Rongjie Lai

Hao Liu, Alex Havrilla, Rongjie Lai et al. · gatech

Autoencoders have demonstrated remarkable success in learning low-dimensional latent features of high-dimensional data across various applications. Assuming that data are sampled near a low-dimensional manifold, we employ chart autoencoders, which encode data into low-dimensional latent features on a collection of charts, preserving the topology and geometry of the data manifold. Our paper establishes statistical guarantees on the generalization error of chart autoencoders, and we demonstrate their denoising capabilities by considering $n$ noisy training samples, along with their noise-free counterparts, on a $d$-dimensional manifold. By training autoencoders, we show that chart autoencoders can effectively denoise the input data with normal noise. We prove that, under proper network architectures, chart autoencoders achieve a squared generalization error in the order of $\displaystyle n^{-\frac{2}{d+2}}\log^4 n$, which depends on the intrinsic dimension of the manifold and only weakly depends on the ambient dimension and noise level. We further extend our theory on data with noise containing both normal and tangential components, where chart autoencoders still exhibit a denoising effect for the normal component. As a special case, our theory also applies to classical autoencoders, as long as the data manifold has a global parametrization. Our results provide a solid theoretical foundation for the effectiveness of autoencoders, which is further validated through several numerical experiments.

N. Joseph Tatro, Payel Das, Pin-Yu Chen et al. · ibm-research

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

Rongjie Lai, Jianfeng Lu

The committor functions provide useful information to the understanding of transitions of a stochastic system between disjoint regions in phase space. In this work, we develop a point cloud discretization for Fokker-Planck operators to numerically calculate the committor function, with the assumption that the transition occurs on an intrinsically low-dimensional manifold in the ambient potentially high dimensional configurational space of the stochastic system. Numerical examples on model systems validate the effectiveness of the proposed method.

Han Huang, Jiajia Yu, Jie Chen et al.

Mean-field games (MFGs) are a modeling framework for systems with a large number of interacting agents. They have applications in economics, finance, and game theory. Normalizing flows (NFs) are a family of deep generative models that compute data likelihoods by using an invertible mapping, which is typically parameterized by using neural networks. They are useful for density modeling and data generation. While active research has been conducted on both models, few noted the relationship between the two. In this work, we unravel the connections between MFGs and NFs by contextualizing the training of an NF as solving the MFG. This is achieved by reformulating the MFG problem in terms of agent trajectories and parameterizing a discretization of the resulting MFG with flow architectures. With this connection, we explore two research directions. First, we employ expressive NF architectures to accurately solve high-dimensional MFGs, sidestepping the curse of dimensionality in traditional numerical methods. Compared with other deep learning approaches, our trajectory-based formulation encodes the continuity equation in the neural network, resulting in a better approximation of the population dynamics. Second, we regularize the training of NFs with transport costs and show the effectiveness on controlling the model's Lipschitz bound, resulting in better generalization performance. We demonstrate numerical results through comprehensive experiments on a variety of synthetic and real-life datasets.

Stefan C. Schonsheck, Scott Mahan, Timo Klock et al.

Autoencoding is a popular method in representation learning. Conventional autoencoders employ symmetric encoding-decoding procedures and a simple Euclidean latent space to detect hidden low-dimensional structures in an unsupervised way. Some modern approaches to novel data generation such as generative adversarial networks askew this symmetry, but still employ a pair of massive networks--one to generate the image and another to judge the images quality based on priors learned from a training set. This work introduces a chart autoencoder with an asymmetric encoding-decoding process that can incorporate additional semi-supervised information such as class labels. Besides enhancing the capability for handling data with complicated topological and geometric structures, the proposed model can successfully differentiate nearby but disjoint manifolds and intersecting manifolds with only a small amount of supervision. Moreover, this model only requires a low-complexity encoding operation, such as a locally defined linear projection. We discuss the approximation power of such networks and derive a bound that essentially depends on the intrinsic dimension of the data manifold rather than the dimension of ambient space. Next we incorporate bounds for the sampling rate of training data need to faithfully represent a given data manifold. We present numerical experiments that verify that the proposed model can effectively manage data with multi-class nearby but disjoint manifolds of different classes, overlapping manifolds, and manifolds with non-trivial topology. Finally, we conclude with some experiments on computer vision and molecular dynamics problems which showcase the efficacy of our methods on real-world data.

