arXiv subjects

Bin Shao

Publications and source records attributed to Bin Shao.

At least 19 recordsLinked to original sources

arXiv2026

Fine-Tuning Small Language Models for Reliable VASP INCAR Generation

Language models can prepare VASP INCAR files from natural-language requests, but so far only large proprietary cloud models come close to handling the tightly coupled, physics-sensitive settings reliably, a dependence that fits poorly with local, high-throughput materials workflows where privacy, cost, and offline deployment matter. We show that a small language model (SLM) can close this gap. The SLM is fine-tuned on reference VASP calculations and paired with VASPGuard, a deterministic post-processor that checks syntax, workflow, and material-dependent constraints; we call the combined model INCAR-SLM. On INCARBench, a benchmark for VASP INCAR generation, INCAR-SLM built on Qwen3-4B outperforms every general-purpose LLM evaluated, exceeding GPT-5.4 by 15.55 points on the 100-point INCAR Score. Most of this gain comes from fine-tuning, with VASPGuard correcting the errors that remain. We further find that model size matters less than expected: once fine-tuning and post-processing are applied, performance saturates at a few billion parameters, and Qwen3-4B outperforms larger models in the same family.

cond-mat.mtrl-sci↗

arXiv2026

INCARBench: A Benchmark for Scientific Configuration in VASP INCAR by Large Language Models

Large language models (LLMs) are increasingly being integrated into first-principles computational workflows, yet their ability to configure scientific calculations remains poorly understood. Here, we introduce INCARBench, a benchmark for evaluating LLMs on input configuration for the Vienna Ab initio Simulation Package (VASP) through both configuration generation and repair tasks. Evaluating 19 model configurations reveals substantial capability differences among current frontier models. While several models achieve high semantic and policy accuracy, task-critical correctness remains substantially lower, demonstrating that parameter-level correctness does not necessarily imply scientifically valid configurations. Failure analysis shows that errors concentrate in physically coupled settings involving DFT+$U$, magnetism, and correlated materials, where multiple constraints must be satisfied simultaneously. Repair evaluation further reveals that correcting incorrect settings and preserving already-valid configurations are distinct capabilities, with configuration preservation remaining a major challenge. These findings establish scientific configuration as a measurable capability of large language models and provide a foundation for developing more reliable AI systems for computational materials science.

cond-mat.mtrl-sci↗

arXiv2026

Accelerating Locality-Driven Integration in Quantum Chemistry with Block-Structured Matrix Multiplication

Locality-driven integration is a pervasive computational pattern in quantum chemistry, arising whenever spatially localized basis functions interact through numerical quadrature or integral screening. The dominant matrix multiplications in these tasks exhibit dynamic, structured sparsity driven by spatial locality, posing significant challenges for both dense batched kernels and generic sparse formats on GPUs. We present KerneLDI, a GPU-oriented framework that addresses this regime by co-designing data layout, screening logic, and matrix-computation operators to realize block-structured matrix multiplication for locality-driven integration. KerneLDI reorganizes operand matrices into a unified block-filtered representation that retains only spatially relevant blocks, and executes the resulting contractions with customized dense block multipliers that adapt proven dense-matmul optimizations to retained block pairs. We develop and evaluate KerneLDI on exchange--correlation (EXC) integration in Kohn--Sham density functional theory, a representative and computationally critical instance of this pattern. Across diverse molecular systems, KerneLDI preserves numerical accuracy while delivering up to 10$\times$ speedup for EXC evaluation over a dense GPU baseline, scales favorably with increasing system size and multi-GPU parallelism, accelerates end-to-end self-consistent field calculations, and yields nearly 6$\times$ throughput improvement for ab initio molecular dynamics.

