ICML24_Molecules_Generation.md

[ICML24] Molecules Generation

This is a repository summarizing the papers on molecular generation from ICML24.

Controllable Molecular generation

• Context-Guided Diffusion for Out-of-Distribution Molecular and Protein Design
  Leo Klarner, Tim G. J. Rudner, Garrett Morris, Charlotte Deane, Yee-Whye Teh

• Projecting Molecules into Synthesizable Chemical Spaces
  Shitong Luo, Wenhao Gao, Zuofan Wu, Jian Peng, Connor Coley, Jianzhu Ma

• Conditional Normalizing Flows for Active Learning of Coarse-Grained Molecular Representations
  Henrik Schopmans, Pascal Friederich

• Preference Optimization for Molecule Synthesis with Conditional Residual Energy-based Models
  Songtao Liu, Hanjun Dai, Yue Zhao, Peng Liu

• Generative Enzyme Design Guided by Functionally Important Sites and Small-Molecule Substrates
  Zhenqiao Song, Yunlong Zhao, Wenxian Shi, Wengong Jin, Yang Yang, Lei Li

Molecular Representation Learning

• Mol-AE: Auto-Encoder Based Molecular Representation Learning With 3D Cloze Test Objective
  Junwei Yang, Kangjie Zheng, Siyu Long, Zaiqing Nie, Ming Zhang, Xinyu Dai, Wei-Ying Ma, Hao Zhou

• Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers
  Md Shamim Hussain, Mohammed Zaki, Dharmashankar Subramanian

• GeoMFormer: A General Architecture for Geometric Molecular Representation Learning
  Tianlang Chen, Shengjie Luo, Di He, Shuxin Zheng, Tie-Yan Liu, Liwei Wang

• Representing Molecules as Random Walks Over Interpretable Grammars
  Michael Sun, Minghao Guo, Weize Yuan, Veronika Thost, Crystal Owens, Aristotle Grosz, Sharvaa Selvan, Katelyn Zhou, Hassan Mohiuddin, Benjamin Pedretti, Zachary Smith, Jie Chen, Wojciech Matusik

Molecular Interaction

• Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning
  Xiangzhe Kong, Wenbing Huang, Yang Liu
• Interaction-based Retrieval-augmented Diffusion Models for Protein-specific 3D Molecule Generation
  Zhilin Huang, Ling Yang, Xiangxin Zhou, Chujun Qin, Yijie Yu, Xiawu Zheng, Zikun Zhou, Wentao Zhang, Yu Wang, Wenming Yang

Data-Efficient

• Data-Efficient Molecular Generation with Hierarchical Textual Inversion
  Seojin Kim, Jaehyun Nam, Sihyun Yu, Younghoon Shin, Jinwoo Shin textual inversion
• Representing Molecules as Random Walks Over Interpretable Grammars
  Michael Sun, Minghao Guo, Weize Yuan, Veronika Thost, Crystal Owens, Aristotle Grosz, Sharvaa Selvan, Katelyn Zhou, Hassan Mohiuddin, Benjamin Pedretti, Zachary Smith, Jie Chen, Wojciech Matusik
• Domain-Aware Guidance for Out-of-Distribution Molecular Design
  Leo Klarner, Tim G. J. Rudner, Garrett Morris, Charlotte Deane, Yee-Whye Teh

Else

• Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks
  Duy Nguyen, Nina Lukashina, Tai Nguyen, An Thai Le, TrungTin Nguyen, Nhat Ho, Jan Peters, Daniel Sonntag, Viktor Zaverkin, Mathias Niepert
• Surface-VQMAE: Vector-quantized Masked Auto-encoders on Molecular Surfaces
  Fang Wu, Stan Z Li
• ESM All-Atom: Multi-Scale Protein Language Model for Unified Molecular Modeling
  Kangjie Zheng, Siyu Long, Tianyu Lu, Junwei Yang, Xinyu Dai, Ming Zhang, Zaiqing Nie, Wei-Ying Ma, Hao Zhou
• Re-Dock: Towards Flexible and Realistic Molecular Docking with Diffusion Bridge
  Yufei Huang, Odin Zhang, Lirong Wu, Cheng Tan, Haitao Lin, Zhangyang Gao, Siyuan Li, Stan Z Li