arXiv subjects

Yongchao Xu

Publications and source records attributed to Yongchao Xu.

At least 37 records · Page 2Linked to original sources

arXiv2025

Pathological Prior-Guided Multiple Instance Learning For Mitigating Catastrophic Forgetting in Breast Cancer Whole Slide Image Classification

In histopathology, intelligent diagnosis of Whole Slide Images (WSIs) is essential for automating and objectifying diagnoses, reducing the workload of pathologists. However, diagnostic models often face the challenge of forgetting previously learned data during incremental training on datasets from different sources. To address this issue, we propose a new framework PaGMIL to mitigate catastrophic forgetting in breast cancer WSI classification. Our framework introduces two key components into the common MIL model architecture. First, it leverages microscopic pathological prior to select more accurate and diverse representative patches for MIL. Secondly, it trains separate classification heads for each task and uses macroscopic pathological prior knowledge, treating the thumbnail as a prompt guide (PG) to select the appropriate classification head. We evaluate the continual learning performance of PaGMIL across several public breast cancer datasets. PaGMIL achieves a better balance between the performance of the current task and the retention of previous tasks, outperforming other continual learning methods. Our code will be open-sourced upon acceptance.

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arXiv2025

Consistent-Point: Consistent Pseudo-Points for Semi-Supervised Crowd Counting and Localization

Crowd counting and localization are important in applications such as public security and traffic management. Existing methods have achieved impressive results thanks to extensive laborious annotations. This paper propose a novel point-localization-based semi-supervised crowd counting and localization method termed Consistent-Point. We identify and address two inconsistencies of pseudo-points, which have not been adequately explored. To enhance their position consistency, we aggregate the positions of neighboring auxiliary proposal-points. Additionally, an instance-wise uncertainty calibration is proposed to improve the class consistency of pseudo-points. By generating more consistent pseudo-points, Consistent-Point provides more stable supervision to the training process, yielding improved results. Extensive experiments across five widely used datasets and three different labeled ratio settings demonstrate that our method achieves state-of-the-art performance in crowd localization while also attaining impressive crowd counting results. The code will be available.

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arXiv2024

CellSeg1: Robust Cell Segmentation with One Training Image

Recent trends in cell segmentation have shifted towards universal models to handle diverse cell morphologies and imaging modalities. However, for continuously emerging cell types and imaging techniques, these models still require hundreds or thousands of annotated cells for fine-tuning. We introduce CellSeg1, a practical solution for segmenting cells of arbitrary morphology and modality with a few dozen cell annotations in 1 image. By adopting Low-Rank Adaptation of the Segment Anything Model (SAM), we achieve robust cell segmentation. Tested on 19 diverse cell datasets, CellSeg1 trained on 1 image achieved 0.81 average mAP at 0.5 IoU, performing comparably to existing models trained on over 500 images. It also demonstrated superior generalization in cross-dataset tests on TissueNet. We found that high-quality annotation of a few dozen densely packed cells of varied sizes is key to effective segmentation. CellSeg1 provides an efficient solution for cell segmentation with minimal annotation effort.

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arXiv2024

Shape Transformation Driven by Active Contour for Class-Imbalanced Semi-Supervised Medical Image Segmentation

Annotating 3D medical images demands expert knowledge and is time-consuming. As a result, semi-supervised learning (SSL) approaches have gained significant interest in 3D medical image segmentation. The significant size differences among various organs in the human body lead to imbalanced class distribution, which is a major challenge in the real-world application of these SSL approaches. To address this issue, we develop a novel Shape Transformation driven by Active Contour (STAC), that enlarges smaller organs to alleviate imbalanced class distribution across different organs. Inspired by curve evolution theory in active contour methods, STAC employs a signed distance function (SDF) as the level set function, to implicitly represent the shape of organs, and deforms voxels in the direction of the steepest descent of SDF (i.e., the normal vector). To ensure that the voxels far from expansion organs remain unchanged, we design an SDF-based weight function to control the degree of deformation for each voxel. We then use STAC as a data-augmentation process during the training stage. Experimental results on two benchmark datasets demonstrate that the proposed method significantly outperforms some state-of-the-art methods. Source code is publicly available at https://github.com/GuGuLL123/STAC.

