Xiaojing Ye

Wanyu Bian, Qingchao Zhang, Xiaojing Ye et al.

Generating multi-contrasts/modal MRI of the same anatomy enriches diagnostic information but is limited in practice due to excessive data acquisition time. In this paper, we propose a novel deep-learning model for joint reconstruction and synthesis of multi-modal MRI using incomplete k-space data of several source modalities as inputs. The output of our model includes reconstructed images of the source modalities and high-quality image synthesized in the target modality. Our proposed model is formulated as a variational problem that leverages several learnable modality-specific feature extractors and a multimodal synthesis module. We propose a learnable optimization algorithm to solve this model, which induces a multi-phase network whose parameters can be trained using multi-modal MRI data. Moreover, a bilevel-optimization framework is employed for robust parameter training. We demonstrate the effectiveness of our approach using extensive numerical experiments.

Chi Ding, Qingchao Zhang, Ge Wang et al.

We propose a novel Learned Alternating Minimization Algorithm (LAMA) for dual-domain sparse-view CT image reconstruction. LAMA is naturally induced by a variational model for CT reconstruction with learnable nonsmooth nonconvex regularizers, which are parameterized as composite functions of deep networks in both image and sinogram domains. To minimize the objective of the model, we incorporate the smoothing technique and residual learning architecture into the design of LAMA. We show that LAMA substantially reduces network complexity, improves memory efficiency and reconstruction accuracy, and is provably convergent for reliable reconstructions. Extensive numerical experiments demonstrate that LAMA outperforms existing methods by a wide margin on multiple benchmark CT datasets.

Nathan Gaby, Xiaojing Ye, Haomin Zhou

We develop a novel computational framework to approximate solution operators of evolution partial differential equations (PDEs). By employing a general nonlinear reduced-order model, such as a deep neural network, to approximate the solution of a given PDE, we realize that the evolution of the model parameter is a control problem in the parameter space. Based on this observation, we propose to approximate the solution operator of the PDE by learning the control vector field in the parameter space. From any initial value, this control field can steer the parameter to generate a trajectory such that the corresponding reduced-order model solves the PDE. This allows for substantially reduced computational cost to solve the evolution PDE with arbitrary initial conditions. We also develop comprehensive error analysis for the proposed method when solving a large class of semilinear parabolic PDEs. Numerical experiments on different high-dimensional evolution PDEs with various initial conditions demonstrate the promising results of the proposed method.

Steven Zhou, Xiaojing Ye

In this paper, we compute numerical approximations of the minimal surfaces, an essential type of Partial Differential Equation (PDE), in higher dimensions. Classical methods cannot handle it in this case because of the Curse of Dimensionality, where the computational cost of these methods increases exponentially fast in response to higher problem dimensions, far beyond the computing capacity of any modern supercomputers. Only in the past few years have machine learning researchers been able to mitigate this problem. The solution method chosen here is a model known as a Physics-Informed Neural Network (PINN) which trains a deep neural network (DNN) to solve the minimal surface PDE. It can be scaled up into higher dimensions and trained relatively quickly even on a laptop with no GPU. Due to the inability to view the high-dimension output, our data is presented as snippets of a higher-dimension shape with enough fixed axes so that it is viewable with 3-D graphs. Not only will the functionality of this method be tested, but we will also explore potential limitations in the method's performance.

Xiaojing Ye

This draft book offers a comprehensive and rigorous treatment of the mathematical principles underlying modern deep learning. The book spans core theoretical topics, from the approximation capabilities of deep neural networks, the theory and algorithms of optimal control and reinforcement learning integrated with deep learning techniques, to contemporary generative models that drive today's advances in artificial intelligence.

Chi Ding, Qingchao Zhang, Ge Wang et al.

Inverse problems arise in many applications, especially tomographic imaging. We develop a Learned Alternating Minimization Algorithm (LAMA) to solve such problems via two-block optimization by synergizing data-driven and classical techniques with proven convergence. LAMA is naturally induced by a variational model with learnable regularizers in both data and image domains, parameterized as composite functions of neural networks trained with domain-specific data. We allow these regularizers to be nonconvex and nonsmooth to extract features from data effectively. We minimize the overall objective function using Nesterov's smoothing technique and residual learning architecture. It is demonstrated that LAMA reduces network complexity, improves memory efficiency, and enhances reconstruction accuracy, stability, and interpretability. Extensive experiments show that LAMA significantly outperforms state-of-the-art methods on popular benchmark datasets for Computed Tomography.

