Yuxiao Cheng

Runzhao Yang, Tingxiong Xiao, Yuxiao Cheng et al. · tsinghua

Implicit neural representation (INR) can describe the target scenes with high fidelity using a small number of parameters, and is emerging as a promising data compression technique. However, limited spectrum coverage is intrinsic to INR, and it is non-trivial to remove redundancy in diverse complex data effectively. Preliminary studies can only exploit either global or local correlation in the target data and thus of limited performance. In this paper, we propose a Tree-structured Implicit Neural Compression (TINC) to conduct compact representation for local regions and extract the shared features of these local representations in a hierarchical manner. Specifically, we use Multi-Layer Perceptrons (MLPs) to fit the partitioned local regions, and these MLPs are organized in tree structure to share parameters according to the spatial distance. The parameter sharing scheme not only ensures the continuity between adjacent regions, but also jointly removes the local and non-local redundancy. Extensive experiments show that TINC improves the compression fidelity of INR, and has shown impressive compression capabilities over commercial tools and other deep learning based methods. Besides, the approach is of high flexibility and can be tailored for different data and parameter settings. The source code can be found at https://github.com/RichealYoung/TINC .

Runzhao Yang, Tingxiong Xiao, Yuxiao Cheng et al. · tsinghua

Massive collection and explosive growth of biomedical data, demands effective compression for efficient storage, transmission and sharing. Readily available visual data compression techniques have been studied extensively but tailored for natural images/videos, and thus show limited performance on biomedical data which are of different features and larger diversity. Emerging implicit neural representation (INR) is gaining momentum and demonstrates high promise for fitting diverse visual data in target-data-specific manner, but a general compression scheme covering diverse biomedical data is so far absent. To address this issue, we firstly derive a mathematical explanation for INR's spectrum concentration property and an analytical insight on the design of INR based compressor. Further, we propose a Spectrum Concentrated Implicit neural compression (SCI) which adaptively partitions the complex biomedical data into blocks matching INR's concentrated spectrum envelop, and design a funnel shaped neural network capable of representing each block with a small number of parameters. Based on this design, we conduct compression via optimization under given budget and allocate the available parameters with high representation accuracy. The experiments show SCI's superior performance to state-of-the-art methods including commercial compressors, data-driven ones, and INR based counterparts on diverse biomedical data. The source code can be found at https://github.com/RichealYoung/ImplicitNeuralCompression.git.

Tingxiong Xiao, Weihang Zhang, Yuxiao Cheng et al. · tsinghua

Despite their remarkable performance, deep neural networks remain mostly ``black boxes'', suggesting inexplicability and hindering their wide applications in fields requiring making rational decisions. Here we introduce HOPE (High-order Polynomial Expansion), a method for expanding a network into a high-order Taylor polynomial on a reference input. Specifically, we derive the high-order derivative rule for composite functions and extend the rule to neural networks to obtain their high-order derivatives quickly and accurately. From these derivatives, we can then derive the Taylor polynomial of the neural network, which provides an explicit expression of the network's local interpretations. Numerical analysis confirms the high accuracy, low computational complexity, and good convergence of the proposed method. Moreover, we demonstrate HOPE's wide applications built on deep learning, including function discovery, fast inference, and feature selection. The code is available at https://github.com/HarryPotterXTX/HOPE.git.

Zhihong Zhang, Runzhao Yang, Jinli Suo et al. · tsinghua

The demand for compact cameras capable of recording high-speed scenes with high resolution is steadily increasing. However, achieving such capabilities often entails high bandwidth requirements, resulting in bulky, heavy systems unsuitable for low-capacity platforms. To address this challenge, leveraging a coded exposure setup to encode a frame sequence into a blurry snapshot and subsequently retrieve the latent sharp video presents a lightweight solution. Nevertheless, restoring motion from blur remains a formidable challenge due to the inherent ill-posedness of motion blur decomposition, the intrinsic ambiguity in motion direction, and the diverse motions present in natural videos. In this study, we propose a novel approach to address these challenges by combining the classical coded exposure imaging technique with the emerging implicit neural representation for videos. We strategically embed motion direction cues into the blurry image during the imaging process. Additionally, we develop a novel implicit neural representation based blur decomposition network to sequentially extract the latent video frames from the blurry image, leveraging the embedded motion direction cues. To validate the effectiveness and efficiency of our proposed framework, we conduct extensive experiments using benchmark datasets and real-captured blurry images. The results demonstrate that our approach significantly outperforms existing methods in terms of both quality and flexibility. The code for our work is available at .https://github.com/zhihongz/BDINR

Yuxiao Cheng, Runzhao Yang, Tingxiong Xiao et al. · tsinghua

Causal discovery from time-series data has been a central task in machine learning. Recently, Granger causality inference is gaining momentum due to its good explainability and high compatibility with emerging deep neural networks. However, most existing methods assume structured input data and degenerate greatly when encountering data with randomly missing entries or non-uniform sampling frequencies, which hampers their applications in real scenarios. To address this issue, here we present CUTS, a neural Granger causal discovery algorithm to jointly impute unobserved data points and build causal graphs, via plugging in two mutually boosting modules in an iterative framework: (i) Latent data prediction stage: designs a Delayed Supervision Graph Neural Network (DSGNN) to hallucinate and register unstructured data which might be of high dimension and with complex distribution; (ii) Causal graph fitting stage: builds a causal adjacency matrix with imputed data under sparse penalty. Experiments show that CUTS effectively infers causal graphs from unstructured time-series data, with significantly superior performance to existing methods. Our approach constitutes a promising step towards applying causal discovery to real applications with non-ideal observations.

