arXiv subjects

Yubo Fan

Publications and source records attributed to Yubo Fan.

At least 19 recordsLinked to original sources

arXiv2026

Roles of vortices and turbulent eddies in particle preferential concentration and deposition in the human respiratory tract

Precise targeting of pharmaceutical aerosols is critical to the efficacy and safety of inhaled therapies. This study focused on the influences of vortices and turbulent eddies on preferential concentration and deposition of pharmaceutical aerosols within the human respiratory tract. By reconstructing a high-fidelity respiratory tract geometry spanning the nasal cavity down to sequential bronchi from computed tomography (CT) images and assigning physiologically realistic transient breathing profiles, an unsteady Reynolds-averaged Navier-Stokes (URANS) framework using the shear stress transport (SST) k-w turbulence model and a stress-blended eddy simulation (SBES) framework of human respiratory tract were built. Beyond flow field analyses, Vorono diagrams and a set of newly-defined spatial accuracy metrics were adopted to quantitatively characterize particle distributions and localized prediction discrepancies. Spectral analysis revealed that the SBES simulations adequately recovered the prominent Kolmogorov -5/3 inertial scaling law. Such turbulent motion induces pronounced radial turbulent dispersion, forming particle clusters with higher cluster fractal dimensions D> 1.2 on the mid-plane of the laryngopharynx. Spatial accuracy metrics uncovered a critical dual deficiency of the URANS model: globally over-smears near-wall deposition by roughly 20%, simultaneously fails to resolve most high-concentration `hotspots' (the top 5% local extrema). These findings highlighted that the numerical resolution of transient vortices and turbulent eddies constitutes an indispensable prerequisite for accurately predicting of particle transport and deposition in the human respiratory tract.

physics.bio-ph↗

arXiv2026

Process-Reward Tactic Evolution for Long-Horizon Bioinformatics Workflows

LLM agents can write code and call tools, but reliable bioinformatics work requires long-horizon interaction with workflow software, typed data objects, provenance, and biological checks. We study this setting through Galaxy workflow execution. The agent must explore task data, construct or adapt an executable workflow DAG, bind inputs and dataset collections, monitor execution, debug failures, and validate biological outputs. We propose Process-Reward Tactic Evolution, a Galaxy-based training framework that turns verified workflow rollouts into reusable \tactics. During training, agents practice on curriculum-organized Galaxy tasks in Agent Gym; process verifiers score workflow construction, software interaction, execution, and biological correctness; successful and failed traces are distilled into a tactic library. At inference, the trained executor, Process-Reward Tactic Evolution, uses this library to execute held-out peer reviewed Galaxy workflow converted BioWorkflow Bench and BioAgent Bench tasks in isolated environments. The paper evaluates whether process-supervised tactic accumulation improves long-horizon bioinformatics workflow completion, biological correctness, and execution efficiency over no-memory and reflection-style baselines.

cs.AI↗

arXiv2026

IntraStyler: Intra-Domain Style Synthesis for Cross-Modality MRI Domain Adaptation

Segmentation of vestibular schwannoma and cochlea from T2 MRI is clinically important yet annotation-intensive. Domain adaptation (DA) has been widely adopted to bridge the gap between labeled contrast-enhanced T1 and unlabeled T2 datasets. While existing methods focus on cross-domain alignment, intra-domain variability within the target domain remains largely overlooked. Images from the same domain may vary substantially due to different scanners, field strengths, and acquisition protocols. Ignoring this variability produces homogeneous synthetic images that limit the generalizability of downstream segmentation models. To address this, we propose IntraStyler, a 3D unpaired image translation method that automatically discovers fine-grained intra-domain styles without any predefined sub-domains, and synthesizes diverse target domain images using per-image style references. To this end, we design a 3D style encoder trained with a novel contrastive learning objective to extract style-only embeddings disentangled from anatomy. IntraStyler is built upon the 1st place CrossMoDA challenge solution and further advances it, generating more diverse synthetic data and achieving more reliable downstream segmentation. Code is available at https://github.com/MedICL-VU/IntraStyler.