Abiy Tasissa, Rongjie Lai

This paper considers theoretical analysis of recovering a low rank matrix given a few expansion coefficients with respect to any basis. The current approach generalizes the existing analysis for the low-rank matrix completion problem with sampling under entry sensing or with respect to a symmetric orthonormal basis. The analysis is based on dual certificates using a dual basis approach and does not assume the restricted isometry property (RIP). We introduce a condition on the basis called the correlation condition. This condition can be computed in time $O(n^3)$ and holds for many cases of deterministic basis where RIP might not hold or is NP hard to verify. If the correlation condition holds and the underlying low rank matrix obeys the coherence condition with parameter $ν$, under additional mild assumptions, our main result shows that the true matrix can be recovered with very high probability from $O(nrν\log^2n)$ uniformly random expansion coefficients.

Alexander Hsu, Zhaiming Shen, Wenjing Liao et al.

Pre-trained transformers are able to learn from examples provided as part of the prompt without any weight updates, a remarkable ability known as in-context learning (ICL). Despite its demonstrated efficacy across various domains, the theoretical understanding of ICL is still developing. Whereas most existing theory has focused on linear models, we study ICL in the nonlinear regression setting. Through the interaction mechanism in attention, we explicitly construct transformer networks to realize nonlinear features, such as polynomial or spline bases, which span a wide class of functions. Based on this construction, we establish a framework to analyze end-to-end in-context nonlinear regression with the constructed features. Our theory provides finite-sample generalization error bounds in terms of context length and training set size. We numerically validate the theory on synthetic regression tasks.

Dayang Wang, Feng-Lei Fan, Bo-Jian Hou et al.

A neural network with the widely-used ReLU activation has been shown to partition the sample space into many convex polytopes for prediction. However, the parameterized way a neural network and other machine learning models use to partition the space has imperfections, \textit{e}.\textit{g}., the compromised interpretability for complex models, the inflexibility in decision boundary construction due to the generic character of the model, and the risk of being trapped into shortcut solutions. In contrast, although the non-parameterized models can adorably avoid or downplay these issues, they are usually insufficiently powerful either due to over-simplification or the failure to accommodate the manifold structures of data. In this context, we first propose a new type of machine learning models referred to as Manifoldron that directly derives decision boundaries from data and partitions the space via manifold structure discovery. Then, we systematically analyze the key characteristics of the Manifoldron such as manifold characterization capability and its link to neural networks. The experimental results on 4 synthetic examples, 20 public benchmark datasets, and 1 real-world application demonstrate that the proposed Manifoldron performs competitively compared to the mainstream machine learning models. We have shared our code in \url{https://github.com/wdayang/Manifoldron} for free download and evaluation.

Feng-Lei Fan, Mengzhou Li, Fei Wang et al.

Inspired by the diversity of biological neurons, quadratic artificial neurons can play an important role in deep learning models. The type of quadratic neurons of our interest replaces the inner-product operation in the conventional neuron with a quadratic function. Despite promising results so far achieved by networks of quadratic neurons, there are important issues not well addressed. Theoretically, the superior expressivity of a quadratic network over either a conventional network or a conventional network via quadratic activation is not fully elucidated, which makes the use of quadratic networks not well grounded. Practically, although a quadratic network can be trained via generic backpropagation, it can be subject to a higher risk of collapse than the conventional counterpart. To address these issues, we first apply the spline theory and a measure from algebraic geometry to give two theorems that demonstrate better model expressivity of a quadratic network than the conventional counterpart with or without quadratic activation. Then, we propose an effective training strategy referred to as ReLinear to stabilize the training process of a quadratic network, thereby unleashing the full potential in its associated machine learning tasks. Comprehensive experiments on popular datasets are performed to support our findings and confirm the performance of quadratic deep learning. We have shared our code in \url{https://github.com/FengleiFan/ReLinear}.