Yuxiao Cheng, Ziqian Wang, Tingxiong Xiao et al. · tsinghua

Time-series causal discovery (TSCD) is a fundamental problem of machine learning. However, existing synthetic datasets cannot properly evaluate or predict the algorithms' performance on real data. This study introduces the CausalTime pipeline to generate time-series that highly resemble the real data and with ground truth causal graphs for quantitative performance evaluation. The pipeline starts from real observations in a specific scenario and produces a matching benchmark dataset. Firstly, we harness deep neural networks along with normalizing flow to accurately capture realistic dynamics. Secondly, we extract hypothesized causal graphs by performing importance analysis on the neural network or leveraging prior knowledge. Thirdly, we derive the ground truth causal graphs by splitting the causal model into causal term, residual term, and noise term. Lastly, using the fitted network and the derived causal graph, we generate corresponding versatile time-series proper for algorithm assessment. In the experiments, we validate the fidelity of the generated data through qualitative and quantitative experiments, followed by a benchmarking of existing TSCD algorithms using these generated datasets. CausalTime offers a feasible solution to evaluating TSCD algorithms in real applications and can be generalized to a wide range of fields. For easy use of the proposed approach, we also provide a user-friendly website, hosted on www.causaltime.cc.

Zhihong Zhang, Yuxiao Cheng, Jinli Suo et al.

Under low-light environment, handheld photography suffers from severe camera shake under long exposure settings. Although existing deblurring algorithms have shown promising performance on well-exposed blurry images, they still cannot cope with low-light snapshots. Sophisticated noise and saturation regions are two dominating challenges in practical low-light deblurring. In this work, we propose a novel non-blind deblurring method dubbed image and feature space Wiener deconvolution network (INFWIDE) to tackle these problems systematically. In terms of algorithm design, INFWIDE proposes a two-branch architecture, which explicitly removes noise and hallucinates saturated regions in the image space and suppresses ringing artifacts in the feature space, and integrates the two complementary outputs with a subtle multi-scale fusion network for high quality night photograph deblurring. For effective network training, we design a set of loss functions integrating a forward imaging model and backward reconstruction to form a close-loop regularization to secure good convergence of the deep neural network. Further, to optimize INFWIDE's applicability in real low-light conditions, a physical-process-based low-light noise model is employed to synthesize realistic noisy night photographs for model training. Taking advantage of the traditional Wiener deconvolution algorithm's physically driven characteristics and arisen deep neural network's representation ability, INFWIDE can recover fine details while suppressing the unpleasant artifacts during deblurring. Extensive experiments on synthetic data and real data demonstrate the superior performance of the proposed approach.

Ruoran Li, Runzhao Yang, Wenxin Xiang et al. · tsinghua

Functional Magnetic Resonance Imaging (fMRI) data is a widely used kind of four-dimensional biomedical data, which requires effective compression. However, fMRI compressing poses unique challenges due to its intricate temporal dynamics, low signal-to-noise ratio, and complicated underlying redundancies. This paper reports a novel compression paradigm specifically tailored for fMRI data based on Implicit Neural Representation (INR). The proposed approach focuses on removing the various redundancies among the time series by employing several methods, including (i) conducting spatial correlation modeling for intra-region dynamics, (ii) decomposing reusable neuronal activation patterns, and (iii) using proper initialization together with nonlinear fusion to describe the inter-region similarity. This scheme appropriately incorporates the unique features of fMRI data, and experimental results on publicly available datasets demonstrate the effectiveness of the proposed method, surpassing state-of-the-art algorithms in both conventional image quality evaluation metrics and fMRI downstream tasks. This work in this paper paves the way for sharing massive fMRI data at low bandwidth and high fidelity.

Jiayun Li, Yuxiao Cheng, Yiwen Lu et al.

Activation functions are essential to introduce nonlinearity into neural networks, with the Rectified Linear Unit (ReLU) often favored for its simplicity and effectiveness. Motivated by the structural similarity between a shallow Feedforward Neural Network (FNN) and a single iteration of the Projected Gradient Descent (PGD) algorithm, a standard approach for solving constrained optimization problems, we consider ReLU as a projection from R onto the nonnegative half-line R+. Building on this interpretation, we extend ReLU by substituting it with a generalized projection operator onto a convex cone, such as the Second-Order Cone (SOC) projection, thereby naturally extending it to a Multivariate Projection Unit (MPU), an activation function with multiple inputs and multiple outputs. We further provide mathematical proof establishing that FNNs activated by SOC projections outperform those utilizing ReLU in terms of expressive power. Experimental evaluations on widely-adopted architectures further corroborate MPU's effectiveness against a broader range of existing activation functions.