Yunmei Chen, Chi Ding, Xiaojing Ye

We develop a novel transfer learning framework to tackle the challenge of limited training data in image reconstruction problems. The proposed framework consists of two training steps, both of which are formed as bi-level optimizations. In the first step, we train a powerful universal feature-extractor that is capable of learning important knowledge from large, heterogeneous data sets in various domains. In the second step, we train a task-specific domain-adapter for a new target domain or task with only a limited amount of data available for training. Then the composition of the adapter and the universal feature-extractor effectively explores feature which serve as an important component of image regularization for the new domains, and this leads to high-quality reconstruction despite the data limitation issue. We apply this framework to reconstruct under-sampled MR images with limited data by using a collection of diverse data samples from different domains, such as images of other anatomies, measurements of various sampling ratios, and even different image modalities, including natural images. Experimental results demonstrate a promising transfer learning capability of the proposed method.

Chi Ding, Qingchao Zhang, Ge Wang et al.

We propose a learnable variational model that learns the features and leverages complementary information from both image and measurement domains for image reconstruction. In particular, we introduce a learned alternating minimization algorithm (LAMA) from our prior work, which tackles two-block nonconvex and nonsmooth optimization problems by incorporating a residual learning architecture in a proximal alternating framework. In this work, our goal is to provide a complete and rigorous convergence proof of LAMA and show that all accumulation points of a specified subsequence of LAMA must be Clarke stationary points of the problem. LAMA directly yields a highly interpretable neural network architecture called LAMA-Net. Notably, in addition to the results shown in our prior work, we demonstrate that the convergence property of LAMA yields outstanding stability and robustness of LAMA-Net in this work. We also show that the performance of LAMA-Net can be further improved by integrating a properly designed network that generates suitable initials, which we call iLAMA-Net. To evaluate LAMA-Net/iLAMA-Net, we conduct several experiments and compare them with several state-of-the-art methods on popular benchmark datasets for Sparse-View Computed Tomography.

Nathan Gaby, Xiaojing Ye

We develop a general theoretical framework for optimal probability density control and propose a numerical algorithm that is scalable to solve the control problem in high dimensions. Specifically, we establish the Pontryagin Maximum Principle (PMP) for optimal density control and construct the Hamilton-Jacobi-Bellman (HJB) equation of the value functional through rigorous derivations without any concept from Wasserstein theory. To solve the density control problem numerically, we propose to use reduced-order models, such as deep neural networks (DNNs), to parameterize the control vector-field and the adjoint function, which allows us to tackle problems defined on high-dimensional state spaces. We also prove several convergence properties of the proposed algorithm. Numerical results demonstrate promising performances of our algorithm on a variety of density control problems with obstacles and nonlinear interaction challenges in high dimensions.

Nathan Gaby, Xiaojing Ye

We propose a finite-dimensional control-based method to approximate solution operators for evolutional partial differential equations (PDEs), particularly in high-dimensions. By employing a general reduced-order model, such as a deep neural network, we connect the evolution of the model parameters with trajectories in a corresponding function space. Using the computational technique of neural ordinary differential equation, we learn the control over the parameter space such that from any initial starting point, the controlled trajectories closely approximate the solutions to the PDE. Approximation accuracy is justified for a general class of second-order nonlinear PDEs. Numerical results are presented for several high-dimensional PDEs, including real-world applications to solving Hamilton-Jacobi-Bellman equations. These are demonstrated to show the accuracy and efficiency of the proposed method.

Zhiwei Tang, Tsung-Hui Chang, Xiaojing Ye et al.

