arXiv subjects

Dan Wu

Publications and source records attributed to Dan Wu.

At least 37 records · Page 2Linked to original sources

arXiv2025

Surface Vision Mamba: Leveraging Bidirectional State Space Model for Efficient Spherical Manifold Representation

Attention-based methods have demonstrated exceptional performance in modelling long-range dependencies on spherical cortical surfaces, surpassing traditional Geometric Deep Learning (GDL) models. However, their extensive inference time and high memory demands pose challenges for application to large datasets with limited computing resources. Inspired by the state space model in computer vision, we introduce the attention-free Vision Mamba (Vim) to spherical surfaces, presenting a domain-agnostic architecture for analyzing data on spherical manifolds. Our method achieves surface patching by representing spherical data as a sequence of triangular patches derived from a subdivided icosphere. The proposed Surface Vision Mamba (SiM) is evaluated on multiple neurodevelopmental phenotype regression tasks using cortical surface metrics from neonatal brains. Experimental results demonstrate that SiM outperforms both attention- and GDL-based methods, delivering 4.8 times faster inference and achieving 91.7% lower memory consumption compared to the Surface Vision Transformer (SiT) under the Ico-4 grid partitioning. Sensitivity analysis further underscores the potential of SiM to identify subtle cognitive developmental patterns. The code is available at https://github.com/Rongzhao-He/surface-vision-mamba.

cs.CV↗

arXiv2025

Data-aware Dynamic Execution of Irregular Workloads on Heterogeneous Systems

Current approaches to scheduling workloads on heterogeneous systems with specialized accelerators often rely on manual partitioning, offloading tasks with specific compute patterns to accelerators. This method requires extensive experimentation and human effort to identify the tasks suitable for the accelerator. To solve this problem, we introduce DyPe, a scheduling framework tailored for heterogeneous systems with specialized accelerators. Our method automatically partitions, deploys, and reschedules execution when necessary by dynamically analyzing the characteristics of the input data and leveraging the interoperator parallelism among heterogeneous devices. DyPe navigates a multi-objective, multi-constraint design space that considers both system constraints and application requirements, which allows it to discover Pareto-optimal mapping configurations, improving the system's overall performance and effectively managing energy-performance trade-offs. To demonstrate the benefits of our approach on real hardware, we build a heterogeneous system of GPUs and FPGAs with peer-to-peer data transfers. The experiments show that conventional static scheduling is optimal for 13 out of 86 cases for different workloads and system settings while DyPe is adaptable and able to find the optimal schedule in 77 out of 86 cases, with an average of only 3.95% performance or energy efficiency loss in the sub-optimal cases. Performance evaluation of DyPe shows an average of 1.53x throughput and 1.09x energy efficiency improvement over the static schedule baseline and 1.44x throughput and 1.66x energy efficiency over the GPU-only baseline.

cs.DC↗

arXiv2025

Hybrid Parallel Collaborative Simulation Framework Integrating Device Physics with Circuit Dynamics for PDAE-Modeled Power Electronic Equipment

Optimizing high-performance power electronic equipment, such as power converters, requires multiscale simulations that incorporate the physics of power semiconductor devices and the dynamics of other circuit components, especially in conducting Design of Experiments (DoEs), defining the safe operating area of devices, and analyzing failures related to semiconductor devices. However, current methodologies either overlook the intricacies of device physics or do not achieve satisfactory computational speeds. To bridge this gap, this paper proposes a Hybrid-Parallel Collaborative (HPC) framework specifically designed to analyze the Partial Differential Algebraic Equation (PDAE) modeled power electronic equipment, integrating the device physics and circuit dynamics. The HPC framework employs a dynamic iteration to tackle the challenges inherent in solving the coupled nonlinear PDAE system, and utilizes a hybrid-parallel computing strategy to reduce computing time. Physics-based system partitioning along with hybrid-process-thread parallelization on shared and distributed memory are employed, facilitating the simulation of hundreds of partial differential equations (PDEs)-modeled devices simultaneously without compromising speed. Experiments based on the hybrid line commutated converter and reverse-blocking integrated gate-commutated thyristors are conducted under 3 typical real-world scenarios: semiconductor device optimization for the converter; converter design optimization; and device failure analysis. The HPC framework delivers simulation speed up to 60 times faster than the leading commercial software, while maintaining carrier-level accuracy in the experiments. This shows great potential for comprehensive analysis and collaborative optimization of devices and electronic power equipment, particularly in extreme conditions and failure scenarios.

