Zhi-Ming Ma

Weitao Du, Yuanqi Du, Limei Wang et al.

Geometric deep learning enables the encoding of physical symmetries in modeling 3D objects. Despite rapid progress in encoding 3D symmetries into Graph Neural Networks (GNNs), a comprehensive evaluation of the expressiveness of these networks through a local-to-global analysis lacks today. In this paper, we propose a local hierarchy of 3D isomorphism to evaluate the expressive power of equivariant GNNs and investigate the process of representing global geometric information from local patches. Our work leads to two crucial modules for designing expressive and efficient geometric GNNs; namely local substructure encoding (LSE) and frame transition encoding (FTE). To demonstrate the applicability of our theory, we propose LEFTNet which effectively implements these modules and achieves state-of-the-art performance on both scalar-valued and vector-valued molecular property prediction tasks. We further point out the design space for future developments of equivariant graph neural networks. Our codes are available at \url{https://github.com/yuanqidu/LeftNet}.

Shuchen Xue, Mingyang Yi, Weijian Luo et al.

Diffusion Probabilistic Models (DPMs) have achieved considerable success in generation tasks. As sampling from DPMs is equivalent to solving diffusion SDE or ODE which is time-consuming, numerous fast sampling methods built upon improved differential equation solvers are proposed. The majority of such techniques consider solving the diffusion ODE due to its superior efficiency. However, stochastic sampling could offer additional advantages in generating diverse and high-quality data. In this work, we engage in a comprehensive analysis of stochastic sampling from two aspects: variance-controlled diffusion SDE and linear multi-step SDE solver. Based on our analysis, we propose \textit{SA-Solver}, which is an improved efficient stochastic Adams method for solving diffusion SDE to generate data with high quality. Our experiments show that \textit{SA-Solver} achieves: 1) improved or comparable performance compared with the existing state-of-the-art (SOTA) sampling methods for few-step sampling; 2) SOTA FID on substantial benchmark datasets under a suitable number of function evaluations (NFEs). Code is available at https://github.com/scxue/SA-Solver.

Rui Zhang, Qi Meng, Rongchan Zhu et al.

In scenarios with limited available data, training the function-to-function neural PDE solver in an unsupervised manner is essential. However, the efficiency and accuracy of existing methods are constrained by the properties of numerical algorithms, such as finite difference and pseudo-spectral methods, integrated during the training stage. These methods necessitate careful spatiotemporal discretization to achieve reasonable accuracy, leading to significant computational challenges and inaccurate simulations, particularly in cases with substantial spatiotemporal variations. To address these limitations, we propose the Monte Carlo Neural PDE Solver (MCNP Solver) for training unsupervised neural solvers via the PDEs' probabilistic representation, which regards macroscopic phenomena as ensembles of random particles. Compared to other unsupervised methods, MCNP Solver naturally inherits the advantages of the Monte Carlo method, which is robust against spatiotemporal variations and can tolerate coarse step size. In simulating the trajectories of particles, we employ Heun's method for the convection process and calculate the expectation via the probability density function of neighbouring grid points during the diffusion process. These techniques enhance accuracy and circumvent the computational issues associated with Monte Carlo sampling. Our numerical experiments on convection-diffusion, Allen-Cahn, and Navier-Stokes equations demonstrate significant improvements in accuracy and efficiency compared to other unsupervised baselines. The source code will be publicly available at: https://github.com/optray/MCNP.

Rui Zhang, Qi Meng, Zhi-Ming Ma

Neural operators have been explored as surrogate models for simulating physical systems to overcome the limitations of traditional partial differential equation (PDE) solvers. However, most existing operator learning methods assume that the data originate from a single physical mechanism, limiting their applicability and performance in more realistic scenarios. To this end, we propose Physical Invariant Attention Neural Operator (PIANO) to decipher and integrate the physical invariants (PI) for operator learning from the PDE series with various physical mechanisms. PIANO employs self-supervised learning to extract physical knowledge and attention mechanisms to integrate them into dynamic convolutional layers. Compared to existing techniques, PIANO can reduce the relative error by 13.6\%-82.2\% on PDE forecasting tasks across varying coefficients, forces, or boundary conditions. Additionally, varied downstream tasks reveal that the PI embeddings deciphered by PIANO align well with the underlying invariants in the PDE systems, verifying the physical significance of PIANO. The source code will be publicly available at: https://github.com/optray/PIANO.

