arXiv subjects

Guanglei Zhang

Publications and source records attributed to Guanglei Zhang.

12 recordsLinked to original sources

arXiv2026

SegMix:Shuffle-based Feedback Learning for Semantic Segmentation of Pathology Images

Segmentation is a critical task in computational pathology, as it identifies areas affected by disease or abnormal growth and is essential for diagnosis and treatment. However, acquiring high-quality pixel-level supervised segmentation data requires significant workload demands from experienced pathologists, limiting the application of deep learning. To overcome this challenge, relaxing the label conditions to image-level classification labels allows for more data to be used and more scenarios to be enabled. One approach is to leverage Class Activation Map (CAM) to generate pseudo pixel-level annotations for semantic segmentation with only image-level labels. However, this method fails to thoroughly explore the essential characteristics of pathology images, thus identifying only small areas that are insufficient for pseudo masking. In this paper, we propose a novel shuffle-based feedback learning method inspired by curriculum learning to generate higher-quality pseudo-semantic segmentation masks. Specifically, we perform patch level shuffle of pathology images, with the model adaptively adjusting the shuffle strategy based on feedback from previous learning. Experimental results demonstrate that our proposed approach outperforms state-of-the-arts on three different datasets.

cs.CV↗

arXiv2024

MDiff-FMT: Morphology-aware Diffusion Model for Fluorescence Molecular Tomography with Small-scale Datasets

Fluorescence molecular tomography (FMT) is a sensitive optical imaging technology widely used in biomedical research. However, the ill-posedness of the inverse problem poses a huge challenge to FMT reconstruction. Although end-to-end deep learning algorithms have been widely used to address this critical issue, they still suffer from high data dependency and poor morphological restoration. In this paper, we report for the first time a morphology-aware diffusion model, MDiff-FMT, based on denoising diffusion probabilistic model (DDPM) to achieve high-fidelity morphological reconstruction for FMT. First, we use the noise addition of DDPM to simulate the process of the gradual degradation of morphological features, and achieve fine-grained reconstruction of morphological features through a stepwise probabilistic sampling mechanism, avoiding problems such as loss of structure details that may occur in end-to-end deep learning methods. Additionally, we introduce the conditional fluorescence image as structural prior information to sample a high-fidelity reconstructed image from the noisy images. Numerous numerical and real phantom experimental results show that the proposed MDiff-FMT achieves SOTA results in morphological reconstruction of FMT without relying on large-scale datasets.

eess.IV↗

arXiv2023

Generating Progressive Images from Pathological Transitions via Diffusion Model

Deep learning is widely applied in computer-aided pathological diagnosis, which alleviates the pathologist workload and provide timely clinical analysis. However, most models generally require large-scale annotated data for training, which faces challenges due to the sampling and annotation scarcity in pathological images. The rapid developing generative models shows potential to generate more training samples from recent studies. However, they also struggle in generalization diversity with limited training data, incapable of generating effective samples. Inspired by the pathological transitions between different stages, we propose an adaptive depth-controlled diffusion (ADD) network to generate pathological progressive images for effective data augmentation. This novel approach roots in domain migration, where a hybrid attention strategy guides the bidirectional diffusion, blending local and global attention priorities. With feature measuring, the adaptive depth-controlled strategy ensures the migration and maintains locational similarity in simulating the pathological feature transition. Based on tiny training set (samples less than 500), the ADD yields cross-domain progressive images with corresponding soft-labels. Experiments on two datasets suggest significant improvements in generation diversity, and the effectiveness with generated progressive samples are highlighted in downstream classifications. The code is available at https://github.com/Rowerliu/ADD.

