arXiv subjects

Yuwen Chen

Publications and source records attributed to Yuwen Chen.

At least 37 records · Page 2Linked to original sources

arXiv2025

CrowdTrack: A Benchmark for Difficult Multiple Pedestrian Tracking in Real Scenarios

Multi-object tracking is a classic field in computer vision. Among them, pedestrian tracking has extremely high application value and has become the most popular research category. Existing methods mainly use motion or appearance information for tracking, which is often difficult in complex scenarios. For the motion information, mutual occlusions between objects often prevent updating of the motion state; for the appearance information, non-robust results are often obtained due to reasons such as only partial visibility of the object or blurred images. Although learning how to perform tracking in these situations from the annotated data is the simplest solution, the existing MOT dataset fails to satisfy this solution. Existing methods mainly have two drawbacks: relatively simple scene composition and non-realistic scenarios. Although some of the video sequences in existing dataset do not have the above-mentioned drawbacks, the number is far from adequate for research purposes. To this end, we propose a difficult large-scale dataset for multi-pedestrian tracking, shot mainly from the first-person view and all from real-life complex scenarios. We name it ``CrowdTrack'' because there are numerous objects in most of the sequences. Our dataset consists of 33 videos, containing a total of 5,185 trajectories. Each object is annotated with a complete bounding box and a unique object ID. The dataset will provide a platform to facilitate the development of algorithms that remain effective in complex situations. We analyzed the dataset comprehensively and tested multiple SOTA models on our dataset. Besides, we analyzed the performance of the foundation models on our dataset. The dataset and project code is released at: https://github.com/loseevaya/CrowdTrack .

cs.CV↗

arXiv2025

SegmentAnyMuscle: A universal muscle segmentation model across different locations in MRI

The quantity and quality of muscles are increasingly recognized as important predictors of health outcomes. While MRI offers a valuable modality for such assessments, obtaining precise quantitative measurements of musculature remains challenging. This study aimed to develop a publicly available model for muscle segmentation in MRIs and demonstrate its applicability across various anatomical locations and imaging sequences. A total of 362 MRIs from 160 patients at a single tertiary center (Duke University Health System, 2016-2020) were included, with 316 MRIs from 114 patients used for model development. The model was tested on two separate sets: one with 28 MRIs representing common sequence types, achieving an average Dice Similarity Coefficient (DSC) of 88.45%, and another with 18 MRIs featuring less frequent sequences and abnormalities such as muscular atrophy, hardware, and significant noise, achieving 86.21% DSC. These results demonstrate the feasibility of a fully automated deep learning algorithm for segmenting muscles on MRI across diverse settings. The public release of this model enables consistent, reproducible research into the relationship between musculature and health.

eess.SP↗

arXiv2025

Fréchet Radiomic Distance (FRD): A Versatile Metric for Comparing Medical Imaging Datasets

Determining whether two sets of images belong to the same or different distributions or domains is a crucial task in modern medical image analysis and deep learning; for example, to evaluate the output quality of image generative models. Currently, metrics used for this task either rely on the (potentially biased) choice of some downstream task, such as segmentation, or adopt task-independent perceptual metrics (e.g., Fréchet Inception Distance/FID) from natural imaging, which we show insufficiently capture anatomical features. To this end, we introduce a new perceptual metric tailored for medical images, FRD (Fréchet Radiomic Distance), which utilizes standardized, clinically meaningful, and interpretable image features. We show that FRD is superior to other image distribution metrics for a range of medical imaging applications, including out-of-domain (OOD) detection, the evaluation of image-to-image translation (by correlating more with downstream task performance as well as anatomical consistency and realism), and the evaluation of unconditional image generation. Moreover, FRD offers additional benefits such as stability and computational efficiency at low sample sizes, sensitivity to image corruptions and adversarial attacks, feature interpretability, and correlation with radiologist-perceived image quality. Additionally, we address key gaps in the literature by presenting an extensive framework for the multifaceted evaluation of image similarity metrics in medical imaging -- including the first large-scale comparative study of generative models for medical image translation -- and release an accessible codebase to facilitate future research. Our results are supported by thorough experiments spanning a variety of datasets, modalities, and downstream tasks, highlighting the broad potential of FRD for medical image analysis.

