arXiv subjects

Ying Xiao

Publications and source records attributed to Ying Xiao.

At least 19 recordsLinked to original sources

arXiv2026

A Digital Pathology Resource for Liver Cancer Quantification with Datasets, Benchmarks, and Tools

Liver cancer, especially hepatocellular carcinoma (HCC), imposes a substantial global disease burden. Accurate diagnosis and prognostic assessment directly influence treatment selection and patient survival, and pathological examination remains the gold standard for liver cancer diagnosis. Identifying diverse tissue components and pathological subtypes on histopathology slides is crucial for estimating postoperative recurrence risk and overall prognosis. However, most publicly available resources are still provided at the whole-slide image (WSI) level, and well-annotated datasets for fine-grained tissue component identification in liver cancer are scarce, which hinders reproducible model development and the deployment of quantitative analysis tools. To address this gap, we release HepatoBench, a patch-level image database for liver cancer with annotations for seven key tissue categories. Based on HepatoBench, we train and open-source a deep learning classification model as a tissue recognition tool. Furthermore, we train a WSI-level tumor/non-tumor segmentation model to automatically localize lesion regions across entire slides. By integrating the patch-level tissue classifier with the WSI-level segmentation model, we build HepatoQuant, an end-to-end, disease-specific regional quantification tool for liver cancer, enabling a unified workflow from WSIs to tissue composition parsing and quantitative statistics. We also open-source HepatoBench, the benchmarking protocol, and supporting tools, providing a solid foundation for automated regional quantification and fair method comparison in liver cancer pathology.

cs.CV↗

arXiv2026

LLMs Are Not a Silver Bullet: A Case Study on Software Fairness

Fairness is a critical requirement for human-related, high-stakes software systems, motivating extensive research on bias mitigation. Prior work has largely focused on tabular data settings using traditional Machine Learning (ML) methods. With the rapid rise of Large Language Models (LLMs), recent studies have begun to explore their use for bias mitigation in the same setting. However, it remains unclear whether LLM-based methods offer advantages over traditional ML methods, leaving software engineers without clear guidance for practical adoption. To address this gap, we present a large-scale study comparing state-of-the-art ML- and LLM-based bias mitigation methods. We find that ML-based methods consistently outperform LLM-based methods in both fairness and predictive performance, with even strong LLMs failing to surpass established ML baselines. To understand why prior LLM-based studies report favorable results, we analyze their evaluation settings and show that these gains are largely driven by artificially balanced test data rather than realistic imbalanced distributions. We further observe that existing LLM-based methods primarily rely on in-context learning and thus fail to leverage all available training data. Motivated by this, we explore supervised fine-tuning on the full training set and find that, while it achieves competitive results, its advantages over traditional ML methods remain limited. These findings suggest that LLMs are not a silver bullet for software fairness.

cs.SE↗

arXiv2026

EET: Experience-Driven Early Termination for Cost-Efficient Software Engineering Agents

Software engineering (SE) agents powered by large language models are increasingly adopted in practice, yet they often incur substantial monetary cost. We introduce EET, an experience-driven early termination approach that reduces the cost of SE agents while preserving task performance. EET extracts structured experience from prior issue-resolution executions and leverages it to guide early termination during patch generation and selection, reducing unproductive iterations. We evaluate EET on the SWE-bench Verified benchmark across three representative SE agents. EET consistently reduces total cost by 19%-55% (32% on average), with negligible loss in resolution rate (at most 0.2%). These efficiency gains are achieved, on average, by identifying early-termination opportunities for 11% of issues and reducing API calls, input tokens, and output tokens by 21%, 30%, and 25%, respectively. We release the code, prompts, and data at https://github.com/IanWalls/EET.

cs.SE↗

arXiv2025

Fairness Is Not Just Ethical: Performance Trade-Off via Data Correlation Tuning to Mitigate Bias in ML Software

