Tiejun Li

Yunfei Liu, Hao Wang, Yuhang Qi et al.

High-fidelity computational fluid dynamics is essential for aerospace design, but engineering-scale simulations of practical three-dimensional aircraft remain computationally expensive. Learning-based flow-field initialization can improve efficiency by reducing the numerical distance between the initial and converged solutions, yet existing deep learning approaches remain difficult to scale to large three-dimensional aircraft flows with multiscale regional heterogeneity. Most prior studies therefore focus on two-dimensional problems, surface quantities, integral aerodynamic coefficients, or simplified three-dimensional cases with limited grid resolution.Here we propose MHLF, a multigrid-hierarchical learning framework for accelerating engineering-scale aircraft flow simulations while preserving high-fidelity numerical accuracy. MHLF combines a topologically consistent geometric multigrid representation with a hierarchical strategy that captures regional flow heterogeneity during both prediction and subsequent CFD correction. Across three engineering-scale aircraft cases spanning Mach 0.15 to 6.0 and covering subsonic, transonic and supersonic regimes, MHLF accelerates convergence without sacrificing flow-field accuracy, achieving a 3 to 8 times efficiency improvement over conventional initialization. These results demonstrate practical full-flow-field prediction for large three-dimensional aircraft within the CFD domain and provide a foundation for data-driven acceleration of high-fidelity aircraft flow simulation.

Yue Zhao, Wei Zhang, Tiejun Li

We present EPR-Net, a novel and effective deep learning approach that tackles a crucial challenge in biophysics: constructing potential landscapes for high-dimensional non-equilibrium steady-state (NESS) systems. EPR-Net leverages a nice mathematical fact that the desired negative potential gradient is simply the orthogonal projection of the driving force of the underlying dynamics in a weighted inner-product space. Remarkably, our loss function has an intimate connection with the steady entropy production rate (EPR), enabling simultaneous landscape construction and EPR estimation. We introduce an enhanced learning strategy for systems with small noise, and extend our framework to include dimensionality reduction and state-dependent diffusion coefficient case in a unified fashion. Comparative evaluations on benchmark problems demonstrate the superior accuracy, effectiveness, and robustness of EPR-Net compared to existing methods. We apply our approach to challenging biophysical problems, such as an 8D limit cycle and a 52D multi-stability problem, which provide accurate solutions and interesting insights on constructed landscapes. With its versatility and power, EPR-Net offers a promising solution for diverse landscape construction problems in biophysics.

Qiangwei Peng, Zihan Wang, Junda Ying et al.

The Wasserstein-Fisher-Rao (WFR) metric extends dynamic optimal transport (OT) by coupling displacement with change of mass, providing a principled geometry for modeling unbalanced snapshot dynamics. Existing WFR solvers, however, are often unstable, computationally expensive, and difficult to scale. Here we introduce WFR Flow Matching (WFR-FM), a simulation-free training algorithm that unifies flow matching with dynamic unbalanced OT. Unlike classical flow matching which regresses only a transport vector field, WFR-FM simultaneously regresses a vector field for displacement and a scalar growth rate function for birth-death dynamics, yielding continuous flows under the WFR geometry. Theoretically, we show that minimizing the WFR-FM loss exactly recovers WFR geodesics. Empirically, WFR-FM yields more accurate and robust trajectory inference in single-cell biology, reconstructing consistent dynamics with proliferation and apoptosis, estimating time-varying growth fields, and applying to generative dynamics under imbalanced data. It outperforms state-of-the-art baselines in efficiency, stability, and reconstruction accuracy. Overall, WFR-FM establishes a unified and efficient paradigm for learning dynamical systems from unbalanced snapshots, where not only states but also mass evolve over time. The Python code is available at https://github.com/QiangweiPeng/WFR-FM.

Jing Xiao, Xinhai Chen, Jiaming Peng et al.

Symbolic Regression (SR) aims to discover interpretable equations from observational data, with the potential to reveal underlying principles behind natural phenomena. However, existing approaches often fall into the Pseudo-Equation Trap: producing equations that fit observations well but remain inconsistent with fundamental scientific principles. A key reason is that these approaches are dominated by empirical risk minimization, lacking explicit constraints to ensure scientific consistency. To bridge this gap, we propose PG-SR, a prior-guided SR framework built upon a three-stage pipeline consisting of warm-up, evolution, and refinement. Throughout the pipeline, PG-SR introduces a prior constraint checker that explicitly encodes domain priors as executable constraint programs, and employs a Prior Annealing Constrained Evaluation (PACE) mechanism during the evolution stage to progressively steer discovery toward scientifically consistent regions. Theoretically, we prove that PG-SR reduces the Rademacher complexity of the hypothesis space, yielding tighter generalization bounds and establishing a guarantee against pseudo-equations. Experimentally, PG-SR outperforms state-of-the-art baselines across diverse domains, maintaining robustness to varying prior quality, noisy data, and data scarcity.

Yuhao Sun, Zhenyi Zhang, Zihan Wang et al.

