mlsanityData to 14 Oct 2026

Deciphering antibody affinity maturation with language models and weakly supervised learning

arXiv 2112.07782 ↗First posted 14 Dec 2021q-bio.BM cs.LGcited by 53

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Abstract (arXiv)

In response to pathogens, the adaptive immune system generates specific antibodies that bind and neutralize foreign antigens. Understanding the composition of an individual's immune repertoire can provide insights into this process and reveal potential therapeutic antibodies. In this work, we explore the application of antibody-specific language models to aid understanding of immune repertoires. We introduce AntiBERTy, a language model trained on 558M natural antibody sequences. We find that within repertoires, our model clusters antibodies into trajectories resembling affinity maturation. Importantly, we show that models trained to predict highly redundant sequences under a multiple instance learning framework identify key binding residues in the process. With further development, the methods presented here will provide new insights into antigen binding from repertoire sequences alone.

Key facts. Cited by 53 papers in the map (data through 14 Oct 2026). Builds on 7 of its 23 references that are in the map. First posted on arXiv 14 Dec 2021.

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7 of 23 references.

References · 7

  1. 2017Attention Is All You Needcited by 60,361
  2. 2018BERT: Pre-training of Deep Bidirectional Transformers for Language Understandingcited by 40,399
  3. 2014Adam: A Method for Stochastic Optimizationcited by 37,240
  4. 2018UMAP: Uniform Manifold Approximation and Projection for Dimension Reductioncited by 2,898
  5. 2019HuggingFace's Transformers: State-of-the-art Natural Language Processingcited by 2,218
  6. 2018Attention-based Deep Multiple Instance Learningcited by 1,095
  7. 2020ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computingcited by 162

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Cited by year (2026 to 14 Oct)

Citing papers per year: 2022: 7; 2023: 9; 2024: 14; 2025: 14; 2026: 9.

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  1. 2022ProGen2: Exploring the Boundaries of Protein Language Modelscited by 159
  2. 2022Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoderscited by 102
  3. 2022Conditional Antibody Design as 3D Equivariant Graph Translationcited by 75
  4. 2023Large AI Models in Health Informatics: Applications, Challenges, and the Futurecited by 61
  5. 2024xTrimoPGLM: Unified 100B-Scale Pre-trained Transformer for Deciphering the Language of Proteincited by 50
  6. 2023End-to-End Full-Atom Antibody Designcited by 49
  7. 2023AbDiffuser: Full-Atom Generation of in vitro Functioning Antibodiescited by 35
  8. 2024Antigen-Specific Antibody Design via Direct Energy-based Preference Optimizationcited by 30
  9. 2024A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generationcited by 29
  10. 2024ProteinBench: A Holistic Evaluation of Protein Foundation Modelscited by 25
  11. 2024Large scale paired antibody language modelscited by 16
  12. 2023Data-Efficient Protein 3D Geometric Pretraining via Refinement of Diffused Protein Structure Decoycited by 10
38 more
  1. 2024HELM: Hierarchical Encoding for mRNA Language Modelingcited by 10
  2. 2025dyAb: Flow Matching for Flexible Antibody Design with AlphaFold-driven Pre-binding Antigencited by 10
  3. 2024Retrieval Augmented Diffusion Model for Structure-informed Antibody Design and Optimizationcited by 9
  4. 2025Antibody Design and Optimization with Multi-scale Equivariant Graph Diffusion Models for Accurate Complex Antigen Bindingcited by 9
  5. 2023Cross-Gate MLP with Protein Complex Invariant Embedding is A One-Shot Antibody Designercited by 8
  6. 2024AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Predictioncited by 8
  7. 2022Linguistically inspired roadmap for building biologically reliable protein language modelscited by 7
  8. 2025Computational Protein Science in the Era of Large Language Models (LLMs)cited by 6
  9. 2023On Pre-trained Language Models for Antibodycited by 4
  10. 2025AbBiBench: A Benchmark for Antibody Binding Affinity Maturation and Designcited by 4
  11. 2022Incorporating Pre-training Paradigm for Antibody Sequence-Structure Co-designcited by 3
  12. 2023AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactionscited by 3
  13. 2024A SARS-CoV-2 Interaction Dataset and VHH Sequence Corpus for Antibody Language Modelscited by 3
  14. 2024Generative Humanization for Therapeutic Antibodiescited by 3
  15. 2025AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Rankingcited by 3
  16. 2026Speaking the Language of Science: Toward a General-Purpose Generative Foundation Model for the Natural Sciencescited by 3
  17. 2022ImmunoLingo: Linguistics-based formalization of the antibody languagecited by 2
  18. 2022xTrimoABFold: De novo Antibody Structure Prediction without MSAcited by 2
  19. 2024S2ALM: Sequence-Structure Pre-trained Large Language Model for Comprehensive Antibody Representation Learningcited by 2
  20. 2025AffinityFlow: Guided Flows for Antibody Affinity Maturationcited by 1
  21. 2026AbLWR:A Context-Aware Listwise Ranking Framework for Antibody-Antigen Binding Affinity Prediction via Positive-Unlabeled Learningcited by 1
  22. 2023Solvent: A Framework for Protein Foldingcited by 0
  23. 2023AntiBARTy Diffusion for Property Guided Antibody Designcited by 0
  24. 2024Improving Antibody Humanness Prediction using Patent Datacited by 0
  25. 2024Decoupled Sequence and Structure Generation for Realistic Antibody Designcited by 0
  26. 2024Harnessing Preference Optimisation in Protein LMs for Hit Maturation in Cell Therapycited by 0
  27. 2025Customizing Spider Silk: Generative Models with Mechanical Property Conditioning for Protein Engineeringcited by 0
  28. 2025NbBench: Benchmarking Language Models for Comprehensive Nanobody Taskscited by 0
  29. 2025Llama-Affinity: A Predictive Antibody Antigen Binding Model Integrating Antibody Sequences with Llama3 Backbone Architecturecited by 0
  30. 2025Antibody Foundational Model : Ab-RoBERTacited by 0
  31. 2025Sequence-based protein-protein interaction prediction and its applications in drug discoverycited by 0
  32. 2025ABConformer: Physics-inspired Sliding Attention for Antibody-Antigen Interface Predictioncited by 0
  33. 2025FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equationcited by 0
  34. 2025DuaDeep-SeqAffinity: Dual-Branch Deep Learning for Tri-Stream Sequence-Based Antibody--Antigen Affinity Predictioncited by 0
  35. 2026Conditionally Site-Independent Neural Evolution of Antibody Sequencescited by 0
  36. 2026Biologically-Grounded Multi-Encoder Architectures as Developability Oracles for Antibody Designcited by 0
  37. 2026Conditional generation of antibody sequences with classifier-guided germline-absorbing discrete diffusioncited by 0
  38. 2026Computational Modeling of Antibody-Antigen Complexes: PLM-Based and MSA-Based Approachescited by 0

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