arXiv subjects

Libin Lu

Publications and source records attributed to Libin Lu.

10 recordsLinked to original sources

arXiv2026

Prolate spheroidal wave functions enable fast and exponent-aware long-range machine learning interatomic potentials

Long-range interactions such as electrostatics and dispersion remain a central bottleneck for machine learning interatomic potentials (MLIPs), especially in ionic, polar and interfacial systems. Ewald-based reciprocal-space mechanisms provide a physically grounded route for capturing these nonlocal effects, but often require dense Fourier grids and can become memory-limited at scale. This problem is particularly pronounced in molecular dynamics, where high efficiency requirements make accurate long-range modelling particularly costly. Here we introduce PSWF-LR, an exponent-aware long-range framework based on prolate spheroidal wave functions (PSWFs) that can be easily incorporated into existing model architectures. Its core components are PSWF-based mollification and atom-grid spreading, which enable compact and efficient representation of arbitrary inverse-power channels $1/r^p$ while treating the decay exponent as a physical prior. Across diverse long-range benchmarks, PSWF-LR reduces Fourier-mode requirements, improves energy and force accuracy, accelerates production-level simulations by about threefold, and extends long-range MLIP simulations beyond the memory limits of conventional MLIPs.

physics.chem-ph↗

arXiv2026

Fast Ewald Summation with Prolates for Charged Systems in the NPT Ensemble

We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework, this work focuses on rigorous and thermodynamically consistent pressure/stress evaluation in the isothermal--isobaric ensemble. ESP employs prolate spheroidal wave functions as both splitting and spreading kernels, reducing the Fourier grid size needed to reach a prescribed pressure accuracy compared with current widely used mesh-Ewald methods based on Gaussian splitting and B-spline spreading. We derive a unified pressure-tensor formulation applicable to isotropic, semi-isotropic, anisotropic, and fully flexible cells, and show that the long-range pressure can be evaluated with a single forward FFT followed by diagonal scaling, whereas force evaluation requires both forward and inverse transforms. We provide production implementations in LAMMPS and GROMACS and validate pressure and force accuracy on bulk water, LiTFSI ionic liquids, and a transmembrane system. Benchmarks on up to $3\times 10^3$ CPU cores demonstrate strong scaling and reduced communication cost at matched accuracy, particularly for NPT pressure evaluation.

math.NA↗

arXiv2025

Accelerating Molecular Dynamics Simulations using Fast Ewald Summation with Prolates

The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast Fourier transform to achieve near-linear scaling. We introduce ESP -- Ewald summation with prolate spheroidal wave functions (PSWFs) -- which leads to a more efficient Fourier representation and a reduction in the required grid size, global communication, and particle-grid operations, without loss of accuracy. We have integrated the ESP method into two widely-used open-source MD packages, LAMMPS and GROMACS, enabling rapid comparison and adoption. Relative to PME/PPPM baselines at error tolerances $10^{-3}$ to $10^{-4}$, ESP gives roughly a $3$-fold acceleration of electrostatic interactions, and a $2.5$-fold speed-up in the MD simulation when using about $10^3$ compute cores. At high accuracy ($10^{-5}$), these increase to $10$-fold for the far-field electrostatics and $5$-fold for MD simulation. Furthermore, we show that the accelerated codes have improved strong scaling with core count, and validate them in realistic long-time biological and material simulations. ESP thus offers a practical, drop-in path to reduce the time-to-solution and energy footprint of MD workflows.

math.NA↗

arXiv2025

WaveNet-SF: A Hybrid Network for Retinal Disease Detection Based on Wavelet Transform in Spatial-Frequency Domain

Retinal diseases are a leading cause of vision impairment and blindness, with timely diagnosis being critical for effective treatment. Optical Coherence Tomography (OCT) has become a standard imaging modality for retinal disease diagnosis, but OCT images often suffer from issues such as speckle noise, complex lesion shapes, and varying lesion sizes, making interpretation challenging. In this paper, we propose a novel framework, WaveNet-SF, to enhance retinal disease detection by integrating the spatial-domain and frequency-domain learning. The framework utilizes wavelet transforms to decompose OCT images into low- and high-frequency components, enabling the model to extract both global structural features and fine-grained details. To improve lesion detection, we introduce a Multi-Scale Wavelet Spatial Attention (MSW-SA) module, which enhances the model's focus on regions of interest at multiple scales. Additionally, a High-Frequency Feature Compensation (HFFC) block is incorporated to recover edge information lost during wavelet decomposition, suppress noise, and preserve fine details crucial for lesion detection. Our approach achieves state-of-the-art (SOTA) classification accuracies of 97.82% and 99.58% on the OCT-C8 and OCT2017 datasets, respectively, surpassing existing methods. These results demonstrate the efficacy of WaveNet-SF in addressing the challenges of OCT image analysis and its potential as a powerful tool for retinal disease diagnosis.

eess.IV↗

arXiv2023

Fusing Structural and Functional Connectivities using Disentangled VAE for Detecting MCI

Brain network analysis is a useful approach to studying human brain disorders because it can distinguish patients from healthy people by detecting abnormal connections. Due to the complementary information from multiple modal neuroimages, multimodal fusion technology has a lot of potential for improving prediction performance. However, effective fusion of multimodal medical images to achieve complementarity is still a challenging problem. In this paper, a novel hierarchical structural-functional connectivity fusing (HSCF) model is proposed to construct brain structural-functional connectivity matrices and predict abnormal brain connections based on functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI). Specifically, the prior knowledge is incorporated into the separators for disentangling each modality of information by the graph convolutional networks (GCN). And a disentangled cosine distance loss is devised to ensure the disentanglement's effectiveness. Moreover, the hierarchical representation fusion module is designed to effectively maximize the combination of relevant and effective features between modalities, which makes the generated structural-functional connectivity more robust and discriminative in the cognitive disease analysis. Results from a wide range of tests performed on the public Alzheimer's Disease Neuroimaging Initiative (ADNI) database show that the proposed model performs better than competing approaches in terms of classification evaluation. In general, the proposed HSCF model is a promising model for generating brain structural-functional connectivities and identifying abnormal brain connections as cognitive disease progresses.

