arXiv subjects

Zhongkai Hao

Publications and source records attributed to Zhongkai Hao.

32 records · Page 2Linked to original sources

arXiv2024

Preconditioning for Physics-Informed Neural Networks

Physics-informed neural networks (PINNs) have shown promise in solving various partial differential equations (PDEs). However, training pathologies have negatively affected the convergence and prediction accuracy of PINNs, which further limits their practical applications. In this paper, we propose to use condition number as a metric to diagnose and mitigate the pathologies in PINNs. Inspired by classical numerical analysis, where the condition number measures sensitivity and stability, we highlight its pivotal role in the training dynamics of PINNs. We prove theorems to reveal how condition number is related to both the error control and convergence of PINNs. Subsequently, we present an algorithm that leverages preconditioning to improve the condition number. Evaluations of 18 PDE problems showcase the superior performance of our method. Significantly, in 7 of these problems, our method reduces errors by an order of magnitude. These empirical findings verify the critical role of the condition number in PINNs' training.

cs.LG↗

arXiv2023

Full-Atom Protein Pocket Design via Iterative Refinement

The design of \emph{de novo} functional proteins that bind specific ligand molecules is paramount in therapeutics and bio-engineering. A critical yet formidable task in this endeavor is the design of the protein pocket, which is the cavity region of the protein where the ligand binds. Current methods are plagued by inefficient generation, inadequate context modeling of the ligand molecule, and the inability to generate side-chain atoms. Here, we present the Full-Atom Iterative Refinement (FAIR) method, designed to address these challenges by facilitating the co-design of protein pocket sequences, specifically residue types, and their corresponding 3D structures. FAIR operates in two steps, proceeding in a coarse-to-fine manner (transitioning from protein backbone to atoms, including side chains) for a full-atom generation. In each iteration, all residue types and structures are simultaneously updated, a process termed full-shot refinement. In the initial stage, the residue types and backbone coordinates are refined using a hierarchical context encoder, complemented by two structure refinement modules that capture both inter-residue and pocket-ligand interactions. The subsequent stage delves deeper, modeling the side-chain atoms of the pockets and updating residue types to ensure sequence-structure congruence. Concurrently, the structure of the binding ligand is refined across iterations to accommodate its inherent flexibility. Comprehensive experiments show that FAIR surpasses existing methods in designing superior pocket sequences and structures, producing average improvement exceeding 10\% in AAR and RMSD metrics. FAIR is available at \url{https://github.com/zaixizhang/FAIR}.

q-bio.BM↗

arXiv2023

PINNacle: A Comprehensive Benchmark of Physics-Informed Neural Networks for Solving PDEs

While significant progress has been made on Physics-Informed Neural Networks (PINNs), a comprehensive comparison of these methods across a wide range of Partial Differential Equations (PDEs) is still lacking. This study introduces PINNacle, a benchmarking tool designed to fill this gap. PINNacle provides a diverse dataset, comprising over 20 distinct PDEs from various domains, including heat conduction, fluid dynamics, biology, and electromagnetics. These PDEs encapsulate key challenges inherent to real-world problems, such as complex geometry, multi-scale phenomena, nonlinearity, and high dimensionality. PINNacle also offers a user-friendly toolbox, incorporating about 10 state-of-the-art PINN methods for systematic evaluation and comparison. We have conducted extensive experiments with these methods, offering insights into their strengths and weaknesses. In addition to providing a standardized means of assessing performance, PINNacle also offers an in-depth analysis to guide future research, particularly in areas such as domain decomposition methods and loss reweighting for handling multi-scale problems and complex geometry. To the best of our knowledge, it is the largest benchmark with a diverse and comprehensive evaluation that will undoubtedly foster further research in PINNs.

cs.LG↗

arXiv2023

GNOT: A General Neural Operator Transformer for Operator Learning

Learning partial differential equations' (PDEs) solution operators is an essential problem in machine learning. However, there are several challenges for learning operators in practical applications like the irregular mesh, multiple input functions, and complexity of the PDEs' solution. To address these challenges, we propose a general neural operator transformer (GNOT), a scalable and effective transformer-based framework for learning operators. By designing a novel heterogeneous normalized attention layer, our model is highly flexible to handle multiple input functions and irregular meshes. Besides, we introduce a geometric gating mechanism which could be viewed as a soft domain decomposition to solve the multi-scale problems. The large model capacity of the transformer architecture grants our model the possibility to scale to large datasets and practical problems. We conduct extensive experiments on multiple challenging datasets from different domains and achieve a remarkable improvement compared with alternative methods. Our code and data are publicly available at \url{https://github.com/thu-ml/GNOT}.

cs.LG↗

arXiv2023

MultiAdam: Parameter-wise Scale-invariant Optimizer for Multiscale Training of Physics-informed Neural Networks

