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"cancer detection": models, code, and papers

MIXCAPS: A Capsule Network-based Mixture of Experts for Lung Nodule Malignancy Prediction

Aug 13, 2020
Parnian Afshar, Farnoosh Naderkhani, Anastasia Oikonomou, Moezedin Javad Rafiee, Arash Mohammadi, Konstantinos N. Plataniotis

Lung diseases including infections such as Pneumonia, Tuberculosis, and novel Coronavirus (COVID-19), together with Lung Cancer are significantly widespread and are, typically, considered life threatening. In particular, lung cancer is among the most common and deadliest cancers with a low 5-year survival rate. Timely diagnosis of lung cancer is, therefore, of paramount importance as it can save countless lives. In this regard, deep learning radiomics solutions have the promise of extracting the most useful features on their own in an end-to-end fashion without having access to the annotated boundaries. Among different deep learning models, Capsule Networks are proposed to overcome shortcomings of the Convolutional Neural Networks (CNN) such as their inability to recognize detailed spatial relations. Capsule networks have so far shown satisfying performance in medical imaging problems. Capitalizing on their success, in this study, we propose a novel capsule network-based mixture of experts, referred to as the MIXCAPS. The proposed MIXCAPS architecture takes advantage of not only the capsule network's capabilities to handle small datasets, but also automatically splitting dataset through a convolutional gating network. MIXCAPS enables capsule network experts to specialize on different subsets of the data. Our results show that MIXCAPS outperforms a single capsule network and a mixture of CNNs, with an accuracy of 92.88%, sensitivity of 93.2%, specificity of 92.3% and area under the curve of 0.963. Our experiments also show that there is a relation between the gate outputs and a couple of hand-crafted features, illustrating explainable nature of the proposed MIXCAPS. To further evaluate generalization capabilities of the proposed MIXCAPS architecture, additional experiments on a brain tumor dataset are performed showing potentials of MIXCAPS for detection of tumors related to other organs.


A Pragmatic Machine Learning Approach to Quantify Tumor Infiltrating Lymphocytes in Whole Slide Images

Feb 14, 2022
Nikita Shvetsov, Morten Grønnesby, Edvard Pedersen, Kajsa Møllersen, Lill-Tove Rasmussen Busund, Ruth Schwienbacher, Lars Ailo Bongo, Thomas K. Kilvaer

Increased levels of tumor infiltrating lymphocytes (TILs) in cancer tissue indicate favourable outcomes in many types of cancer. Manual quantification of immune cells is inaccurate and time consuming for pathologists. Our aim is to leverage a computational solution to automatically quantify TILs in whole slide images (WSIs) of standard diagnostic haematoxylin and eosin stained sections (H&E slides) from lung cancer patients. Our approach is to transfer an open source machine learning method for segmentation and classification of nuclei in H&E slides trained on public data to TIL quantification without manual labeling of our data. Our results show that additional augmentation improves model transferability when training on few samples/limited tissue types. Models trained with sufficient samples/tissue types do not benefit from our additional augmentation policy. Further, the resulting TIL quantification correlates to patient prognosis and compares favorably to the current state-of-the-art method for immune cell detection in non-small lung cancer (current standard CD8 cells in DAB stained TMAs HR 0.34 95% CI 0.17-0.68 vs TILs in HE WSIs: HoVer-Net PanNuke Aug Model HR 0.30 95% CI 0.15-0.60, HoVer-Net MoNuSAC Aug model HR 0.27 95% CI 0.14-0.53). Moreover, we implemented a cloud based system to train, deploy and visually inspect machine learning based annotation for H&E slides. Our pragmatic approach bridges the gap between machine learning research, translational clinical research and clinical implementation. However, validation in prospective studies is needed to assert that the method works in a clinical setting.