Frank Cole, Dixi Wang, Yineng Chen et al.

We introduce \emph{in-context operator learning on probability measure spaces} for optimal transport (OT). The goal is to learn a single solution operator that maps a pair of distributions to the OT map, using only few-shot samples from each distribution as a prompt and \emph{without} gradient updates at inference. We parameterize the solution operator and develop scaling-law theory in two regimes. In the \emph{nonparametric} setting, when tasks concentrate on a low-intrinsic-dimension manifold of source--target pairs, we establish generalization bounds that quantify how in-context accuracy scales with prompt size, intrinsic task dimension, and model capacity. In the \emph{parametric} setting (e.g., Gaussian families), we give an explicit architecture that recovers the exact OT map in context and provide finite-sample excess-risk bounds. Our numerical experiments on synthetic transports and generative-modeling benchmarks validate the framework.

Xue Feng, Li Wang, Deanna Needell et al.

The Jordan-Kinderlehrer-Otto (JKO) scheme provides a stable variational framework for computing Wasserstein gradient flows, but its practical use is often limited by the high computational cost of repeatedly solving the JKO subproblems. We propose a self-supervised approach for learning a JKO solution operator without requiring numerical solutions of any JKO trajectories. The learned operator maps an input density directly to the minimizer of the corresponding JKO subproblem, and can be iteratively applied to efficiently generate the gradient-flow evolution. A key challenge is that only a number of initial densities are typically available for training. To address this, we introduce a Learn-to-Evolve algorithm that jointly learns the JKO operator and its induced trajectories by alternating between trajectory generation and operator updates. As training progresses, the generated data increasingly approximates true JKO trajectories. Meanwhile, this Learn-to-Evolve strategy serves as a natural form of data augmentation, significantly enhancing the generalization ability of the learned operator. Numerical experiments demonstrate the accuracy, stability, and robustness of the proposed method across various choices of energies and initial conditions.

Bongsoo Yi, Rongjie Lai, Yao Li

Adversarial training has been shown to be successful in enhancing the robustness of deep neural networks against adversarial attacks. However, this robustness is accompanied by a significant decline in accuracy on clean data. In this paper, we propose a novel method, called Tangent Direction Guided Adversarial Training (TART), that leverages the tangent space of the data manifold to ameliorate the existing adversarial defense algorithms. We argue that training with adversarial examples having large normal components significantly alters the decision boundary and hurts accuracy. TART mitigates this issue by estimating the tangent direction of adversarial examples and allocating an adaptive perturbation limit according to the norm of their tangential component. To the best of our knowledge, our paper is the first work to consider the concept of tangent space and direction in the context of adversarial defense. We validate the effectiveness of TART through extensive experiments on both simulated and benchmark datasets. The results demonstrate that TART consistently boosts clean accuracy while retaining a high level of robustness against adversarial attacks. Our findings suggest that incorporating the geometric properties of data can lead to more effective and efficient adversarial training methods.

Zhaiming Shen, Alexander Hsu, Rongjie Lai et al.

While in-context learning (ICL) has achieved remarkable success in natural language and vision domains, its theoretical understanding-particularly in the context of structured geometric data-remains unexplored. This paper initiates a theoretical study of ICL for regression of Hölder functions on manifolds. We establish a novel connection between the attention mechanism and classical kernel methods, demonstrating that transformers effectively perform kernel-based prediction at a new query through its interaction with the prompt. This connection is validated by numerical experiments, revealing that the learned query-prompt scores for Hölder functions are highly correlated with the Gaussian kernel. Building on this insight, we derive generalization error bounds in terms of the prompt length and the number of training tasks. When a sufficient number of training tasks are observed, transformers give rise to the minimax regression rate of Hölder functions on manifolds, which scales exponentially with the intrinsic dimension of the manifold, rather than the ambient space dimension. Our result also characterizes how the generalization error scales with the number of training tasks, shedding light on the complexity of transformers as in-context kernel algorithm learners. Our findings provide foundational insights into the role of geometry in ICL and novels tools to study ICL of nonlinear models.