Recovering the dynamics from a few snapshots of a high-dimensional system is a challenging task in statistical physics and machine learning, with important applications in computational biology. Many algorithms have been developed to tackle this problem, based on frameworks such as optimal transport and the Schrödinger bridge. A notable recent framework is Regularized Unbalanced Optimal Transport (RUOT), which integrates both stochastic dynamics and unnormalized distributions. However, since many existing methods do not explicitly enforce optimality conditions, their solutions often struggle to satisfy the principle of least action and meet challenges to converge in a stable and reliable way. To address these issues, we propose Variational RUOT (Var-RUOT), a new framework to solve the RUOT problem. By incorporating the optimal necessary conditions for the RUOT problem into both the parameterization of the search space and the loss function design, Var-RUOT only needs to learn a scalar field to solve the RUOT problem and can search for solutions with lower action. We also examined the challenge of selecting a growth penalty function in the widely used Wasserstein-Fisher-Rao metric and proposed a solution that better aligns with biological priors in Var-RUOT. We validated the effectiveness of Var-RUOT on both simulated data and real single-cell datasets. Compared with existing algorithms, Var-RUOT can find solutions with lower action while exhibiting faster convergence and improved training stability. Our code is available at https://github.com/ZerooVector/VarRUOT.

Xinyu Wang, Ruoyu Wang, Qiangwei Peng et al.

Reconstructing dynamical evolution from limited observations is a fundamental challenge in single-cell biology, where dynamic unbalanced optimal transport provides a principled framework for modeling coupled transport and mass variation. However, existing approaches rely on trajectory simulation at inference time, making inference a key bottleneck for scalable applications. In this work, we propose a mean-flow framework for unbalanced flow matching that summarizes both transport and mass-growth dynamics over arbitrary time intervals using mean velocity and mass-growth fields, enabling fast one-step generation without trajectory simulation. To solve dynamic unbalanced optimal transport under the Wasserstein-Fisher-Rao geometry, we further build on this framework to develop Wasserstein-Fisher-Rao Mean Flow Matching (WFR-MFM). Across synthetic and real single-cell RNA sequencing datasets, WFR-MFM achieves orders-of-magnitude faster inference than a range of existing baselines while maintaining high predictive accuracy, and enables efficient perturbation response prediction on large synthetic datasets with thousands of conditions.

Chengqian Zhang, Yucheng Jin, Duo Zhang et al.

Crystal generative models mainly learn what stable crystals look like, with little explicit supervision for what makes them stable. We reveal a substantial representation gap between state-of-the-art crystal generative models and pretrained universal machine learning interatomic potentials (MLIPs) via energy probing, and show this gap can be closed by a simple training-time alignment. We propose Crystal REPresentation Alignment (CrystalREPA), a plug-and-play framework that aligns the atom-wise hidden states of generative encoders with frozen MLIP representations through an element-aware contrastive objective, transferring stability-aware atomistic priors with marginal training overhead and no additional inference cost. Across three generative frameworks, ten MLIP teachers, and two benchmark datasets, CrystalREPA consistently improves the thermodynamic stability, structural validity, and structural fidelity of generated crystals. Equally important, we find that an MLIP's transfer effectiveness is poorly predicted by its accuracy on standard leaderboards (e.g., Matbench Discovery) but strongly predicted by the distinguishability of its atom-wise representation space, yielding a practical, accuracy-independent criterion for selecting MLIP teachers for generative transfer.

Siqing Fu, Lizhou Wu, Tiejun Li et al.

Monte Carlo particle transport problems play a vital role in scientific computing, but solving them on exiting von Neumann architectures suffers from random branching and irregular memory access, causing computing inefficiency due to a fundamental mismatch between stochastic algorithms and deterministic hardware. To bridge this gap, we propose MCPT-Solver, a spin-based hardware true random number generator (TRNG) with tunable output probability enabled by a Bayesian inference network architecture. It is dedicated for efficiently solving stochastic applications including Monte Carlo particle transport problems. First, we leverage the stochastic switching property of spin devices to provide a high-quality entropy source for the TRNG and achieve high generating throughput and process-voltage-temperature tolerance through optimized control logic and write mechanism designs. Next, we propose a hardware Bayesian inference network to enable probability-tunable random number outputs. Finally, we present a system-level simulation framework to evaluate MCPT-Solver. Experimental results show that MCPT-Solver achieves a mean squared error of 7.6e-6 for solving transport problems while demonstrating a dramatic acceleration effect over general-purpose processors. Additionally, the MCPT-Solver's throughput reaches 185 Mb/s with an area of 27.8 um2/bit and energy consumption of 8.6 pJ/bit, making it the first spin-based TRNG that offers both process-voltage-temperature tolerance and adjustable probability.