Traditional software fairness research typically emphasizes ethical and social imperatives, neglecting that fairness fundamentally represents a core software quality issue arising directly from performance disparities across sensitive user groups. Recognizing fairness explicitly as a software quality dimension yields practical benefits beyond ethical considerations, notably improved predictive performance for unprivileged groups, enhanced out-of-distribution generalization, and increased geographic transferability in real-world deployments. Nevertheless, existing bias mitigation methods face a critical dilemma: while pre-processing methods offer broad applicability across model types, they generally fall short in effectiveness compared to post-processing techniques. To overcome this challenge, we propose Correlation Tuning (CoT), a novel pre-processing approach designed to mitigate bias by adjusting data correlations. Specifically, CoT introduces the Phi-coefficient, an intuitive correlation measure, to systematically quantify correlation between sensitive attributes and labels, and employs multi-objective optimization to address the proxy biases. Extensive evaluations demonstrate that CoT increases the true positive rate of unprivileged groups by an average of 17.5% and reduces three key bias metrics, including statistical parity difference (SPD), average odds difference (AOD), and equal opportunity difference (EOD), by more than 50% on average. CoT outperforms state-of-the-art methods by three and ten percentage points in single attribute and multiple attributes scenarios, respectively. We will publicly release our experimental results and source code to facilitate future research.

cs.SE↗

arXiv2025

Software Fairness Dilemma: Is Bias Mitigation a Zero-Sum Game?

Fairness is a critical requirement for Machine Learning (ML) software, driving the development of numerous bias mitigation methods. Previous research has identified a leveling-down effect in bias mitigation for computer vision and natural language processing tasks, where fairness is achieved by lowering performance for all groups without benefiting the unprivileged group. However, it remains unclear whether this effect applies to bias mitigation for tabular data tasks, a key area in fairness research with significant real-world applications. This study evaluates eight bias mitigation methods for tabular data, including both widely used and cutting-edge approaches, across 44 tasks using five real-world datasets and four common ML models. Contrary to earlier findings, our results show that these methods operate in a zero-sum fashion, where improvements for unprivileged groups are related to reduced benefits for traditionally privileged groups. However, previous research indicates that the perception of a zero-sum trade-off might complicate the broader adoption of fairness policies. To explore alternatives, we investigate an approach that applies the state-of-the-art bias mitigation method solely to unprivileged groups, showing potential to enhance benefits of unprivileged groups without negatively affecting privileged groups or overall ML performance. Our study highlights potential pathways for achieving fairness improvements without zero-sum trade-offs, which could help advance the adoption of bias mitigation methods.

cs.LG↗

arXiv2025

Subspecialty-Specific Foundation Model for Intelligent Gastrointestinal Pathology

Gastrointestinal (GI) diseases represent a clinically significant burden, necessitating precise diagnostic approaches to optimize patient outcomes. Conventional histopathological diagnosis suffers from limited reproducibility and diagnostic variability. To overcome these limitations, we develop Digepath, a specialized foundation model for GI pathology. Our framework introduces a dual-phase iterative optimization strategy combining pretraining with fine-screening, specifically designed to address the detection of sparsely distributed lesion areas in whole-slide images. Digepath is pretrained on over 353 million multi-scale images from 210,043 H&E-stained slides of GI diseases. It attains state-of-the-art performance on 33 out of 34 tasks related to GI pathology, including pathological diagnosis, protein expression status prediction, gene mutation prediction, and prognosis evaluation. We further translate the intelligent screening module for early GI cancer and achieve near-perfect 99.70% sensitivity across nine independent medical institutions. This work not only advances AI-driven precision pathology for GI diseases but also bridge critical gaps in histopathological practice.

eess.IV↗

arXiv2025

FairMedQA: Benchmarking Bias in Large Language Models for Medical Question Answering