Mingyang Yi, Ruoyu Wang, Jiachen Sun et al.

Recently, generalization on out-of-distribution (OOD) data with correlation shift has attracted great attentions. The correlation shift is caused by the spurious attributes that correlate to the class label, as the correlation between them may vary in training and test data. For such a problem, we show that given the class label, the models that are conditionally independent of spurious attributes are OOD generalizable. Based on this, a metric Conditional Spurious Variation (CSV) which controls the OOD generalization error, is proposed to measure such conditional independence. To improve the OOD generalization, we regularize the training process with the proposed CSV. Under mild assumptions, our training objective can be formulated as a nonconvex-concave mini-max problem. An algorithm with a provable convergence rate is proposed to solve the problem. Extensive empirical results verify our algorithm's efficacy in improving OOD generalization.

Bohan Wang, Yushun Zhang, Huishuai Zhang et al.

Adam is widely adopted in practical applications due to its fast convergence. However, its theoretical analysis is still far from satisfactory. Existing convergence analyses for Adam rely on the bounded smoothness assumption, referred to as the \emph{L-smooth condition}. Unfortunately, this assumption does not hold for many deep learning tasks. Moreover, we believe that this assumption obscures the true benefit of Adam, as the algorithm can adapt its update magnitude according to local smoothness. This important feature of Adam becomes irrelevant when assuming globally bounded smoothness. This paper studies the convergence of randomly reshuffled Adam (RR Adam) with diminishing learning rate, which is the major version of Adam adopted in deep learning tasks. We present the first convergence analysis of RR Adam without the bounded smoothness assumption. We demonstrate that RR Adam can maintain its convergence properties when smoothness is linearly bounded by the gradient norm, referred to as the \emph{$(L_0, L_1)$-smooth condition. We further compare Adam to SGD when both methods use diminishing learning rate. We refine the existing lower bound of SGD and show that SGD can be slower than Adam. To our knowledge, this is the first time that Adam and SGD are rigorously compared in the same setting and the advantage of Adam is revealed.

Rui Zhang, Peiyan Hu, Qi Meng et al.

Navier-Stokes equations are significant partial differential equations that describe the motion of fluids such as liquids and air. Due to the importance of Navier-Stokes equations, the development on efficient numerical schemes is important for both science and engineer. Recently, with the development of AI techniques, several approaches have been designed to integrate deep neural networks in simulating and inferring the fluid dynamics governed by incompressible Navier-Stokes equations, which can accelerate the simulation or inferring process in a mesh-free and differentiable way. In this paper, we point out that the capability of existing deep Navier-Stokes informed methods is limited to handle non-smooth or fractional equations, which are two critical situations in reality. To this end, we propose the \emph{Deep Random Vortex Method} (DRVM), which combines the neural network with a random vortex dynamics system equivalent to the Navier-Stokes equation. Specifically, the random vortex dynamics motivates a Monte Carlo based loss function for training the neural network, which avoids the calculation of derivatives through auto-differentiation. Therefore, DRVM not only can efficiently solve Navier-Stokes equations involving rough path, non-differentiable initial conditions and fractional operators, but also inherits the mesh-free and differentiable benefits of the deep-learning-based solver. We conduct experiments on the Cauchy problem, parametric solver learning, and the inverse problem of both 2-d and 3-d incompressible Navier-Stokes equations. The proposed method achieves accurate results for simulation and inference of Navier-Stokes equations. Especially for the cases that include singular initial conditions, DRVM significantly outperforms existing PINN method.

Peiyan Hu, Qi Meng, Bingguang Chen et al.