cs.CV↗

arXiv2025

Rapid MRI-Based Synthetic CT Simulations for Precise tFUS Targeting

Accurate targeting is critical for the effectiveness of transcranial focused ultrasound (tFUS) neuromodulation. While CT provides accurate skull acoustic properties, its ionizing radiation and poor soft tissue contrast limit clinical applicability. In contrast, MRI offers superior neuroanatomical visualization without radiation exposure but lacks skull property mapping. This study proposes a novel, fully CT free simulation framework that integrates MRI-derived synthetic CT (sCT) with efficient modeling techniques for rapid and precise tFUS targeting. We trained a deep-learning model to generate sCT from T1-weighted MRI and integrated it with both full-wave (k-Wave) and accelerated simulation methods, hybrid angular spectrum (kWASM) and Rayleigh-Sommerfeld ASM (RSASM). Across five skull models, both full-wave and hybrid pipelines using sCT demonstrated sub-millimeter targeting deviation, focal shape consistency (FWHM ~3.3-3.8 mm), and <0.2 normalized pressure error compared to CT-based gold standard. Notably, the kW-ASM and RS-ASM pipelines reduced simulation time from ~3320 s to 187 s and 34 s respectively, achieving ~94% and ~90% time savings. These results confirm that MRI-derived sCT combined with innovative rapid simulation techniques enables fast, accurate, and radiation-free tFUS planning, supporting its feasibility for scalable clinical applications.

physics.med-ph↗

arXiv2025

Human Locomotion Implicit Modeling Based Real-Time Gait Phase Estimation

Gait phase estimation based on inertial measurement unit (IMU) signals facilitates precise adaptation of exoskeletons to individual gait variations. However, challenges remain in achieving high accuracy and robustness, particularly during periods of terrain changes. To address this, we develop a gait phase estimation neural network based on implicit modeling of human locomotion, which combines temporal convolution for feature extraction with transformer layers for multi-channel information fusion. A channel-wise masked reconstruction pre-training strategy is proposed, which first treats gait phase state vectors and IMU signals as joint observations of human locomotion, thus enhancing model generalization. Experimental results demonstrate that the proposed method outperforms existing baseline approaches, achieving a gait phase RMSE of $2.729 \pm 1.071%$ and phase rate MAE of $0.037 \pm 0.016%$ under stable terrain conditions with a look-back window of 2 seconds, and a phase RMSE of $3.215 \pm 1.303%$ and rate MAE of $0.050 \pm 0.023%$ under terrain transitions. Hardware validation on a hip exoskeleton further confirms that the algorithm can reliably identify gait cycles and key events, adapting to various continuous motion scenarios. This research paves the way for more intelligent and adaptive exoskeleton systems, enabling safer and more efficient human-robot interaction across diverse real-world environments.

cs.RO↗

arXiv2025

crossMoDA Challenge: Evolution of Cross-Modality Domain Adaptation Techniques for Vestibular Schwannoma and Cochlea Segmentation from 2021 to 2023