Large language models (LLMs) are approaching expert-level performance in medical question answering (QA), demonstrating strong potential to improve public healthcare. However, underlying biases related to sensitive attributes such as sex and race pose life-critical risks. The extent to which such sensitive attributes affect diagnosis remains an open question and requires comprehensive empirical investigation. Additionally, even the latest Counterfactual Patient Variations (CPV) benchmark can hardly distinguish the bias levels of different LLMs. To further explore these dynamics, we propose a new benchmark, FairMedQA, and benchmark 12 representative LLMs. FairMedQA contains 4,806 counterfactual question pairs constructed from 801 clinical vignettes. Our results reveal substantial accuracy disparity ranging from 3 to 19 percentage points across sensitive demographic groups. Notably, FairMedQA exposes biases that are at least 12 percentage points larger than those identified by the latest CPV benchmark, presenting superior benchmarking sensitivity. Our results underscore an urgent need for targeted debiasing techniques and more rigorous, identity-aware validation protocols before LLMs can be safely integrated into practical clinical decision-support systems.

cs.AI↗

arXiv2025

Natural van der Waals canalization lens for non-destructive nanoelectronic circuit imaging and inspection

Optical inspection has long served as a cornerstone non-destructive method in semiconductor wafer manufacturing, particularly for surface and defect analysis. However, conventional techniques such as bright-field and dark-field scattering optics face significant limitations, including insufficient resolution and the inability to penetrate and detect buried structures. Atomic force microscopy (AFM), while offering higher resolution and precise surface characterization, is constrained by slow speed, limited to surface-level imaging, and incapable of resolving subsurface features. Here, we propose an approach that integrates the strengths of dark-field scattering optics and AFM by leveraging a van der Waals (vdW) canalization lens based on natural biaxial {\alpha}-MoO3 crystals. This method enables ultrahigh-resolution subwavelength imaging with the ability to visualize both surface and buried structures, achieving a spatial resolution of 15 nm and grating pitch detection down to 100 nm. The underlying mechanism relies on the unique anisotropic properties of {\alpha}-MoO3, where its atomic-scale unit cells and biaxial symmetry facilitate the diffraction-free propagation of both evanescent and propagating waves via a flat-band canalization regime. Unlike metamaterial-based superlenses and hyperlenses, which suffer from high plasmonic losses, fabrication imperfections, and uniaxial constraints, {\alpha}-MoO3 provides robust and aberration-free imaging in multiple directions. We successfully applied this approach to high-resolution inspection of buried nanoscale electronic circuits, offering unprecedented capabilities essential for next-generation semiconductor manufacturing.

physics.optics↗

arXiv2024

Fairness Testing of Large Language Models in Role-Playing

Large Language Models (LLMs) have become foundational in modern language-driven software applications, profoundly influencing daily life. A critical technique in leveraging their potential is role-playing, where LLMs simulate diverse roles to enhance their real-world utility. However, while research has highlighted the presence of social biases in LLM outputs, it remains unclear whether and to what extent these biases emerge during role-playing scenarios. In this paper, we conduct an empirical study on fairness testing of LLMs in role-playing scenarios. To enable this testing, we use LLMs to generate 550 social roles spanning a comprehensive set of 11 demographic attributes, producing 33,000 role-specific questions that target various forms of bias. These questions, covering Yes/No, multiple-choice, and open-ended formats, are designed to prompt LLMs to adopt specific roles and respond accordingly. We employ a combination of rule-based and LLM-based strategies to identify biased responses, rigorously validated through human evaluation. Using the generated questions as the test cases, we conduct extensive evaluations of 10 advanced LLMs. The evaluation reveal 107,580 biased responses across the studied LLMs, with individual models yielding between 7,579 and 16,963 biased responses, underscoring the prevalence of bias in role-playing contexts. To support future research, we have publicly released the dataset, along with all scripts and experimental results.

cs.CY↗

arXiv2024

Rosette spectroscopic imaging for whole-brain metabolite mapping at 7T: acceleration potential and reproducibility