Stochastic partial differential equations (SPDEs) are significant tools for modeling dynamics in many areas including atmospheric sciences and physics. Neural Operators, generations of neural networks with capability of learning maps between infinite-dimensional spaces, are strong tools for solving parametric PDEs. However, they lack the ability to modeling SPDEs which usually have poor regularity due to the driving noise. As the theory of regularity structure has achieved great successes in analyzing SPDEs and provides the concept model feature vectors that well-approximate SPDEs' solutions, we propose the Neural Operator with Regularity Structure (NORS) which incorporates the feature vectors for modeling dynamics driven by SPDEs. We conduct experiments on various of SPDEs including the dynamic Phi41 model and the 2d stochastic Navier-Stokes equation, and the results demonstrate that the NORS is resolution-invariant, efficient, and achieves one order of magnitude lower error with a modest amount of data.

Yuyan Ni, Shikun Feng, Xin Hong et al.

Deep learning methods have been considered promising for accelerating molecular screening in drug discovery and material design. Due to the limited availability of labelled data, various self-supervised molecular pre-training methods have been presented. While many existing methods utilize common pre-training tasks in computer vision (CV) and natural language processing (NLP), they often overlook the fundamental physical principles governing molecules. In contrast, applying denoising in pre-training can be interpreted as an equivalent force learning, but the limited noise distribution introduces bias into the molecular distribution. To address this issue, we introduce a molecular pre-training framework called fractional denoising (Frad), which decouples noise design from the constraints imposed by force learning equivalence. In this way, the noise becomes customizable, allowing for incorporating chemical priors to significantly improve molecular distribution modeling. Experiments demonstrate that our framework consistently outperforms existing methods, establishing state-of-the-art results across force prediction, quantum chemical properties, and binding affinity tasks. The refined noise design enhances force accuracy and sampling coverage, which contribute to the creation of physically consistent molecular representations, ultimately leading to superior predictive performance.

Yuyan Ni, Shikun Feng, Wei-Ying Ma et al.

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42\% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.

Peiyan Hu, Rui Wang, Xiang Zheng et al.

Simulating and controlling physical systems described by partial differential equations (PDEs) are crucial tasks across science and engineering. Recently, diffusion generative models have emerged as a competitive class of methods for these tasks due to their ability to capture long-term dependencies and model high-dimensional states. However, diffusion models typically struggle with handling system states with abrupt changes and generalizing to higher resolutions. In this work, we propose Wavelet Diffusion Neural Operator (WDNO), a novel PDE simulation and control framework that enhances the handling of these complexities. WDNO comprises two key innovations. Firstly, WDNO performs diffusion-based generative modeling in the wavelet domain for the entire trajectory to handle abrupt changes and long-term dependencies effectively. Secondly, to address the issue of poor generalization across different resolutions, which is one of the fundamental tasks in modeling physical systems, we introduce multi-resolution training. We validate WDNO on five physical systems, including 1D advection equation, three challenging physical systems with abrupt changes (1D Burgers' equation, 1D compressible Navier-Stokes equation and 2D incompressible fluid), and a real-world dataset ERA5, which demonstrates superior performance on both simulation and control tasks over state-of-the-art methods, with significant improvements in long-term and detail prediction accuracy. Remarkably, in the challenging context of the 2D high-dimensional and indirect control task aimed at reducing smoke leakage, WDNO reduces the leakage by 78% compared to the second-best baseline. The code can be found at https://github.com/AI4Science-WestlakeU/wdno.git.