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arXiv2024

Progressive Retinal Image Registration via Global and Local Deformable Transformations

Retinal image registration plays an important role in the ophthalmological diagnosis process. Since there exist variances in viewing angles and anatomical structures across different retinal images, keypoint-based approaches become the mainstream methods for retinal image registration thanks to their robustness and low latency. These methods typically assume the retinal surfaces are planar, and adopt feature matching to obtain the homography matrix that represents the global transformation between images. Yet, such a planar hypothesis inevitably introduces registration errors since retinal surface is approximately curved. This limitation is more prominent when registering image pairs with significant differences in viewing angles. To address this problem, we propose a hybrid registration framework called HybridRetina, which progressively registers retinal images with global and local deformable transformations. For that, we use a keypoint detector and a deformation network called GAMorph to estimate the global transformation and local deformable transformation, respectively. Specifically, we integrate multi-level pixel relation knowledge to guide the training of GAMorph. Additionally, we utilize an edge attention module that includes the geometric priors of the images, ensuring the deformation field focuses more on the vascular regions of clinical interest. Experiments on two widely-used datasets, FIRE and FLoRI21, show that our proposed HybridRetina significantly outperforms some state-of-the-art methods. The code is available at https://github.com/lyp-deeplearning/awesome-retinal-registration.

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arXiv2024

Shape-intensity knowledge distillation for robust medical image segmentation

Many medical image segmentation methods have achieved impressive results. Yet, most existing methods do not take into account the shape-intensity prior information. This may lead to implausible segmentation results, in particular for images of unseen datasets. In this paper, we propose a novel approach to incorporate joint shape-intensity prior information into the segmentation network. Specifically, we first train a segmentation network (regarded as the teacher network) on class-wise averaged training images to extract valuable shape-intensity information, which is then transferred to a student segmentation network with the same network architecture as the teacher via knowledge distillation. In this way, the student network regarded as the final segmentation model can effectively integrate the shape-intensity prior information, yielding more accurate segmentation results. Despite its simplicity, experiments on five medical image segmentation tasks of different modalities demonstrate that the proposed Shape-Intensity Knowledge Distillation (SIKD) consistently improves several baseline models (including recent MaxStyle and SAMed) under intra-dataset evaluation, and significantly improves the cross-dataset generalization ability. The code is available at https://github.com/whdong-whu/SIKD.

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arXiv2024

Prompting Segment Anything Model with Domain-Adaptive Prototype for Generalizable Medical Image Segmentation

Deep learning based methods often suffer from performance degradation caused by domain shift. In recent years, many sophisticated network structures have been designed to tackle this problem. However, the advent of large model trained on massive data, with its exceptional segmentation capability, introduces a new perspective for solving medical segmentation problems. In this paper, we propose a novel Domain-Adaptive Prompt framework for fine-tuning the Segment Anything Model (termed as DAPSAM) to address single-source domain generalization (SDG) in segmenting medical images. DAPSAM not only utilizes a more generalization-friendly adapter to fine-tune the large model, but also introduces a self-learning prototype-based prompt generator to enhance model's generalization ability. Specifically, we first merge the important low-level features into intermediate features before feeding to each adapter, followed by an attention filter to remove redundant information. This yields more robust image embeddings. Then, we propose using a learnable memory bank to construct domain-adaptive prototypes for prompt generation, helping to achieve generalizable medical image segmentation. Extensive experimental results demonstrate that our DAPSAM achieves state-of-the-art performance on two SDG medical image segmentation tasks with different modalities. The code is available at https://github.com/wkklavis/DAPSAM.

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arXiv2024

HFGS: 4D Gaussian Splatting with Emphasis on Spatial and Temporal High-Frequency Components for Endoscopic Scene Reconstruction

Robot-assisted minimally invasive surgery benefits from enhancing dynamic scene reconstruction, as it improves surgical outcomes. While Neural Radiance Fields (NeRF) have been effective in scene reconstruction, their slow inference speeds and lengthy training durations limit their applicability. To overcome these limitations, 3D Gaussian Splatting (3D-GS) based methods have emerged as a recent trend, offering rapid inference capabilities and superior 3D quality. However, these methods still struggle with under-reconstruction in both static and dynamic scenes. In this paper, we propose HFGS, a novel approach for deformable endoscopic reconstruction that addresses these challenges from spatial and temporal frequency perspectives. Our approach incorporates deformation fields to better handle dynamic scenes and introduces Spatial High-Frequency Emphasis Reconstruction (SHF) to minimize discrepancies in spatial frequency spectra between the rendered image and its ground truth. Additionally, we introduce Temporal High-Frequency Emphasis Reconstruction (THF) to enhance dynamic awareness in neural rendering by leveraging flow priors, focusing optimization on motion-intensive parts. Extensive experiments on two widely used benchmarks demonstrate that HFGS achieves superior rendering quality.