Han Huang, Rongjie Lai

Recent advances in deep learning has witnessed many innovative frameworks that solve high dimensional mean-field games (MFG) accurately and efficiently. These methods, however, are restricted to solving single-instance MFG and demands extensive computational time per instance, limiting practicality. To overcome this, we develop a novel framework to learn the MFG solution operator. Our model takes a MFG instances as input and output their solutions with one forward pass. To ensure the proposed parametrization is well-suited for operator learning, we introduce and prove the notion of sampling invariance for our model, establishing its convergence to a continuous operator in the sampling limit. Our method features two key advantages. First, it is discretization-free, making it particularly suitable for learning operators of high-dimensional MFGs. Secondly, it can be trained without the need for access to supervised labels, significantly reducing the computational overhead associated with creating training datasets in existing operator learning methods. We test our framework on synthetic and realistic datasets with varying complexity and dimensionality to substantiate its robustness.

Zhaiming Shen, Alex Havrilla, Rongjie Lai et al.

Transformers serve as the foundational architecture for large language and video generation models, such as GPT, BERT, SORA and their successors. Empirical studies have demonstrated that real-world data and learning tasks exhibit low-dimensional structures, along with some noise or measurement error. The performance of transformers tends to depend on the intrinsic dimension of the data/tasks, though theoretical understandings remain largely unexplored for transformers. This work establishes a theoretical foundation by analyzing the performance of transformers for regression tasks involving noisy input data on a manifold. Specifically, the input data are in a tubular neighborhood of a manifold, while the ground truth function depends on the projection of the noisy data onto the manifold. We prove approximation and generalization errors which crucially depend on the intrinsic dimension of the manifold. Our results demonstrate that transformers can leverage low-complexity structures in learning task even when the input data are perturbed by high-dimensional noise. Our novel proof technique constructs representations of basic arithmetic operations by transformers, which may hold independent interest.

Biraj Dahal, Jiahui Cheng, Hao Liu et al.

Many problems in science and engineering involve time-dependent, high dimensional datasets arising from complex physical processes, which are costly to simulate. In this work, we propose WeldNet: Windowed Encoders for Learning Dynamics, a data-driven nonlinear model reduction framework to build a low-dimensional surrogate model for complex evolution systems. Given time-dependent training data, we split the time domain into multiple overlapping windows, within which nonlinear dimension reduction is performed by auto-encoders to capture latent codes. Once a low-dimensional representation of the data is learned, a propagator network is trained to capture the evolution of the latent codes in each window, and a transcoder is trained to connect the latent codes between adjacent windows. The proposed windowed decomposition significantly simplifies propagator training by breaking long-horizon dynamics into multiple short, manageable segments, while the transcoders ensure consistency across windows. In addition to the algorithmic framework, we develop a mathematical theory establishing the representation power of WeldNet under the manifold hypothesis, justifying the success of nonlinear model reduction via deep autoencoder-based architectures. Our numerical experiments on various differential equations indicate that WeldNet can capture nonlinear latent structures and their underlying dynamics, outperforming both traditional projection-based approaches and recently developed nonlinear model reduction methods.

Hao Liu, Biraj Dahal, Rongjie Lai et al.

Many physical processes in science and engineering are naturally represented by operators between infinite-dimensional function spaces. The problem of operator learning, in this context, seeks to extract these physical processes from empirical data, which is challenging due to the infinite or high dimensionality of data. An integral component in addressing this challenge is model reduction, which reduces both the data dimensionality and problem size. In this paper, we utilize low-dimensional nonlinear structures in model reduction by investigating Auto-Encoder-based Neural Network (AENet). AENet first learns the latent variables of the input data and then learns the transformation from these latent variables to corresponding output data. Our numerical experiments validate the ability of AENet to accurately learn the solution operator of nonlinear partial differential equations. Furthermore, we establish a mathematical and statistical estimation theory that analyzes the generalization error of AENet. Our theoretical framework shows that the sample complexity of training AENet is intricately tied to the intrinsic dimension of the modeled process, while also demonstrating the remarkable resilience of AENet to noise.