cs.CV↗

arXiv2023

PuzzleTuning: Explicitly Bridge Pathological and Natural Image with Puzzles

Pathological image analysis is a crucial field in computer vision. Due to the annotation scarcity in the pathological field, pre-training with self-supervised learning (SSL) is widely applied to learn on unlabeled images. However, the current SSL-based pathological pre-training: (1) does not explicitly explore the essential focuses of the pathological field, and (2) does not effectively bridge with and thus take advantage of the knowledge from natural images. To explicitly address them, we propose our large-scale PuzzleTuning framework, containing the following innovations. Firstly, we define three task focuses that can effectively bridge knowledge of pathological and natural domain: appearance consistency, spatial consistency, and restoration understanding. Secondly, we devise a novel multiple puzzle restoring task, which explicitly pre-trains the model regarding these focuses. Thirdly, we introduce an explicit prompt-tuning process to incrementally integrate the domain-specific knowledge. It builds a bridge to align the large domain gap between natural and pathological images. Additionally, a curriculum-learning training strategy is designed to regulate task difficulty, making the model adaptive to the puzzle restoring complexity. Experimental results show that our PuzzleTuning framework outperforms the previous state-of-the-art methods in various downstream tasks on multiple datasets. The code, demo, and pre-trained weights are available at https://github.com/sagizty/PuzzleTuning.

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arXiv2023

CPIA Dataset: A Comprehensive Pathological Image Analysis Dataset for Self-supervised Learning Pre-training

Pathological image analysis is a crucial field in computer-aided diagnosis, where deep learning is widely applied. Transfer learning using pre-trained models initialized on natural images has effectively improved the downstream pathological performance. However, the lack of sophisticated domain-specific pathological initialization hinders their potential. Self-supervised learning (SSL) enables pre-training without sample-level labels, which has great potential to overcome the challenge of expensive annotations. Thus, studies focusing on pathological SSL pre-training call for a comprehensive and standardized dataset, similar to the ImageNet in computer vision. This paper presents the comprehensive pathological image analysis (CPIA) dataset, a large-scale SSL pre-training dataset combining 103 open-source datasets with extensive standardization. The CPIA dataset contains 21,427,877 standardized images, covering over 48 organs/tissues and about 100 kinds of diseases, which includes two main data types: whole slide images (WSIs) and characteristic regions of interest (ROIs). A four-scale WSI standardization process is proposed based on the uniform resolution in microns per pixel (MPP), while the ROIs are divided into three scales artificially. This multi-scale dataset is built with the diagnosis habits under the supervision of experienced senior pathologists. The CPIA dataset facilitates a comprehensive pathological understanding and enables pattern discovery explorations. Additionally, to launch the CPIA dataset, several state-of-the-art (SOTA) baselines of SSL pre-training and downstream evaluation are specially conducted. The CPIA dataset along with baselines is available at https://github.com/zhanglab2021/CPIA_Dataset.

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arXiv2023

CellMix: A General Instance Relationship based Method for Data Augmentation Towards Pathology Image Classification

In pathology image analysis, obtaining and maintaining high-quality annotated samples is an extremely labor-intensive task. To overcome this challenge, mixing-based methods have emerged as effective alternatives to traditional preprocessing data augmentation techniques. Nonetheless, these methods fail to fully consider the unique features of pathology images, such as local specificity, global distribution, and inner/outer-sample instance relationships. To better comprehend these characteristics and create valuable pseudo samples, we propose the CellMix framework, which employs a novel distribution-oriented in-place shuffle approach. By dividing images into patches based on the granularity of pathology instances and shuffling them within the same batch, the absolute relationships between instances can be effectively preserved when generating new samples. Moreover, we develop a curriculum learning-inspired, loss-driven strategy to handle perturbations and distribution-related noise during training, enabling the model to adaptively fit the augmented data. Our experiments in pathology image classification tasks demonstrate state-of-the-art (SOTA) performance on 7 distinct datasets. This innovative instance relationship-centered method has the potential to inform general data augmentation approaches for pathology image classification. The associated codes are available at https://github.com/sagizty/CellMix.

cs.CV↗

arXiv2022

Shuffle Instances-based Vision Transformer for Pancreatic Cancer ROSE Image Classification