eess.SY↗

arXiv2025

ThinTact:Thin Vision-Based Tactile Sensor by Lensless Imaging

Vision-based tactile sensors have drawn increasing interest in the robotics community. However, traditional lens-based designs impose minimum thickness constraints on these sensors, limiting their applicability in space-restricted settings. In this paper, we propose ThinTact, a novel lensless vision-based tactile sensor with a sensing field of over 200 mm2 and a thickness of less than 10 mm.ThinTact utilizes the mask-based lensless imaging technique to map the contact information to CMOS signals. To ensure real-time tactile sensing, we propose a real-time lensless reconstruction algorithm that leverages a frequency-spatial-domain joint filter based on discrete cosine transform (DCT). This algorithm achieves computation significantly faster than existing optimization-based methods. Additionally, to improve the sensing quality, we develop a mask optimization method based on the generic algorithm and the corresponding system matrix calibration algorithm.We evaluate the performance of our proposed lensless reconstruction and tactile sensing through qualitative and quantitative experiments. Furthermore, we demonstrate ThinTact's practical applicability in diverse applications, including texture recognition and contact-rich object manipulation. The paper will appear in the IEEE Transactions on Robotics: https://ieeexplore.ieee.org/document/10842357. Video: https://youtu.be/YrOO9BDMAHo

cs.RO↗

arXiv2024

7 Tesla multimodal MRI dataset of ex-vivo human brain

Ex-vivo MRI offers invaluable insights into the complexity of the human brain, enabling high-resolution anatomical delineation and integration with histopathology, and thus, contributes to both basic and clinical studies on normal and pathological brains. However, ex-vivo MRI is challenging in sample preparation, acquisition, and data analysis, and existing ex-vivo MRI datasets are often single image modality and lack of ethnic diversity. In our study, we aimed to address these limitations by constructing a comprehensive multimodal MRI database acquired from six ex-vivo Chinese human brains. This database included structural MRI, high-angular resolution diffusion MRI, quantitative susceptibility mapping, and quantitative T1 and T2 maps, which enabled multifaceted depiction of brain microstructure and connectivity. Furthermore, we generated population-averaged multimodal templates and the segmentation labels to facilitate analysis of ex-vivo brain MRI. This public database offers a collection of high-resolution and multi-parametric ex-vivo human brain MRI and filled the gap of lacking Asian brain samples in existing databases.

q-bio.QM↗

arXiv2024

Considerations and Recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging

Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the resultant data. This work aims to present selected recommendations and guidelines from the diffusion community, on best practices for preclinical dMRI of in vivo animals. We describe the general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss why some may be more or less appropriate for different studies. We then give guidelines for in vivo acquisition protocols, including decisions on hardware, animal preparation, and imaging sequences, followed by advice for data processing including pre-processing, model-fitting, and tractography. Finally, we provide an online resource which lists publicly available preclinical dMRI datasets and software packages, to promote responsible and reproducible research. In each section, we attempt to provide guides and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should focus. While we mainly cover the central nervous system (on which most preclinical dMRI studies are focused), we also provide, where possible and applicable, recommendations for other organs of interest. An overarching goal herein is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

physics.med-ph↗

arXiv2024

Queueing Delay Minimization in Overloaded Networks

We develop link rate control policies to minimize the queueing delay of packets in overloaded networks. We show that increasing link rates does not guarantee delay reduction during overload. We consider a fluid queueing model that facilitates explicit characterization of the queueing delay of packets, and establish explicit conditions on link rates that can minimize the average and maximum queueing delay in both single-hop and multi-stage (switching) networks. These min-delay conditions require maintaining an identical ratio between the ingress and egress rates of different nodes at the same layer of the network. We term the policies that follow these conditions rate-proportional policies. We further generalize the rate-proportional policies to queue-proportional policies, which minimize the queueing delay asymptotically based on the time-varying queue length while remaining agnostic of packet arrival rates. We validate that the proposed policies lead to minimum queueing delay under various network topologies and settings, compared with benchmarks including the backpressure policy that maximizes network throughput and the max-link-rate policy that fully utilizes bandwidth. We further remark that the explicit min-delay policy design in multi-stage networks facilitates co-optimization with other metrics, such as minimizing total bandwidth, balancing link utilization and node buffer usage. This demonstrates the wider utility of our main results in data center network optimization in practice.