physics.comp-ph↗

arXiv2025

Turbo2K: Towards Ultra-Efficient and High-Quality 2K Video Synthesis

Demand for 2K video synthesis is rising with increasing consumer expectations for ultra-clear visuals. While diffusion transformers (DiTs) have demonstrated remarkable capabilities in high-quality video generation, scaling them to 2K resolution remains computationally prohibitive due to quadratic growth in memory and processing costs. In this work, we propose Turbo2K, an efficient and practical framework for generating detail-rich 2K videos while significantly improving training and inference efficiency. First, Turbo2K operates in a highly compressed latent space, reducing computational complexity and memory footprint, making high-resolution video synthesis feasible. However, the high compression ratio of the VAE and limited model size impose constraints on generative quality. To mitigate this, we introduce a knowledge distillation strategy that enables a smaller student model to inherit the generative capacity of a larger, more powerful teacher model. Our analysis reveals that, despite differences in latent spaces and architectures, DiTs exhibit structural similarities in their internal representations, facilitating effective knowledge transfer. Second, we design a hierarchical two-stage synthesis framework that first generates multi-level feature at lower resolutions before guiding high-resolution video generation. This approach ensures structural coherence and fine-grained detail refinement while eliminating redundant encoding-decoding overhead, further enhancing computational efficiency.Turbo2K achieves state-of-the-art efficiency, generating 5-second, 24fps, 2K videos with significantly reduced computational cost. Compared to existing methods, Turbo2K is up to 20$\times$ faster for inference, making high-resolution video generation more scalable and practical for real-world applications.

cs.CV↗

arXiv2025

Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems

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 required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

physics.chem-ph↗

arXiv2025

Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity

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-order tensor product (TP) operations--restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network, that incorporates adaptive SParsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70%. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact. Our code can be found at https://github.com/microsoft/SPHNet.

cs.LG↗

arXiv2024

MagicEraser: Erasing Any Objects via Semantics-Aware Control

The traditional image inpainting task aims to restore corrupted regions by referencing surrounding background and foreground. However, the object erasure task, which is in increasing demand, aims to erase objects and generate harmonious background. Previous GAN-based inpainting methods struggle with intricate texture generation. Emerging diffusion model-based algorithms, such as Stable Diffusion Inpainting, exhibit the capability to generate novel content, but they often produce incongruent results at the locations of the erased objects and require high-quality text prompt inputs. To address these challenges, we introduce MagicEraser, a diffusion model-based framework tailored for the object erasure task. It consists of two phases: content initialization and controllable generation. In the latter phase, we develop two plug-and-play modules called prompt tuning and semantics-aware attention refocus. Additionally, we propose a data construction strategy that generates training data specially suitable for this task. MagicEraser achieves fine and effective control of content generation while mitigating undesired artifacts. Experimental results highlight a valuable advancement of our approach in the object erasure task.

cs.CV↗

arXiv2024

Neural P$^3$M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this challenge, we introduce Neural P$^3$M, a versatile enhancer of geometric GNNs to expand the scope of their capabilities by incorporating mesh points alongside atoms and reimaging traditional mathematical operations in a trainable manner. Neural P$^3$M exhibits flexibility across a wide range of molecular systems and demonstrates remarkable accuracy in predicting energies and forces, outperforming on benchmarks such as the MD22 dataset. It also achieves an average improvement of 22% on the OE62 dataset while integrating with various architectures.

cs.LG↗

arXiv2024

Long-Short-Range Message-Passing: A Physics-Informed Framework to Capture Non-Local Interaction for Scalable Molecular Dynamics Simulation

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 description of long-range and many-body interactions, respectively. Inspired by fragmentation-based methods, we propose the Long-Short-Range Message-Passing (LSR-MP) framework as a generalization of the existing equivariant graph neural networks (EGNNs) with the intent to incorporate long-range interactions efficiently and effectively. We apply the LSR-MP framework to the recently proposed ViSNet and demonstrate the state-of-the-art results with up to 40% MAE reduction for molecules in MD22 and Chignolin datasets. Consistent improvements to various EGNNs will also be discussed to illustrate the general applicability and robustness of our LSR-MP framework. The code for our experiments and trained model weights could be found at https://github.com/liyy2/LSR-MP.

