ProteinAE: Protein Diffusion Autoencoders for Structure Encoding
Fuente:
arXiv
Saved in:
| Main Authors: | Li, Shaoning, Zhuo, Le, Wang, Yusong, Li, Mingyu, He, Xinheng, Wu, Fandi, Li, Hongsheng, Heng, Pheng-Ann |
|---|---|
| Format: | Preprint |
| Published: |
2025
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
Similar Items
Improving AlphaFlow for Efficient Protein Ensembles Generation
by: Li, Shaoning, et al.
Published: (2024)
by: Li, Shaoning, et al.
Published: (2024)
Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
by: He, Xinheng, et al.
Published: (2025)
by: He, Xinheng, et al.
Published: (2025)
Neural P$^3$M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs
by: Wang, Yusong, et al.
Published: (2024)
by: Wang, Yusong, et al.
Published: (2024)
Protein Inverse Folding From Structure Feedback
by: Xu, Junde, et al.
Published: (2025)
by: Xu, Junde, et al.
Published: (2025)
F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching
by: Li, Shaoning, et al.
Published: (2024)
by: Li, Shaoning, et al.
Published: (2024)
PPDiff: Diffusing in Hybrid Sequence-Structure Space for Protein-Protein Complex Design
by: Song, Zhenqiao, et al.
Published: (2025)
by: Song, Zhenqiao, et al.
Published: (2025)
T2I-R1: Reinforcing Image Generation with Collaborative Semantic-level and Token-level CoT
by: Jiang, Dongzhi, et al.
Published: (2025)
by: Jiang, Dongzhi, et al.
Published: (2025)
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
by: Zhou, Xiangxin, et al.
Published: (2025)
by: Zhou, Xiangxin, et al.
Published: (2025)
Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model
by: Li, Guanlue, et al.
Published: (2025)
by: Li, Guanlue, et al.
Published: (2025)
From Static Structures to Ensembles: Studying and Harnessing Protein Structure Tokenization
by: Liu, Zijing, et al.
Published: (2025)
by: Liu, Zijing, et al.
Published: (2025)
Hashing for Protein Structure Similarity Search
by: Han, Jin, et al.
Published: (2024)
by: Han, Jin, et al.
Published: (2024)
StrAE: Autoencoding for Pre-Trained Embeddings using Explicit Structure
by: Opper, Mattia, et al.
Published: (2023)
by: Opper, Mattia, et al.
Published: (2023)
Towards Interpretable Protein Structure Prediction with Sparse Autoencoders
by: Parsan, Nithin, et al.
Published: (2025)
by: Parsan, Nithin, et al.
Published: (2025)
DEL-Ranking: Ranking-Correction Denoising Framework for Elucidating Molecular Affinities in DNA-Encoded Libraries
by: Cao, Hanqun, et al.
Published: (2024)
by: Cao, Hanqun, et al.
Published: (2024)
Flow Autoencoders are Effective Protein Tokenizers
by: Dilip, Rohit, et al.
Published: (2025)
by: Dilip, Rohit, et al.
Published: (2025)
General Multimodal Protein Design Enables DNA-Encoding of Chemistry
by: Rector-Brooks, Jarrid, et al.
Published: (2026)
by: Rector-Brooks, Jarrid, et al.
Published: (2026)
RiboSphere: Learning Unified and Efficient Representations of RNA Structures
by: Zhang, Zhou, et al.
Published: (2026)
by: Zhang, Zhou, et al.
Published: (2026)
Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries
by: Gu, Chunbin, et al.
Published: (2024)
by: Gu, Chunbin, et al.
Published: (2024)
Robust Inference-Time Steering of Protein Diffusion Models via Embedding Optimization
by: Li, Minhuan, et al.
Published: (2026)
by: Li, Minhuan, et al.
Published: (2026)
Lightweight MSA Design Advances Protein Folding From Evolutionary Embeddings
by: Cao, Hanqun, et al.
Published: (2025)
by: Cao, Hanqun, et al.
Published: (2025)
MAPE-PPI: Towards Effective and Efficient Protein-Protein Interaction Prediction via Microenvironment-Aware Protein Embedding
by: Wu, Lirong, et al.
Published: (2024)
by: Wu, Lirong, et al.
