4 papers
AntigenLM: Structure-Aware DNA Language Modeling for Influenza
Yue Pei, Xuebin Chi, Yu Kang
Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA langua…
A Scalable and Quantum-Accurate Foundation Model for Biomolecular Force Field via Linearly Tensorized Quadrangle Attention
Qun Su, Kai Zhu, Qiaolin Gou +11
Accurate atomistic biomolecular simulations are vital for disease mechanism understanding, drug discovery, and biomaterial design, but existing simulation methods exhibit significa…
Graph Neural Networks in Modern AI-aided Drug Discovery
Odin Zhang, Haitao Lin, Xujun Zhang +9
Graph neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on m…
Descriptors-free Collective Variables From Geometric Graph Neural Networks
Jintu Zhang, Luigi Bonati, Enrico Trizio +4
Enhanced sampling simulations make the computational study of rare events feasible. A large family of such methods crucially depends on the definition of some collective variables…