cs.CV↗

arXiv2025

PHT-CAD: Efficient CAD Parametric Primitive Analysis with Progressive Hierarchical Tuning

Computer-Aided Design (CAD) plays a pivotal role in industrial manufacturing, yet 2D Parametric Primitive Analysis (PPA) remains underexplored due to two key challenges: structural constraint reasoning and advanced semantic understanding. To tackle these challenges, we first propose an Efficient Hybrid Parametrization (EHP) for better representing 2D engineering drawings. EHP contains four types of atomic component i.e., point, line, circle, and arc). Additionally, we propose PHT-CAD, a novel 2D PPA framework that harnesses the modality alignment and reasoning capabilities of Vision-Language Models (VLMs) for precise engineering drawing analysis. In PHT-CAD, we introduce four dedicated regression heads to predict corresponding atomic components. To train PHT-CAD, a three-stage training paradigm Progressive Hierarchical Tuning (PHT) is proposed to progressively enhance PHT-CAD's capability to perceive individual primitives, infer structural constraints, and align annotation layers with their corresponding geometric representations. Considering that existing datasets lack complete annotation layers and real-world engineering drawings, we introduce ParaCAD, the first large-scale benchmark that explicitly integrates both the geometric and annotation layers. ParaCAD comprises over 10 million annotated drawings for training and 3,000 real-world industrial drawings with complex topological structures and physical constraints for test. Extensive experiments demonstrate the effectiveness of PHT-CAD and highlight the practical significance of ParaCAD in advancing 2D PPA research.

cs.CV↗

arXiv2025

GuidedMorph: Two-Stage Deformable Registration for Breast MRI

Accurately registering breast MR images from different time points enables the alignment of anatomical structures and tracking of tumor progression, supporting more effective breast cancer detection, diagnosis, and treatment planning. However, the complexity of dense tissue and its highly non-rigid nature pose challenges for conventional registration methods, which primarily focus on aligning general structures while overlooking intricate internal details. To address this, we propose \textbf{GuidedMorph}, a novel two-stage registration framework designed to better align dense tissue. In addition to a single-scale network for global structure alignment, we introduce a framework that utilizes dense tissue information to track breast movement. The learned transformation fields are fused by introducing the Dual Spatial Transformer Network (DSTN), improving overall alignment accuracy. A novel warping method based on the Euclidean distance transform (EDT) is also proposed to accurately warp the registered dense tissue and breast masks, preserving fine structural details during deformation. The framework supports paradigms that require external segmentation models and with image data only. It also operates effectively with the VoxelMorph and TransMorph backbones, offering a versatile solution for breast registration. We validate our method on ISPY2 and internal dataset, demonstrating superior performance in dense tissue, overall breast alignment, and breast structural similarity index measure (SSIM), with notable improvements by over 13.01% in dense tissue Dice, 3.13% in breast Dice, and 1.21% in breast SSIM compared to the best learning-based baseline.

eess.IV↗

arXiv2025

Temporal Gaussian Copula For Clinical Multivariate Time Series Data Imputation

The imputation of the Multivariate time series (MTS) is particularly challenging since the MTS typically contains irregular patterns of missing values due to various factors such as instrument failures, interference from irrelevant data, and privacy regulations. Existing statistical methods and deep learning methods have shown promising results in time series imputation. In this paper, we propose a Temporal Gaussian Copula Model (TGC) for three-order MTS imputation. The key idea is to leverage the Gaussian Copula to explore the cross-variable and temporal relationships based on the latent Gaussian representation. Subsequently, we employ an Expectation-Maximization (EM) algorithm to improve robustness in managing data with varying missing rates. Comprehensive experiments were conducted on three real-world MTS datasets. The results demonstrate that our TGC substantially outperforms the state-of-the-art imputation methods. Additionally, the TGC model exhibits stronger robustness to the varying missing ratios in the test dataset. Our code is available at https://github.com/MVL-Lab/TGC-MTS.