N. Joseph Tatro, Pin-Yu Chen, Payel Das et al.

The loss landscapes of deep neural networks are not well understood due to their high nonconvexity. Empirically, the local minima of these loss functions can be connected by a learned curve in model space, along which the loss remains nearly constant; a feature known as mode connectivity. Yet, current curve finding algorithms do not consider the influence of symmetry in the loss surface created by model weight permutations. We propose a more general framework to investigate the effect of symmetry on landscape connectivity by accounting for the weight permutations of the networks being connected. To approximate the optimal permutation, we introduce an inexpensive heuristic referred to as neuron alignment. Neuron alignment promotes similarity between the distribution of intermediate activations of models along the curve. We provide theoretical analysis establishing the benefit of alignment to mode connectivity based on this simple heuristic. We empirically verify that the permutation given by alignment is locally optimal via a proximal alternating minimization scheme. Empirically, optimizing the weight permutation is critical for efficiently learning a simple, planar, low-loss curve between networks that successfully generalizes. Our alignment method can significantly alleviate the recently identified robust loss barrier on the path connecting two adversarial robust models and find more robust and accurate models on the path.

Rui Xiang, Rongjie Lai, Hongkai Zhao

In this work, a simple and efficient dual iterative refinement (DIR) method is proposed for dense correspondence between two nearly isometric shapes. The key idea is to use dual information, such as spatial and spectral, or local and global features, in a complementary and effective way, and extract more accurate information from current iteration to use for the next iteration. In each DIR iteration, starting from current correspondence, a zoom-in process at each point is used to select well matched anchor pairs by a local mapping distortion criterion. These selected anchor pairs are then used to align spectral features (or other appropriate global features) whose dimension adaptively matches the capacity of the selected anchor pairs. Thanks to the effective combination of complementary information in a data-adaptive way, DIR is not only efficient but also robust to render accurate results within a few iterations. By choosing appropriate dual features, DIR has the flexibility to handle patch and partial matching as well. Extensive experiments on various data sets demonstrate the superiority of DIR over other state-of-the-art methods in terms of both accuracy and efficiency.

N. Joseph Tatro, Stefan C. Schonsheck, Rongjie Lai

Geometric disentanglement, the separation of latent codes for intrinsic (i.e. identity) and extrinsic(i.e. pose) geometry, is a prominent task for generative models of non-Euclidean data such as 3D deformable models. It provides greater interpretability of the latent space, and leads to more control in generation. This work introduces a mesh feature, the conformal factor and normal feature (CFAN),for use in mesh convolutional autoencoders. We further propose CFAN-VAE, a novel architecture that disentangles identity and pose using the CFAN feature. Requiring no label information on the identity or pose during training, CFAN-VAE achieves geometric disentanglement in an unsupervisedway. Our comprehensive experiments, including reconstruction, interpolation, generation, and identity/pose transfer, demonstrate CFAN-VAE achieves state-of-the-art performance on unsupervised geometric disentanglement. We also successfully detect a level of geometric disentanglement in mesh convolutional autoencoders that encode xyz-coordinates directly by registering its latent space to that of CFAN-VAE.

