Protein Representation Learning

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5 papers in the last four weeks, level with the four weeks before. 0.0% of all new papers.

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PIT-GCL: Protein Interaction using Topological Graph Contrastive Learning
Oct 4, 2026Jae Won Choi, Ryoonki Hong, Alan Liang +5Protein-Protein Interaction Prediction Protein Representation Learning
Department of Computer Science, University of Southern California
StabilityArc: Decoding Protein Sequence Embeddings into Generalizable Stability Landscapes
Sep 30, 2026Aaron L. Feller, Andrew D. Ellington, Claus O. WilkeTransfer Learning Molecular Property Prediction
The University of Texas at Austin Interdisciplinary Life Sciences · The University of Texas at Austin Integrative Biology
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
From Surfaces to Volumes: Registered Geometry for Protein Representation Learning
Sep 28, 2026Siyuan Chen, Cai Zhou, Jinrui Zhang +8Protein-Protein Interaction Prediction 3D Representation Learning
University of British Columbia · Massachusetts Institute of Technology · Carnegie Mellon University +2
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
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
Benchmarking Peptide-Protein Affinity Prediction Across Peptide and Target Shifts
Aug 31, 2026Jiaxin Tian, Darren An, Jun LiProtein-Ligand Binding Affinity Prediction OOD Generalization
College of Biology, Hunan University, Changsha, Hunan, China · 2Lingang Laboratory, Shanghai, China
Hyper-Fold: Exploring the Expressive Limit of Sequence-Geometry Learning for Proteins via Hypergraph Modeling
Aug 29, 2026Yifan Feng, Guanjie Cheng, Shihui Ying +2Hypergraph Neural Networks Molecular Property Prediction
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
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
Probing and steering biology across Boltz-1s trunk-diffusion boundary
Aug 11, 2026Piotr Jedryszek, Tongmeng Xie, Adam Winnifrith +5Protein Structure Prediction Activation Steering
Department of Biology, University of Oxford, Oxford, UK · Evolvere Biosciences, London, UK · Independent Researcher +4
Inter-Residue Geometry Attention for Antibody-Specific Epitope Prediction
Aug 2, 2026Chuanliu Fan, Nan Yu, Junjie Wu +1Rotary Positional Embeddings Positional Encoding
School of Computer Science and Technology, Soochow University · Institute of Artificial Intelligence, Soochow University
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
Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design
Jul 22, 2026Xiaoliang Shi, Zichen Wang, Runze Ma +2Multimodal Pretraining Protein Design
Shanghai Jiao Tong University
Neural spectroscopy of AlphaFold2 reveals encoded protein conformational landscapes
Jul 17, 2026Kaustav MehtaProtein Structure Prediction Neural Network Interpretability
Independent researcher, India
Accurate, Interdisciplinary and Transparent Structure-property Understanding with Deep Native Structural Reasoning
Jul 8, 2026Chen Tang, Yizhou Wang, Jianyu Wu +26Scientific Reasoning Materials Property Prediction
Shanghai Artificial Intelligence Laboratory, China. · The Chinese University of Hong Kong, Hong Kong. · Shanghai Jiao Tong University, China. +8
MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction
Jul 2, 2026Wenbo ZhangKG Embedding Protein-Protein Interaction Prediction
College of Computer and Information Science, Southwest University, Chongqing, Chongqing, China
Enhancing Protein Representation Learning via Manifold Restore Mixing
Jun 21, 2026Yizhou Dang, Chuang Zhao, Lianbo Ma +3Data Augmentation Mixup
Software College, Northeastern University Shenyang, China · Tianjin University Tianjin, China · School of Computer Science and Engineering, Northeastern University Shenyang, China +1
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
Protein Representation Learning with Secondary-Structure and Energy-Filtered Hydrogen-Bond Graphs
Jun 12, 2026Mohamed Mouhajir, Limei Wang, El Houcine Bergou +3Graph Neural Networks Protein Representation Learning
College of Computing, UM6P Morocco · Independent USA
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
CryoProt: A Protein Pretraining Framework with Cross-Box Interactions on Cryo-EM Density Maps
May 31, 2026Dan Luo, Xuan Lin, Peng Zhou +4Cryo-Electron Microscopy 3D Representation Learning
College of Computer Science and Electronic Engineering, Hunan University · School of Computer Science, Xiangtan University
Enhancing Protein-Protein Interaction Prediction with Hierarchical Motif-based Multimodal Protein Embedding
May 30, 2026Zaifei Yang, Samuel Ping-Man Choi, James KwokHierarchical Representation Learning Multimodal Embedding
Department of Computer Science and Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong. · Lee Shau Kee School of Business and Administration, The Hong Kong Metropolitan University, Ho Man Tin, Kowloon, Hong Kong.
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
Atom-level Protein Representation Learning Improves Protein Structure Prediction
May 21, 2026Taewon Kim, Hyosoon Jang, Hyunjin Seo +6Protein Structure Prediction Self-Supervised Pre-Training
Graduate School of AI, KAIST · Department of Chemistry, KAIST · HITS Inc. +3
Protein Fold Classification at Scale: Benchmarking and Pretraining
May 18, 2026Dexiong Chen, Andrei Manolache, Mathias Niepert +1Masked Autoencoders Self-Supervised Pre-Training
Max Planck Institute of Biochemistry, Martinsried, Germany · Computer Science Department, University of Stuttgart, Germany · Bitdefender, Romania
Structure-Aware Masking for Protein Representation Learning
May 15, 2026Thomas Walton, Ayan Goel, Amirali AghazadehProtein Fitness Prediction Masked Language Modeling
Georgia Institute of Technology
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
Learning Protein Structure-Function Relationships through Knowledge-guided Representation Decomposition
May 12, 2026Mingqing Wang, Zhiwei Nie, Athanasios V. Vasilakos +2Representation Disentanglement 3D Representation Learning
Shenzhen International Graduate School, Tsinghua University, Shenzhen, China · Pengcheng Laboratory, Shenzhen, China · School of Electronic and Computer Engineering, Peking University, Shenzhen, China +2
Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning
May 9, 2026Siddhant Dutta, Edward Tan Beng Wai, Soumick Sarker +2Graph Neural Networks Protein Language Models
Nanyang Technological University, Singapore