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arXiv2024

WIA-LD2ND: Wavelet-based Image Alignment for Self-supervised Low-Dose CT Denoising

In clinical examinations and diagnoses, low-dose computed tomography (LDCT) is crucial for minimizing health risks compared with normal-dose computed tomography (NDCT). However, reducing the radiation dose compromises the signal-to-noise ratio, leading to degraded quality of CT images. To address this, we analyze LDCT denoising task based on experimental results from the frequency perspective, and then introduce a novel self-supervised CT image denoising method called WIA-LD2ND, only using NDCT data. The proposed WIA-LD2ND comprises two modules: Wavelet-based Image Alignment (WIA) and Frequency-Aware Multi-scale Loss (FAM). First, WIA is introduced to align NDCT with LDCT by mainly adding noise to the high-frequency components, which is the main difference between LDCT and NDCT. Second, to better capture high-frequency components and detailed information, Frequency-Aware Multi-scale Loss (FAM) is proposed by effectively utilizing multi-scale feature space. Extensive experiments on two public LDCT denoising datasets demonstrate that our WIA-LD2ND, only uses NDCT, outperforms existing several state-of-the-art weakly-supervised and self-supervised methods. Source code is available at https://github.com/zhaohaoyu376/WI-LD2ND.

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arXiv2024

MoreStyle: Relax Low-frequency Constraint of Fourier-based Image Reconstruction in Generalizable Medical Image Segmentation

The task of single-source domain generalization (SDG) in medical image segmentation is crucial due to frequent domain shifts in clinical image datasets. To address the challenge of poor generalization across different domains, we introduce a Plug-and-Play module for data augmentation called MoreStyle. MoreStyle diversifies image styles by relaxing low-frequency constraints in Fourier space, guiding the image reconstruction network. With the help of adversarial learning, MoreStyle further expands the style range and pinpoints the most intricate style combinations within latent features. To handle significant style variations, we introduce an uncertainty-weighted loss. This loss emphasizes hard-to-classify pixels resulting only from style shifts while mitigating true hard-to-classify pixels in both MoreStyle-generated and original images. Extensive experiments on two widely used benchmarks demonstrate that the proposed MoreStyle effectively helps to achieve good domain generalization ability, and has the potential to further boost the performance of some state-of-the-art SDG methods. Source code is available at https://github.com/zhaohaoyu376/morestyle.

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arXiv2024

Position-Guided Prompt Learning for Anomaly Detection in Chest X-Rays

Anomaly detection in chest X-rays is a critical task. Most methods mainly model the distribution of normal images, and then regard significant deviation from normal distribution as anomaly. Recently, CLIP-based methods, pre-trained on a large number of medical images, have shown impressive performance on zero/few-shot downstream tasks. In this paper, we aim to explore the potential of CLIP-based methods for anomaly detection in chest X-rays. Considering the discrepancy between the CLIP pre-training data and the task-specific data, we propose a position-guided prompt learning method. Specifically, inspired by the fact that experts diagnose chest X-rays by carefully examining distinct lung regions, we propose learnable position-guided text and image prompts to adapt the task data to the frozen pre-trained CLIP-based model. To enhance the model's discriminative capability, we propose a novel structure-preserving anomaly synthesis method within chest x-rays during the training process. Extensive experiments on three datasets demonstrate that our proposed method outperforms some state-of-the-art methods. The code of our implementation is available at https://github.com/sunzc-sunny/PPAD.

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arXiv2024

Spatial-aware Attention Generative Adversarial Network for Semi-supervised Anomaly Detection in Medical Image

Medical anomaly detection is a critical research area aimed at recognizing abnormal images to aid in diagnosis.Most existing methods adopt synthetic anomalies and image restoration on normal samples to detect anomaly. The unlabeled data consisting of both normal and abnormal data is not well explored. We introduce a novel Spatial-aware Attention Generative Adversarial Network (SAGAN) for one-class semi-supervised generation of health images.Our core insight is the utilization of position encoding and attention to accurately focus on restoring abnormal regions and preserving normal regions. To fully utilize the unlabelled data, SAGAN relaxes the cyclic consistency requirement of the existing unpaired image-to-image conversion methods, and generates high-quality health images corresponding to unlabeled data, guided by the reconstruction of normal images and restoration of pseudo-anomaly images.Subsequently, the discrepancy between the generated healthy image and the original image is utilized as an anomaly score.Extensive experiments on three medical datasets demonstrate that the proposed SAGAN outperforms the state-of-the-art methods.

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arXiv2024

Development of Skip Connection in Deep Neural Networks for Computer Vision and Medical Image Analysis: A Survey

Deep learning has made significant progress in computer vision, specifically in image classification, object detection, and semantic segmentation. The skip connection has played an essential role in the architecture of deep neural networks,enabling easier optimization through residual learning during the training stage and improving accuracy during testing. Many neural networks have inherited the idea of residual learning with skip connections for various tasks, and it has been the standard choice for designing neural networks. This survey provides a comprehensive summary and outlook on the development of skip connections in deep neural networks. The short history of skip connections is outlined, and the development of residual learning in deep neural networks is surveyed. The effectiveness of skip connections in the training and testing stages is summarized, and future directions for using skip connections in residual learning are discussed. Finally, we summarize seminal papers, source code, models, and datasets that utilize skip connections in computer vision, including image classification, object detection, semantic segmentation, and image reconstruction. We hope this survey could inspire peer researchers in the community to develop further skip connections in various forms and tasks and the theory of residual learning in deep neural networks. The project page can be found at https://github.com/apple1986/Residual_Learning_For_Images

