2022-03-29 更新
Deep ensembles in bioimage segmentation
Authors:Loris Nanni, Daniela Cuza, Alessandra Lumini, Andrea Loreggia, Sheryl Brahnam
Semantic segmentation consists in classifying each pixel of an image by assigning it to a specific label chosen from a set of all the available ones. During the last few years, a lot of attention shifted to this kind of task. Many computer vision researchers tried to apply autoencoder structures to develop models that can learn the semantics of the image as well as a low-level representation of it. In an autoencoder architecture, given an input, an encoder computes a low dimensional representation of the input that is then used by a decoder to reconstruct the original data. In this work, we propose an ensemble of convolutional neural networks (CNNs). In ensemble methods, many different models are trained and then used for classification, the ensemble aggregates the outputs of the single classifiers. The approach leverages on differences of various classifiers to improve the performance of the whole system. Diversity among the single classifiers is enforced by using different loss functions. In particular, we present a new loss function that results from the combination of Dice and Structural Similarity Index. The proposed ensemble is implemented by combining different backbone networks using the DeepLabV3+ and HarDNet environment. The proposal is evaluated through an extensive empirical evaluation on two real-world scenarios: polyp and skin segmentation. All the code is available online at https://github.com/LorisNanni.
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Colorectal Polyp Classification from White-light Colonoscopy Images via Domain Alignment
Authors:Qin Wang, Hui Che, Weizhen Ding, Li Xiang, Guanbin Li, Zhen Li, Shuguang Cui
Differentiation of colorectal polyps is an important clinical examination. A computer-aided diagnosis system is required to assist accurate diagnosis from colonoscopy images. Most previous studies at-tempt to develop models for polyp differentiation using Narrow-Band Imaging (NBI) or other enhanced images. However, the wide range of these models’ applications for clinical work has been limited by the lagging of imaging techniques. Thus, we propose a novel framework based on a teacher-student architecture for the accurate colorectal polyp classification (CPC) through directly using white-light (WL) colonoscopy images in the examination. In practice, during training, the auxiliary NBI images are utilized to train a teacher network and guide the student network to acquire richer feature representation from WL images. The feature transfer is realized by domain alignment and contrastive learning. Eventually the final student network has the ability to extract aligned features from only WL images to facilitate the CPC task. Besides, we release the first public-available paired CPC dataset containing WL-NBI pairs for the alignment training. Quantitative and qualitative evaluation indicates that the proposed method outperforms the previous methods in CPC, improving the accuracy by 5.6%with very fast speed.
PDF Accepted in MICCAI-21
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A Comparative Study on Polyp Classification using Convolutional Neural Networks
Authors:Krushi Patel, Kaidong Li, Ke Tao, Quan Wang, Ajay Bansal, Amit Rastogi, Guanghui Wang
Colorectal cancer is the third most common cancer diagnosed in both men and women in the United States. Most colorectal cancers start as a growth on the inner lining of the colon or rectum, called ‘polyp’. Not all polyps are cancerous, but some can develop into cancer. Early detection and recognition of the type of polyps is critical to prevent cancer and change outcomes. However, visual classification of polyps is challenging due to varying illumination conditions of endoscopy, variant texture, appearance, and overlapping morphology between polyps. More importantly, evaluation of polyp patterns by gastroenterologists is subjective leading to a poor agreement among observers. Deep convolutional neural networks have proven very successful in object classification across various object categories. In this work, we compare the performance of the state-of-the-art general object classification models for polyp classification. We trained a total of six CNN models end-to-end using a dataset of 157 video sequences composed of two types of polyps: hyperplastic and adenomatous. Our results demonstrate that the state-of-the-art CNN models can successfully classify polyps with an accuracy comparable or better than reported among gastroenterologists. The results of this study can guide future research in polyp classification.
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Colonoscopy Polyp Detection and Classification: Dataset Creation and Comparative Evaluations
Authors:Kaidong Li, Mohammad I. Fathan, Krushi Patel, Tianxiao Zhang, Cuncong Zhong, Ajay Bansal, Amit Rastogi, Jean S. Wang, Guanghui Wang
Colorectal cancer (CRC) is one of the most common types of cancer with a high mortality rate. Colonoscopy is the preferred procedure for CRC screening and has proven to be effective in reducing CRC mortality. Thus, a reliable computer-aided polyp detection and classification system can significantly increase the effectiveness of colonoscopy. In this paper, we create an endoscopic dataset collected from various sources and annotate the ground truth of polyp location and classification results with the help of experienced gastroenterologists. The dataset can serve as a benchmark platform to train and evaluate the machine learning models for polyp classification. We have also compared the performance of eight state-of-the-art deep learning-based object detection models. The results demonstrate that deep CNN models are promising in CRC screening. This work can serve as a baseline for future research in polyp detection and classification.
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HarDNet-MSEG: A Simple Encoder-Decoder Polyp Segmentation Neural Network that Achieves over 0.9 Mean Dice and 86 FPS
Authors:Chien-Hsiang Huang, Hung-Yu Wu, Youn-Long Lin
We propose a new convolution neural network called HarDNet-MSEG for polyp segmentation. It achieves SOTA in both accuracy and inference speed on five popular datasets. For Kvasir-SEG, HarDNet-MSEG delivers 0.904 mean Dice running at 86.7 FPS on a GeForce RTX 2080 Ti GPU. It consists of a backbone and a decoder. The backbone is a low memory traffic CNN called HarDNet68, which has been successfully applied to various CV tasks including image classification, object detection, multi-object tracking and semantic segmentation, etc. The decoder part is inspired by the Cascaded Partial Decoder, known for fast and accurate salient object detection. We have evaluated HarDNet-MSEG using those five popular datasets. The code and all experiment details are available at Github. https://github.com/james128333/HarDNet-MSEG
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