arXiv subjects

Yunlu Feng

Publications and source records attributed to Yunlu Feng.

6 recordsLinked to original sources

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

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.

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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.

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