7 accepted papers
Protein foundation models have advanced rapidly, with most approaches falling into two dominant paradigms. Sequence-only language models (e.g., ESM-2) capture sequence semantics at scale but lack structural grounding. MSA-based predictors (e.g., AlphaFold 2/3) achieve accurate folding by exploiting…
Equivariant Graph Neural Networks (EGNNs) have demonstrated significant success in modeling microscale systems, including those in chemistry, biology and materials science. However, EGNNs face substantial computational challenges due to the high cost of constructing edge features via spherical tenso…
Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost—driven by high-orde…
Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources requ…
In this study, we introduce a unified neural network architecture, the Deep Equilibrium Density Functional Theory Hamiltonian (DEQH) model, which incorporates Deep Equilibrium Models (DEQs) for predicting Density Functional Theory (DFT) Hamiltonians. The DEQH model inherently captures the self-consi…
Computational simulation of chemical and biological systems using *ab initio* molecular dynamics has been a challenge over decades. Researchers have attempted to address the problem with machine learning and fragmentation-based methods. However, the two approaches fail to give a satisfactory descrip…
Predicting the mean-field Hamiltonian matrix in density functional theory is a fundamental formulation to leverage machine learning for solving molecular science problems. Yet, its applicability is limited by insufficient labeled data for training. In this work, we highlight that Hamiltonian predict…