We study a matrix recovery problem with unknown correspondence: given the observation matrix $M_o=[A,\tilde P B]$, where $\tilde P$ is an unknown permutation matrix, we aim to recover the underlying matrix $M=[A,B]$. Such problem commonly arises in many applications where heterogeneous data are utilized and the correspondence among them are unknown, e.g., due to privacy concerns. We show that it is possible to recover $M$ via solving a nuclear norm minimization problem under a proper low-rank condition on $M$, with provable non-asymptotic error bound for the recovery of $M$. We propose an algorithm, $\text{M}^3\text{O}$ (Matrix recovery via Min-Max Optimization) which recasts this combinatorial problem as a continuous minimax optimization problem and solves it by proximal gradient with a Max-Oracle. $\text{M}^3\text{O}$ can also be applied to a more general scenario where we have missing entries in $M_o$ and multiple groups of data with distinct unknown correspondence. Experiments on simulated data, the MovieLens 100K dataset and Yale B database show that $\text{M}^3\text{O}$ achieves state-of-the-art performance over several baselines and can recover the ground-truth correspondence with high accuracy.

Wanyu Bian, Yunmei Chen, Xiaojing Ye et al.

Purpose: This work aims at developing a generalizable MRI reconstruction model in the meta-learning framework. The standard benchmarks in meta-learning are challenged by learning on diverse task distributions. The proposed network learns the regularization function in a variational model and reconstructs MR images with various under-sampling ratios or patterns that may or may not be seen in the training data by leveraging a heterogeneous dataset. Methods: We propose an unrolling network induced by learnable optimization algorithms (LOA) for solving our nonconvex nonsmooth variational model for MRI reconstruction. In this model, the learnable regularization function contains a task-invariant common feature encoder and task-specific learner represented by a shallow network. To train the network we split the training data into two parts: training and validation, and introduce a bilevel optimization algorithm. The lower-level optimization trains task-invariant parameters for the feature encoder with fixed parameters of the task-specific learner on the training dataset, and the upper-level optimizes the parameters of the task-specific learner on the validation dataset. Results: The average PSNR increases significantly compared to the network trained through conventional supervised learning on the seen CS ratios. We test the result of quick adaption on the unseen tasks after meta-training and in the meanwhile saving half of the training time; Conclusion: We proposed a meta-learning framework consisting of the base network architecture, design of regularization, and bi-level optimization-based training. The network inherits the convergence property of the LOA and interpretation of the variational model. The generalization ability is improved by the designated regularization and bilevel optimization-based training algorithm.

Nathan Gaby, Fumin Zhang, Xiaojing Ye

We develop a versatile deep neural network architecture, called Lyapunov-Net, to approximate Lyapunov functions of dynamical systems in high dimensions. Lyapunov-Net guarantees positive definiteness, and thus it can be easily trained to satisfy the negative orbital derivative condition, which only renders a single term in the empirical risk function in practice. This significantly reduces the number of hyper-parameters compared to existing methods. We also provide theoretical justifications on the approximation power of Lyapunov-Net and its complexity bounds. We demonstrate the efficiency of the proposed method on nonlinear dynamical systems involving up to 30-dimensional state spaces, and show that the proposed approach significantly outperforms the state-of-the-art methods.

Wanyu Bian, Yunmei Chen, Xiaojing Ye

Goal: This work aims at developing a novel calibration-free fast parallel MRI (pMRI) reconstruction method incorporate with discrete-time optimal control framework. The reconstruction model is designed to learn a regularization that combines channels and extracts features by leveraging the information sharing among channels of multi-coil images. We propose to recover both magnitude and phase information by taking advantage of structured convolutional networks in image and Fourier spaces. Methods: We develop a novel variational model with a learnable objective function that integrates an adaptive multi-coil image combination operator and effective image regularization in the image and Fourier spaces. We cast the reconstruction network as a structured discrete-time optimal control system, resulting in an optimal control formulation of parameter training where the parameters of the objective function play the role of control variables. We demonstrate that the Lagrangian method for solving the control problem is equivalent to back-propagation, ensuring the local convergence of the training algorithm. Results: We conduct a large number of numerical experiments of the proposed method with comparisons to several state-of-the-art pMRI reconstruction networks on real pMRI datasets. The numerical results demonstrate the promising performance of the proposed method evidently. Conclusion: We conduct a large number of numerical experiments of the proposed method with comparisons to several state-of-the-art pMRI reconstruction networks on real pMRI datasets. The numerical results demonstrate the promising performance of the proposed method evidently. Significance: By learning multi-coil image combination operator and performing regularizations in both image domain and k-space domain, the proposed method achieves a highly efficient image reconstruction network for pMRI.

