Cats or CAT scans: transfer learning from natural or medical image source datasets?

Transfer learning is a widely used strategy in medical image analysis. Instead of only training a network with a limited amount of data from the target task of interest, we can first train the network with other, potentially larger source datasets, creating a more robust model. The source datasets do not have to be related to the target task. For a classification task in lung CT images, we could use both head CT images, or images of cats, as the source. While head CT images appear more similar to lung CT images, the number and diversity of cat images might lead to a better model overall. In this survey we review a number of papers that have performed similar comparisons. Although the answer to which strategy is best seems to be "it depends", we discuss a number of research directions we need to take as a community, to gain more understanding of this topic.Comment: Accepted to Current Opinion in Biomedical Engineerin

A comparative study on polyp classification using convolutional neural networks

This work is licensed under a Creative Commons Attribution 4.0 International License.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.University of Kansas grant (2228901

Classification of Colorectal Cancer Polyps via Transfer Learning and Vision-Based Tactile Sensing

In this study, to address the current high earlydetection miss rate of colorectal cancer (CRC) polyps, we explore the potentials of utilizing transfer learning and machine learning (ML) classifiers to precisely and sensitively classify the type of CRC polyps. Instead of using the common colonoscopic images, we applied three different ML algorithms on the 3D textural image outputs of a unique vision-based surface tactile sensor (VS-TS). To collect realistic textural images of CRC polyps for training the utilized ML classifiers and evaluating their performance, we first designed and additively manufactured 48 types of realistic polyp phantoms with different hardness, type, and textures. Next, the performance of the used three ML algorithms in classifying the type of fabricated polyps was quantitatively evaluated using various statistical metrics.Comment: Accepted to IEEE Sensors 2022 Conferenc

Artificial intelligence and computer-aided diagnosis in colonoscopy: current evidence and future directions

Computer-aided diagnosis offers a promising solution to reduce variation in colonoscopy performance. Pooled miss rates for polyps are as high as 22%, and associated interval colorectal cancers after colonoscopy are of concern. Optical biopsy, whereby in-vivo classification of polyps based on enhanced imaging replaces histopathology, has not been incorporated into routine practice because it is limited by interobserver variability and generally only meets accepted standards in expert settings. Real-time decision-support software has been developed to detect and characterise polyps, and also to offer feedback on the technical quality of inspection. Some of the current algorithms, particularly with recent advances in artificial intelligence techniques, match human expert performance for optical biopsy. In this Review, we summarise the evidence for clinical applications of computer-aided diagnosis and artificial intelligence in colonoscopy

Supervised cnn strategies for optical image segmentation and classification in interventional medicine

The analysis of interventional images is a topic of high interest for the medical-image analysis community. Such an analysis may provide interventional-medicine professionals with both decision support and context awareness, with the final goal of improving patient safety. The aim of this chapter is to give an overview of some of the most recent approaches (up to 2018) in the field, with a focus on Convolutional Neural Networks (CNNs) for both segmentation and classification tasks. For each approach, summary tables are presented reporting the used dataset, involved anatomical region and achieved performance. Benefits and disadvantages of each approach are highlighted and discussed. Available datasets for algorithm training and testing and commonly used performance metrics are summarized to offer a source of information for researchers that are approaching the field of interventional-image analysis. The advancements in deep learning for medical-image analysis are involving more and more the interventional-medicine field. However, these advancements are undeniably slower than in other fields (e.g. preoperative-image analysis) and considerable work still needs to be done in order to provide clinicians with all possible support during interventional-medicine procedures

Rethinking the transfer learning for FCN based polyp segmentation in colonoscopy

Besides the complex nature of colonoscopy frames with intrinsic frame formation artefacts such as light reflections and the diversity of polyp types/shapes, the publicly available polyp segmentation training datasets are limited, small and imbalanced. In this case, the automated polyp segmentation using a deep neural network remains an open challenge due to the overfitting of training on small datasets. We proposed a simple yet effective polyp segmentation pipeline that couples the segmentation (FCN) and classification (CNN) tasks. We find the effectiveness of interactive weight transfer between dense and coarse vision tasks that mitigates the overfitting in learning. And It motivates us to design a new training scheme within our segmentation pipeline. Our method is evaluated on CVC-EndoSceneStill and Kvasir-SEG datasets. It achieves 4.34% and 5.70% Polyp-IoU improvements compared to the state-of-the-art methods on the EndoSceneStill and Kvasir-SEG datasets, respectively.Comment: 11 pages, 10 figures, submit versio

Machine Learning/Deep Learning in Medical Image Processing

Many recent studies on medical image processing have involved the use of machine learning (ML) and deep learning (DL). This special issue, “Machine Learning/Deep Learning in Medical Image Processing”, has been launched to provide an opportunity for researchers in the area of medical image processing to highlight recent developments made in their fields with ML/DL. Seven excellent papers that cover a wide variety of medical/clinical aspects are selected in this special issue

Deep learning to find colorectal polyps in colonoscopy: A systematic literature review

Colorectal cancer has a great incidence rate worldwide, but its early detection significantly increases the survival rate. Colonoscopy is the gold standard procedure for diagnosis and removal of colorectal lesions with potential to evolve into cancer and computer-aided detection systems can help gastroenterologists to increase the adenoma detection rate, one of the main indicators for colonoscopy quality and predictor for colorectal cancer prevention. The recent success of deep learning approaches in computer vision has also reached this field and has boosted the number of proposed methods for polyp detection, localization and segmentation. Through a systematic search, 35 works have been retrieved. The current systematic review provides an analysis of these methods, stating advantages and disadvantages for the different categories used; comments seven publicly available datasets of colonoscopy images; analyses the metrics used for reporting and identifies future challenges and recommendations. Convolutional neural networks are the most used architecture together with an important presence of data augmentation strategies, mainly based on image transformations and the use of patches. End-to-end methods are preferred over hybrid methods, with a rising tendency. As for detection and localization tasks, the most used metric for reporting is the recall, while Intersection over Union is highly used in segmentation. One of the major concerns is the difficulty for a fair comparison and reproducibility of methods. Even despite the organization of challenges, there is still a need for a common validation framework based on a large, annotated and publicly available database, which also includes the most convenient metrics to report results. Finally, it is also important to highlight that efforts should be focused in the future on proving the clinical value of the deep learning based methods, by increasing the adenoma detection rate.This work was partially supported by PICCOLO project. This project has received funding from the European Union's Horizon2020 Research and Innovation Programme under grant agreement No. 732111. The sole responsibility of this publication lies with the author. The European Union is not responsible for any use that may be made of the information contained therein. The authors would also like to thank Dr. Federico Soria for his support on this manuscript and Dr. José Carlos Marín, from Hospital 12 de Octubre, and Dr. Ángel Calderón and Dr. Francisco Polo, from Hospital de Basurto, for the images in Fig. 4