cs.LG↗

arXiv2024

SAM & SAM 2 in 3D Slicer: SegmentWithSAM Extension for Annotating Medical Images

Creating annotations for 3D medical data is time-consuming and often requires highly specialized expertise. Various tools have been implemented to aid this process. Segment Anything Model 2 (SAM 2) offers a general-purpose prompt-based segmentation algorithm designed to annotate videos. In this paper, we adapt this model to the annotation of 3D medical images and offer our implementation in the form of an extension to the popular annotation software: 3D Slicer. Our extension allows users to place point prompts on 2D slices to generate annotation masks and propagate these annotations across entire volumes in either single-directional or bi-directional manners. Our code is publicly available on https://github.com/mazurowski-lab/SlicerSegmentWithSAM and can be easily installed directly from the Extension Manager of 3D Slicer as well.

eess.IV↗

arXiv2024

Segment anything model 2: an application to 2D and 3D medical images

Segment Anything Model (SAM) has gained significant attention because of its ability to segment various objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we extensively evaluate SAM 2's ability to segment both 2D and 3D medical images by first collecting 21 medical imaging datasets, including surgical videos, common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. Two evaluation settings of SAM 2 are considered: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former only applies to videos and 3D modalities, while the latter applies to all datasets. Our results show that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc. We believe our work enhances the understanding of SAM 2's behavior in the medical field and provides directions for future work in adapting SAM 2 to this domain. Our code is available at: https://github.com/mazurowski-lab/segment-anything2-medical-evaluation.

cs.CV↗

arXiv2024

Anatomically-Controllable Medical Image Generation with Segmentation-Guided Diffusion Models

Diffusion models have enabled remarkably high-quality medical image generation, yet it is challenging to enforce anatomical constraints in generated images. To this end, we propose a diffusion model-based method that supports anatomically-controllable medical image generation, by following a multi-class anatomical segmentation mask at each sampling step. We additionally introduce a random mask ablation training algorithm to enable conditioning on a selected combination of anatomical constraints while allowing flexibility in other anatomical areas. We compare our method ("SegGuidedDiff") to existing methods on breast MRI and abdominal/neck-to-pelvis CT datasets with a wide range of anatomical objects. Results show that our method reaches a new state-of-the-art in the faithfulness of generated images to input anatomical masks on both datasets, and is on par for general anatomical realism. Finally, our model also enjoys the extra benefit of being able to adjust the anatomical similarity of generated images to real images of choice through interpolation in its latent space. SegGuidedDiff has many applications, including cross-modality translation, and the generation of paired or counterfactual data. Our code is available at https://github.com/mazurowski-lab/segmentation-guided-diffusion.

eess.IV↗

arXiv2024

Clarabel: An interior-point solver for conic programs with quadratic objectives

We present a general-purpose interior-point solver for convex optimization problems with conic constraints. Our method is based on a homogeneous embedding method originally developed for general monotone complementarity problems and more recently applied to operator splitting methods, and here specialized to an interior-point method for problems with quadratic objectives. We allow for a variety of standard symmetric and non-symmetric cones, and provide support for chordal decomposition methods in the case of semidefinite cones. We describe the implementation of this method in the open-source solver Clarabel, and provide a detailed numerical evaluation of its performance versus several state-of-the-art solvers on a wide range of standard benchmarks problems. Clarabel is faster and more robust than competing commercial and open-source solvers across a range of test sets, with a particularly large performance advantage for problems with quadratic objectives. Clarabel is currently distributed as a standard solver for the Python CVXPY optimization suite.

math.OC↗

arXiv2024

Rethinking Perceptual Metrics for Medical Image Translation

Modern medical image translation methods use generative models for tasks such as the conversion of CT images to MRI. Evaluating these methods typically relies on some chosen downstream task in the target domain, such as segmentation. On the other hand, task-agnostic metrics are attractive, such as the network feature-based perceptual metrics (e.g., FID) that are common to image translation in general computer vision. In this paper, we investigate evaluation metrics for medical image translation on two medical image translation tasks (GE breast MRI to Siemens breast MRI and lumbar spine MRI to CT), tested on various state-of-the-art translation methods. We show that perceptual metrics do not generally correlate with segmentation metrics due to them extending poorly to the anatomical constraints of this sub-field, with FID being especially inconsistent. However, we find that the lesser-used pixel-level SWD metric may be useful for subtle intra-modality translation. Our results demonstrate the need for further research into helpful metrics for medical image translation.