cs.NI↗

arXiv2024

An Ordinary Differential Equation Framework for Stability Analysis of Networks with Finite Buffers

We consider the problem of network stability in finite-buffer systems. We observe that finite buffer may affect stability even in simplest network structure, and we propose an ordinary differential equation (ODE) model to capture the queuing dynamics and analyze the stability in buffered communication networks with general topology. For single-commodity systems, we propose a sufficient condition, which follows the fundamental idea of backpressure, for local transmission policies to stabilize the networks based on ODE stability theory. We further extend the condition to multi-commodity systems, with an additional restriction on the coupling level between different commodities, which can model networks with per-commodity buffers and shared buffers. The framework characterizes a set of policies that can stabilize buffered networks, and is useful for analyzing the effect of finite buffers on network stability.

cs.NI↗

arXiv2024

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 2 -- Ex vivo imaging: added value and acquisition

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher signal-to-noise ratio and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts. Another major advantage of ex vivo dMRI is the direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a 3-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We give general considerations and foundational knowledge that must be considered when designing experiments. We describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge.

physics.med-ph↗

arXiv2024

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3 -- Ex vivo imaging: data processing, comparisons with microscopy, and tractography

Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages that facilitate high spatial resolution and high signal-to-noise ratio (SNR) images, cutting-edge diffusion contrasts, and direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work concludes a 3-part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre-processing, data processing and model fitting, and tractography. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. We end by providing guidelines on code sharing and data sharing, and point towards open-source software and databases specific to small animal and ex vivo imaging.

physics.med-ph↗

arXiv2024

A Multi-scenario Attention-based Generative Model for Personalized Blood Pressure Time Series Forecasting

Continuous blood pressure (BP) monitoring is essential for timely diagnosis and intervention in critical care settings. However, BP varies significantly across individuals, this inter-patient variability motivates the development of personalized models tailored to each patient's physiology. In this work, we propose a personalized BP forecasting model mainly using electrocardiogram (ECG) and photoplethysmogram (PPG) signals. This time-series model incorporates 2D representation learning to capture complex physiological relationships. Experiments are conducted on datasets collected from three diverse scenarios with BP measurements from 60 subjects total. Results demonstrate that the model achieves accurate and robust BP forecasts across scenarios within the Association for the Advancement of Medical Instrumentation (AAMI) standard criteria. This reliable early detection of abnormal fluctuations in BP is crucial for at-risk patients undergoing surgery or intensive care. The proposed model provides a valuable addition for continuous BP tracking to reduce mortality and improve prognosis.

cs.LG↗

arXiv2024

A robust hybridizable discontinuous Galerkin scheme with harmonic averaging technique for steady state of real-world semiconductor devices

Solving real-world nonlinear semiconductor device problems modeled by the drift-diffusion equations coupled with the Poisson equation (also known as the Poisson-Nernst-Planck equations) necessitates an accurate and efficient numerical scheme which can avoid non-physical oscillations even for problems with extremely sharp doping profiles. In this paper, we propose a flexible and high-order hybridizable discontinuous Galerkin (HDG) scheme with harmonic averaging (HA) technique to tackle these challenges. The proposed HDG-HA scheme combines the robustness of finite volume Scharfetter-Gummel (FVSG) method with the high-order accuracy and $hp$-flexibility offered by the locally conservative HDG scheme. The coupled Poisson equation and two drift-diffusion equations are simultaneously solved by the Newton method. Indicators based on the gradient of net doping $N$ and solution variables are proposed to switch between cells with HA technique and high-order conventional HDG cells, utilizing the flexibility of HDG scheme. Numerical results suggest that the proposed scheme does not exhibit oscillations or convergence issues, even when applied to heavily doped and sharp PN-junctions. Devices with circular junctions and realistic doping profiles are simulated in two dimensions, qualifying this scheme for practical simulation of real-world semiconductor devices.

