanghai Artificial Intelligence Laboratory · Generative Symbolic Intelligence Lab (GenSI), Tsinghua University · Institute for AI Industry Research (AIR), Tsinghua University +1
MT-ProtBERT: Multi-task Learning ProtBERT for Intrinsically Disordered Proteins Classification with Scarce Data
Sep 21, 2026Jian Sun, Kingshuk Ghosh, Lilianna Houston +1Protein Language Models Multi-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
MI-PEFT: Mixture-of-Experts Integrated Parameter-Efficient Fine-Tuning Protein Language Models Improves Acidophilic Proteins Classification
Sep 7, 2026Honghan ShenMixture of Experts Protein Language Models
University of Wisconsin–Madison, Madison, WI 53706, USA
ProtLingo: Efficient Protein Language Modeling via Conditional Memory and Expert Routing
Sep 7, 2026Mingrui Li, Sixian Shen, Minzhang Li +4Mixture-of-Experts Language Models Protein Fitness Prediction
ShanghaiTech University
SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding
Sep 1, 2026Handong Wang, Jiaxin Qi, Baisheng Lai +1Protein Language Models Protein Design
Computer Network Information Center, Chinese Academy of Sciences · University of Chinese Academy of Sciences
Learning Task-Specific Antibody Representations via Function-Aware Masking
Sep 1, 2026Ayan Goel, Thomas A. Walton, Amirali AghazadehMasked Language Modeling Protein Language Models
School of Computer Science, Georgia Institute of Technology · School of Electrical and Computer Engineering, Georgia Institute of Technology
Task- and dataset-specific information in protein language models
Aug 12, 2026Roman Joeres, Ilya Senatorov, Anastasia Kolchina +2Protein Language Models Protein 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
LC-SEPLM: long-range contact-supervised adaptation for sequence-only protein representation learning
Jul 24, 2026Chen Wang, Boming Kang, Qinghua CuiProtein Language Models Protein 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
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 Models Protein 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
Residue-Level Attributions in Protein Language Models Do Not Recover Allergen Epitopes
Jun 20, 2026Jianzhou Yao, Anxiong Song, Katja Baerenfaller +1Gradient-Based Attribution Protein Language Models
Swiss Institute of Allergy and Asthma Research, Davos, Switzerland · ETH Zurich, Zurich, Switzerland · Swiss Institute of Bioinformatics, Lausanne, Switzerland
BioMatrix: Towards a Comprehensive Biological Foundation Model Spanning the Modality Matrix of Sequences, Structures, and Language
Jun 20, 2026Qizhi Pei, Zhimeng Zhou, Yi Duan +9Unified Multimodal Models Multimodal 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
Protein contacts are already in the attention: a single-forward-pass alternative to the Categorical Jacobian
Jun 20, 2026Rome ThorstensonProtein Structure Prediction Attention Head Analysis
Independent Researcher
Be Your Own Teacher: Steering Protein Language Models via Unsupervised Reward Optimization
Jun 17, 2026Lanqing Li, Shentong Mo, Yang Yu +1RL for Language Models Reinforcement Learning
The Chinese University of Hong Kong · MBZUAI · Hong Kong University of Science and Technology
Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment
Jun 17, 2026Yanjun Shao, Yundi Chen, Yashvi Patel +2Contrastive Learning Protein Language Models
Biomedical Informatics and Data Science, Yale School of Medicine, United States · Institute of Computational Life Sciences, Zürich University of Applied Sciences (ZHAW), Switzerland
Protein-Based Fish Species Identification: Dataset, Models, and Insights from Native Bangladeshi Fish
Jun 16, 2026Md Nasiat Hasan Fahim, Md. Abid Ullah Muhib, Mohammad Shahidur RahmanHybrid CNN-Transformer Architectures Protein Language Models
Shahjalal University of Science and Technology, Sylhet
Circuit Tracing in Autoregressive Protein Language Models
Jun 14, 2026Darin Tsui, William Deinzer, Daniel Saeedi +1Circuit Discovery Protein Fitness Prediction
School of Electrical and Computer Engineering, Georgia Institute of Technology, Atltanta, GA.
Viral Proteins Reveal Geometry of Protein Language Models
Jun 10, 2026Arthur Bigot, Harmon Bhasin, Core Francisco Park +2Protein Language Models Protein Representation Learning
Department of Computer Science, ETH Zurich, Zurich, Switzerland · Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA · TwentyTwo, USA +2
Constraint-Aware Optimization for Robust Protein Stability Prediction
Jun 6, 2026A Shivram, Aneesh S. Chivukula, Manik Gupta +1OOD Generalization Protein Language Models
Department of Computer Science and Information Systems, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, 500078, Telangana, India · Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, 500078, Telangana, India
AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design
Jun 1, 2026Sahil Rahman, Maxx Richard RahmanRL for Language Models Direct Preference Optimization
Bedford College, London, United Kingdom · Saarland University, Saarbrücken, Germany
AMix-2: Establishing Protein as a Native Modality in Large Language Models
May 29, 2026Keyue Qiu, Yixin Wu, Lihao Wang +19Multimodal Large Language Models Protein Language Models
1Shanghai Artificial Intelligence Laboratory · Institute for AI Industry Research (AIR), Tsinghua University
PROTOCOL: Late Interaction Retrieval for Protein Homolog Search
May 27, 2026Gabrielle Cohn, Rohan Gumaste, Minh Hoang +1Late Interaction Retrieval Protein Language Models
MIT · Princeton University
Computational Modeling of Antibody-Antigen Complexes: PLM-Based and MSA-Based Approaches
May 27, 2026Xiao LuoProtein Structure Prediction AI-Assisted Scientific Research
TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO, CHICAGO, ILLINOIS
EvoStruct: Bridging Evolutionary and Structural Priors for Antibody CDR Design via Protein Language Model Adaptation
May 20, 2026Mansoor Ahmed, Sujin Lee, Umar Khayaz +1Protein Language Models Equivariant GNNs
Georgia State University, Atlanta, USA · Georgia Institute of Technology, Atlanta, USA
Structure-Aware Masking for Protein Representation Learning
May 15, 2026Thomas Walton, Ayan Goel, Amirali AghazadehProtein Fitness Prediction Masked Language Modeling
Georgia Institute of Technology
Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design
May 15, 2026Chen Wei, Fanding Xu, Minghao Sun +5Protein Language Models Diffusion Language Model Decoding
Xi’an University of Posts & Telecommunications · National University of Singapore · Xi’an Jiaotong University +1
ENSEMBITS: an alphabet of protein conformational ensembles
May 13, 2026Kaiwen Shi, Carlos OliverProtein Language Models Protein Representation Learning
Department of Computer Science, Vanderbilt University · Center for AI in Protein Dynamics, Vanderbilt University · Department of Molecular Physiology and Biophysics, Vanderbilt University

