Jianhong Chen

Jianhong Chen, Naichen Shi, Xubo Yue

Causal discovery is a data-driven paradigm for analyzing complex systems, while physics-based models, such as ordinary differential equations (ODEs), provide mechanistic structure for real-world dynamical processes. Integrating these paradigms can improve identifiability, stability, and robustness. However, real dynamical systems often exhibit cyclic interactions and nonstationarity, whereas many causal discovery methods rely on acyclicity, stationarity, or equilibrium assumptions. We propose an integrative causal discovery framework for dynamical systems that leverages partial physical knowledge through stochastic differential equations (SDEs). The drift term encodes known ODE dynamics, while the diffusion term captures unknown causal couplings beyond the prescribed physics. We develop a scalable sparsity-inducing maximum quasi-likelihood estimator with a theoretically justified stabilization technique to improve the optimization landscape. Under mild conditions, we establish causal graph recovery guarantees for both stable and unstable SDEs. We also analyze robustness of our causal graph estimate to ODE misspecification and clarify how the introduced stabilization technique balances numerical stability and statistical recoverability. Experiments on linear SDEs and nonlinear benchmarks, including Lotka-Volterra and Lorenz dynamics with acyclic and cyclic structures, show improved graph recovery and robustness over data-driven baselines. We also demonstrate practical utility on real-world epidemic data by reconstructing stochastic SIR dynamics within our causal discovery framework.

Jianhong Chen, Ying Ma, Xubo Yue

Traditionally, learning the structure of a Dynamic Bayesian Network has been centralized, requiring all data to be pooled in one location. However, in real-world scenarios, data are often distributed across multiple entities (e.g., companies, devices) that seek to collaboratively learn a Dynamic Bayesian Network while preserving data privacy and security. More importantly, due to the presence of diverse clients, the data may follow different distributions, resulting in data heterogeneity. This heterogeneity poses additional challenges for centralized approaches. In this study, we first introduce a federated learning approach for estimating the structure of a Dynamic Bayesian Network from homogeneous time series data that are horizontally distributed across different parties. We then extend this approach to heterogeneous time series data by incorporating a proximal operator as a regularization term in a personalized federated learning framework. To this end, we propose \texttt{FDBNL} and \texttt{PFDBNL}, which leverage continuous optimization, ensuring that only model parameters are exchanged during the optimization process. Experimental results on synthetic and real-world datasets demonstrate that our method outperforms state-of-the-art techniques, particularly in scenarios with many clients and limited individual sample sizes.

Jianhong Chen, Meng Zhao, Mostafa Reisi Gahrooei et al.

Temporal causal representation learning is a powerful tool for uncovering complex patterns in observational studies, which are often represented as low-dimensional time series. However, in many real-world applications, data are high-dimensional with varying input lengths and naturally take the form of irregular tensors. To analyze such data, irregular tensor decomposition is critical for extracting meaningful clusters that capture essential information. In this paper, we focus on modeling causal representation learning based on the transformed information. First, we present a novel causal formulation for a set of latent clusters. We then propose CaRTeD, a joint learning framework that integrates temporal causal representation learning with irregular tensor decomposition. Notably, our framework provides a blueprint for downstream tasks using the learned tensor factors, such as modeling latent structures and extracting causal information, and offers a more flexible regularization design to enhance tensor decomposition. Theoretically, we show that our algorithm converges to a stationary point. More importantly, our results fill the gap in theoretical guarantees for the convergence of state-of-the-art irregular tensor decomposition. Experimental results on synthetic and real-world electronic health record (EHR) datasets (MIMIC-III), with extensive benchmarks from both phenotyping and network recovery perspectives, demonstrate that our proposed method outperforms state-of-the-art techniques and enhances the explainability of causal representations.

Jianhong Chen, Shihao Yang

Parameter estimation and trajectory reconstruction for data-driven dynamical systems governed by ordinary differential equations (ODEs) are essential tasks in fields such as biology, engineering, and physics. These inverse problems -- estimating ODE parameters from observational data -- are particularly challenging when the data are noisy, sparse, and the dynamics are nonlinear. We propose the Eigen-Fourier Physics-Informed Gaussian Process (EFiGP), an algorithm that integrates Fourier transformation and eigen-decomposition into a physics-informed Gaussian Process framework. This approach eliminates the need for numerical integration, significantly enhancing computational efficiency and accuracy. Built on a principled Bayesian framework, EFiGP incorporates the ODE system through probabilistic conditioning, enforcing governing equations in the Fourier domain while truncating high-frequency terms to achieve denoising and computational savings. The use of eigen-decomposition further simplifies Gaussian Process covariance operations, enabling efficient recovery of trajectories and parameters even in dense-grid settings. We validate the practical effectiveness of EFiGP on three benchmark examples, demonstrating its potential for reliable and interpretable modeling of complex dynamical systems while addressing key challenges in trajectory recovery and computational cost.

Jonathan W. Siegel, Jianhong Chen, Pengchuan Zhang et al.

Pruning the weights of neural networks is an effective and widely-used technique for reducing model size and inference complexity. We develop and test a novel method based on compressed sensing which combines the pruning and training into a single step. Specifically, we utilize an adaptively weighted $\ell^1$ penalty on the weights during training, which we combine with a generalization of the regularized dual averaging (RDA) algorithm in order to train sparse neural networks. The adaptive weighting we introduce corresponds to a novel regularizer based on the logarithm of the absolute value of the weights. We perform a series of ablation studies demonstrating the improvement provided by the adaptive weighting and generalized RDA algorithm. Furthermore, numerical experiments on the CIFAR-10, CIFAR-100, and ImageNet datasets demonstrate that our method 1) trains sparser, more accurate networks than existing state-of-the-art methods; 2) can be used to train sparse networks from scratch, i.e. from a random initialization, as opposed to initializing with a well-trained base model; 3) acts as an effective regularizer, improving generalization accuracy.

Jianhong Chen, Huang Huang, Wenrui Hao et al.

Pulse feeling, representing the tactile arterial palpation of the heartbeat, has been widely used in traditional Chinese medicine (TCM) to diagnose various diseases. The quantitative relationship between the pulse wave and health conditions however has not been investigated in modern medicine. In this paper, we explored the correlation between pulse pressure wave (PPW), rather than the pulse key features in TCM, and pregnancy by using deep learning technology. This computational approach shows that the accuracy of pregnancy detection by the PPW is 84% with an AUC of 91%. Our study is a proof of concept of pulse diagnosis and will also motivate further sophisticated investigations on pulse waves.