1 code implementation • 17 Jul 2023 • Xuan Zhang, Limei Wang, Jacob Helwig, Youzhi Luo, Cong Fu, Yaochen Xie, Meng Liu, Yuchao Lin, Zhao Xu, Keqiang Yan, Keir Adams, Maurice Weiler, Xiner Li, Tianfan Fu, Yucheng Wang, Haiyang Yu, Yuqing Xie, Xiang Fu, Alex Strasser, Shenglong Xu, Yi Liu, Yuanqi Du, Alexandra Saxton, Hongyi Ling, Hannah Lawrence, Hannes Stärk, Shurui Gui, Carl Edwards, Nicholas Gao, Adriana Ladera, Tailin Wu, Elyssa F. Hofgard, Aria Mansouri Tehrani, Rui Wang, Ameya Daigavane, Montgomery Bohde, Jerry Kurtin, Qian Huang, Tuong Phung, Minkai Xu, Chaitanya K. Joshi, Simon V. Mathis, Kamyar Azizzadenesheli, Ada Fang, Alán Aspuru-Guzik, Erik Bekkers, Michael Bronstein, Marinka Zitnik, Anima Anandkumar, Stefano Ermon, Pietro Liò, Rose Yu, Stephan Günnemann, Jure Leskovec, Heng Ji, Jimeng Sun, Regina Barzilay, Tommi Jaakkola, Connor W. Coley, Xiaoning Qian, Xiaofeng Qian, Tess Smidt, Shuiwang Ji
Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences.
1 code implementation • 6 May 2023 • Cong Fu, Keqiang Yan, Limei Wang, Wing Yee Au, Michael McThrow, Tao Komikado, Koji Maruhashi, Kanji Uchino, Xiaoning Qian, Shuiwang Ji
Proteins are complex biomolecules that perform a variety of crucial functions within living organisms.
1 code implementation • NeurIPS 2023 • Weitao Du, Yuanqi Du, Limei Wang, Dieqiao Feng, Guifeng Wang, Shuiwang Ji, Carla Gomes, Zhi-Ming Ma
Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects.
1 code implementation • 26 Jul 2022 • Limei Wang, Haoran Liu, Yi Liu, Jerry Kurtin, Shuiwang Ji
In this work, we propose to develop a novel hierarchical graph network, known as ProNet, to capture the relations.
1 code implementation • 17 Jun 2022 • Limei Wang, Yi Liu, Yuchao Lin, Haoran Liu, Shuiwang Ji
To incorporate 3D information completely and efficiently, we propose a novel message passing scheme that operates within 1-hop neighborhood.
Ranked #4 on Drug Discovery on QM9
1 code implementation • 16 Jun 2022 • Shurui Gui, Xiner Li, Limei Wang, Shuiwang Ji
Our GOOD benchmark is a growing project and expects to expand in both quantity and variety of resources as the area develops.
1 code implementation • 14 Jun 2022 • Haiyang Yu, Limei Wang, Bokun Wang, Meng Liu, Tianbao Yang, Shuiwang Ji
GraphFM-IB applies FM to in-batch sampled data, while GraphFM-OB applies FM to out-of-batch data that are 1-hop neighborhood of in-batch data.
1 code implementation • NeurIPS Workshop AI4Scien 2021 • Meng Liu, Cong Fu, Xuan Zhang, Limei Wang, Yaochen Xie, Hao Yuan, Youzhi Luo, Zhao Xu, Shenglong Xu, Shuiwang Ji
We employ our methods to participate in the 2021 KDD Cup on OGB Large-Scale Challenge (OGB-LSC), which aims to predict the HOMO-LUMO energy gap of molecules.
1 code implementation • 23 Mar 2021 • Meng Liu, Youzhi Luo, Limei Wang, Yaochen Xie, Hao Yuan, Shurui Gui, Haiyang Yu, Zhao Xu, Jingtun Zhang, Yi Liu, Keqiang Yan, Haoran Liu, Cong Fu, Bora Oztekin, Xuan Zhang, Shuiwang Ji
Although there exist several libraries for deep learning on graphs, they are aiming at implementing basic operations for graph deep learning.
1 code implementation • ICLR 2022 • Yi Liu, Limei Wang, Meng Liu, Xuan Zhang, Bora Oztekin, Shuiwang Ji
Based on such observations, we propose the spherical message passing (SMP) as a novel and powerful scheme for 3D molecular learning.
Ranked #3 on Drug Discovery on QM9
1 code implementation • 2 Dec 2020 • Zhengyang Wang, Meng Liu, Youzhi Luo, Zhao Xu, Yaochen Xie, Limei Wang, Lei Cai, Qi Qi, Zhuoning Yuan, Tianbao Yang, Shuiwang Ji
Here we develop a suite of comprehensive machine learning methods and tools spanning different computational models, molecular representations, and loss functions for molecular property prediction and drug discovery.