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"cancer detection": models, code, and papers

Multi-resolution Super Learner for Voxel-wise Classification of Prostate Cancer Using Multi-parametric MRI

Jul 02, 2020
Jin Jin, Lin Zhang, Ethan Leng, Gregory J. Metzger, Joseph S. Koopmeiners

While current research has shown the importance of Multi-parametric MRI (mpMRI) in diagnosing prostate cancer (PCa), further investigation is needed for how to incorporate the specific structures of the mpMRI data, such as the regional heterogeneity and between-voxel correlation within a subject. This paper proposes a machine learning-based method for improved voxel-wise PCa classification by taking into account the unique structures of the data. We propose a multi-resolution modeling approach to account for regional heterogeneity, where base learners trained locally at multiple resolutions are combined using the super learner, and account for between-voxel correlation by efficient spatial Gaussian kernel smoothing. The method is flexible in that the super learner framework allows implementation of any classifier as the base learner, and can be easily extended to classifying cancer into more sub-categories. We describe detailed classification algorithm for the binary PCa status, as well as the ordinal clinical significance of PCa for which a weighted likelihood approach is implemented to enhance the detection of the less prevalent cancer categories. We illustrate the advantages of the proposed approach over conventional modeling and machine learning approaches through simulations and application to in vivo data.

* 23 pages, 3 figures, 5 tables 
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Computer-aided Tumor Diagnosis in Automated Breast Ultrasound using 3D Detection Network

Jul 31, 2020
Junxiong Yu, Chaoyu Chen, Xin Yang, Yi Wang, Dan Yan, Jianxing Zhang, Dong Ni

Automated breast ultrasound (ABUS) is a new and promising imaging modality for breast cancer detection and diagnosis, which could provide intuitive 3D information and coronal plane information with great diagnostic value. However, manually screening and diagnosing tumors from ABUS images is very time-consuming and overlooks of abnormalities may happen. In this study, we propose a novel two-stage 3D detection network for locating suspected lesion areas and further classifying lesions as benign or malignant tumors. Specifically, we propose a 3D detection network rather than frequently-used segmentation network to locate lesions in ABUS images, thus our network can make full use of the spatial context information in ABUS images. A novel similarity loss is designed to effectively distinguish lesions from background. Then a classification network is employed to identify the located lesions as benign or malignant. An IoU-balanced classification loss is adopted to improve the correlation between classification and localization task. The efficacy of our network is verified from a collected dataset of 418 patients with 145 benign tumors and 273 malignant tumors. Experiments show our network attains a sensitivity of 97.66% with 1.23 false positives (FPs), and has an area under the curve(AUC) value of 0.8720.

* Early Accepted by MICCAI 2020 
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Automated Pulmonary Nodule Detection via 3D ConvNets with Online Sample Filtering and Hybrid-Loss Residual Learning

Aug 13, 2017
Qi Dou, Hao Chen, Yueming Jin, Huangjing Lin, Jing Qin, Pheng-Ann Heng

In this paper, we propose a novel framework with 3D convolutional networks (ConvNets) for automated detection of pulmonary nodules from low-dose CT scans, which is a challenging yet crucial task for lung cancer early diagnosis and treatment. Different from previous standard ConvNets, we try to tackle the severe hard/easy sample imbalance problem in medical datasets and explore the benefits of localized annotations to regularize the learning, and hence boost the performance of ConvNets to achieve more accurate detections. Our proposed framework consists of two stages: 1) candidate screening, and 2) false positive reduction. In the first stage, we establish a 3D fully convolutional network, effectively trained with an online sample filtering scheme, to sensitively and rapidly screen the nodule candidates. In the second stage, we design a hybrid-loss residual network which harnesses the location and size information as important cues to guide the nodule recognition procedure. Experimental results on the public large-scale LUNA16 dataset demonstrate superior performance of our proposed method compared with state-of-the-art approaches for the pulmonary nodule detection task.

* Accepted to MICCAI 2017 
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Skin Cancer Segmentation and Classification with NABLA-N and Inception Recurrent Residual Convolutional Networks

Apr 25, 2019
Md Zahangir Alom, Theus Aspiras, Tarek M. Taha, Vijayan K. Asari

In the last few years, Deep Learning (DL) has been showing superior performance in different modalities of biomedical image analysis. Several DL architectures have been proposed for classification, segmentation, and detection tasks in medical imaging and computational pathology. In this paper, we propose a new DL architecture, the NABLA-N network, with better feature fusion techniques in decoding units for dermoscopic image segmentation tasks. The NABLA-N network has several advances for segmentation tasks. First, this model ensures better feature representation for semantic segmentation with a combination of low to high-level feature maps. Second, this network shows better quantitative and qualitative results with the same or fewer network parameters compared to other methods. In addition, the Inception Recurrent Residual Convolutional Neural Network (IRRCNN) model is used for skin cancer classification. The proposed NABLA-N network and IRRCNN models are evaluated for skin cancer segmentation and classification on the benchmark datasets from the International Skin Imaging Collaboration 2018 (ISIC-2018). The experimental results show superior performance on segmentation tasks compared to the Recurrent Residual U-Net (R2U-Net). The classification model shows around 87% testing accuracy for dermoscopic skin cancer classification on ISIC2018 dataset.

