arXiv subjects

Shuo-Hui Li

Publications and source records attributed to Shuo-Hui Li.

7 recordsLinked to original sources

arXiv2026

Predicting Solvation Free Energies of Molecules and Ions via First-Principles and Machine-Learning Molecular Dynamics

The solvation free energy (SFE) of molecules and ions is a fundamental property governing their solvation behavior and solubility. Molecular simulations offer a route to compute SFEs using alchemical free energy methods, such as thermodynamic integration or free energy perturbation. However, these methods suffer from the infamous end-point singularity, which leads to numerical instability when atoms approach closely, a challenge that becomes particularly acute in ab initio and machine learning molecular dynamics simulations. Here, we introduce the bubble method to calculate the SFEs of molecules and ions from first principles. Our approach avoids the end-state problem in both ab initio and machine learning molecular dynamics simulations and is applicable to molecules and ions of arbitrary shape. When calculating the SFEs of ions using periodic density functional theory, we incorporate corrections for the neutralizing background charge, spurious interactions between periodic images, and the vacuum-water interface potential. To validate our method, we successfully computed the SFEs of methane, methanol, water, and sodium ions using classical, ab initio, and machine learning molecular dynamics simulations. Importantly, our method requires no experimental inputs or empirical data. This makes it particularly well-suited for studying systems under extreme conditions, such as high pressure-temperature environments or under nanoconfinement, situations where experimental investigations are challenging and classical force fields, typically parameterized under ambient conditions, may be unreliable.

physics.chem-ph↗

arXiv2026

Differentiable free energy surface: a variational approach to directly observing rare events using generative deep-learning models

Rare events are central to the evolution of complex many-body systems, characterized as key transitional configurations on the free energy surface (FES). Conventional methods require adequate sampling of rare event transitions to obtain the FES, which is computationally very demanding. Here we introduce the variational free energy surface (VaFES), a dataset-free framework that directly models FESs using tractable-density generative models. Rare events can then be immediately identified from the FES with their configurations generated directly via one-shot sampling of generative models. By extending a coarse-grained collective variable (CV) into its reversible equivalent, VaFES constructs a latent space of intermediate representation in which the CVs explicitly occupy a subset of dimensions. This latent-space construction preserves the physical interpretability and transparent controllability of the CVs by design, while accommodating arbitrary CV formulations. The reversibility makes the system energy exactly accessible, enabling variational optimization of the FES without pre-generated simulation data. A single optimization yields a continuous, differentiable FES together with one-shot generation of rare-event configurations. Our method can reproduce the exact analytical solution for the bistable dimer potential and identify a chignolin native folded state in close alignment with the experimental NMR structure. Our approach thus establishes a scalable, systematic framework for advancing the study of complex statistical systems.

physics.comp-ph↗

arXiv2024

Deep generative modelling of canonical ensemble with differentiable thermal properties

It is a long-standing challenge to accurately and efficiently compute thermodynamic quantities of many-body systems at thermal equilibrium. The conventional methods, e.g., Markov chain Monte Carlo, require many steps to equilibrate. The recently developed deep learning methods can perform direct sampling, but only work at a single trained temperature point and risk biased sampling. Here, we propose a variational method for canonical ensembles with differentiable temperature, which gives thermodynamic quantities as continuous functions of temperature akin to an analytical solution. The proposed method is a general framework that works with any tractable density generative model. At optimal, the model is theoretically guaranteed to be the unbiased Boltzmann distribution. We validated our method by calculating phase transitions in the Ising and XY models, demonstrating that our direct-sampling simulations are as accurate as Markov chain Monte Carlo, but more efficient. Moreover, our differentiable free energy aligns closely with the exact one to the second-order derivative, indicating that the variational model captures the subtle thermal transitions at the phase transitions. This functional dependence on external parameters is a fundamental advancement in combining the exceptional fitting ability of deep learning with rigorous physical analysis.

cond-mat.stat-mech↗

arXiv2022

Learning Non-linear Wavelet Transformation via Normalizing Flow

Wavelet transformation stands as a cornerstone in modern data analysis and signal processing. Its mathematical essence is an invertible transformation that discerns slow patterns from fast ones in the frequency domain. Such an invertible transformation can be learned by a designed normalizing flow model. With a generalized lifting scheme as coupling layers, a factor-out layer resembling the downsampling, and parameter sharing at different levels of the model, one can train the normalizing flow to filter high-frequency elements at different levels, thus extending traditional linear wavelet transformations to learnable non-linear deep learning models. In this paper, a way of building such flow is proposed, along with a numerical analysis of the learned transformation. Then, we demonstrate the model's ability in image lossless compression, show it can achieve SOTA compression scores while achieving a small model size, substantial generalization ability, and the ability to handle high-dimensional data.

cs.LG↗

arXiv2020

Neural Canonical Transformation with Symplectic Flows

Canonical transformation plays a fundamental role in simplifying and solving classical Hamiltonian systems. We construct flexible and powerful canonical transformations as generative models using symplectic neural networks. The model transforms physical variables towards a latent representation with an independent harmonic oscillator Hamiltonian. Correspondingly, the phase space density of the physical system flows towards a factorized Gaussian distribution in the latent space. Since the canonical transformation preserves the Hamiltonian evolution, the model captures nonlinear collective modes in the learned latent representation. We present an efficient implementation of symplectic neural coordinate transformations and two ways to train the model. The variational free energy calculation is based on the analytical form of physical Hamiltonian. While the phase space density estimation only requires samples in the coordinate space for separable Hamiltonians. We demonstrate appealing features of neural canonical transformation using toy problems including two-dimensional ring potential and harmonic chain. Finally, we apply the approach to real-world problems such as identifying slow collective modes in alanine dipeptide and conceptual compression of the MNIST dataset.

cond-mat.stat-mech↗

arXiv2019

Machine Learning Holographic Mapping by Neural Network Renormalization Group

The exact holographic mapping (EHM) provides an explicit duality map between a conformal field theory (CFT) configuration and a massive field propagating on an emergent classical geometry. However, designing the optimal holographic mapping is challenging. Here we introduce the neural network renormalization group as a universal approach to design generic EHM for interacting field theories. Given a field theory action, we train a flow-based hierarchical deep generative neural network to reproduce the boundary field ensemble from uncorrelated bulk field fluctuations. In this way, the neural network develops the optimal renormalization group transformations. Using the machine-designed EHM to map the CFT back to a bulk effective action, we determine the bulk geodesic distance from the residual mutual information. We apply this approach to the complex $ϕ^4$ theory in two-dimensional Euclidian spacetime in its critical phase, and show that the emergent bulk geometry matches the three-dimensional hyperbolic geometry.

cond-mat.dis-nn↗

arXiv2018

Neural Network Renormalization Group

We present a variational renormalization group (RG) approach using a deep generative model based on normalizing flows. The model performs hierarchical change-of-variables transformations from the physical space to a latent space with reduced mutual information. Conversely, the neural net directly maps independent Gaussian noises to physical configurations following the inverse RG flow. The model has an exact and tractable likelihood, which allows unbiased training and direct access to the renormalized energy function of the latent variables. To train the model, we employ probability density distillation for the bare energy function of the physical problem, in which the training loss provides a variational upper bound of the physical free energy. We demonstrate practical usage of the approach by identifying mutually independent collective variables of the Ising model and performing accelerated hybrid Monte Carlo sampling in the latent space. Lastly, we comment on the connection of the present approach to the wavelet formulation of RG and the modern pursuit of information preserving RG.

cond-mat.stat-mech↗