Physics-informed Neural Networks (PINNs) have recently achieved remarkable progress in solving Partial Differential Equations (PDEs) in various fields by minimizing a weighted sum of PDE loss and boundary loss. However, there are several critical challenges in the training of PINNs, including the lack of theoretical frameworks and the imbalance between PDE loss and boundary loss. In this paper, we present an analysis of second-order non-homogeneous PDEs, which are classified into three categories and applicable to various common problems. We also characterize the connections between the training loss and actual error, guaranteeing convergence under mild conditions. The theoretical analysis inspires us to further propose MultiAdam, a scale-invariant optimizer that leverages gradient momentum to parameter-wisely balance the loss terms. Extensive experiment results on multiple problems from different physical domains demonstrate that our MultiAdam solver can improve the predictive accuracy by 1-2 orders of magnitude compared with strong baselines.

cs.LG↗

arXiv2023

A Unified Hard-Constraint Framework for Solving Geometrically Complex PDEs

We present a unified hard-constraint framework for solving geometrically complex PDEs with neural networks, where the most commonly used Dirichlet, Neumann, and Robin boundary conditions (BCs) are considered. Specifically, we first introduce the "extra fields" from the mixed finite element method to reformulate the PDEs so as to equivalently transform the three types of BCs into linear equations. Based on the reformulation, we derive the general solutions of the BCs analytically, which are employed to construct an ansatz that automatically satisfies the BCs. With such a framework, we can train the neural networks without adding extra loss terms and thus efficiently handle geometrically complex PDEs, alleviating the unbalanced competition between the loss terms corresponding to the BCs and PDEs. We theoretically demonstrate that the "extra fields" can stabilize the training process. Experimental results on real-world geometrically complex PDEs showcase the effectiveness of our method compared with state-of-the-art baselines.

cs.LG↗

arXiv2023

NUNO: A General Framework for Learning Parametric PDEs with Non-Uniform Data

The neural operator has emerged as a powerful tool in learning mappings between function spaces in PDEs. However, when faced with real-world physical data, which are often highly non-uniformly distributed, it is challenging to use mesh-based techniques such as the FFT. To address this, we introduce the Non-Uniform Neural Operator (NUNO), a comprehensive framework designed for efficient operator learning with non-uniform data. Leveraging a K-D tree-based domain decomposition, we transform non-uniform data into uniform grids while effectively controlling interpolation error, thereby paralleling the speed and accuracy of learning from non-uniform data. We conduct extensive experiments on 2D elasticity, (2+1)D channel flow, and a 3D multi-physics heatsink, which, to our knowledge, marks a novel exploration into 3D PDE problems with complex geometries. Our framework has reduced error rates by up to 60% and enhanced training speeds by 2x to 30x. The code is now available at https://github.com/thu-ml/NUNO.

cs.LG↗

arXiv2023

On the Reuse Bias in Off-Policy Reinforcement Learning

Importance sampling (IS) is a popular technique in off-policy evaluation, which re-weights the return of trajectories in the replay buffer to boost sample efficiency. However, training with IS can be unstable and previous attempts to address this issue mainly focus on analyzing the variance of IS. In this paper, we reveal that the instability is also related to a new notion of Reuse Bias of IS -- the bias in off-policy evaluation caused by the reuse of the replay buffer for evaluation and optimization. We theoretically show that the off-policy evaluation and optimization of the current policy with the data from the replay buffer result in an overestimation of the objective, which may cause an erroneous gradient update and degenerate the performance. We further provide a high-probability upper bound of the Reuse Bias, and show that controlling one term of the upper bound can control the Reuse Bias by introducing the concept of stability for off-policy algorithms. Based on these analyses, we finally present a novel Bias-Regularized Importance Sampling (BIRIS) framework along with practical algorithms, which can alleviate the negative impact of the Reuse Bias. Experimental results show that our BIRIS-based methods can significantly improve the sample efficiency on a series of continuous control tasks in MuJoCo.

cs.LG↗

arXiv2023

Bi-level Physics-Informed Neural Networks for PDE Constrained Optimization using Broyden's Hypergradients

Deep learning based approaches like Physics-informed neural networks (PINNs) and DeepONets have shown promise on solving PDE constrained optimization (PDECO) problems. However, existing methods are insufficient to handle those PDE constraints that have a complicated or nonlinear dependency on optimization targets. In this paper, we present a novel bi-level optimization framework to resolve the challenge by decoupling the optimization of the targets and constraints. For the inner loop optimization, we adopt PINNs to solve the PDE constraints only. For the outer loop, we design a novel method by using Broyden's method based on the Implicit Function Theorem (IFT), which is efficient and accurate for approximating hypergradients. We further present theoretical explanations and error analysis of the hypergradients computation. Extensive experiments on multiple large-scale and nonlinear PDE constrained optimization problems demonstrate that our method achieves state-of-the-art results compared with strong baselines.

cs.LG↗

arXiv2023

Physics-Informed Machine Learning: A Survey on Problems, Methods and Applications