Ziqian Wang, Yuxiao Cheng, Jinli Suo

Explainability is essential for neural networks that model long time series, yet most existing explainable AI methods only produce point-wise importance scores and fail to capture temporal structures such as trends, cycles, and regime changes. This limitation weakens human interpretability and trust in long-horizon models. To address these issues, we identify four key requirements for interpretable time-series modeling: temporal continuity, pattern-centric explanation, causal disentanglement, and faithfulness to the model's inference process. We propose EXCAP, a unified framework that satisfies all four requirements. EXCAP combines an attention-based segmenter that extracts coherent temporal patterns, a causally structured decoder guided by a pre-trained causal graph, and a latent aggregation mechanism that enforces representation stability. Our theoretical analysis shows that EXCAP provides smooth and stable explanations over time and is robust to perturbations in causal masks. Extensive experiments on classification and forecasting benchmarks demonstrate that EXCAP achieves strong predictive accuracy while generating coherent and causally grounded explanations. These results show that EXCAP offers a principled and scalable approach to interpretable modeling of long time series with relevance to high-stakes domains such as healthcare and finance.

Yuxiao Cheng, Jinli Suo · tsinghua

Health informatics research is characterized by diverse data modalities, rapid knowledge expansion, and the need to integrate insights across biomedical science, data analytics, and clinical practice. These characteristics make it particularly well-suited for agent-based approaches that can automate knowledge exploration, manage complex workflows, and generate clinically meaningful outputs. Recent progress in large language model (LLM)-based agents has demonstrated promising capabilities in literature synthesis, data analysis, and even end-to-end research execution. However, existing systems remain limited for health informatics because they lack mechanisms to interpret medical visualizations and often overlook domain-specific quality requirements. To address these gaps, we introduce OpenLens AI, a fully automated framework tailored to health informatics. OpenLens AI integrates specialized agents for literature review, data analysis, code generation, and manuscript preparation, enhanced by vision-language feedback for medical visualization and quality control for reproducibility. The framework automates the entire research pipeline, producing publication-ready LaTeX manuscripts with transparent and traceable workflows, thereby offering a domain-adapted solution for advancing health informatics research.

Yuxiao Cheng, Xinxin Song, Ziqian Wang et al. · tsinghua

Recent advances in deep learning (DL) have prompted the development of high-performing early warning score (EWS) systems, predicting clinical deteriorations such as acute kidney injury, acute myocardial infarction, or circulatory failure. DL models have proven to be powerful tools for various tasks but come with the cost of lacking interpretability and limited generalizability, hindering their clinical applications. To develop a practical EWS system applicable to various outcomes, we propose causally-informed explainable early prediction model, which leverages causal discovery to identify the underlying causal relationships of prediction and thus owns two unique advantages: demonstrating the explicit interpretation of the prediction while exhibiting decent performance when applied to unfamiliar environments. Benefiting from these features, our approach achieves superior accuracy for 6 different critical deteriorations and achieves better generalizability across different patient groups, compared to various baseline algorithms. Besides, we provide explicit causal pathways to serve as references for assistant clinical diagnosis and potential interventions. The proposed approach enhances the practical application of deep learning in various medical scenarios.

Tingxiong Xiao, Runzhao Yang, Yuxiao Cheng et al.

Solving partial differential equations (PDEs) has been a fundamental problem in computational science and of wide applications for both scientific and engineering research. Due to its universal approximation property, neural network is widely used to approximate the solutions of PDEs. However, existing works are incapable of solving high-order PDEs due to insufficient calculation accuracy of higher-order derivatives, and the final network is a black box without explicit explanation. To address these issues, we propose a deep learning framework to solve high-order PDEs, named SHoP. Specifically, we derive the high-order derivative rule for neural network, to get the derivatives quickly and accurately; moreover, we expand the network into a Taylor series, providing an explicit solution for the PDEs. We conduct experimental validations four high-order PDEs with different dimensions, showing that we can solve high-order PDEs efficiently and accurately.

Yuxiao Cheng, Lianglong Li, Tingxiong Xiao et al.

Causal discovery in time-series is a fundamental problem in the machine learning community, enabling causal reasoning and decision-making in complex scenarios. Recently, researchers successfully discover causality by combining neural networks with Granger causality, but their performances degrade largely when encountering high-dimensional data because of the highly redundant network design and huge causal graphs. Moreover, the missing entries in the observations further hamper the causal structural learning. To overcome these limitations, We propose CUTS+, which is built on the Granger-causality-based causal discovery method CUTS and raises the scalability by introducing a technique called Coarse-to-fine-discovery (C2FD) and leveraging a message-passing-based graph neural network (MPGNN). Compared to previous methods on simulated, quasi-real, and real datasets, we show that CUTS+ largely improves the causal discovery performance on high-dimensional data with different types of irregular sampling.