Oct 4, 2026, cs.LGJ/K move · Enter open · S save

PIT-GCL: Protein Interaction using Topological Graph Contrastive Learning

Jae Won Choi, Ryoonki Hong, Alan Liang, Manjula Adiveppa Wader+4

Department of Computer Science, University of Southern California

Protein-Protein Interaction Prediction Protein Representation Learning

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Protein binding prediction is central to target identification, therapeutic binder design, and large scale screening, yet remains challenging because binding depends on sequence, three dimensional geometry, and global structural organization. Recent folding models such as AlphaFold3 and Boltz-2 have substantially improved structure prediction, but their confidence outputs (pLDDT, pTM, ipTM) are not specifically designed for binary binding prediction, and dedicated structure aware predictors often require bound complex structures that are unavailable at screening scale. We introduce PIT-GCL, a dual tower structure aware framework that encodes each protein independently from its amino acid sequence, Cα point cloud, and a global persistent homology descriptor. Each tower combines residue ESM-2 embeddings with a topological summary computed from the H0 and H1 persistence landscapes of a Vietoris-Rips filtration, and processes the resulting tokens with a structure aware Transformer in which pairwise Cα distances enter as a learned attention bias. A bidirectional cross attention module then performs latent space soft docking between the two per-protein representations, and the model is trained with a combined binary cross entropy and NT-Xent contrastive objective. On three binary interaction prediction benchmarks, general PPI on PPIRef, TCRpMHC binding on STAG, and whole chain pairs on PPB-Affinity, PIT-GCL outperforms representative sequence based, structure aware, and task specific baselines on general PPI under our evaluation, and is the only method above chance on PPB-Affinity; on TCR-pMHC it leads at a fixed decision threshold but is outranked by a task specific sequence model. Because each protein is encoded independently in the first phase, its representation can be precomputed and reused across candidate pairs, which is convenient for large scale screening.

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