Recent advances of data-driven machine learning have revolutionized fields like computer vision, reinforcement learning, and many scientific and engineering domains. In many real-world and scientific problems, systems that generate data are governed by physical laws. Recent work shows that it provides potential benefits for machine learning models by incorporating the physical prior and collected data, which makes the intersection of machine learning and physics become a prevailing paradigm. By integrating the data and mathematical physics models seamlessly, it can guide the machine learning model towards solutions that are physically plausible, improving accuracy and efficiency even in uncertain and high-dimensional contexts. In this survey, we present this learning paradigm called Physics-Informed Machine Learning (PIML) which is to build a model that leverages empirical data and available physical prior knowledge to improve performance on a set of tasks that involve a physical mechanism. We systematically review the recent development of physics-informed machine learning from three perspectives of machine learning tasks, representation of physical prior, and methods for incorporating physical prior. We also propose several important open research problems based on the current trends in the field. We argue that encoding different forms of physical prior into model architectures, optimizers, inference algorithms, and significant domain-specific applications like inverse engineering design and robotic control is far from being fully explored in the field of physics-informed machine learning. We believe that the interdisciplinary research of physics-informed machine learning will significantly propel research progress, foster the creation of more effective machine learning models, and also offer invaluable assistance in addressing long-standing problems in related disciplines.

cs.LG↗

arXiv2023

Equivariant Energy-Guided SDE for Inverse Molecular Design

Inverse molecular design is critical in material science and drug discovery, where the generated molecules should satisfy certain desirable properties. In this paper, we propose equivariant energy-guided stochastic differential equations (EEGSDE), a flexible framework for controllable 3D molecule generation under the guidance of an energy function in diffusion models. Formally, we show that EEGSDE naturally exploits the geometric symmetry in 3D molecular conformation, as long as the energy function is invariant to orthogonal transformations. Empirically, under the guidance of designed energy functions, EEGSDE significantly improves the baseline on QM9, in inverse molecular design targeted to quantum properties and molecular structures. Furthermore, EEGSDE is able to generate molecules with multiple target properties by combining the corresponding energy functions linearly.

physics.chem-ph↗

arXiv2022

GSmooth: Certified Robustness against Semantic Transformations via Generalized Randomized Smoothing

Certified defenses such as randomized smoothing have shown promise towards building reliable machine learning systems against $\ell_p$-norm bounded attacks. However, existing methods are insufficient or unable to provably defend against semantic transformations, especially those without closed-form expressions (such as defocus blur and pixelate), which are more common in practice and often unrestricted. To fill up this gap, we propose generalized randomized smoothing (GSmooth), a unified theoretical framework for certifying robustness against general semantic transformations via a novel dimension augmentation strategy. Under the GSmooth framework, we present a scalable algorithm that uses a surrogate image-to-image network to approximate the complex transformation. The surrogate model provides a powerful tool for studying the properties of semantic transformations and certifying robustness. Experimental results on several datasets demonstrate the effectiveness of our approach for robustness certification against multiple kinds of semantic transformations and corruptions, which is not achievable by the alternative baselines.

cs.LG↗

arXiv2022

Cluster Attack: Query-based Adversarial Attacks on Graphs with Graph-Dependent Priors

While deep neural networks have achieved great success in graph analysis, recent work has shown that they are vulnerable to adversarial attacks. Compared with adversarial attacks on image classification, performing adversarial attacks on graphs is more challenging because of the discrete and non-differential nature of the adjacent matrix for a graph. In this work, we propose Cluster Attack -- a Graph Injection Attack (GIA) on node classification, which injects fake nodes into the original graph to degenerate the performance of graph neural networks (GNNs) on certain victim nodes while affecting the other nodes as little as possible. We demonstrate that a GIA problem can be equivalently formulated as a graph clustering problem; thus, the discrete optimization problem of the adjacency matrix can be solved in the context of graph clustering. In particular, we propose to measure the similarity between victim nodes by a metric of Adversarial Vulnerability, which is related to how the victim nodes will be affected by the injected fake node, and to cluster the victim nodes accordingly. Our attack is performed in a practical and unnoticeable query-based black-box manner with only a few nodes on the graphs that can be accessed. Theoretical analysis and extensive experiments demonstrate the effectiveness of our method by fooling the node classifiers with only a small number of queries.

cs.LG↗

arXiv2020

ASGN: An Active Semi-supervised Graph Neural Network for Molecular Property Prediction

Molecular property prediction (e.g., energy) is an essential problem in chemistry and biology. Unfortunately, many supervised learning methods usually suffer from the problem of scarce labeled molecules in the chemical space, where such property labels are generally obtained by Density Functional Theory (DFT) calculation which is extremely computational costly. An effective solution is to incorporate the unlabeled molecules in a semi-supervised fashion. However, learning semi-supervised representation for large amounts of molecules is challenging, including the joint representation issue of both molecular essence and structure, the conflict between representation and property leaning. Here we propose a novel framework called Active Semi-supervised Graph Neural Network (ASGN) by incorporating both labeled and unlabeled molecules. Specifically, ASGN adopts a teacher-student framework. In the teacher model, we propose a novel semi-supervised learning method to learn general representation that jointly exploits information from molecular structure and molecular distribution. Then in the student model, we target at property prediction task to deal with the learning loss conflict. At last, we proposed a novel active learning strategy in terms of molecular diversities to select informative data during the whole framework learning. We conduct extensive experiments on several public datasets. Experimental results show the remarkable performance of our ASGN framework.

cs.LG↗