math.NA↗

arXiv2024

SCREENER: A general framework for task-specific experiment design in quantitative MRI

Quantitative magnetic resonance imaging (qMRI) is increasingly investigated for use in a variety of clinical tasks from diagnosis, through staging, to treatment monitoring. However, experiment design in qMRI, the identification of the optimal acquisition protocols, has been focused on obtaining the most precise parameter estimations, with no regard for the specific requirements of downstream tasks. Here we propose SCREENER: A general framework for task-specific experiment design in quantitative MRI. SCREENER incorporates a task-specific objective and seeks the optimal protocol with a deep-reinforcement-learning (DRL) based optimization strategy. To illustrate this framework, we employ a task of classifying the inflammation status of bone marrow using diffusion MRI data with intravoxel incoherent motion (IVIM) modelling. Results demonstrate SCREENER outperforms previous ad hoc and optimized protocols under clinical signal-to-noise ratio (SNR) conditions, achieving significant improvement, both in binary classification tasks, e.g. from 67% to 89%, and in a multi-class classification task, from 46% to 59%. Additionally, we show this improvement is robust to the SNR. Lastly, we demonstrate the advantage of DRL-based optimization strategy, enabling zero-shot discovery of near-optimal protocols for a range of SNRs not used in training. In conclusion, SCREENER has the potential to enable wider uptake of qMRI in the clinic.

cs.CV↗

arXiv2023

Approximating Voltage Stability Boundary Under High Variability of Renewables Using Differential Geometry

This paper proposes a novel method rooted in differential geometry to approximate the voltage stability boundary of power systems under high variability of renewable generation. We extract intrinsic geometric information of the power flow solution manifold at a given operating point. Specifically, coefficients of the Levi-Civita connection are constructed to approximate the geodesics of the manifold starting at an operating point along any interested directions that represent possible fluctuations in generation and load. Then, based on the geodesic approximation, we further predict the voltage collapse point by solving a few univariate quadratic equations. Conventional methods mostly rely on either expensive numerical continuation at specified directions or numerical optimization. Instead, the proposed approach constructs the Christoffel symbols of the second kind from the Riemannian metric tensors to characterize the complete local geometry which is then extended to the proximity of the stability boundary with efficient computations. As a result, this approach is suitable to handle high-dimensional variability in operating points due to the large-scale integration of renewable resources. Using various case studies, we demonstrate the advantages of the proposed method and provide additional insights and discussions on voltage stability in renewable-rich power systems.

eess.SY↗

arXiv2023

InkStream: Real-time GNN Inference on Streaming Graphs via Incremental Update

Classic Graph Neural Network (GNN) inference approaches, designed for static graphs, are ill-suited for streaming graphs that evolve with time. The dynamism intrinsic to streaming graphs necessitates constant updates, posing unique challenges to acceleration on GPU. We address these challenges based on two key insights: (1) Inside the $k$-hop neighborhood, a significant fraction of the nodes is not impacted by the modified edges when the model uses min or max as aggregation function; (2) When the model weights remain static while the graph structure changes, node embeddings can incrementally evolve over time by computing only the impacted part of the neighborhood. With these insights, we propose a novel method, InkStream, designed for real-time inference with minimal memory access and computation, while ensuring an identical output to conventional methods. InkStream operates on the principle of propagating and fetching data only when necessary. It uses an event-based system to control inter-layer effect propagation and intra-layer incremental updates of node embedding. InkStream is highly extensible and easily configurable by allowing users to create and process customized events. We showcase that less than 10 lines of additional user code are needed to support popular GNN models such as GCN, GraphSAGE, and GIN. Our experiments with three GNN models on four large graphs demonstrate that InkStream accelerates by 2.5-427$\times$ on a CPU cluster and 2.4-343$\times$ on two different GPU clusters while producing identical outputs as GNN model inference on the latest graph snapshot.