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

SiYuan Ma, Canran Xiao, Zikai Xiao, Albert Gao+4

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

Protein Fitness Prediction Protein Language Models Latent Space Optimization

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Model-guided directed evolution seeks to identify high-fitness protein variants under limited oracle budgets. Protein language models (PLMs) provide rich representations for this task, but task-agnostic zero-shot scores can be misaligned with a target assay, while supervised search in high-dimensional embedding spaces can make surrogate modeling and uncertainty estimation sample-inefficient. We propose the Linear Fitness Subspace (LFS) hypothesis: within mutation-induced residue-level representation changes, a compact, assay-specific set of directions makes fitness variation linearly accessible from few labeled variants. This is a local, supervision-recoverable statement rather than a claim that protein fitness landscapes or global PLM geometry are universally linear. Building on this observation, we introduce Subspace-Guided Evolutionary Search (SGES), which estimates an LFS from a small initial sample and performs surrogate modeling, uncertainty estimation, and acquisition in the learned subspace. Across 10 core ProteinGym assays, 87 extended static-validation assays, and an 18-assay budgeted-search evaluation, SGES improves fitness prediction and search efficiency over zero-shot PLMs and recent ML-guided protein optimization baselines. Controlled comparisons with PCA, random projections, label-shuffled PLS, classical mutation features, and acquisition ablations further isolate the benefit of a fitness-aligned site-delta coordinate.

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