physics.chem-ph↗

arXiv2024

UltraPixel: Advancing Ultra-High-Resolution Image Synthesis to New Peaks

Ultra-high-resolution image generation poses great challenges, such as increased semantic planning complexity and detail synthesis difficulties, alongside substantial training resource demands. We present UltraPixel, a novel architecture utilizing cascade diffusion models to generate high-quality images at multiple resolutions (\textit{e.g.}, 1K to 6K) within a single model, while maintaining computational efficiency. UltraPixel leverages semantics-rich representations of lower-resolution images in the later denoising stage to guide the whole generation of highly detailed high-resolution images, significantly reducing complexity. Furthermore, we introduce implicit neural representations for continuous upsampling and scale-aware normalization layers adaptable to various resolutions. Notably, both low- and high-resolution processes are performed in the most compact space, sharing the majority of parameters with less than 3$\%$ additional parameters for high-resolution outputs, largely enhancing training and inference efficiency. Our model achieves fast training with reduced data requirements, producing photo-realistic high-resolution images and demonstrating state-of-the-art performance in extensive experiments.

cs.CV↗

arXiv2024

Acceleration without Disruption: DFT Software as a Service

Density functional theory (DFT) has been a cornerstone in computational chemistry, physics, and materials science for decades, benefiting from advancements in computational power and theoretical methods. This paper introduces a novel, cloud-native application, Accelerated DFT, which offers an order of magnitude acceleration in DFT simulations. By integrating state-of-the-art cloud infrastructure and redesigning algorithms for graphic processing units (GPUs), Accelerated DFT achieves high-speed calculations without sacrificing accuracy. It provides an accessible and scalable solution for the increasing demands of DFT calculations in scientific communities. The implementation details, examples, and benchmark results illustrate how Accelerated DFT can significantly expedite scientific discovery across various domains.

physics.chem-ph↗

arXiv2024

Infusing Self-Consistency into Density Functional Theory Hamiltonian Prediction via Deep Equilibrium Models

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-consistency nature of Hamiltonian, a critical aspect often overlooked by traditional machine learning approaches for Hamiltonian prediction. By employing DEQ within our model architecture, we circumvent the need for DFT calculations during the training phase to introduce the Hamiltonian's self-consistency, thus addressing computational bottlenecks associated with large or complex systems. We propose a versatile framework that combines DEQ with off-the-shelf machine learning models for predicting Hamiltonians. When benchmarked on the MD17 and QH9 datasets, DEQHNet, an instantiation of the DEQH framework, has demonstrated a significant improvement in prediction accuracy. Beyond a predictor, the DEQH model is a Hamiltonian solver, in the sense that it uses the fixed-point solving capability of the deep equilibrium model to iteratively solve for the Hamiltonian. Ablation studies of DEQHNet further elucidate the network's effectiveness, offering insights into the potential of DEQ-integrated networks for Hamiltonian learning. We open source our implementation at https://github.com/Zun-Wang/DEQHNet.

cs.LG↗

arXiv2024

Self-Consistency Training for Density-Functional-Theory Hamiltonian Prediction

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 prediction possesses a self-consistency principle, based on which we propose self-consistency training, an exact training method that does not require labeled data. It distinguishes the task from predicting other molecular properties by the following benefits: (1) it enables the model to be trained on a large amount of unlabeled data, hence addresses the data scarcity challenge and enhances generalization; (2) it is more efficient than running DFT to generate labels for supervised training, since it amortizes DFT calculation over a set of queries. We empirically demonstrate the better generalization in data-scarce and out-of-distribution scenarios, and the better efficiency over DFT labeling. These benefits push forward the applicability of Hamiltonian prediction to an ever-larger scale.

cs.LG↗

arXiv2024

SE3Set: Harnessing equivariant hypergraph neural networks for molecular representation learning

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 extension of traditional graphs; they are pivotal for modeling high-order relationships, a capability that conventional equivariant graph-based methods lack due to their inherent limitations in representing intricate many-body interactions. To achieve this, we first construct hypergraphs via proposing a new fragmentation method that considers both chemical and three-dimensional spatial information of molecular system. We then design SE3Set, which incorporates equivariance into the hypergragh neural network. This ensures that the learned molecular representations are invariant to spatial transformations, thereby providing robustness essential for accurate prediction of molecular properties. SE3Set has shown performance on par with state-of-the-art (SOTA) models for small molecule datasets like QM9 and MD17. It excels on the MD22 dataset, achieving a notable improvement of approximately 20% in accuracy across all molecules, which highlights the prevalence of complex many-body interactions in larger molecules. This exceptional performance of SE3Set across diverse molecular structures underscores its transformative potential in computational chemistry, offering a route to more accurate and physically nuanced modeling.