eess.IV↗

arXiv2024

Recent advances on the spherical metal oxides for sustainable degradation of antibiotics

Due to the permanent harm to human health and ecosystem balance, antibiotic pollution in water has become an important direction of current environmental governance. Spherical metal oxides (SMOs) have been frequently utilized as effective heterogeneous photocatalysts for the efficient degradation of antibiotics due to the unique properties (e.g., strong light absorption ability, high separation efficiency of photo-generated electron hole pairs, and good catalytic activity). This review will firstly focus on summarizing the rational design and synthesis of SMOs with various tuned microstructures such as hollow, porous shell, yolk shell, core shell, and nanoflowers. These structures can expose more active sites, achieve a higher utilization rate of light, enhance the mass transfer efficiency and improve the effective diffusion of reactive oxygen species (ROS). Secondly, this review will mainly analyze the intrinsic relationship between the structure of SMOs and its photocatalytic property, the ability to generate ROS, and the degradation pathway for antibiotics. Moreover, the photocatalytic mechanisms and recent progress of different SMOs catalysts for degrading typical antibiotics are compared in detail. Finally, challenges and prospects of future direction in the development of SMOs for antibiotic degradation are reviewed. It is expected to provide a rational design of SMOs catalysts for efficient photocatalytic degradation of environmental pollutants.

physics.bio-ph↗

arXiv2024

Facile synthesis of micro-flower NiCo2O4 assembled by nanosheets efficient for electrocatalysis of water

Effective regulation of the morphology of transition metal spinel structures is crucial for creating efficient and stable bifunctional catalysts for electrocatalysis of water. In this work, micro-flower NiCo2O4 (F-NCO) assembled by nanosheets via a chemical template method for the simultaneous promotion of hydrogen evolution reaction (HER) and oxygen evolution reaction (OER). Electronic microscope analysis revealed that the thickness of the F-NCO catalyst was only 2.7% of that of the NiCo2O4 bulk (B-NCO), and this ultrathin lamellar structure was conducive to further exposure of the active site and improved reaction kinetics. The F-NCO catalyst exhibited superior HER and OER performance (10 = 236 and 310 mV) and robust long-term stability over the B-NCO catalyst in 1.0 M KOH, with a 2.68-fold and 4.16-fold increase in active surface area and a 0.42-fold and 0.61-fold decrease in charge transfer resistance values, respectively. This micro-flower-structured electrode has remarkable electrocatalytic property and long-term durability, providing a novel insight for characterizing cost-effective and high-performance bifunctional electrocatalysts.

physics.chem-ph↗

arXiv2024

Acceleration of Fe$^{3+}$/Fe$^{2+}$ cycle in garland-like MIL-101(Fe)/MoS$_2$ nanosheets to promote peroxymonosulfate activation for sulfamethoxazole degradation

Iron-based molybdenum disulfide (Fe-MoS$_2$) has emerged as a Fenton-like catalyst for the highly efficient degradation of antibiotics, but the structure-activity relationship remains elusive. Herein, garland-like MIL-101(Fe)/MoS$_2$ nanosheets (MMS) with dual metal active sites (Fe and Mo) and rich sulfur vacancies were fabricated to directly activate peroxymonosulfate (PMS) for fast degradation of different organic pollutants (phenols, dyes and drugs), even in real water bodies. The MMS exhibited extremely fast catalytic rate constant of 0.289 min$^{-1}$ in the degradation of sulfamethoxazole (SMX), which was about 36 and 29 times that of single MoS$_2$ (0.008 min$^{-1}$) and MIL-101(Fe) (0.01 min$^{-1}$). Moreover, MMS with good stability and reusability could reach 92% degradation of SMX after 5 cycles. Quenching experiments and electron spin resonance (ESR) tests revealed that hydroxyl radicals (.OH) and singlet oxygen ($^1$O$_2$) were the dominant reactive oxygen species (ROS) for SMX degradation. The integration of experimental works, characterization techniques and density functional theory (DFT) calculations unraveled that the formation of sulfur vacancies in MMS catalyst could expose more Mo sites, improve the charge density and boost the electron transfer, which was conducive to accelerating the Fe$^{3+}$/Fe$^{2+}$ cycle for enhancing the activation of PMS. Finally, the C-N, N-O, S-N, C-O and C-S bonds of SMX were easily attacked by ROS to generate the nontoxic intermediates in the MMS/PMS/SMX system. This study offers a new approach to designing high-performance Fe-MoS$_2$ catalysts for the removal of organic pollutants.

