We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks.

B: Overview of the proposed PhiSNet architecture.

Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 2,399 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications.

We consider the task of predicting Hamiltonian matrices to accelerate electronic structure calculations, which plays an important role in physics, chemistry, and materials science. Motivated by the inherent relationship between the off-diagonal blocks of the Hamiltonian matrix and the SO(2) local frame, we propose a novel and efficient network, called QHNetV2, that achieves global SO(3) equivariance without the costly SO(3) Clebsch-Gordan tensor products. This is achieved by introducing a set of new efficient and powerful SO(2)-equivariant operations and performing all off-diagonal feature updates and message passing within SO(2) local frames, thereby eliminating the need of SO(3) tensor products. Moreover, a continuous SO(2) tensor product is performed within the SO(2) local frame at each node to fuse node features, mimicking the symmetric contraction operation. Extensive experiments on the large QH9 and MD17 datasets demonstrate that our model achieves superior performance across a wide range of molecular structures and trajectories, highlighting its strong generalization capability. The proposed SO(2) operations on SO(2) local frames offer a promising direction for scalable and symmetry-aware learning of electronic structures. Our code will be released as part of the AIRS library https://github.com/divelab/AIRS.

Recently, sophisticated deep learning-based approaches have been developed for generating efficient initial guesses to accelerate the convergence of density functional theory (DFT) calculations. While the actual initial guesses are often density matrices (DM), quantities that can convert into density matrices also qualify as alternative forms of initial guesses. Hence, existing works mostly rely on the prediction of the Hamiltonian matrix for obtaining high-quality initial guesses. However, the Hamiltonian matrix is both numerically difficult to predict and intrinsically non-transferable, hindering the application of such models in real scenarios. In light of this, we propose a method that constructs DFT initial guesses by predicting the electron density in a compact auxiliary basis representation using E(3)-equivariant neural networks. Trained on small molecules with up to 20 atoms, our model is able to achieve an average 33.3% self-consistent field (SCF) step reduction on systems up to 60 atoms, substantially outperforming Hamiltonian-centric and DM-centric models. Critically, this acceleration remains nearly constant with increasing system sizes and exhibits strong transferring behaviors across orbital basis sets and exchange-correlation (XC) functionals. To the best of our knowledge, this work represents the first and robust candidate for a universally transferable DFT acceleration method. We are also releasing the SCFbench dataset and its accompanying code to facilitate future research in this promising direction.

We also introduce a novel benchmark for evaluating NNPs in molecular property prediction, Hamiltonian prediction, and conformational optimization tasks.

Deep learning methods for electronic-structure Hamiltonian prediction has offered significant computational efficiency advantages over traditional density functional theory (DFT), yet the diversity of atomic types, structural patterns, and the high-dimensional complexity of Hamiltonians pose substantial challenges to the generalization performance. In this work, we contribute on both the methodology and dataset sides to advance universal deep learning paradigm for Hamiltonian prediction. On the method side, we propose NextHAM, a neural E(3)-symmetry and expressive correction method for efficient and generalizable materials electronic-structure Hamiltonian prediction. First, we introduce the zeroth-step Hamiltoni-ans, which can be efficiently constructed by the initial charge density of DFT, as informative descriptors of neural regression model in the input level and initial estimates of the target Hamiltonian in the output level, so that the regression model directly predicts the correction terms to the target ground truths, thereby significantly simplifying the input-output mapping and facilitating fine-grained predictions. Second, we present a neural Transformer architecture with strict E(3)-Symmetry and high non-linear expressiveness for Hamiltonian prediction. Third, we propose a novel training objective to ensure the accuracy performance of Hamiltonians in both real space and reciprocal space, preventing error amplification and the occurrence of "ghost states" caused by the large condition number of the overlap matrix. Experimental results on Materials-HAM-SOC demonstrate that NextHAM achieves excellent accuracy in predicting Hamiltonians and band structures, with spin-off-diagonal block reaching the accuracy of sub-µeV scale. These results establish NextHAM as a universal and highly accurate deep learning model for electronic-structure prediction, delivering DFT -level precision with dramatically improved computational efficiency. Understanding the electronic structure is fundamental to unraveling how electrons govern the properties of condensed matter systems. This knowledge is essential for predicting a wide range of material characteristics, such as electrical conductivity, magnetism, optical behavior, and chemical activity, which are vital for technologies spanning from electronics to sustainable energy and advanced catalysis. At the heart of these calculations is the challenge of determining the system's Hamiltonian matrix, whose eigenvalues and eigenstates yield important quantities like energy levels, band structures, and electronic wavefunctions. Traditionally, Density Functional Theory (DFT) (Hohenberg & Kohn, 1964; Kohn & Sham, 1965) has been the standard approach for these problems. Recently, deep learning has emerged as a powerful tool in the physical sciences (Zhang et al., 2025).