Published: (2024)
SVD-AE: Simple Autoencoders for Collaborative Filtering
by: Hong, Seoyoung, et al.
Published: (2024)
by: Hong, Seoyoung, et al.
Published: (2024)
SaDiT: Efficient Protein Backbone Design via Latent Structural Tokenization and Diffusion Transformers
by: Mo, Shentong, et al.
Published: (2026)
by: Mo, Shentong, et al.
Published: (2026)
ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction
by: Jin, Mingyu, et al.
Published: (2024)
by: Jin, Mingyu, et al.
Published: (2024)
Dynamics-inspired Structure Hallucination for Protein-protein Interaction Modeling
by: Wu, Fang, et al.
Published: (2026)
by: Wu, Fang, et al.
Published: (2026)
ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training
by: Zhuo, Le, et al.
Published: (2024)
by: Zhuo, Le, et al.
Published: (2024)
DiffBP: Generative Diffusion of 3D Molecules for Target Protein Binding
by: Lin, Haitao, et al.
Published: (2022)
by: Lin, Haitao, et al.
Published: (2022)
From Supervision to Exploration: What Does Protein Language Model Learn During Reinforcement Learning?
by: Cao, Hanqun, et al.
Published: (2025)
by: Cao, Hanqun, et al.
Published: (2025)
AE SemRL: Learning Semantic Association Rules with Autoencoders
by: Karabulut, Erkan, et al.
Published: (2024)
by: Karabulut, Erkan, et al.
Published: (2024)
ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design
by: Zhang, Yulin, et al.
Published: (2026)
by: Zhang, Yulin, et al.
Published: (2026)
Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model
by: Li, Guanlue, et al.
Published: (2025)
by: Li, Guanlue, et al.
Published: (2025)
NODE-AdvGAN: Improving the transferability and perceptual similarity of adversarial examples by dynamic-system-driven adversarial generative model
by: Xie, Xinheng, et al.
Published: (2024)
by: Xie, Xinheng, et al.
Published: (2024)
Interpreting and Steering Protein Language Models through Sparse Autoencoders
by: Garcia, Edith Natalia Villegas, et al.
Published: (2025)
by: Garcia, Edith Natalia Villegas, et al.
Published: (2025)
RSAttAE: An Information-Aware Attention-based Autoencoder Recommender System
by: Taromi, Amirhossein Dadashzadeh, et al.
Published: (2025)
by: Taromi, Amirhossein Dadashzadeh, et al.
Published: (2025)
SeaDAG: Semi-autoregressive Diffusion for Conditional Directed Acyclic Graph Generation
by: Zhou, Xinyi, et al.
Published: (2024)
by: Zhou, Xinyi, et al.
Published: (2024)
ProteinZero: Self-Improving Protein Generation via Online Reinforcement Learning
by: Wang, Ziwen, et al.
Published: (2025)
by: Wang, Ziwen, et al.
Published: (2025)
SiDGen: Structure-informed Diffusion for Generative modeling of Ligands for Proteins
by: Sanghvi, Samyak, et al.
Published: (2025)
by: Sanghvi, Samyak, et al.
Published: (2025)
Efficiently Predicting Mutational Effect on Homologous Proteins by Evolution Encoding
by: Zhong, Zhiqiang, et al.
Published: (2024)
by: Zhong, Zhiqiang, et al.
Published: (2024)
Extracting Inter-Protein Interactions Via Multitasking Graph Structure Learning
by: Li, Jiang, et al.
Published: (2025)
by: Li, Jiang, et al.
Published: (2025)
PSC-CPI: Multi-Scale Protein Sequence-Structure Contrasting for Efficient and Generalizable Compound-Protein Interaction Prediction
by: Wu, Lirong, et al.
Published: (2024)
by: Wu, Lirong, et al.
Published: (2024)
Similar Items
-
Improving AlphaFlow for Efficient Protein Ensembles Generation
by: Li, Shaoning, et al.
Published: (2024) -
Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding
by: He, Xinheng, et al.
Published: (2025) -
Neural P$^3$M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs
by: Wang, Yusong, et al.
Published: (2024) -
Protein Inverse Folding From Structure Feedback
by: Xu, Junde, et al.
Published: (2025) -
F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching
by: Li, Shaoning, et al.
Published: (2024)