4 papers
AMix-2: Establishing Protein as a Native Modality in Large Language Models
Keyue Qiu, Yixin Wu, Lihao Wang +19
We present AMix-2, a protein-text foundation model that establishes protein as a native modality in large language models (LLMs), unifying protein understanding and sequence design…
Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates
Kaiyuan Gao, Yusong Wang, Haoxiang Guan +5
The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics…
Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models
Zun Wang, Chang Liu, Nianlong Zou +5
In this study, we introduce a unified neural network architecture, the Deep Equilibrium Density Functional Theory Hamiltonian (DEQH) model, which incorporates Deep Equilibrium Mode…
SE3Set: Harnessing equivariant hypergraph neural networks for molecular representation learning
Hongfei Wu, Lijun Wu, Guoqing Liu +3
In this paper, we develop SE3Set, an SE(3) equivariant hypergraph neural network architecture tailored for advanced molecular representation learning. Hypergraphs are not merely an…