* 19 pages, 5 figures, 2 tables, 11 supplementary pages 

Towards Automatic Detection of Misinformation in Online Medical Videos

Sep 04, 2019
Rui Hou, VerĂłnica PĂ©rez-Rosas, Stacy Loeb, Rada Mihalcea

Recent years have witnessed a significant increase in the online sharing of medical information, with videos representing a large fraction of such online sources. Previous studies have however shown that more than half of the health-related videos on platforms such as YouTube contain misleading information and biases. Hence, it is crucial to build computational tools that can help evaluate the quality of these videos so that users can obtain accurate information to help inform their decisions. In this study, we focus on the automatic detection of misinformation in YouTube videos. We select prostate cancer videos as our entry point to tackle this problem. The contribution of this paper is twofold. First, we introduce a new dataset consisting of 250 videos related to prostate cancer manually annotated for misinformation. Second, we explore the use of linguistic, acoustic, and user engagement features for the development of classification models to identify misinformation. Using a series of ablation experiments, we show that we can build automatic models with accuracies of up to 74%, corresponding to a 76.5% precision and 73.2% recall for misinformative instances.


Nanorobot queue: Cooperative treatment of cancer based on team member communication and image processing

Nov 23, 2021
Xinyu Zhou

Although nanorobots have been used as clinical prescriptions for work such as gastroscopy, and even photoacoustic tomography technology has been proposed to control nanorobots to deliver drugs at designated delivery points in real time, and there are cases of eliminating "superbacteria" in blood through nanorobots, most technologies are immature, either with low efficiency or low accuracy, Either it can not be mass produced, so the most effective way to treat cancer diseases at this stage is through chemotherapy and radiotherapy. Patients are suffering and can not be cured. Therefore, this paper proposes an ideal model of a treatment method that can completely cure cancer, a cooperative treatment method based on nano robot queue through team member communication and computer vision image classification (target detection).

* 9pages,4figures 

Quantifying the Scanner-Induced Domain Gap in Mitosis Detection

Mar 30, 2021
Marc Aubreville, Christof Bertram, Mitko Veta, Robert Klopfleisch, Nikolas Stathonikos, Katharina Breininger, Natalie ter Hoeve, Francesco Ciompi, Andreas Maier

Automated detection of mitotic figures in histopathology images has seen vast improvements, thanks to modern deep learning-based pipelines. Application of these methods, however, is in practice limited by strong variability of images between labs. This results in a domain shift of the images, which causes a performance drop of the models. Hypothesizing that the scanner device plays a decisive role in this effect, we evaluated the susceptibility of a standard mitosis detection approach to the domain shift introduced by using a different whole slide scanner. Our work is based on the MICCAI-MIDOG challenge 2021 data set, which includes 200 tumor cases of human breast cancer and four scanners. Our work indicates that the domain shift induced not by biochemical variability but purely by the choice of acquisition device is underestimated so far. Models trained on images of the same scanner yielded an average F1 score of 0.683, while models trained on a single other scanner only yielded an average F1 score of 0.325. Training on another multi-domain mitosis dataset led to mean F1 scores of 0.52. We found this not to be reflected by domain-shifts measured as proxy A distance-derived metric.

* 3 pages, 1 figure, 1 table, submitted as short paper to MIDL 

Neural Networks for Infectious Diseases Detection: Prospects and Challenges

Dec 07, 2021
Muhammad Azeem, Shumaila Javaid, Hamza Fahim, Nasir Saeed

Artificial neural network (ANN) ability to learn, correct errors, and transform a large amount of raw data into useful medical decisions for treatment and care have increased its popularity for enhanced patient safety and quality of care. Therefore, this paper reviews the critical role of ANNs in providing valuable insights for patients' healthcare decisions and efficient disease diagnosis. We thoroughly review different types of ANNs presented in the existing literature that advanced ANNs adaptation for complex applications. Moreover, we also investigate ANN's advances for various disease diagnoses and treatments such as viral, skin, cancer, and COVID-19. Furthermore, we propose a novel deep Convolutional Neural Network (CNN) model called ConXNet for improving the detection accuracy of COVID-19 disease. ConXNet is trained and tested using different datasets, and it achieves more than 97% detection accuracy and precision, which is significantly better than existing models. Finally, we highlight future research directions and challenges such as complexity of the algorithms, insufficient available data, privacy and security, and integration of biosensing with ANNs. These research directions require considerable attention for improving the scope of ANNs for medical diagnostic and treatment applications.