Rui Xiang, Rongjie Lai, Hongkai Zhao

In this work, we introduce a novel local pairwise descriptor and then develop a simple, effective iterative method to solve the resulting quadratic assignment through sparsity control for shape correspondence between two approximate isometric surfaces. Our pairwise descriptor is based on the stiffness and mass matrix of finite element approximation of the Laplace-Beltrami differential operator, which is local in space, sparse to represent, and extremely easy to compute while containing global information. It allows us to deal with open surfaces, partial matching, and topological perturbations robustly. To solve the resulting quadratic assignment problem efficiently, the two key ideas of our iterative algorithm are: 1) select pairs with good (approximate) correspondence as anchor points, 2) solve a regularized quadratic assignment problem only in the neighborhood of selected anchor points through sparsity control. These two ingredients can improve and increase the number of anchor points quickly while reducing the computation cost in each quadratic assignment iteration significantly. With enough high-quality anchor points, one may use various pointwise global features with reference to these anchor points to further improve the dense shape correspondence. We use various experiments to show the efficiency, quality, and versatility of our method on large data sets, patches, and point clouds (without global meshes).

Feng-Lei Fan, Rongjie Lai, Ge Wang

While classic studies proved that wide networks allow universal approximation, recent research and successes of deep learning demonstrate the power of deep networks. Based on a symmetric consideration, we investigate if the design of artificial neural networks should have a directional preference, and what the mechanism of interaction is between the width and depth of a network. Inspired by the De Morgan law, we address this fundamental question by establishing a quasi-equivalence between the width and depth of ReLU networks in two aspects. First, we formulate two transforms for mapping an arbitrary ReLU network to a wide network and a deep network respectively for either regression or classification so that the essentially same capability of the original network can be implemented. Then, we replace the mainstream artificial neuron type with a quadratic counterpart, and utilize the factorization and continued fraction representations of the same polynomial function to construct a wide network and a deep network, respectively. Based on our findings, a deep network has a wide equivalent, and vice versa, subject to an arbitrarily small error.

Stefan Schonsheck, Jie Chen, Rongjie Lai

Deep generative models have made tremendous advances in image and signal representation learning and generation. These models employ the full Euclidean space or a bounded subset as the latent space, whose flat geometry, however, is often too simplistic to meaningfully reflect the manifold structure of the data. In this work, we advocate the use of a multi-chart latent space for better data representation. Inspired by differential geometry, we propose a \textbf{Chart Auto-Encoder (CAE)} and prove a universal approximation theorem on its representation capability. We show that the training data size and the network size scale exponentially in approximation error with an exponent depending on the intrinsic dimension of the data manifold. CAE admits desirable manifold properties that auto-encoders with a flat latent space fail to obey, predominantly proximity of data. We conduct extensive experimentation with synthetic and real-life examples to demonstrate that CAE provides reconstruction with high fidelity, preserves proximity in the latent space, and generates new data remaining near the manifold. These experiments show that CAE is advantageous over existing auto-encoders and variants by preserving the topology of the data manifold as well as its geometry.

Pengfei Jin, Tianhao Lai, Rongjie Lai et al.

Convolution plays a crucial role in various applications in signal and image processing, analysis, and recognition. It is also the main building block of convolution neural networks (CNNs). Designing appropriate convolution neural networks on manifold-structured point clouds can inherit and empower recent advances of CNNs to analyzing and processing point cloud data. However, one of the major challenges is to define a proper way to "sweep" filters through the point cloud as a natural generalization of the planar convolution and to reflect the point cloud's geometry at the same time. In this paper, we consider generalizing convolution by adapting parallel transport on the point cloud. Inspired by a triangulated surface-based method [Stefan C. Schonsheck, Bin Dong, and Rongjie Lai, arXiv:1805.07857.], we propose the Narrow-Band Parallel Transport Convolution (NPTC) using a specifically defined connection on a voxel-based narrow-band approximation of point cloud data. With that, we further propose a deep convolutional neural network based on NPTC (called NPTC-net) for point cloud classification and segmentation. Comprehensive experiments show that the proposed NPTC-net achieves similar or better results than current state-of-the-art methods on point cloud classification and segmentation.