cs.LG↗

arXiv2023

Flip: Data-Centric Edge CGRA Accelerator

Coarse-Grained Reconfigurable Arrays (CGRA) are promising edge accelerators due to the outstanding balance in flexibility, performance, and energy efficiency. Classic CGRAs statically map compute operations onto the processing elements (PE) and route the data dependencies among the operations through the Network-on-Chip. However, CGRAs are designed for fine-grained static instruction-level parallelism and struggle to accelerate applications with dynamic and irregular data-level parallelism, such as graph processing. To address this limitation, we present Flip, a novel accelerator that enhances traditional CGRA architectures to boost the performance of graph applications. Flip retains the classic CGRA execution model while introducing a special data-centric mode for efficient graph processing. Specifically, it exploits the natural data parallelism of graph algorithms by mapping graph vertices onto processing elements (PEs) rather than the operations, and supporting dynamic routing of temporary data according to the runtime evolution of the graph frontier. Experimental results demonstrate that Flip achieves up to 36$\times$ speedup with merely 19% more area compared to classic CGRAs. Compared to state-of-the-art large-scale graph processors, Flip has similar energy efficiency and 2.2$\times$ better area efficiency at a much-reduced power/area budget.

cs.AR↗

arXiv2023

A Motion Assessment Method for Reference Stack Selection in Fetal Brain MRI Reconstruction Based on Tensor Rank Approximation

Purpose: Slice-to-volume registration and super-resolution reconstruction (SVR-SRR) is commonly used to generate 3D volumes of the fetal brain from 2D stacks of slices acquired in multiple orientations. A critical initial step in this pipeline is to select one stack with the minimum motion as a reference for registration. An accurate and unbiased motion assessment (MA) is thus crucial for successful selection. Methods: We presented a MA method that determines the minimum motion stack based on 3D low-rank approximation using CANDECOMP/PARAFAC (CP) decomposition. Compared to the current 2D singular value decomposition (SVD) based method that requires flattening stacks into matrices to obtain ranks, in which the spatial information is lost, the CP-based method can factorize 3D stack into low-rank and sparse components in a computationally efficient manner. The difference between the original stack and its low-rank approximation was proposed as the motion indicator. Results: Compared to SVD-based methods, our proposed CP-based MA demonstrated higher sensitivity in detecting small motion with a lower baseline bias. Experiments on randomly simulated motion illustrated that the proposed CP method achieved a higher success rate of 95.45% in identifying the minimum motion stack, compared to SVD-based method with a success rate of 58.18%. We further demonstrated that combining CP-based MA with existing SRR-SVR pipeline significantly improved 3D volume reconstruction. Conclusion: The proposed CP-based MA method showed superior performance compared to SVD-based methods with higher sensitivity to motion, success rate, and lower baseline bias, and can be used as a prior step to improve fetal brain reconstruction.

eess.IV↗

arXiv2023

Cyber-resilient Automatic Generation Control for Systems of AC Microgrids

In this paper we propose a co-design of the secondary frequency regulation in systems of AC microgrids and its cyber securty solutions. We term the secondary frequency regulator a Micro-Automatic Generation Control (Micro-AGC) for highlighting its same functionality as the AGC in bulk power systems. We identify sensory challenges and cyber threats facing the Micro-AGC. To address the sensory challenges, we introduce a new microgrid model by exploiting the rank-one deficiency property of microgrid dynamics. This model is used to pose an optimal Micro-AGC control problem that is easily implemented, because it does not require fast frequency measurements. An end-to-end cyber security solution to the False Data Injection (FDI) attack detection and mitigation is developed for the proposed Micro-AGC. The front-end barrier of applying off-the-shelf algorithms for cyber attack detection is removed by introducing a data-driven modeling approach. Finally, we propose an observer-based corrective control for an islanded microgrid and a collaborative mitigation schemes in systems of AC microgrids. We demonstrate a collaborative role of systems of microgrids during cyber attacks. The performance of the proposed cyber-resilient Micro-AGC is tested in a system of two networked microgrids.

eess.SY↗