Shushan He, Hongyuan Zha, Xiaojing Ye

We propose a novel learning framework using neural mean-field (NMF) dynamics for inference and estimation problems on heterogeneous diffusion networks. Our new framework leverages the Mori-Zwanzig formalism to obtain an exact evolution equation of the individual node infection probabilities, which renders a delay differential equation with memory integral approximated by learnable time convolution operators. Directly using information diffusion cascade data, our framework can simultaneously learn the structure of the diffusion network and the evolution of node infection probabilities. Connections between parameter learning and optimal control are also established, leading to a rigorous and implementable algorithm for training NMF. Moreover, we show that the projected gradient descent method can be employed to solve the challenging influence maximization problem, where the gradient is computed extremely fast by integrating NMF forward in time just once in each iteration. Extensive empirical studies show that our approach is versatile and robust to variations of the underlying diffusion network models, and significantly outperform existing approaches in accuracy and efficiency on both synthetic and real-world data.

Qingchao Zhang, Mehrdad Alvandipour, Wenjun Xia et al.

We propose a provably convergent method, called Efficient Learned Descent Algorithm (ELDA), for low-dose CT (LDCT) reconstruction. ELDA is a highly interpretable neural network architecture with learned parameters and meanwhile retains convergence guarantee as classical optimization algorithms. To improve reconstruction quality, the proposed ELDA also employs a new non-local feature mapping and an associated regularizer. We compare ELDA with several state-of-the-art deep image methods, such as RED-CNN and Learned Primal-Dual, on a set of LDCT reconstruction problems. Numerical experiments demonstrate improvement of reconstruction quality using ELDA with merely 19 layers, suggesting the promising performance of ELDA in solution accuracy and parameter efficiency.

Yujia Xie, Yixiu Mao, Simiao Zuo et al.

We consider a variant of regression problem, where the correspondence between input and output data is not available. Such shuffled data is commonly observed in many real world problems. Taking flow cytometry as an example, the measuring instruments may not be able to maintain the correspondence between the samples and the measurements. Due to the combinatorial nature of the problem, most existing methods are only applicable when the sample size is small, and limited to linear regression models. To overcome such bottlenecks, we propose a new computational framework -- ROBOT -- for the shuffled regression problem, which is applicable to large data and complex nonlinear models. Specifically, we reformulate the regression without correspondence as a continuous optimization problem. Then by exploiting the interaction between the regression model and the data correspondence, we develop a hypergradient approach based on differentiable programming techniques. Such a hypergradient approach essentially views the data correspondence as an operator of the regression, and therefore allows us to find a better descent direction for the model parameter by differentiating through the data correspondence. ROBOT can be further extended to the inexact correspondence setting, where there may not be an exact alignment between the input and output data. Thorough numerical experiments show that ROBOT achieves better performance than existing methods in both linear and nonlinear regression tasks, including real-world applications such as flow cytometry and multi-object tracking.

Wanyu Bian, Yunmei Chen, Xiaojing Ye

We propose a novel deep neural network architecture by mapping the robust proximal gradient scheme for fast image reconstruction in parallel MRI (pMRI) with regularization function trained from data. The proposed network learns to adaptively combine the multi-coil images from incomplete pMRI data into a single image with homogeneous contrast, which is then passed to a nonlinear encoder to efficiently extract sparse features of the image. Unlike most of existing deep image reconstruction networks, our network does not require knowledge of sensitivity maps, which can be difficult to estimate accurately, and have been a major bottleneck of image reconstruction in real-world pMRI applications. The experimental results demonstrate the promising performance of our method on a variety of pMRI imaging data sets.

Yunmei Chen, Hongcheng Liu, Xiaojing Ye et al.