The cross-Modality Domain Adaptation (crossMoDA) challenge series, initiated in 2021 in conjunction with the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), focuses on unsupervised cross-modality segmentation, learning from contrast-enhanced T1 (ceT1) and transferring to T2 MRI. The task is an extreme example of domain shift chosen to serve as a meaningful and illustrative benchmark. From a clinical application perspective, it aims to automate Vestibular Schwannoma (VS) and cochlea segmentation on T2 scans for more cost-effective VS management. Over time, the challenge objectives have evolved to enhance its clinical relevance. The challenge evolved from using single-institutional data and basic segmentation in 2021 to incorporating multi-institutional data and Koos grading in 2022, and by 2023, it included heterogeneous routine data and sub-segmentation of intra- and extra-meatal tumour components. In this work, we report the findings of the 2022 and 2023 editions and perform a retrospective analysis of the challenge progression over the years. The observations from the successive challenge contributions indicate that the number of outliers decreases with an expanding dataset. This is notable since the diversity of scanning protocols of the datasets concurrently increased. The winning approach of the 2023 edition reduced the number of outliers on the 2021 and 2022 testing data, demonstrating how increased data heterogeneity can enhance segmentation performance even on homogeneous data. However, the cochlea Dice score declined in 2023, likely due to the added complexity from tumour sub-annotations affecting overall segmentation performance. While progress is still needed for clinically acceptable VS segmentation, the plateauing performance suggests that a more challenging cross-modal task may better serve future benchmarking.

eess.IV↗

arXiv2024

Hybrid roles of adaptation and optimization in formation of vascular network

It was hypothesized that the structures of biological transport networks are the result of either energy consumption or adaptation dynamics. Although approaches based on these hypotheses can produce optimal network and form loop structures, we found that neither possesses complete ability to generate complex networks that resemble vascular network in living organisms, which motivated us to propose a hybrid approach. This approach can replicate the path dependency phenomenon of main branches and produce an optimal network that resembles the real vascular network. We further show that there is a clear transition in the structural pattern of the vascular network, shifting from `chive-like' to dendritic configuration after a period of sequenced adaptation and optimization.

physics.bio-ph↗

arXiv2024

Predicting fluorescent labels in label-free microscopy images with pix2pix and adaptive loss in Light My Cells challenge

Fluorescence labeling is the standard approach to reveal cellular structures and other subcellular constituents for microscopy images. However, this invasive procedure may perturb or even kill the cells and the procedure itself is highly time-consuming and complex. Recently, in silico labeling has emerged as a promising alternative, aiming to use machine learning models to directly predict the fluorescently labeled images from label-free microscopy. In this paper, we propose a deep learning-based in silico labeling method for the Light My Cells challenge. Built upon pix2pix, our proposed method can be trained using the partially labeled datasets with an adaptive loss. Moreover, we explore the effectiveness of several training strategies to handle different input modalities, such as training them together or separately. The results show that our method achieves promising performance for in silico labeling. Our code is available at https://github.com/MedICL-VU/LightMyCells.

eess.IV↗

arXiv2024

Terrain-Aware Stride-Level Trajectory Forecasting for a Powered Hip Exoskeleton via Vision and Kinematics Fusion

Powered hip exoskeletons have shown the ability for locomotion assistance during treadmill walking. However, providing suitable assistance in real-world walking scenarios which involve changing terrain remains challenging. Recent research suggests that forecasting the lower limb joint's angles could provide target trajectories for exoskeletons and prostheses, and the performance could be improved with visual information. In this letter, We share a real-world dataset of 10 healthy subjects walking through five common types of terrain with stride-level label. We design a network called Sandwich Fusion Transformer for Image and Kinematics (SFTIK), which predicts the thigh angle of the ensuing stride given the terrain images at the beginning of the preceding and the ensuing stride and the IMU time series during the preceding stride. We introduce width-level patchify, tailored for egocentric terrain images, to reduce the computational demands. We demonstrate the proposed sandwich input and fusion mechanism could significantly improve the forecasting performance. Overall, the SFTIK outperforms baseline methods, achieving a computational efficiency of 3.31 G Flops, and root mean square error (RMSE) of 3.445 \textpm \ 0.804\textdegree \ and Pearson's correlation coefficient (PCC) of 0.971 \textpm\ 0.025. The results demonstrate that SFTIK could forecast the thigh's angle accurately with low computational cost, which could serve as a terrain adaptive trajectory planning method for hip exoskeletons. Codes and data are available at https://github.com/RuoqiZhao116/SFTIK.

