1 code implementation • 12 Dec 2023 • Alexandre Duval, Simon V. Mathis, Chaitanya K. Joshi, Victor Schmidt, Santiago Miret, Fragkiskos D. Malliaros, Taco Cohen, Pietro Liò, Yoshua Bengio, Michael Bronstein
In these graphs, the geometric attributes transform according to the inherent physical symmetries of 3D atomic systems, including rotations and translations in Euclidean space, as well as node permutations.
no code implementations • 7 Dec 2023 • Divya Nori, Simon V. Mathis, Amir Shanehsazzadeh
The success of therapeutic antibodies relies on their ability to selectively bind antigens.
1 code implementation • 14 Aug 2023 • Jos Torge, Charles Harris, Simon V. Mathis, Pietro Lio
Scaffold hopping is a drug discovery strategy to generate new chemical entities by modifying the core structure, the \emph{scaffold}, of a known active compound.
2 code implementations • 14 Aug 2023 • Charles Harris, Kieran Didi, Arian R. Jamasb, Chaitanya K. Joshi, Simon V. Mathis, Pietro Lio, Tom Blundell
Deep generative models for structure-based drug design (SBDD), where molecule generation is conditioned on a 3D protein pocket, have received considerable interest in recent years.
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 • 23 Jan 2023 • Chaitanya K. Joshi, Cristian Bodnar, Simon V. Mathis, Taco Cohen, Pietro Liò
The expressive power of Graph Neural Networks (GNNs) has been studied extensively through the Weisfeiler-Leman (WL) graph isomorphism test.