We propose a general learning based framework for solving nonsmooth and nonconvex image reconstruction problems. We model the regularization function as the composition of the $l_{2,1}$ norm and a smooth but nonconvex feature mapping parametrized as a deep convolutional neural network. We develop a provably convergent descent-type algorithm to solve the nonsmooth nonconvex minimization problem by leveraging the Nesterov's smoothing technique and the idea of residual learning, and learn the network parameters such that the outputs of the algorithm match the references in training data. Our method is versatile as one can employ various modern network structures into the regularization, and the resulting network inherits the guaranteed convergence of the algorithm. We also show that the proposed network is parameter-efficient and its performance compares favorably to the state-of-the-art methods in a variety of image reconstruction problems in practice.

Shushan He, Hongyuan Zha, Xiaojing Ye

We propose a novel learning framework based on neural mean-field dynamics for inference and estimation problems of diffusion on networks. Our new framework is derived from the Mori-Zwanzig formalism to obtain an exact evolution of the node infection probabilities, which renders a delay differential equation with memory integral approximated by learnable time convolution operators, resulting in a highly structured and interpretable RNN. Directly using cascade data, our framework can jointly learn the structure of the diffusion network and the evolution of infection probabilities, which are cornerstone to important downstream applications such as influence maximization. Connections between parameter learning and optimal control are also established. Empirical study shows that our approach is versatile and robust to variations of the underlying diffusion network models, and significantly outperform existing approaches in accuracy and efficiency on both synthetic and real-world data.

Qingchao Zhang, Xiaojing Ye, Hongcheng Liu et al.

Optimization algorithms for solving nonconvex inverse problem have attracted significant interests recently. However, existing methods require the nonconvex regularization to be smooth or simple to ensure convergence. In this paper, we propose a novel gradient descent type algorithm, by leveraging the idea of residual learning and Nesterov's smoothing technique, to solve inverse problems consisting of general nonconvex and nonsmooth regularization with provable convergence. Moreover, we develop a neural network architecture intimating this algorithm to learn the nonlinear sparsity transformation adaptively from training data, which also inherits the convergence to accommodate the general nonconvex structure of this learned transformation. Numerical results demonstrate that the proposed network outperforms the state-of-the-art methods on a variety of different image reconstruction problems in terms of efficiency and accuracy.

Gang Bao, Xiaojing Ye, Yaohua Zang et al.

We consider a weak adversarial network approach to numerically solve a class of inverse problems, including electrical impedance tomography and dynamic electrical impedance tomography problems. We leverage the weak formulation of PDE in the given inverse problem, and parameterize the solution and the test function as deep neural networks. The weak formulation and the boundary conditions induce a minimax problem of a saddle function of the network parameters. As the parameters are alternatively updated, the network gradually approximates the solution of the inverse problem. We provide theoretical justifications on the convergence of the proposed algorithm. Our method is completely mesh-free without any spatial discretization, and is particularly suitable for problems with high dimensionality and low regularity on solutions. Numerical experiments on a variety of test inverse problems demonstrate the promising accuracy and efficiency of our approach.

Shaojun Ma, Haodong Sun, Xiaojing Ye et al.

Inverse optimal transport (OT) refers to the problem of learning the cost function for OT from observed transport plan or its samples. In this paper, we derive an unconstrained convex optimization formulation of the inverse OT problem, which can be further augmented by any customizable regularization. We provide a comprehensive characterization of the properties of inverse OT, including uniqueness of solutions. We also develop two numerical algorithms, one is a fast matrix scaling method based on the Sinkhorn-Knopp algorithm for discrete OT, and the other one is a learning based algorithm that parameterizes the cost function as a deep neural network for continuous OT. The novel framework proposed in the work avoids repeatedly solving a forward OT in each iteration which has been a thorny computational bottleneck for the bi-level optimization in existing inverse OT approaches. Numerical results demonstrate promising efficiency and accuracy advantages of the proposed algorithms over existing state-of-the-art methods.

Ruilin Li, Xiaojing Ye, Haomin Zhou et al.