cs.RO↗

arXiv2024

Generating Synthetic Computed Tomography for Radiotherapy: SynthRAD2023 Challenge Report

Radiation therapy plays a crucial role in cancer treatment, necessitating precise delivery of radiation to tumors while sparing healthy tissues over multiple days. Computed tomography (CT) is integral for treatment planning, offering electron density data crucial for accurate dose calculations. However, accurately representing patient anatomy is challenging, especially in adaptive radiotherapy, where CT is not acquired daily. Magnetic resonance imaging (MRI) provides superior soft-tissue contrast. Still, it lacks electron density information while cone beam CT (CBCT) lacks direct electron density calibration and is mainly used for patient positioning. Adopting MRI-only or CBCT-based adaptive radiotherapy eliminates the need for CT planning but presents challenges. Synthetic CT (sCT) generation techniques aim to address these challenges by using image synthesis to bridge the gap between MRI, CBCT, and CT. The SynthRAD2023 challenge was organized to compare synthetic CT generation methods using multi-center ground truth data from 1080 patients, divided into two tasks: 1) MRI-to-CT and 2) CBCT-to-CT. The evaluation included image similarity and dose-based metrics from proton and photon plans. The challenge attracted significant participation, with 617 registrations and 22/17 valid submissions for tasks 1/2. Top-performing teams achieved high structural similarity indices (>0.87/0.90) and gamma pass rates for photon (>98.1%/99.0%) and proton (>97.3%/97.0%) plans. However, no significant correlation was found between image similarity metrics and dose accuracy, emphasizing the need for dose evaluation when assessing the clinical applicability of sCT. SynthRAD2023 facilitated the investigation and benchmarking of sCT generation techniques, providing insights for developing MRI-only and CBCT-based adaptive radiotherapy.

physics.med-ph↗

arXiv2023

Learning Site-specific Styles for Multi-institutional Unsupervised Cross-modality Domain Adaptation

Unsupervised cross-modality domain adaptation is a challenging task in medical image analysis, and it becomes more challenging when source and target domain data are collected from multiple institutions. In this paper, we present our solution to tackle the multi-institutional unsupervised domain adaptation for the crossMoDA 2023 challenge. First, we perform unpaired image translation to translate the source domain images to the target domain, where we design a dynamic network to generate synthetic target domain images with controllable, site-specific styles. Afterwards, we train a segmentation model using the synthetic images and further reduce the domain gap by self-training. Our solution achieved the 1st place during both the validation and testing phases of the challenge. The code repository is publicly available at https://github.com/MedICL-VU/crossmoda2023.

cs.CV↗

arXiv2023

MLP Based Continuous Gait Recognition of a Powered Ankle Prosthesis with Serial Elastic Actuator

Powered ankle prostheses effectively assist people with lower limb amputation to perform daily activities. High performance prostheses with adjustable compliance and capability to predict and implement amputee's intent are crucial for them to be comparable to or better than a real limb. However, current designs fail to provide simple yet effective compliance of the joint with full potential of modification, and lack accurate gait prediction method in real time. This paper proposes an innovative design of powered ankle prosthesis with serial elastic actuator (SEA), and puts forward a MLP based gait recognition method that can accurately and continuously predict more gait parameters for motion sensing and control. The prosthesis mimics biological joint with similar weight, torque, and power which can assist walking of up to 4 m/s. A new design of planar torsional spring is proposed for the SEA, which has better stiffness, endurance, and potential of modification than current designs. The gait recognition system simultaneously generates locomotive speed, gait phase, ankle angle and angular velocity only utilizing signals of single IMU, holding advantage in continuity, adaptability for speed range, accuracy, and capability of multi-functions.

cs.RO↗

arXiv2023

Nucleus-aware Self-supervised Pretraining Using Unpaired Image-to-image Translation for Histopathology Images