Peiyan Hu, Yue Wang, Zhi-Ming Ma

Recently, neural networks have been extensively employed to solve partial differential equations (PDEs) in physical system modeling. While major studies focus on learning system evolution on predefined static mesh discretizations, some methods utilize reinforcement learning or supervised learning techniques to create adaptive and dynamic meshes, due to the dynamic nature of these systems. However, these approaches face two primary challenges: (1) the need for expensive optimal mesh data, and (2) the change of the solution space's degree of freedom and topology during mesh refinement. To address these challenges, this paper proposes a neural PDE solver with a neural mesh adapter. To begin with, we introduce a novel data-free neural mesh adaptor, called Data-free Mesh Mover (DMM), with two main innovations. Firstly, it is an operator that maps the solution to adaptive meshes and is trained using the Monge-Ampère equation without optimal mesh data. Secondly, it dynamically changes the mesh by moving existing nodes rather than adding or deleting nodes and edges. Theoretical analysis shows that meshes generated by DMM have the lowest interpolation error bound. Based on DMM, to efficiently and accurately model dynamic systems, we develop a moving mesh based neural PDE solver (MM-PDE) that embeds the moving mesh with a two-branch architecture and a learnable interpolation framework to preserve information within the data. Empirical experiments demonstrate that our method generates suitable meshes and considerably enhances accuracy when modeling widely considered PDE systems. The code can be found at: https://github.com/Peiyannn/MM-PDE.git.

Shuchen Xue, Chongjian Ge, Shilong Zhang et al.

Reinforcement Learning (RL) has emerged as a central paradigm for advancing Large Language Models (LLMs), where pre-training and RL post-training share the same log-likelihood formulation. In contrast, recent RL approaches for diffusion models, most notably Denoising Diffusion Policy Optimization (DDPO), optimize an objective different from the pretraining objectives--score/flow matching loss. In this work, we establish a novel theoretical analysis: DDPO is an implicit form of score/flow matching with noisy targets, which increases variance and slows convergence. Building on this analysis, we introduce \textbf{Advantage Weighted Matching (AWM)}, a policy-gradient method for diffusion. It uses the same score/flow-matching loss as pretraining to obtain a lower-variance objective and reweights each sample by its advantage. In effect, AWM raises the influence of high-reward samples and suppresses low-reward ones while keeping the modeling objective identical to pretraining. This unifies pretraining and RL conceptually and practically, is consistent with policy-gradient theory, reduces variance, and yields faster convergence. This simple yet effective design yields substantial benefits: on GenEval, OCR, and PickScore benchmarks, AWM delivers up to a $24\times$ speedup over Flow-GRPO (which builds on DDPO), when applied to Stable Diffusion 3.5 Medium and FLUX, without compromising generation quality. Code is available at https://github.com/scxue/advantage_weighted_matching.

Zekun Wang, Mingyang Yi, Shuchen Xue et al.

Diffusion Probabilistic Models (DPMs) have achieved significant success in generative tasks. However, their training and sampling processes suffer from the issue of distribution mismatch. During the denoising process, the input data distributions differ between the training and inference stages, potentially leading to inaccurate data generation. To obviate this, we analyze the training objective of DPMs and theoretically demonstrate that this mismatch can be alleviated through Distributionally Robust Optimization (DRO), which is equivalent to performing robustness-driven Adversarial Training (AT) on DPMs. Furthermore, for the recently proposed Consistency Model (CM), which distills the inference process of the DPM, we prove that its training objective also encounters the mismatch issue. Fortunately, this issue can be mitigated by AT as well. Based on these insights, we propose to conduct efficient AT on both DPM and CM. Finally, extensive empirical studies validate the effectiveness of AT in diffusion-based models. The code is available at https://github.com/kugwzk/AT_Diff.

Shikun Feng, Yuyan Ni, Yan Lu et al.

Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can learn meaningful data representations that enhance predictive tasks, we explore the potential for developing a unified generative model in the molecular domain that effectively addresses both molecular generation and property prediction tasks. However, the integration of these tasks is challenging due to inherent inconsistencies, making simple multi-task learning ineffective. To address this, we propose UniGEM, the first unified model to successfully integrate molecular generation and property prediction, delivering superior performance in both tasks. Our key innovation lies in a novel two-phase generative process, where predictive tasks are activated in the later stages, after the molecular scaffold is formed. We further enhance task balance through innovative training strategies. Rigorous theoretical analysis and comprehensive experiments demonstrate our significant improvements in both tasks. The principles behind UniGEM hold promise for broader applications, including natural language processing and computer vision.