cs.LG↗

arXiv2024

F$^3$low: Frame-to-Frame Coarse-grained Molecular Dynamics with SE(3) Guided Flow Matching

Molecular dynamics (MD) is a crucial technique for simulating biological systems, enabling the exploration of their dynamic nature and fostering an understanding of their functions and properties. To address exploration inefficiency, emerging enhanced sampling approaches like coarse-graining (CG) and generative models have been employed. In this work, we propose a \underline{Frame-to-Frame} generative model with guided \underline{Flow}-matching (F$3$low) for enhanced sampling, which (a) extends the domain of CG modeling to the SE(3) Riemannian manifold; (b) retreating CGMD simulations as autoregressively sampling guided by the former frame via flow-matching models; (c) targets the protein backbone, offering improved insights into secondary structure formation and intricate folding pathways. Compared to previous methods, F$3$low allows for broader exploration of conformational space. The ability to rapidly generate diverse conformations via force-free generative paradigm on SE(3) paves the way toward efficient enhanced sampling methods.

q-bio.QM↗

arXiv2024

Overcoming the Barrier of Orbital-Free Density Functional Theory for Molecular Systems Using Deep Learning

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a lower cost scaling than the prevailing Kohn-Sham DFT, which is increasingly desired for contemporary molecular research. However, its accuracy is limited by the kinetic energy density functional, which is notoriously hard to approximate for non-periodic molecular systems. Here we propose M-OFDFT, an OFDFT approach capable of solving molecular systems using a deep learning functional model. We build the essential non-locality into the model, which is made affordable by the concise density representation as expansion coefficients under an atomic basis. With techniques to address unconventional learning challenges therein, M-OFDFT achieves a comparable accuracy with Kohn-Sham DFT on a wide range of molecules untouched by OFDFT before. More attractively, M-OFDFT extrapolates well to molecules much larger than those seen in training, which unleashes the appealing scaling of OFDFT for studying large molecules including proteins, representing an advancement of the accuracy-efficiency trade-off frontier in quantum chemistry.

stat.ML↗

arXiv2023

Orthogonality catastrophe and quantum speed limit for dynamical quantum phase transition

We investigate the orthogonality catastrophe and quantum speed limit in the Creutz model for dynamical quantum phase transitions. We demonstrate that exact zeros of the Loschmidt echo can exist in finite-size systems for specific discrete values. We highlight the role of the zero-energy mode when analyzing quench dynamics near the critical point. We also examine the behavior of the time for the first exact zeros of the Loschmidt echo and the corresponding quantum speed limit time as the system size increases. While the bound is not tight, it can be attributed to the scaling properties of the band gap and energy variance with respect to system size. As such, we establish a relation between the orthogonality catastrophe and quantum speed limit by referencing the full form of the Loschmidt echo. Significantly, we find the possibility of using the quantum speed limit to detect the critical point of a static quantum phase transition, along with a decrease in the amplitude of noise induced quantum speed limit.

quant-ph↗

arXiv2023

ViSNet: an equivariant geometry-enhanced graph neural network with vector-scalar interactive message passing for molecules

Geometric deep learning has been revolutionizing the molecular modeling field. Despite the state-of-the-art neural network models are approaching ab initio accuracy for molecular property prediction, their applications, such as drug discovery and molecular dynamics (MD) simulation, have been hindered by insufficient utilization of geometric information and high computational costs. Here we propose an equivariant geometry-enhanced graph neural network called ViSNet, which elegantly extracts geometric features and efficiently models molecular structures with low computational costs. Our proposed ViSNet outperforms state-of-the-art approaches on multiple MD benchmarks, including MD17, revised MD17 and MD22, and achieves excellent chemical property prediction on QM9 and Molecule3D datasets. Additionally, ViSNet achieved the top winners of PCQM4Mv2 track in the OGB-LCS@NeurIPS2022 competition. Furthermore, through a series of simulations and case studies, ViSNet can efficiently explore the conformational space and provide reasonable interpretability to map geometric representations to molecular structures.

physics.chem-ph↗