Zichen Liu, Tiejun Li

Sampling the free energy surface, namely, the distribution of collective variables (CVs), is a crucial problem in statistical physics, as it underpins a better understanding of chemical reactions and conformational transitions. Traditional methods for free energy surface sampling involve simulation in high-dimensional configuration space and projecting the resulting configurations onto the CV space. To reduce the computational costs of such sampling, we propose FES-FM, a reduced flow matching (FM) method for free energy sampling (FES). We train a dynamical transport map in the CV space, thereby enabling direct sampling of the free energy surface. For many-particle systems, we construct a prior distribution based on the Hessian at a local minimum of the potential, which ensures both rotation-translation invariance and physically meaningful configurations. We evaluate the proposed method across a variety of potential functions and collective variables. Comparative experiments demonstrate that our approach drastically reduces computational costs while delivering superior accuracy per unit sampling time.

Zhenyi Zhang, Yuhao Sun, Qiangwei Peng et al.

Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene expression, offering valuable insights into cellular states at a single time point. Recent advancements in temporally resolved scRNA-seq, spatial transcriptomics (ST), and time-series spatial transcriptomics (temporal-ST) have further revolutionized our ability to study the spatiotemporal dynamics of individual cells. These technologies, when combined with computational frameworks such as Markov chains, stochastic differential equations (SDEs), and generative models like optimal transport and Schrödinger bridges, enable the reconstruction of dynamic cellular trajectories and cell fate decisions. This review discusses how these dynamical system approaches offer new opportunities to model and infer cellular dynamics from a systematic perspective.

Xu Zhu, Yi Zeng, Tiejun Li

This letter studies pilot design for orthogonal frequency-division multiplexing-based time-division duplex (TDD) systems under a sliding-window latest-slot recovery framework that jointly exploits delay--Doppler sparsity across recent slots. Under contiguous-subband and fairness constraints, this viewpoint naturally leads to a geometry-aware time--frequency joint pilot assignment. We show that effective patterns should balance grid coverage and redundant-collinearity suppression, with an additional symmetry-avoidance refinement when complete collinearity elimination is infeasible. Based on these principles, we formulate a mixed-integer construction method compatible with practical TDD allocation. Numerical results show that minimum-coverage-radius and collinearity-control (MCC) pattern improves both surrogate geometry metrics and latest-slot recovery performance.

Zichen Liu, Wei Zhang, Christof Schütte et al.

We propose Riemannian Denoising Diffusion Probabilistic Models (RDDPMs) for learning distributions on submanifolds of Euclidean space that are level sets of functions, including most of the manifolds relevant to applications. Existing methods for generative modeling on manifolds rely on substantial geometric information such as geodesic curves or eigenfunctions of the Laplace-Beltrami operator and, as a result, they are limited to manifolds where such information is available. In contrast, our method, built on a projection scheme, can be applied to more general manifolds, as it only requires being able to evaluate the value and the first order derivatives of the function that defines the submanifold. We provide a theoretical analysis of our method in the continuous-time limit, which elucidates the connection between our RDDPMs and score-based generative models on manifolds. The capability of our method is demonstrated on datasets from previous studies and on new datasets sampled from two high-dimensional manifolds, i.e. $\mathrm{SO}(10)$ and the configuration space of molecular system alanine dipeptide with fixed dihedral angle.

Zichen Liu, Wei Zhang, Tiejun Li

Euclidean diffusion models have achieved remarkable success in generative modeling across diverse domains, and they have been extended to manifold cases in recent advances. Instead of explicitly utilizing the structure of special manifolds as studied in previous works, in this paper we investigate direct sampling of the Euclidean diffusion models for general manifold-structured data. We reveal the multiscale singularity of the score function in the ambient space, which hinders the accuracy of diffusion-generated samples. We then present an elaborate theoretical analysis of the singularity structure of the score function by decomposing it along the tangential and normal directions of the manifold. To mitigate the singularity and improve the sampling accuracy, we propose two novel methods: (1) Niso-DM, which reduces the scale discrepancies in the score function by utilizing a non-isotropic noise, and (2) Tango-DM, which trains only the tangential component of the score function using a tangential-only loss function. Numerical experiments demonstrate that our methods achieve superior performance on distributions over various manifolds with complex geometries.

Yue Zhao, Chenzhuang Du, Hang Zhao et al.

In vision-based reinforcement learning (RL) tasks, it is prevalent to assign auxiliary tasks with a surrogate self-supervised loss so as to obtain more semantic representations and improve sample efficiency. However, abundant information in self-supervised auxiliary tasks has been disregarded, since the representation learning part and the decision-making part are separated. To sufficiently utilize information in auxiliary tasks, we present a simple yet effective idea to employ self-supervised loss as an intrinsic reward, called Intrinsically Motivated Self-Supervised learning in Reinforcement learning (IM-SSR). We formally show that the self-supervised loss can be decomposed as exploration for novel states and robustness improvement from nuisance elimination. IM-SSR can be effortlessly plugged into any reinforcement learning with self-supervised auxiliary objectives with nearly no additional cost. Combined with IM-SSR, the previous underlying algorithms achieve salient improvements on both sample efficiency and generalization in various vision-based robotics tasks from the DeepMind Control Suite, especially when the reward signal is sparse.