Self-supervised pretraining attempts to enhance model performance by obtaining effective features from unlabeled data, and has demonstrated its effectiveness in the field of histopathology images. Despite its success, few works concentrate on the extraction of nucleus-level information, which is essential for pathologic analysis. In this work, we propose a novel nucleus-aware self-supervised pretraining framework for histopathology images. The framework aims to capture the nuclear morphology and distribution information through unpaired image-to-image translation between histopathology images and pseudo mask images. The generation process is modulated by both conditional and stochastic style representations, ensuring the reality and diversity of the generated histopathology images for pretraining. Further, an instance segmentation guided strategy is employed to capture instance-level information. The experiments on 7 datasets show that the proposed pretraining method outperforms supervised ones on Kather classification, multiple instance learning, and 5 dense-prediction tasks with the transfer learning protocol, and yields superior results than other self-supervised approaches on 8 semi-supervised tasks. Our project is publicly available at https://github.com/zhiyuns/UNITPathSSL.

cs.CV↗

arXiv2023

COLosSAL: A Benchmark for Cold-start Active Learning for 3D Medical Image Segmentation

Medical image segmentation is a critical task in medical image analysis. In recent years, deep learning based approaches have shown exceptional performance when trained on a fully-annotated dataset. However, data annotation is often a significant bottleneck, especially for 3D medical images. Active learning (AL) is a promising solution for efficient annotation but requires an initial set of labeled samples to start active selection. When the entire data pool is unlabeled, how do we select the samples to annotate as our initial set? This is also known as the cold-start AL, which permits only one chance to request annotations from experts without access to previously annotated data. Cold-start AL is highly relevant in many practical scenarios but has been under-explored, especially for 3D medical segmentation tasks requiring substantial annotation effort. In this paper, we present a benchmark named COLosSAL by evaluating six cold-start AL strategies on five 3D medical image segmentation tasks from the public Medical Segmentation Decathlon collection. We perform a thorough performance analysis and explore important open questions for cold-start AL, such as the impact of budget on different strategies. Our results show that cold-start AL is still an unsolved problem for 3D segmentation tasks but some important trends have been observed. The code repository, data partitions, and baseline results for the complete benchmark are publicly available at https://github.com/MedICL-VU/COLosSAL.

cs.CV↗

arXiv2023

DRMC: A Generalist Model with Dynamic Routing for Multi-Center PET Image Synthesis

Multi-center positron emission tomography (PET) image synthesis aims at recovering low-dose PET images from multiple different centers. The generalizability of existing methods can still be suboptimal for a multi-center study due to domain shifts, which result from non-identical data distribution among centers with different imaging systems/protocols. While some approaches address domain shifts by training specialized models for each center, they are parameter inefficient and do not well exploit the shared knowledge across centers. To address this, we develop a generalist model that shares architecture and parameters across centers to utilize the shared knowledge. However, the generalist model can suffer from the center interference issue, \textit{i.e.} the gradient directions of different centers can be inconsistent or even opposite owing to the non-identical data distribution. To mitigate such interference, we introduce a novel dynamic routing strategy with cross-layer connections that routes data from different centers to different experts. Experiments show that our generalist model with dynamic routing (DRMC) exhibits excellent generalizability across centers. Code and data are available at: https://github.com/Yaziwel/Multi-Center-PET-Image-Synthesis.

eess.IV↗

arXiv2023

Zero-shot Nuclei Detection via Visual-Language Pre-trained Models

Large-scale visual-language pre-trained models (VLPM) have proven their excellent performance in downstream object detection for natural scenes. However, zero-shot nuclei detection on H\&E images via VLPMs remains underexplored. The large gap between medical images and the web-originated text-image pairs used for pre-training makes it a challenging task. In this paper, we attempt to explore the potential of the object-level VLPM, Grounded Language-Image Pre-training (GLIP) model, for zero-shot nuclei detection. Concretely, an automatic prompts design pipeline is devised based on the association binding trait of VLPM and the image-to-text VLPM BLIP, avoiding empirical manual prompts engineering. We further establish a self-training framework, using the automatically designed prompts to generate the preliminary results as pseudo labels from GLIP and refine the predicted boxes in an iterative manner. Our method achieves a remarkable performance for label-free nuclei detection, surpassing other comparison methods. Foremost, our work demonstrates that the VLPM pre-trained on natural image-text pairs exhibits astonishing potential for downstream tasks in the medical field as well. Code will be released at https://github.com/wuyongjianCODE/VLPMNuD.