The rapid on-site evaluation (ROSE) technique can signifi-cantly accelerate the diagnosis of pancreatic cancer by im-mediately analyzing the fast-stained cytopathological images. Computer-aided diagnosis (CAD) can potentially address the shortage of pathologists in ROSE. However, the cancerous patterns vary significantly between different samples, making the CAD task extremely challenging. Besides, the ROSE images have complicated perturbations regarding color distribution, brightness, and contrast due to different staining qualities and various acquisition device types. To address these challenges, we proposed a shuffle instances-based Vision Transformer (SI-ViT) approach, which can reduce the perturbations and enhance the modeling among the instances. With the regrouped bags of shuffle instances and their bag-level soft labels, the approach utilizes a regression head to make the model focus on the cells rather than various perturbations. Simultaneously, combined with a classification head, the model can effectively identify the general distributive patterns among different instances. The results demonstrate significant improvements in the classification accuracy with more accurate attention regions, indicating that the diverse patterns of ROSE images are effectively extracted, and the complicated perturbations are significantly reduced. It also suggests that the SI-ViT has excellent potential in analyzing cytopathological images. The code and experimental results are available at https://github.com/sagizty/MIL-SI.

eess.IV↗

arXiv2022

Pancreatic Cancer ROSE Image Classification Based on Multiple Instance Learning with Shuffle Instances

The rapid on-site evaluation (ROSE) technique can significantly ac-celerate the diagnostic workflow of pancreatic cancer by immediately analyzing the fast-stained cytopathological images with on-site pathologists. Computer-aided diagnosis (CAD) using the deep learning method has the potential to solve the problem of insufficient pathology staffing. However, the cancerous patterns of ROSE images vary greatly between different samples, making the CAD task extremely challenging. Besides, due to different staining qualities and various types of acquisition devices, the ROSE images also have compli-cated perturbations in terms of color distribution, brightness, and contrast. To address these challenges, we proposed a novel multiple instance learning (MIL) approach using shuffle patches containing the instances, which adopts the patch-based learning strategy of Vision Transformers. With the re-grouped bags of shuffle instances and their bag-level soft labels, the approach utilizes a MIL head to make the model focus on the features from the pancreatic cancer cells, rather than that from various perturbations in ROSE images. Simultaneously, combined with a classification head, the model can effectively identify the gen-eral distributive patterns across different instances. The results demonstrate the significant improvements in the classification accuracy with more accurate at-tention regions, indicating that the diverse patterns of ROSE images are effec-tively extracted, and the complicated perturbations of ROSE images are signifi-cantly eliminated. It also suggests that the MIL with shuffle instances has great potential in the analysis of cytopathological images.

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arXiv2021

MSHT: Multi-stage Hybrid Transformer for the ROSE Image Analysis of Pancreatic Cancer

Pancreatic cancer is one of the most malignant cancers in the world, which deteriorates rapidly with very high mortality. The rapid on-site evaluation (ROSE) technique innovates the workflow by immediately analyzing the fast stained cytopathological images with on-site pathologists, which enables faster diagnosis in this time-pressured process. However, the wider expansion of ROSE diagnosis has been hindered by the lack of experienced pathologists. To overcome this problem, we propose a hybrid high-performance deep learning model to enable the automated workflow, thus freeing the occupation of the valuable time of pathologists. By firstly introducing the Transformer block into this field with our particular multi-stage hybrid design, the spatial features generated by the convolutional neural network (CNN) significantly enhance the Transformer global modeling. Turning multi-stage spatial features as global attention guidance, this design combines the robustness from the inductive bias of CNN with the sophisticated global modeling power of Transformer. A dataset of 4240 ROSE images is collected to evaluate the method in this unexplored field. The proposed multi-stage hybrid Transformer (MSHT) achieves 95.68% in classification accuracy, which is distinctively higher than the state-of-the-art models. Facing the need for interpretability, MSHT outperforms its counterparts with more accurate attention regions. The results demonstrate that the MSHT can distinguish cancer samples accurately at an unprecedented image scale, laying the foundation for deploying automatic decision systems and enabling the expansion of ROSE in clinical practice. The code and records are available at: https://github.com/sagizty/Multi-Stage-Hybrid-Transformer.