Whole-brain proton magnetic resonance spectroscopic imaging (1H-MRSI) is a non-invasive technique for assessing neurochemical distribution in the brain, offering valuable insights into brain functions and neural diseases. It greatly benefits from the improved SNR at ultrahigh field strengths ($\geq$7T). However, 1H-MRSI still faces several challenges, such as long acquisition time and severe signal contaminations from water and lipids. In this study, 2D and 3D short TR/TE 1H-FID-MRSI sequences using rosette trajectories were developed with spatial resolutions of 4.48$\times$4.48 mm$^2$ and 4.48$\times$4.48$\times$4.50 mm$^3$, respectively. Water signals were suppressed using an optimized Five-variable-Angle-gaussian-pulses-with-ShorT-total-duration of 76 ms (FAST) water suppression scheme, and lipid signals were removed using the L2 regularization method. Metabolic maps of major 1H metabolites were obtained within 5:40 min with 16 averages and 1 average for the 2D and 3D acquisitions, respectively. Excellent inter-session reproducibility was shown, with the coefficients of variance (CV) being lower than 6% for N-Acetyle-L-aspartic acid (NAA), Glutamate (Glu), Choline Chloride and glycerophosphocholine (tCho), Creatine and Phosphocreatine (tCr), and Glycine and Myo-inositol (Gly+Ins). To explore the potential of further accelerating the acquisition, compressed sensing was applied retrospectively to the 3D datasets. The structural similarity index (SSIM) remained above 0.85 and 0.8 until $R = 2$ and $R = 3$ for the metabolite maps of Glu, NAA, tCr, and tCho, indicating the possibility for further reduction of acquisition time to around 2min.

physics.med-ph↗

arXiv2024

Fast 3D 31P B1+ mapping with a weighted stack of spiral trajectory at 7 Tesla

Purpose: Phosphorus Magnetic Resonance Spectroscopy (31P MRS) enables non-invasive assessment of energy metabolism, yet its application is hindered by sensitivity limitations. To overcome this, often high magnetic fields are used, leading to challenges such as spatial B_1^+ inhomogeneity and therefore the need for accurate flip angle determination in accelerated acquisitions with short repetition times (T_R). In response to these challenges, we propose a novel short T_R and look-up table-based Double-Angle Method for fast 3D 31P B_1^+ mapping (fDAM). Methods: Our method incorporates 3D weighted stack of spiral gradient echo acquisitions and a frequency-selective pulse to enable efficient B_1^+ mapping based on the phosphocreatine signal at 7T. Protocols were optimised using simulations and validated through phantom experiments. The method was validated in phantom experiments and skeletal muscle applications using a birdcage 1H/31P volume coil. Results: The results of fDAM were compared to the classical DAM (cDAM). A good correlation (r=0.94) was obtained between the two B_1^+ maps. A 3D 31P B_1^+ mapping in the human calf muscle was achieved in about 10 min using a birdcage volume coil, with a 20% extended coverage relative to that of the cDAM (24 min). fDAM also enabled the first full brain coverage 31P 3D B_1^+ mapping in approx. 10 min using a 1 Tx/ 32 Rx coil. Conclusion: fDAM is an efficient method for 31P 3D B_1^+ mapping, showing promise for future applications in rapid 31P MRSI.

physics.med-ph↗

arXiv2024

The status and challenges for prostate SBRT treatments in United States proton therapy centers: An NRG Oncology practice survey

A survey was designed to inquire about the practice of proton SBRT treatment for prostate cancer. The survey was distributed to all 30 proton therapy centers in the United States that participate in the National Clinical Trial Network in Feb. 2023. The survey focused on usage, patient selection criteria, prescriptions, target contours, dose constraints, treatment plan optimization and evaluation methods, patient-specific QA, and IGRT methods. Results: We received responses from 25 centers (83% participation). Only 8 respondent proton centers (32%) reported performing SBRT of the prostate. The remaining 17 centers cited three primary reasons for not offering this treatment: no clinical need, lack of volumetric imaging, and/or lack of clinical evidence. Only 1 center cited the reduction in overall reimbursement as a concern for not offering prostate SBRT. Several common practices among the 8 centers offering SBRT for the prostate were noted, such as using Hydrogel spacers, fiducial markers, and MRI for target delineation. Most proton centers (87.5%) utilized pencil beam scanning (PBS) delivery and completed Imaging and Radiation Oncology Core (IROC) phantom credentialing. Treatment planning typically used parallel opposed lateral beams, and consistent parameters for setup and range uncertainties were used for plan optimization and robustness evaluation. Measurements-based patient-specific QA, beam delivery every other day, fiducial contours for IGRT, and total doses of 35-40 GyRBE were consistent across all centers. However, there was no consensus on the risk levels for patient selection. Conclusion: Prostate SBRT is used in about 1/3 of proton centers in the US. There was a significant consistency in practices among proton centers treating with proton SBRT. It is possible that the adoption of proton SBRT may become more common if proton SBRT is more commonly offered in clinical trials.

