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Proteins inherently possess a consistent sequence-structure duality.
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AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models
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Evolutionary-scale prediction of atomic-level protein structure with a language model
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Language Model Beats Diffusion–Tokenizer is Key to Visual Generation
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OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
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Simulating 500 million years of evolution with a language model
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ProtInvTree: Deliberate Protein Inverse Folding with Reward-guided Tree Search
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GLProtein: Global-and-Local Structure Aware Protein Representation Learning. In Findings of the Association for Computational Linguistics: EMNLP 2025 . Association for Computational Linguistics, Suzhou, China
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Fluid: Scaling autoregressive text-to-image generative models with continuous tokens
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Autoregressive image generation without vector quantization
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Diffusion on language model encodings for protein sequence generation
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Fast and accurate protein structure search with Foldseek
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Diffusion Language Models Are Versatile Protein Learners. In International Conference on Machine Learning
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Improved motif-scaffolding with SE(3) flow matching
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Yunqing Liu, Wenqi Fan, Xiaoyong Wei, and Li Qing. 2025b · 2025
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All-atom protein generation with latent diffusion. In ICLR 2025 Workshop on Generative and Experimental Perspectives for Biomolecular Design
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Tokenized and continuous embedding compressions of protein sequence and structure
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Toward deep learning sequence–structure co-generation for protein design
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Janus: Decoupling visual encoding for unified multimodal understanding and generation. In Proceedings of the Computer Vision and Pattern Recognition Conference . 12966–12977
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Hierarchical protein backbone generation with latent and structure diffusion
Jason Yim, Marouane Jaakik, Ge Liu, Jacob Gershon, Karsten Kreis, David Baker, Regina Barzilay, and Tommi Jaakkola. 2025 · 2025
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Discrete Diffusion in Large Language and Multimodal Models: A Survey
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MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Texts
Jiatong Li, Yunqing Liu, Wei Liu, Jingdi Lei, Di Zhang, Wenqi Fan, Dongzhan Zhou, Yuqiang Li, and Qing Li. 2026 · 2026
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Enhancing Molecular Property Predictions by Learning from Bond Modelling and Interactions. In The Fourteenth International Conference on Learning Representations
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HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens. In 32nd SIGKDD Conference on Knowledge Discovery and Data Mining - AI for Sciences Track
Yi Zhou, Haohao Qu, Yunqing LIU, Shanru Lin, Le Song, and Wenqi Fan. 2026 · 2026
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