eess.IV↗

arXiv2021

Prior Attention Network for Multi-Lesion Segmentation in Medical Images

The accurate segmentation of multiple types of lesions from adjacent tissues in medical images is significant in clinical practice. Convolutional neural networks (CNNs) based on the coarse-to-fine strategy have been widely used in this field. However, multi-lesion segmentation remains to be challenging due to the uncertainty in size, contrast, and high interclass similarity of tissues. In addition, the commonly adopted cascaded strategy is rather demanding in terms of hardware, which limits the potential of clinical deployment. To address the problems above,we propose a novel Prior Attention Network (PANet) that follows the coarse-to-fine strategy to perform multi-lesion segmentation in medical images. The proposed network achieves the two steps of segmentation in a single network by inserting lesion-related spatial attention mechanism in the network. Further, we also propose the intermediate supervision strategy for generating lesion-related attention to acquire the regions of interest (ROIs), which accelerates the convergence and obviously improves the segmentation performance. We have investigated the proposed segmentation framework in two applications: 2D segmentation of multiple lung infections in lung CT slices and 3D segmentation of multiple lesions in brain MRIs. Experimental results show that in both 2D and 3D segmentation tasks our proposed network achieves better performance with less computational cost compared with cascaded networks. The proposed network can be regarded as a universal solution to multi-lesion segmentation in both 2D and 3D tasks. The source code is available at: https://github.com/hsiangyuzhao/PANet.

eess.IV↗

arXiv2021

D2A U-Net: Automatic Segmentation of COVID-19 Lesions from CT Slices with Dilated Convolution and Dual Attention Mechanism

Coronavirus Disease 2019 (COVID-19) has caused great casualties and becomes almost the most urgent public health events worldwide. Computed tomography (CT) is a significant screening tool for COVID-19 infection, and automated segmentation of lung infection in COVID-19 CT images will greatly assist diagnosis and health care of patients. However, accurate and automatic segmentation of COVID-19 lung infections remains to be challenging. In this paper we propose a dilated dual attention U-Net (D2A U-Net) for COVID-19 lesion segmentation in CT slices based on dilated convolution and a novel dual attention mechanism to address the issues above. We introduce a dilated convolution module in model decoder to achieve large receptive field, which refines decoding process and contributes to segmentation accuracy. Also, we present a dual attention mechanism composed of two attention modules which are inserted to skip connection and model decoder respectively. The dual attention mechanism is utilized to refine feature maps and reduce semantic gap between different levels of the model. The proposed method has been evaluated on open-source dataset and outperforms cutting edges methods in semantic segmentation. Our proposed D2A U-Net with pretrained encoder achieves a Dice score of 0.7298 and recall score of 0.7071. Besides, we also build a simplified D2A U-Net without pretrained encoder to provide a fair comparison with other models trained from scratch, which still outperforms popular U-Net family models with a Dice score of 0.7047 and recall score of 0.6626. Our experiment results have shown that by introducing dilated convolution and dual attention mechanism, the number of false positives is significantly reduced, which improves sensitivity to COVID-19 lesions and subsequently brings significant increase to Dice score.

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arXiv2020

Transmission electron microscopy of organic-inorganic hybrid perovskites: myths and truths

Organic-inorganic hybrid perovskites (OIHPs) have attracted extensive research interest as a promising candidate for efficient and inexpensive solar cells. Transmission electron microscopy characterizations that can benefit the fundamental understanding and the degradation mechanism are widely used for these materials. However, their sensitivity to the electron beam illumination and hence structural instabilities usually prevent us from obtaining the intrinsic information or even lead to significant artifacts. Here, we systematacially investigate the structural degradation behaviors under different experimental factors to reveal the optimized conditions for TEM characterizations of OIHPs by using low-dose electron diffraction and imaging techniques. We find that a low temperature does not slow down the beam damage but instead induces a rapid amorphization for OIHPs. Moreover, a less severe damage is observed at a higher accelerating voltage. The beam-sensitivity is found to be facet-dependent that a (100) exposed MAPbI3 surface is more stable than (001) surface. With these guidance, we successfully acquire the atomic structure of pristine MAPbI3 and identify the characterization window that is very narrow. These findings are helpful to guide future electron microscopy characterization of these beam-sensitive materials, which are also useful for finding strategies to improve the stability and the performance of the perovskite solar cells.

physics.app-ph↗