We propose a unified data-driven framework based on inverse optimal transport that can learn adaptive, nonlinear interaction cost function from noisy and incomplete empirical matching matrix and predict new matching in various matching contexts. We emphasize that the discrete optimal transport plays the role of a variational principle which gives rise to an optimization-based framework for modeling the observed empirical matching data. Our formulation leads to a non-convex optimization problem which can be solved efficiently by an alternating optimization method. A key novel aspect of our formulation is the incorporation of marginal relaxation via regularized Wasserstein distance, significantly improving the robustness of the method in the face of noisy or missing empirical matching data. Our model falls into the category of prescriptive models, which not only predict potential future matching, but is also able to explain what leads to empirical matching and quantifies the impact of changes in matching factors. The proposed approach has wide applicability including predicting matching in online dating, labor market, college application and crowdsourcing. We back up our claims with numerical experiments on both synthetic data and real world data sets.

Jiachen Yang, Xiaojing Ye, Rakshit Trivedi et al.

We consider the problem of representing collective behavior of large populations and predicting the evolution of a population distribution over a discrete state space. A discrete time mean field game (MFG) is motivated as an interpretable model founded on game theory for understanding the aggregate effect of individual actions and predicting the temporal evolution of population distributions. We achieve a synthesis of MFG and Markov decision processes (MDP) by showing that a special MFG is reducible to an MDP. This enables us to broaden the scope of mean field game theory and infer MFG models of large real-world systems via deep inverse reinforcement learning. Our method learns both the reward function and forward dynamics of an MFG from real data, and we report the first empirical test of a mean field game model of a real-world social media population.

Shuai Xiao, Mehrdad Farajtabar, Xiaojing Ye et al.

Point processes are becoming very popular in modeling asynchronous sequential data due to their sound mathematical foundation and strength in modeling a variety of real-world phenomena. Currently, they are often characterized via intensity function which limits model's expressiveness due to unrealistic assumptions on its parametric form used in practice. Furthermore, they are learned via maximum likelihood approach which is prone to failure in multi-modal distributions of sequences. In this paper, we propose an intensity-free approach for point processes modeling that transforms nuisance processes to a target one. Furthermore, we train the model using a likelihood-free leveraging Wasserstein distance between point processes. Experiments on various synthetic and real-world data substantiate the superiority of the proposed point process model over conventional ones.

Mehrdad Farajtabar, Jiachen Yang, Xiaojing Ye et al.

We propose the first multistage intervention framework that tackles fake news in social networks by combining reinforcement learning with a point process network activity model. The spread of fake news and mitigation events within the network is modeled by a multivariate Hawkes process with additional exogenous control terms. By choosing a feature representation of states, defining mitigation actions and constructing reward functions to measure the effectiveness of mitigation activities, we map the problem of fake news mitigation into the reinforcement learning framework. We develop a policy iteration method unique to the multivariate networked point process, with the goal of optimizing the actions for maximal total reward under budget constraints. Our method shows promising performance in real-time intervention experiments on a Twitter network to mitigate a surrogate fake news campaign, and outperforms alternatives on synthetic datasets.

Meizhu Liu, Le Lu, Xiaojing Ye et al.

Classification is one of the core problems in Computer-Aided Diagnosis (CAD), targeting for early cancer detection using 3D medical imaging interpretation. High detection sensitivity with desirably low false positive (FP) rate is critical for a CAD system to be accepted as a valuable or even indispensable tool in radiologists' workflow. Given various spurious imagery noises which cause observation uncertainties, this remains a very challenging task. In this paper, we propose a novel, two-tiered coarse-to-fine (CTF) classification cascade framework to tackle this problem. We first obtain classification-critical data samples (e.g., samples on the decision boundary) extracted from the holistic data distributions using a robust parametric model (e.g., \cite{Raykar08}); then we build a graph-embedding based nonparametric classifier on sampled data, which can more accurately preserve or formulate the complex classification boundary. These two steps can also be considered as effective "sample pruning" and "feature pursuing + $k$NN/template matching", respectively. Our approach is validated comprehensively in colorectal polyp detection and lung nodule detection CAD systems, as the top two deadly cancers, using hospital scale, multi-site clinical datasets. The results show that our method achieves overall better classification/detection performance than existing state-of-the-art algorithms using single-layer classifiers, such as the support vector machine variants \cite{Wang08}, boosting \cite{Slabaugh10}, logistic regression \cite{Ravesteijn10}, relevance vector machine \cite{Raykar08}, $k$-nearest neighbor \cite{Murphy09} or spectral projections on graph \cite{Cai08}.