* 7 pages, 7 figures, 2 Tables 
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AI-based Carcinoma Detection and Classification Using Histopathological Images: A Systematic Review

Jan 18, 2022
Swathi Prabhua, Keerthana Prasada, Antonio Robels-Kelly, Xuequan Lu

Histopathological image analysis is the gold standard to diagnose cancer. Carcinoma is a subtype of cancer that constitutes more than 80% of all cancer cases. Squamous cell carcinoma and adenocarcinoma are two major subtypes of carcinoma, diagnosed by microscopic study of biopsy slides. However, manual microscopic evaluation is a subjective and time-consuming process. Many researchers have reported methods to automate carcinoma detection and classification. The increasing use of artificial intelligence (AI) in the automation of carcinoma diagnosis also reveals a significant rise in the use of deep network models. In this systematic literature review, we present a comprehensive review of the state-of-the-art approaches reported in carcinoma diagnosis using histopathological images. Studies are selected from well-known databases with strict inclusion/exclusion criteria. We have categorized the articles and recapitulated their methods based on specific organs of carcinoma origin. Further, we have summarized pertinent literature on AI methods, highlighted critical challenges and limitations, and provided insights on future research direction in automated carcinoma diagnosis. Out of 101 articles selected, most of the studies experimented on private datasets with varied image sizes, obtaining accuracy between 63% and 100%. Overall, this review highlights the need for a generalized AI-based carcinoma diagnostic system. Additionally, it is desirable to have accountable approaches to extract microscopic features from images of multiple magnifications that should mimic pathologists' evaluations.

* accepted to Computers in Biology and Medicine 
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A Quantitative Comparison between Shannon and Tsallis Havrda Charvat Entropies Applied to Cancer Outcome Prediction

Mar 22, 2022
Thibaud Brochet, Jérôme Lapuyade-Lahorgue, Pierre Vera, Su Ruan

In this paper, we propose to quantitatively compare loss functions based on parameterized Tsallis-Havrda-Charvat entropy and classical Shannon entropy for the training of a deep network in the case of small datasets which are usually encountered in medical applications. Shannon cross-entropy is widely used as a loss function for most neural networks applied to the segmentation, classification and detection of images. Shannon entropy is a particular case of Tsallis-Havrda-Charvat entropy. In this work, we compare these two entropies through a medical application for predicting recurrence in patients with head-neck and lung cancers after treatment. Based on both CT images and patient information, a multitask deep neural network is proposed to perform a recurrence prediction task using cross-entropy as a loss function and an image reconstruction task. Tsallis-Havrda-Charvat cross-entropy is a parameterized cross entropy with the parameter $\alpha$. Shannon entropy is a particular case of Tsallis-Havrda-Charvat entropy for $\alpha$ = 1. The influence of this parameter on the final prediction results is studied. In this paper, the experiments are conducted on two datasets including in total 580 patients, of whom 434 suffered from head-neck cancers and 146 from lung cancers. The results show that Tsallis-Havrda-Charvat entropy can achieve better performance in terms of prediction accuracy with some values of $\alpha$.

* Entropy 2022, 24(4), 436; 
* 11 pages, 3 figures 
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Automatic Mass Detection in Breast Using Deep Convolutional Neural Network and SVM Classifier

Jul 09, 2019
Md. Kamrul Hasan, Tajwar Abrar Aleef

Mammography is the most widely used gold standard for screening breast cancer, where, mass detection is considered as the prominent step. Detecting mass in the breast is, however, an arduous problem as they usually have large variations between them in terms of shape, size, boundary, and texture. In this literature, the process of mass detection is automated with the use of transfer learning techniques of Deep Convolutional Neural Networks (DCNN). Pre-trained VGG19 network is used to extract features which are then followed by bagged decision tree for features selection and then a Support Vector Machine (SVM) classifier is trained and used for classifying between the mass and non-mass. Area Under ROC Curve (AUC) is chosen as the performance metric, which is then maximized during classifier selection and hyper-parameter tuning. The robustness of the two selected type of classifiers, C-SVM, and \u{psion}-SVM, are investigated with extensive experiments before selecting the best performing classifier. All experiments in this paper were conducted using the INbreast dataset. The best AUC obtained from the experimental results is 0.994 +/- 0.003 i.e. [0.991, 0.997]. Our results conclude that by using pre-trained VGG19 network, high-level distinctive features can be extracted from Mammograms which when used with the proposed SVM classifier is able to robustly distinguish between the mass and non-mass present in breast.