physics.med-ph↗

arXiv2024

Design and Visual Servoing Control of a Hybrid Dual-Segment Flexible Neurosurgical Robot for Intraventricular Biopsy

Traditional rigid endoscopes have challenges in flexibly treating tumors located deep in the brain, and low operability and fixed viewing angles limit its development. This study introduces a novel dual-segment flexible robotic endoscope MicroNeuro, designed to perform biopsies with dexterous surgical manipulation deep in the brain. Taking into account the uncertainty of the control model, an image-based visual servoing with online robot Jacobian estimation has been implemented to enhance motion accuracy. Furthermore, the application of model predictive control with constraints significantly bolsters the flexible robot's ability to adaptively track mobile objects and resist external interference. Experimental results underscore that the proposed control system enhances motion stability and precision. Phantom testing substantiates its considerable potential for deployment in neurosurgery.

cs.RO↗

arXiv2024

Proton Pencil-Beam Scanning Stereotactic Body Radiation Therapy and Hypofractionated Radiation Therapy for Thoracic Malignancies: Patterns of Practice Survey and Recommendations for Future Development from NRG Oncology and PTCOG

Stereotactic body radiation therapy (SBRT) and hypofractionation using pencil-beam scanning (PBS) proton therapy (PBSPT) is an attractive option for thoracic malignancies. Combining the advantages of target coverage conformity and critical organ sparing from both PBSPT and SBRT, this new delivery technique has great potential to improve the therapeutic ratio, particularly for tumors near critical organs. Safe and effective implementation of PBSPT SBRT/hypofractionation to treat thoracic malignancies is more challenging than the conventionally-fractionated PBSPT due to concerns of amplified uncertainties at the larger dose per fraction. NRG Oncology and Particle Therapy Cooperative Group (PTCOG) Thoracic Subcommittee surveyed US proton centers to identify practice patterns of thoracic PBSPT SBRT/hypofractionation. From these patterns, we present recommendations for future technical development of proton SBRT/hypofractionation for thoracic treatment. Amongst other points, the recommendations highlight the need for volumetric image guidance and multiple CT-based robust optimization and robustness tools to minimize further the impact of uncertainties associated with respiratory motion. Advances in direct motion analysis techniques are urgently needed to supplement current motion management techniques.

physics.med-ph↗

arXiv2023

Twisted Pair Transmission Line Coil -- A Flexible, Self-Decoupled and Extremely Robust Element for 7T MRI

This study evaluates the performance of a twisted pair transmission line coil as a transceive element for 7T MRI in terms of physical flexibility, robustness to shape deformations, and interelement decoupling. Each coil element was created by shaping a twisted pair of wires into a circle. One wire was interrupted at the top, while the other was interrupted at the bottom, and connected to the matching circuit. Electromagnetic simulations were conducted to determine the optimal number of twists per length (in terms of B$_1^+$ field efficiency, SAR efficiency, sensitivity to elongation and interelement decoupling properties) and for investigating the fundamental operational principle of the coil through fields streamline visualization. A comparison between the twisted pair coil and a conventional loop coil in terms of B$_1^+$ fields, maxSAR10g, and stability of $S_{11}$ when the coil was deformed, was performed. Experimentally measured interelement coupling between individual elements of multichannel arrays was also investigated. Increasing the number of twists per length resulted in a more physically robust coil. Poynting vector streamline visualization showed that the twisted pair coil concentrated most of the energy in the near field. The twisted pair coil exhibited comparable B$_1^+$ fields and improved maxSAR10g to the conventional coil but demonstrated exceptional stability with respect to coil deformation and a strong self-decoupling nature when placed in an array configuration. The findings highlight the robustness of the twisted pair coil, showcasing its stability under shape variations. This coil holds great potential as a flexible RF coil for various imaging applications using multiple-element arrays, benefiting from its inherent decoupling.