Stefan C. Schonsheck, Michael M. Bronstein, Rongjie Lai

Surface registration is one of the most fundamental problems in geometry processing. Many approaches have been developed to tackle this problem in cases where the surfaces are nearly isometric. However, it is much more challenging to compute correspondence between surfaces which are intrinsically less similar. In this paper, we propose a variational model to align the Laplace-Beltrami (LB) eigensytems of two non-isometric genus zero shapes via conformal deformations. This method enables us compute to geometric meaningful point-to-point maps between non-isometric shapes. Our model is based on a novel basis pursuit scheme whereby we simultaneously compute a conformal deformation of a 'target shape' and its deformed LB eigensytem. We solve the model using an proximal alternating minimization algorithm hybridized with the augmented Lagrangian method which produces accurate correspondences given only a few landmark points. We also propose a reinitialization scheme to overcome some of the difficulties caused by the non-convexity of the variational problem. Intensive numerical experiments illustrate the effectiveness and robustness of the proposed method to handle non-isometric surfaces with large deformation with respect to both noise on the underlying manifolds and errors within the given landmarks.

Zhiqian Chen, Feng Chen, Rongjie Lai et al.

For node level graph encoding, a recent important state-of-art method is the graph convolutional networks (GCN), which nicely integrate local vertex features and graph topology in the spectral domain. However, current studies suffer from several drawbacks: (1) graph CNNs relies on Chebyshev polynomial approximation which results in oscillatory approximation at jump discontinuities; (2) Increasing the order of Chebyshev polynomial can reduce the oscillations issue, but also incurs unaffordable computational cost; (3) Chebyshev polynomials require degree $Ω$(poly(1/$ε$)) to approximate a jump signal such as $|x|$, while rational function only needs $\mathcal{O}$(poly log(1/$ε$))\cite{liang2016deep,telgarsky2017neural}. However, it's non-trivial to apply rational approximation without increasing computational complexity due to the denominator. In this paper, the superiority of rational approximation is exploited for graph signal recovering. RatioanlNet is proposed to integrate rational function and neural networks. We show that rational function of eigenvalues can be rewritten as a function of graph Laplacian, which can avoid multiplication by the eigenvector matrix. Focusing on the analysis of approximation on graph convolution operation, a graph signal regression task is formulated. Under graph signal regression task, its time complexity can be significantly reduced by graph Fourier transform. To overcome the local minimum problem of neural networks model, a relaxed Remez algorithm is utilized to initialize the weight parameters. Convergence rate of RatioanlNet and polynomial based methods on jump signal is analyzed for a theoretical guarantee. The extensive experimental results demonstrated that our approach could effectively characterize the jump discontinuities, outperforming competing methods by a substantial margin on both synthetic and real-world graphs.

Stefan C. Schonsheck, Bin Dong, Rongjie Lai

Convolution has been playing a prominent role in various applications in science and engineering for many years. It is the most important operation in convolutional neural networks. There has been a recent growth of interests of research in generalizing convolutions on curved domains such as manifolds and graphs. However, existing approaches cannot preserve all the desirable properties of Euclidean convolutions, namely compactly supported filters, directionality, transferability across different manifolds. In this paper we develop a new generalization of the convolution operation, referred to as parallel transport convolution (PTC), on Riemannian manifolds and their discrete counterparts. PTC is designed based on the parallel transportation which is able to translate information along a manifold and to intrinsically preserve directionality. PTC allows for the construction of compactly supported filters and is also robust to manifold deformations. This enables us to preform wavelet-like operations and to define deep convolutional neural networks on curved domains.

Abiy Tasissa, Rongjie Lai

The Euclidean distance geometry problem arises in a wide variety of applications, from determining molecular conformations in computational chemistry to localization in sensor networks. When the distance information is incomplete, the problem can be formulated as a nuclear norm minimization problem. In this paper, this minimization program is recast as a matrix completion problem of a low-rank $r$ Gram matrix with respect to a suitable basis. The well known restricted isometry property can not be satisfied in this scenario. Instead, a dual basis approach is introduced to theoretically analyze the reconstruction problem. If the Gram matrix satisfies certain coherence conditions with parameter $ν$, the main result shows that the underlying configuration of $n$ points can be recovered with very high probability from $O(nrν\log^{2}(n))$ uniformly random samples. Computationally, simple and fast algorithms are designed to solve the Euclidean distance geometry problem. Numerical tests on different three dimensional data and protein molecules validate effectiveness and efficiency of the proposed algorithms.