eess.IV↗

arXiv2022

pmwd: A Differentiable Cosmological Particle-Mesh $N$-body Library

The formation of the large-scale structure, the evolution and distribution of galaxies, quasars, and dark matter on cosmological scales, requires numerical simulations. Differentiable simulations provide gradients of the cosmological parameters, that can accelerate the extraction of physical information from statistical analyses of observational data. The deep learning revolution has brought not only myriad powerful neural networks, but also breakthroughs including automatic differentiation (AD) tools and computational accelerators like GPUs, facilitating forward modeling of the Universe with differentiable simulations. Because AD needs to save the whole forward evolution history to backpropagate gradients, current differentiable cosmological simulations are limited by memory. Using the adjoint method, with reverse time integration to reconstruct the evolution history, we develop a differentiable cosmological particle-mesh (PM) simulation library pmwd (particle-mesh with derivatives) with a low memory cost. Based on the powerful AD library JAX, pmwd is fully differentiable, and is highly performant on GPUs.

astro-ph.IM↗

arXiv2022

Differentiable Cosmological Simulation with Adjoint Method

Rapid advances in deep learning have brought not only myriad powerful neural networks, but also breakthroughs that benefit established scientific research. In particular, automatic differentiation (AD) tools and computational accelerators like GPUs have facilitated forward modeling of the Universe with differentiable simulations. Based on analytic or automatic backpropagation, current differentiable cosmological simulations are limited by memory, and thus are subject to a trade-off between time and space/mass resolution, usually sacrificing both. We present a new approach free of such constraints, using the adjoint method and reverse time integration. It enables larger and more accurate forward modeling at the field level, and will improve gradient based optimization and inference. We implement it in an open-source particle-mesh (PM) $N$-body library pmwd (particle-mesh with derivatives). Based on the powerful AD system JAX, pmwd is fully differentiable, and is highly performant on GPUs.

astro-ph.IM↗

arXiv2019

Scalable Simulation of Realistic Volume Fraction Red Blood Cell Flows through Vascular Networks

High-resolution blood flow simulations have potential for developing better understanding biophysical phenomena at the microscale, such as vasodilation, vasoconstriction and overall vascular resistance. To this end, we present a scalable platform for the simulation of red blood cell (RBC) flows through complex capillaries by modeling the physical system as a viscous fluid with immersed deformable particles. We describe a parallel boundary integral equation solver for general elliptic partial differential equations, which we apply to Stokes flow through blood vessels. We also detail a parallel collision avoiding algorithm to ensure RBCs and the blood vessel remain contact-free. We have scaled our code on Stampede2 at the Texas Advanced Computing Center up to 34,816 cores. Our largest simulation enforces a contact-free state between four billion surface elements and solves for three billion degrees of freedom on one million RBCs and a blood vessel composed from two million patches.

cs.CE↗

arXiv2018

Parallel contact-aware simulations of deformable particles in 3D Stokes flow

We present a parallel-scalable method for simulating non-dilute suspensions of deformable particles immersed in Stokesian fluid in three dimensions. A critical component in these simulations is robust and accurate collision handling. This work complements our previous work [L. Lu, A. Rahimian, and D. Zorin. Contact-aware simulations of particulate Stokesian suspensions. Journal of Computational Physics 347C: 160-182] by extending it to 3D and by introducing new parallel algorithms for collision detection and handling. We use a well-established boundary integral formulation with spectral Galerkin method to solve the fluid flow. The key idea is to ensure an interference-free particle configuration by introducing explicit contact constraints into the system. While such constraints are typically unnecessary in the formulation they make it possible to eliminate catastrophic loss of accuracy in the discretized problem by preventing contact explicitly. The incorporation of contact constraints results in a significant increase in stable time-step size for locally-implicit time-stepping and a reduction in the necessary number of discretization points for stability. Our method maintains the accuracy of previous methods at a significantly lower cost for dense suspensions and the time step size is independent from the volume fraction. Our method permits simulations with high volume fractions; we report results with up to 60% volume fraction. We demonstrated the parallel scaling of the algorithms on up to 16K CPU cores.

math.NA↗

arXiv2016

Contact-aware simulations of particulate Stokesian suspensions

We present an efficient, accurate, and robust method for simulation of dense suspensions of deformable and rigid particles immersed in Stokesian fluid in two dimensions. We use a well-established boundary integral formulation for the problem as the foundation of our approach. This type of formulations, with a high-order spatial discretization and an implicit and adaptive time discretization, have been shown to be able to handle complex interactions between particles with high accuracy. Yet, for dense suspensions, very small time-steps or expensive implicit solves as well as a large number of discretization points are required to avoid non-physical contact and intersections between particles, leading to infinite forces and numerical instability. Our method maintains the accuracy of previous methods at a significantly lower cost for dense suspensions. The key idea is to ensure interference-free configuration by introducing explicit contact constraints into the system. While such constraints are unnecessary in the formulation, in the discrete form of the problem, they make it possible to eliminate catastrophic loss of accuracy by preventing contact explicitly. Introducing contact constraints results in a significant increase in stable time-step size for explicit time-stepping, and a reduction in the number of points adequate for stability.

math.NA↗