Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion
Trajectory Prediction

Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction

28 January 2023

Vijil Chenthamarakshan

Jian Tang

Papers citing "Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction"

16 / 16 papers shown

Title
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji W. Elwasif Linfeng Zhang Guolin Ke 48 0 0 20 Mar 2025
ProtFAD: Introducing function-aware domains as implicit modality towards protein function perception Mingqing Wang Zhiwei Nie Yonghong He Zhixiang Ren 19 0 0 24 May 2024
ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training Le Zhuo Zewen Chi Minghao Xu Heyan Huang Heqi Zheng Conghui He Xian-Ling Mao Wentao Zhang 76 11 0 28 Feb 2024
Feedback Efficient Online Fine-Tuning of Diffusion Models Masatoshi Uehara Yulai Zhao Kevin Black Ehsan Hajiramezanali Gabriele Scalia N. Diamant Alex Tseng Sergey Levine Tommaso Biancalani 27 21 0 26 Feb 2024
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 21 1 0 10 Feb 2024
Structure-Informed Protein Language Model Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 21 8 0 07 Feb 2024
Pre-Training Protein Bi-level Representation Through Span Mask Strategy On 3D Protein Chains Jiale Zhao Wanru Zhuang Jia Song Yaqi Li Shuqi Lu AI4CE 8 5 0 02 Feb 2024
PepHarmony: A Multi-View Contrastive Learning Framework for Integrated Sequence and Structure-Based Peptide Encoding Ruochi Zhang Haoran Wu Chang Liu Hua-Wang Li Yuqian Wu ... Yifan Wang Yifan Deng Jiahui Chen Fengfeng Zhou Xin Gao AI4TS 29 2 0 21 Jan 2024
A Multi-Modal Contrastive Diffusion Model for Therapeutic Peptide Generation Yongkang Wang Xuan Liu Feng Huang Zhankun Xiong Wen Zhang 50 14 0 25 Dec 2023
A Systematic Study of Joint Representation Learning on Protein Sequences and Structures Zuobai Zhang Chuanrui Wang Minghao Xu Vijil Chenthamarakshan A. Lozano Payel Das Jian Tang 27 30 0 11 Mar 2023
DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking Gabriele Corso Hannes Stärk Bowen Jing Regina Barzilay Tommi Jaakkola DiffM 136 409 0 04 Oct 2022
Contrastive Representation Learning for 3D Protein Structures Pedro Hermosilla Timo Ropinski 3DV 46 51 0 31 May 2022
Diffusion-LM Improves Controllable Text Generation Xiang Lisa Li John Thickstun Ishaan Gulrajani Percy Liang Tatsunori B. Hashimoto AI4CE 173 773 0 27 May 2022
Protein Structure and Sequence Generation with Equivariant Denoising Diffusion Probabilistic Models N. Anand Tudor Achim DiffM 183 173 0 26 May 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 112 302 0 07 Oct 2021
Argmax Flows and Multinomial Diffusion: Learning Categorical Distributions Emiel Hoogeboom Didrik Nielsen P. Jaini Patrick Forré Max Welling DiffM 207 394 0 10 Feb 2021