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arXiv2024

Dual Structure-Aware Image Filterings for Semi-supervised Medical Image Segmentation

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

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arXiv2024

Shifted Autoencoders for Point Annotation Restoration in Object Counting

Object counting typically uses 2D point annotations. The complexity of object shapes and the subjectivity of annotators may lead to annotation inconsistency, potentially confusing counting model training. Some sophisticated noise-resistance counting methods have been proposed to alleviate this issue. Differently, we aim to directly refine the initial point annotations before training counting models. For that, we propose the Shifted Autoencoders (SAE), which enhances annotation consistency. Specifically, SAE applies random shifts to initial point annotations and employs a UNet to restore them to their original positions. Similar to MAE reconstruction, the trained SAE captures general position knowledge and ignores specific manual offset noise. This allows to restore the initial point annotations to more general and thus consistent positions. Extensive experiments show that using such refined consistent annotations to train some advanced (including noise-resistance) object counting models steadily/significantly boosts their performances. Remarkably, the proposed SAE helps to set new records on nine datasets. We will make codes and refined point annotations available.

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arXiv2023

Scale-aware Test-time Click Adaptation for Pulmonary Nodule and Mass Segmentation

Pulmonary nodules and masses are crucial imaging features in lung cancer screening that require careful management in clinical diagnosis. Despite the success of deep learning-based medical image segmentation, the robust performance on various sizes of lesions of nodule and mass is still challenging. In this paper, we propose a multi-scale neural network with scale-aware test-time adaptation to address this challenge. Specifically, we introduce an adaptive Scale-aware Test-time Click Adaptation method based on effortlessly obtainable lesion clicks as test-time cues to enhance segmentation performance, particularly for large lesions. The proposed method can be seamlessly integrated into existing networks. Extensive experiments on both open-source and in-house datasets consistently demonstrate the effectiveness of the proposed method over some CNN and Transformer-based segmentation methods. Our code is available at https://github.com/SplinterLi/SaTTCA

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arXiv2023

Not All Pixels Are Equal: Learning Pixel Hardness for Semantic Segmentation

Semantic segmentation has recently witnessed great progress. Despite the impressive overall results, the segmentation performance in some hard areas (e.g., small objects or thin parts) is still not promising. A straightforward solution is hard sample mining, which is widely used in object detection. Yet, most existing hard pixel mining strategies for semantic segmentation often rely on pixel's loss value, which tends to decrease during training. Intuitively, the pixel hardness for segmentation mainly depends on image structure and is expected to be stable. In this paper, we propose to learn pixel hardness for semantic segmentation, leveraging hardness information contained in global and historical loss values. More precisely, we add a gradient-independent branch for learning a hardness level (HL) map by maximizing hardness-weighted segmentation loss, which is minimized for the segmentation head. This encourages large hardness values in difficult areas, leading to appropriate and stable HL map. Despite its simplicity, the proposed method can be applied to most segmentation methods with no and marginal extra cost during inference and training, respectively. Without bells and whistles, the proposed method achieves consistent/significant improvement (1.37% mIoU on average) over most popular semantic segmentation methods on Cityscapes dataset, and demonstrates good generalization ability across domains. The source codes are available at https://github.com/Menoly-xin/Hardness-Level-Learning .

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arXiv2022

Local Intensity Order Transformation for Robust Curvilinear Object Segmentation

Segmentation of curvilinear structures is important in many applications, such as retinal blood vessel segmentation for early detection of vessel diseases and pavement crack segmentation for road condition evaluation and maintenance. Currently, deep learning-based methods have achieved impressive performance on these tasks. Yet, most of them mainly focus on finding powerful deep architectures but ignore capturing the inherent curvilinear structure feature (e.g., the curvilinear structure is darker than the context) for a more robust representation. In consequence, the performance usually drops a lot on cross-datasets, which poses great challenges in practice. In this paper, we aim to improve the generalizability by introducing a novel local intensity order transformation (LIOT). Specifically, we transfer a gray-scale image into a contrast-invariant four-channel image based on the intensity order between each pixel and its nearby pixels along with the four (horizontal and vertical) directions. This results in a representation that preserves the inherent characteristic of the curvilinear structure while being robust to contrast changes. Cross-dataset evaluation on three retinal blood vessel segmentation datasets demonstrates that LIOT improves the generalizability of some state-of-the-art methods. Additionally, the cross-dataset evaluation between retinal blood vessel segmentation and pavement crack segmentation shows that LIOT is able to preserve the inherent characteristic of curvilinear structure with large appearance gaps. An implementation of the proposed method is available at https://github.com/TY-Shi/LIOT.

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