physics.chem-ph↗

arXiv2024

Visible light-assisted peroxymonosulfate activation by high-purity FeS$_2$ nanoplates for dye pollutant control

With the rapid industrial development, many dye pollutants have entered the water, along with heavy metals like As, leading to complex pollution that threatens the ecological environment and human health. Therefore, designing an effective strategy for treating complex dye wastewater is urgent. Herein, we have constructed high-purity pyrite FeS$_2$ nanoplates as bifunctional catalysts for the simultaneous removal of dyes and arsenite (As(III)).

physics.app-ph↗

arXiv2024

Enhanced electron transfer using NiCo2O4@C hollow nanocages with an electron-shuttle effect for efficient tetracycline degradation

Spinel oxides are recognized as promising Fenton-like catalysts for the degradation of antibiotics. However, the catalytic performance is restrained by the poor electron transfer rate (ETR). Herein, hollow NiCo2O4@C nanocages are rationally designed and prepared to accelerate ETR in peroxymonosulfate (PMS) activation for tetracycline (TC) degradation.

cond-mat.mes-hall↗

arXiv2024

Facile synthesis of fine-grained CoFe$_2$O$_4$ anchored on porous carbon for simultaneous removal of tetracycline and arsenite

The coexistence of tetracycline (TC) and arsenite (As(III)) in livestock wastewater threatens public health, and the heterogeneous Fenton-like system is a practical approach for the simultaneous removal of TC and As(III). In this work, fine CoFe$_2$O$_4$ nanoparticles are facilely anchored on heretically porous carbon (CoFe$_2$O$_4$@PC) via a microwave-assisted calcination method and used for eliminating TC and As(III) via peroxymonosulfate (PMS) activation.

physics.app-ph↗

arXiv2024

SegmentAnyBone: A Universal Model that Segments Any Bone at Any Location on MRI

Magnetic Resonance Imaging (MRI) is pivotal in radiology, offering non-invasive and high-quality insights into the human body. Precise segmentation of MRIs into different organs and tissues would be highly beneficial since it would allow for a higher level of understanding of the image content and enable important measurements, which are essential for accurate diagnosis and effective treatment planning. Specifically, segmenting bones in MRI would allow for more quantitative assessments of musculoskeletal conditions, while such assessments are largely absent in current radiological practice. The difficulty of bone MRI segmentation is illustrated by the fact that limited algorithms are publicly available for use, and those contained in the literature typically address a specific anatomic area. In our study, we propose a versatile, publicly available deep-learning model for bone segmentation in MRI across multiple standard MRI locations. The proposed model can operate in two modes: fully automated segmentation and prompt-based segmentation. Our contributions include (1) collecting and annotating a new MRI dataset across various MRI protocols, encompassing over 300 annotated volumes and 8485 annotated slices across diverse anatomic regions; (2) investigating several standard network architectures and strategies for automated segmentation; (3) introducing SegmentAnyBone, an innovative foundational model-based approach that extends Segment Anything Model (SAM); (4) comparative analysis of our algorithm and previous approaches; and (5) generalization analysis of our algorithm across different anatomical locations and MRI sequences, as well as an external dataset. We publicly release our model at https://github.com/mazurowski-lab/SegmentAnyBone.

eess.IV↗