Rongjie Lai, Jia Li

Solutions of partial differential equations (PDEs) on manifolds have provided important applications in different fields in science and engineering. Existing methods are majorly based on discretization of manifolds as implicit functions, triangle meshes, or point clouds, where the manifold structure is approximated by either zero level set of an implicit function or a set of points. In many applications, manifolds might be only provided as an inter-point distance matrix with possible missing values. This paper discusses a framework to discretize PDEs on manifolds represented as incomplete inter-point distance information. Without conducting a time-consuming global coordinates reconstruction, we propose a more efficient strategy by discretizing differential operators only based on point-wisely local reconstruction. Our local reconstruction model is based on the recent advances of low-rank matrix completion theory, where only a very small random portion of distance information is required. This method enables us to conduct analyses of incomplete distance data using solutions of special designed PDEs such as the Laplace-Beltrami (LB) eigen-system. As an application, we demonstrate a new way of manifold reconstruction from an incomplete distance by stitching patches using the spectrum of the LB operator. Intensive numerical experiments demonstrate the effectiveness of the proposed methods.

Wenxiang Cong, Ge Wang, Qingsong Yang et al.

Regularization methods are commonly used in X-ray CT image reconstruction. Different regularization methods reflect the characterization of different prior knowledge of images. In a recent work, a new regularization method called a low-dimensional manifold model (LDMM) is investigated to characterize the low-dimensional patch manifold structure of natural images, where the manifold dimensionality characterizes structural information of an image. In this paper, we propose a CT image reconstruction method based on the prior knowledge of the low-dimensional manifold of CT image. Using the clinical raw projection data from GE clinic, we conduct comparisons for the CT image reconstruction among the proposed method, the simultaneous algebraic reconstruction technique (SART) with the total variation (TV) regularization, and the filtered back projection (FBP) method. Results show that the proposed method can successfully recover structural details of an imaging object, and achieve higher spatial and contrast resolution of the reconstructed image than counterparts of FBP and SART with TV.

Honglin Yuan, Xiaoyi Gu, Rongjie Lai et al.

Orthogonality constrained optimization is widely used in applications from science and engineering. Due to the nonconvex orthogonality constraints, many numerical algorithms often can hardly achieve the global optimality. We aim at establishing an efficient scheme for finding global minimizers under one or more orthogonality constraints. The main concept is based on noisy gradient flow constructed from stochastic differential equations (SDE) on the Stiefel manifold, the differential geometric characterization of orthogonality constraints. We derive an explicit representation of SDE on the Stiefel manifold endowed with a canonical metric and propose a numerically efficient scheme to simulate this SDE based on Cayley transformation with theoretical convergence guarantee. The convergence to global optimizers is proved under second-order continuity. The effectiveness and efficiency of the proposed algorithms are demonstrated on a variety of problems including homogeneous polynomial optimization, computation of stability number, and 3D structure determination from Common Lines in Cryo-EM.

Rongjie Lai, Jia Li

Low-rank structures play important role in recent advances of many problems in image science and data science. As a natural extension of low-rank structures for data with nonlinear structures, the concept of the low-dimensional manifold structure has been considered in many data processing problems. Inspired by this concept, we consider a manifold based low-rank regularization as a linear approximation of manifold dimension. This regularization is less restricted than the global low-rank regularization, and thus enjoy more flexibility to handle data with nonlinear structures. As applications, we demonstrate the proposed regularization to classical inverse problems in image sciences and data sciences including image inpainting, image super-resolution, X-ray computer tomography (CT) image reconstruction and semi-supervised learning. We conduct intensive numerical experiments in several image restoration problems and a semi-supervised learning problem of classifying handwritten digits using the MINST data. Our numerical tests demonstrate the effectiveness of the proposed methods and illustrate that the new regularization methods produce outstanding results by comparing with many existing methods.