physics.med-ph↗

arXiv2023

kNN-Embed: Locally Smoothed Embedding Mixtures For Multi-interest Candidate Retrieval

Candidate retrieval is the first stage in recommendation systems, where a light-weight system is used to retrieve potentially relevant items for an input user. These candidate items are then ranked and pruned in later stages of recommender systems using a more complex ranking model. As the top of the recommendation funnel, it is important to retrieve a high-recall candidate set to feed into downstream ranking models. A common approach is to leverage approximate nearest neighbor (ANN) search from a single dense query embedding; however, this approach this can yield a low-diversity result set with many near duplicates. As users often have multiple interests, candidate retrieval should ideally return a diverse set of candidates reflective of the user's multiple interests. To this end, we introduce kNN-Embed, a general approach to improving diversity in dense ANN-based retrieval. kNN-Embed represents each user as a smoothed mixture over learned item clusters that represent distinct "interests" of the user. By querying each of a user's mixture component in proportion to their mixture weights, we retrieve a high-diversity set of candidates reflecting elements from each of a user's interests. We experimentally compare kNN-Embed to standard ANN candidate retrieval, and show significant improvements in overall recall and improved diversity across three datasets. Accompanying this work, we open source a large Twitter follow-graph dataset (https://huggingface.co/datasets/Twitter/TwitterFollowGraph), to spur further research in graph-mining and representation learning for recommender systems.

cs.IR↗

arXiv2023

DBGSA: A Novel Data Adaptive Bregman Clustering Algorithm

With the development of Big data technology, data analysis has become increasingly important. Traditional clustering algorithms such as K-means are highly sensitive to the initial centroid selection and perform poorly on non-convex datasets. In this paper, we address these problems by proposing a data-driven Bregman divergence parameter optimization clustering algorithm (DBGSA), which combines the Universal Gravitational Algorithm to bring similar points closer in the dataset. We construct a gravitational coefficient equation with a special property that gradually reduces the influence factor as the iteration progresses. Furthermore, we introduce the Bregman divergence generalized power mean information loss minimization to identify cluster centers and build a hyperparameter identification optimization model, which effectively solves the problems of manual adjustment and uncertainty in the improved dataset. Extensive experiments are conducted on four simulated datasets and six real datasets. The results demonstrate that DBGSA significantly improves the accuracy of various clustering algorithms by an average of 63.8\% compared to other similar approaches like enhanced clustering algorithms and improved datasets. Additionally, a three-dimensional grid search was established to compare the effects of different parameter values within threshold conditions, and it was discovered the parameter set provided by our model is optimal. This finding provides strong evidence of the high accuracy and robustness of the algorithm.

cs.LG↗

arXiv2023

Iterative-in-Iterative Super-Resolution Biomedical Imaging Using One Real Image

Deep learning-based super-resolution models have the potential to revolutionize biomedical imaging and diagnoses by effectively tackling various challenges associated with early detection, personalized medicine, and clinical automation. However, the requirement of an extensive collection of high-resolution images presents limitations for widespread adoption in clinical practice. In our experiment, we proposed an approach to effectively train the deep learning-based super-resolution models using only one real image by leveraging self-generated high-resolution images. We employed a mixed metric of image screening to automatically select images with a distribution similar to ground truth, creating an incrementally curated training data set that encourages the model to generate improved images over time. After five training iterations, the proposed deep learning-based super-resolution model experienced a 7.5\% and 5.49\% improvement in structural similarity and peak-signal-to-noise ratio, respectively. Significantly, the model consistently produces visually enhanced results for training, improving its performance while preserving the characteristics of original biomedical images. These findings indicate a potential way to train a deep neural network in a self-revolution manner independent of real-world human data.

physics.med-ph↗