cs.CV↗

arXiv2023

Cyclic Learning: Bridging Image-level Labels and Nuclei Instance Segmentation

Nuclei instance segmentation on histopathology images is of great clinical value for disease analysis. Generally, fully-supervised algorithms for this task require pixel-wise manual annotations, which is especially time-consuming and laborious for the high nuclei density. To alleviate the annotation burden, we seek to solve the problem through image-level weakly supervised learning, which is underexplored for nuclei instance segmentation. Compared with most existing methods using other weak annotations (scribble, point, etc.) for nuclei instance segmentation, our method is more labor-saving. The obstacle to using image-level annotations in nuclei instance segmentation is the lack of adequate location information, leading to severe nuclei omission or overlaps. In this paper, we propose a novel image-level weakly supervised method, called cyclic learning, to solve this problem. Cyclic learning comprises a front-end classification task and a back-end semi-supervised instance segmentation task to benefit from multi-task learning (MTL). We utilize a deep learning classifier with interpretability as the front-end to convert image-level labels to sets of high-confidence pseudo masks and establish a semi-supervised architecture as the back-end to conduct nuclei instance segmentation under the supervision of these pseudo masks. Most importantly, cyclic learning is designed to circularly share knowledge between the front-end classifier and the back-end semi-supervised part, which allows the whole system to fully extract the underlying information from image-level labels and converge to a better optimum. Experiments on three datasets demonstrate the good generality of our method, which outperforms other image-level weakly supervised methods for nuclei instance segmentation, and achieves comparable performance to fully-supervised methods.

cs.CV↗

arXiv2022

Adaptive Contrastive Learning with Dynamic Correlation for Multi-Phase Organ Segmentation

Recent studies have demonstrated the superior performance of introducing ``scan-wise" contrast labels into contrastive learning for multi-organ segmentation on multi-phase computed tomography (CT). However, such scan-wise labels are limited: (1) a coarse classification, which could not capture the fine-grained ``organ-wise" contrast variations across all organs; (2) the label (i.e., contrast phase) is typically manually provided, which is error-prone and may introduce manual biases of defining phases. In this paper, we propose a novel data-driven contrastive loss function that adapts the similar/dissimilar contrast relationship between samples in each minibatch at organ-level. Specifically, as variable levels of contrast exist between organs, we hypothesis that the contrast differences in the organ-level can bring additional context for defining representations in the latent space. An organ-wise contrast correlation matrix is computed with mean organ intensities under one-hot attention maps. The goal of adapting the organ-driven correlation matrix is to model variable levels of feature separability at different phases. We evaluate our proposed approach on multi-organ segmentation with both non-contrast CT (NCCT) datasets and the MICCAI 2015 BTCV Challenge contrast-enhance CT (CECT) datasets. Compared to the state-of-the-art approaches, our proposed contrastive loss yields a substantial and significant improvement of 1.41% (from 0.923 to 0.936, p-value$<$0.01) and 2.02% (from 0.891 to 0.910, p-value$<$0.01) on mean Dice scores across all organs with respect to NCCT and CECT cohorts. We further assess the trained model performance with the MICCAI 2021 FLARE Challenge CECT datasets and achieve a substantial improvement of mean Dice score from 0.927 to 0.934 (p-value$<$0.01). The code is available at: https://github.com/MASILab/DCC_CL

cs.CV↗