Yuyan Ni, Shikun Feng, Haohan Chi et al.

Diffusion-based models have shown great promise in molecular generation but often require a large number of sampling steps to generate valid samples. In this paper, we introduce a novel Straight-Line Diffusion Model (SLDM) to tackle this problem, by formulating the diffusion process to follow a linear trajectory. The proposed process aligns well with the noise sensitivity characteristic of molecular structures and uniformly distributes reconstruction effort across the generative process, thus enhancing learning efficiency and efficacy. Consequently, SLDM achieves state-of-the-art performance on 3D molecule generation benchmarks, delivering a 100-fold improvement in sampling efficiency.

Dingshuo Chen, Shuchen Xue, Liuji Chen et al.

Diffusion probabilistic models (DPMs), widely recognized for their potential to generate high-quality samples, tend to go unnoticed in representation learning. While recent progress has highlighted their potential for capturing visual semantics, adapting DPMs to graph representation learning remains in its infancy. In this paper, we introduce Graffe, a self-supervised diffusion model proposed for graph representation learning. It features a graph encoder that distills a source graph into a compact representation, which, in turn, serves as the condition to guide the denoising process of the diffusion decoder. To evaluate the effectiveness of our model, we first explore the theoretical foundations of applying diffusion models to representation learning, proving that the denoising objective implicitly maximizes the conditional mutual information between data and its representation. Specifically, we prove that the negative logarithm of the denoising score matching loss is a tractable lower bound for the conditional mutual information. Empirically, we conduct a series of case studies to validate our theoretical insights. In addition, Graffe delivers competitive results under the linear probing setting on node and graph classification tasks, achieving state-of-the-art performance on 9 of the 11 real-world datasets. These findings indicate that powerful generative models, especially diffusion models, serve as an effective tool for graph representation learning.

Bohan Wang, Qi Meng, Huishuai Zhang et al.

The momentum acceleration technique is widely adopted in many optimization algorithms. However, there is no theoretical answer on how the momentum affects the generalization performance of the optimization algorithms. This paper studies this problem by analyzing the implicit regularization of momentum-based optimization. We prove that on the linear classification problem with separable data and exponential-tailed loss, gradient descent with momentum (GDM) converges to the L2 max-margin solution, which is the same as vanilla gradient descent. That means gradient descent with momentum acceleration still converges to a low-complexity model, which guarantees their generalization. We then analyze the stochastic and adaptive variants of GDM (i.e., SGDM and deterministic Adam) and show they also converge to the L2 max-margin solution. Technically, to overcome the difficulty of the error accumulation in analyzing the momentum, we construct new potential functions to analyze the gap between the model parameter and the max-margin solution. Numerical experiments are conducted and support our theoretical results.

Mingyang Yi, Ruoyu Wang, Zhi-Ming Ma

We establish upper bounds for the expected excess risk of models trained by proper iterative algorithms which approximate the local minima. Unlike the results built upon the strong globally strongly convexity or global growth conditions e.g., PL-inequality, we only require the population risk to be \emph{locally} strongly convex around its local minima. Concretely, our bound under convex problems is of order $\tilde{\cO}(1/n)$. For non-convex problems with $d$ model parameters such that $d/n$ is smaller than a threshold independent of $n$, the order of $\tilde{\cO}(1/n)$ can be maintained if the empirical risk has no spurious local minima with high probability. Moreover, the bound for non-convex problem becomes $\tilde{\cO}(1/\sqrt{n})$ without such assumption. Our results are derived via algorithmic stability and characterization of the empirical risk's landscape. Compared with the existing algorithmic stability based results, our bounds are dimensional insensitive and without restrictions on the algorithm's implementation, learning rate, and the number of iterations. Our bounds underscore that with locally strongly convex population risk, the models trained by any proper iterative algorithm can generalize well, even for non-convex problems, and $d$ is large.