* Submitted to IEEE/ACM Transactions on Computational Biology and Bioinformatics 

Intelligent Sight and Sound: A Chronic Cancer Pain Dataset

Apr 07, 2022
Catherine Ordun, Alexandra N. Cha, Edward Raff, Byron Gaskin, Alex Hanson, Mason Rule, Sanjay Purushotham, James L. Gulley

Cancer patients experience high rates of chronic pain throughout the treatment process. Assessing pain for this patient population is a vital component of psychological and functional well-being, as it can cause a rapid deterioration of quality of life. Existing work in facial pain detection often have deficiencies in labeling or methodology that prevent them from being clinically relevant. This paper introduces the first chronic cancer pain dataset, collected as part of the Intelligent Sight and Sound (ISS) clinical trial, guided by clinicians to help ensure that model findings yield clinically relevant results. The data collected to date consists of 29 patients, 509 smartphone videos, 189,999 frames, and self-reported affective and activity pain scores adopted from the Brief Pain Inventory (BPI). Using static images and multi-modal data to predict self-reported pain levels, early models show significant gaps between current methods available to predict pain today, with room for improvement. Due to the especially sensitive nature of the inherent Personally Identifiable Information (PII) of facial images, the dataset will be released under the guidance and control of the National Institutes of Health (NIH).

* Published as conference paper at the 35th Conference on Neural Information Processing Systems (NeurIPS 2021) Track on Datasets and Benchmarks 

Skin Cancer Diagnostics with an All-Inclusive Smartphone Application

May 25, 2022
Upender Kalwa, Christopher Legner, Taejoon Kong, Santosh Pandey

Among the different types of skin cancer, melanoma is considered to be the deadliest and is difficult to treat at advanced stages. Detection of melanoma at earlier stages can lead to reduced mortality rates. Desktop-based computer-aided systems have been developed to assist dermatologists with early diagnosis. However, there is significant interest in developing portable, at-home melanoma diagnostic systems which can assess the risk of cancerous skin lesions. Here, we present a smartphone application that combines image capture capabilities with preprocessing and segmentation to extract the Asymmetry, Border irregularity, Color variegation, and Diameter (ABCD) features of a skin lesion. Using the feature sets, classification of malignancy is achieved through support vector machine classifiers. By using adaptive algorithms in the individual data-processing stages, our approach is made computationally light, user friendly, and reliable in discriminating melanoma cases from benign ones. Images of skin lesions are either captured with the smartphone camera or imported from public datasets. The entire process from image capture to classification runs on an Android smartphone equipped with a detachable 10x lens, and processes an image in less than a second. The overall performance metrics are evaluated on a public database of 200 images with Synthetic Minority Over-sampling Technique (SMOTE) (80% sensitivity, 90% specificity, 88% accuracy, and 0.85 area under curve (AUC)) and without SMOTE (55% sensitivity, 95% specificity, 90% accuracy, and 0.75 AUC). The evaluated performance metrics and computation times are comparable or better than previous methods. This all-inclusive smartphone application is designed to be easy-to-download and easy-to-navigate for the end user, which is imperative for the eventual democratization of such medical diagnostic systems.

* Symmetry 2019 

Abnormality Detection in Mammography using Deep Convolutional Neural Networks

Mar 05, 2018
Pengcheng Xi, Chang Shu, Rafik Goubran

Breast cancer is the most common cancer in women worldwide. The most common screening technology is mammography. To reduce the cost and workload of radiologists, we propose a computer aided detection approach for classifying and localizing calcifications and masses in mammogram images. To improve on conventional approaches, we apply deep convolutional neural networks (CNN) for automatic feature learning and classifier building. In computer-aided mammography, deep CNN classifiers cannot be trained directly on full mammogram images because of the loss of image details from resizing at input layers. Instead, our classifiers are trained on labelled image patches and then adapted to work on full mammogram images for localizing the abnormalities. State-of-the-art deep convolutional neural networks are compared on their performance of classifying the abnormalities. Experimental results indicate that VGGNet receives the best overall accuracy at 92.53\% in classifications. For localizing abnormalities, ResNet is selected for computing class activation maps because it is ready to be deployed without structural change or further training. Our approach demonstrates that deep convolutional neural network classifiers have remarkable localization capabilities despite no supervision on the location of abnormalities is provided.

* 6 pages