* 11 pages 
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Skincure: An Innovative Smart Phone-Based Application To Assist In Melanoma Early Detection And Prevention

Jan 06, 2015
Omar Abuzaghleh, Miad Faezipour, Buket D. Barkana

Melanoma spreads through metastasis, and therefore it has been proven to be very fatal. Statistical evidence has revealed that the majority of deaths resulting from skin cancer are as a result of melanoma. Further investigations have shown that the survival rates in patients depend on the stage of the infection; early detection and intervention of melanoma implicates higher chances of cure. Clinical diagnosis and prognosis of melanoma is challenging since the processes are prone to misdiagnosis and inaccuracies due to doctors subjectivity. This paper proposes an innovative and fully functional smart-phone based application to assist in melanoma early detection and prevention. The application has two major components; the first component is a real-time alert to help users prevent skin burn caused by sunlight; a novel equation to compute the time for skin to burn is thereby introduced. The second component is an automated image analysis module which contains image acquisition, hair detection and exclusion, lesion segmentation, feature extraction, and classification. The proposed system exploits PH2 Dermoscopy image database from Pedro Hispano Hospital for development and testing purposes. The image database contains a total of 200 dermoscopy images of lesions, including normal, atypical, and melanoma cases. The experimental results show that the proposed system is efficient, achieving classification of the normal, atypical and melanoma images with accuracy of 96.3%, 95.7% and 97.5%, respectively.

* appears in Signal & Image Processing : An International Journal (SIPIJ) Vol.5, No.6, December 2014 
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SFCN-OPI: Detection and Fine-grained Classification of Nuclei Using Sibling FCN with Objectness Prior Interaction

Dec 22, 2017
Yanning Zhou, Qi Dou, Hao Chen, Jing Qin, Pheng-Ann Heng

Cell nuclei detection and fine-grained classification have been fundamental yet challenging problems in histopathology image analysis. Due to the nuclei tiny size, significant inter-/intra-class variances, as well as the inferior image quality, previous automated methods would easily suffer from limited accuracy and robustness. In the meanwhile, existing approaches usually deal with these two tasks independently, which would neglect the close relatedness of them. In this paper, we present a novel method of sibling fully convolutional network with prior objectness interaction (called SFCN-OPI) to tackle the two tasks simultaneously and interactively using a unified end-to-end framework. Specifically, the sibling FCN branches share features in earlier layers while holding respective higher layers for specific tasks. More importantly, the detection branch outputs the objectness prior which dynamically interacts with the fine-grained classification sibling branch during the training and testing processes. With this mechanism, the fine-grained classification successfully focuses on regions with high confidence of nuclei existence and outputs the conditional probability, which in turn benefits the detection through back propagation. Extensive experiments on colon cancer histology images have validated the effectiveness of our proposed SFCN-OPI and our method has outperformed the state-of-the-art methods by a large margin.

* Accepted at AAAI 2018 
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Deep learning-based detection of intravenous contrast in computed tomography scans

Oct 19, 2021
Zezhong Ye, Jack M. Qian, Ahmed Hosny, Roman Zeleznik, Deborah Plana, Jirapat Likitlersuang, Zhongyi Zhang, Raymond H. Mak, Hugo J. W. L. Aerts, Benjamin H. Kann

Purpose: Identifying intravenous (IV) contrast use within CT scans is a key component of data curation for model development and testing. Currently, IV contrast is poorly documented in imaging metadata and necessitates manual correction and annotation by clinician experts, presenting a major barrier to imaging analyses and algorithm deployment. We sought to develop and validate a convolutional neural network (CNN)-based deep learning (DL) platform to identify IV contrast within CT scans. Methods: For model development and evaluation, we used independent datasets of CT scans of head, neck (HN) and lung cancer patients, totaling 133,480 axial 2D scan slices from 1,979 CT scans manually annotated for contrast presence by clinical experts. Five different DL models were adopted and trained in HN training datasets for slice-level contrast detection. Model performances were evaluated on a hold-out set and on an independent validation set from another institution. DL models was then fine-tuned on chest CT data and externally validated on a separate chest CT dataset. Results: Initial DICOM metadata tags for IV contrast were missing or erroneous in 1,496 scans (75.6%). The EfficientNetB4-based model showed the best overall detection performance. For HN scans, AUC was 0.996 in the internal validation set (n = 216) and 1.0 in the external validation set (n = 595). The fine-tuned model on chest CTs yielded an AUC: 1.0 for the internal validation set (n = 53), and AUC: 0.980 for the external validation set (n = 402). Conclusion: The DL model could accurately detect IV contrast in both HN and chest CT scans with near-perfect performance.

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