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"cancer detection": models, code, and papers

Lung Cancer Lesion Detection in Histopathology Images Using Graph-Based Sparse PCA Network

Oct 27, 2021
Sundaresh Ram, Wenfei Tang, Alexander J. Bell, Cara Spencer, Alexander Buschhaus, Charles R. Hatt, Marina Pasca diMagliano, Jeffrey J. Rodriguez, Stefanie Galban, Craig J. Galban

Early detection of lung cancer is critical for improvement of patient survival. To address the clinical need for efficacious treatments, genetically engineered mouse models (GEMM) have become integral in identifying and evaluating the molecular underpinnings of this complex disease that may be exploited as therapeutic targets. Assessment of GEMM tumor burden on histopathological sections performed by manual inspection is both time consuming and prone to subjective bias. Therefore, an interplay of needs and challenges exists for computer-aided diagnostic tools, for accurate and efficient analysis of these histopathology images. In this paper, we propose a simple machine learning approach called the graph-based sparse principal component analysis (GS-PCA) network, for automated detection of cancerous lesions on histological lung slides stained by hematoxylin and eosin (H&E). Our method comprises four steps: 1) cascaded graph-based sparse PCA, 2) PCA binary hashing, 3) block-wise histograms, and 4) support vector machine (SVM) classification. In our proposed architecture, graph-based sparse PCA is employed to learn the filter banks of the multiple stages of a convolutional network. This is followed by PCA hashing and block histograms for indexing and pooling. The meaningful features extracted from this GS-PCA are then fed to an SVM classifier. We evaluate the performance of the proposed algorithm on H&E slides obtained from an inducible K-rasG12D lung cancer mouse model using precision/recall rates, F-score, Tanimoto coefficient, and area under the curve (AUC) of the receiver operator characteristic (ROC) and show that our algorithm is efficient and provides improved detection accuracy compared to existing algorithms.

* 10 pages, 9 figures, 3 tables 
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Multispectral Spatial Characterization: Application to Mitosis Detection in Breast Cancer Histopathology

Apr 15, 2013
H. Irshad, A. Gouaillard, L. Roux, D. Racoceanu

Accurate detection of mitosis plays a critical role in breast cancer histopathology. Manual detection and counting of mitosis is tedious and subject to considerable inter- and intra-reader variations. Multispectral imaging is a recent medical imaging technology, proven successful in increasing the segmentation accuracy in other fields. This study aims at improving the accuracy of mitosis detection by developing a specific solution using multispectral and multifocal imaging of breast cancer histopathological data. We propose to enable clinical routine-compliant quality of mitosis discrimination from other objects. The proposed framework includes comprehensive analysis of spectral bands and z-stack focus planes, detection of expected mitotic regions (candidates) in selected focus planes and spectral bands, computation of multispectral spatial features for each candidate, selection of multispectral spatial features and a study of different state-of-the-art classification methods for candidates classification as mitotic or non mitotic figures. This framework has been evaluated on MITOS multispectral medical dataset and achieved 60% detection rate and 57% F-Measure. Our results indicate that multispectral spatial features have more information for mitosis classification in comparison with white spectral band features, being therefore a very promising exploration area to improve the quality of the diagnosis assistance in histopathology.

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MS-GWNN:multi-scale graph wavelet neural network for breast cancer diagnosis

Dec 29, 2020
Mo Zhang, Quanzheng Li

Breast cancer is one of the most common cancers in women worldwide, and early detection can significantly reduce the mortality rate of breast cancer. It is crucial to take multi-scale information of tissue structure into account in the detection of breast cancer. And thus, it is the key to design an accurate computer-aided detection (CAD) system to capture multi-scale contextual features in a cancerous tissue. In this work, we present a novel graph convolutional neural network for histopathological image classification of breast cancer. The new method, named multi-scale graph wavelet neural network (MS-GWNN), leverages the localization property of spectral graph wavelet to perform multi-scale analysis. By aggregating features at different scales, MS-GWNN can encode the multi-scale contextual interactions in the whole pathological slide. Experimental results on two public datasets demonstrate the superiority of the proposed method. Moreover, through ablation studies, we find that multi-scale analysis has a significant impact on the accuracy of cancer diagnosis.

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MHSnet: Multi-head and Spatial Attention Network with False-Positive Reduction for Pulmonary Nodules Detection

Feb 16, 2022
Juanyun Mai, Minghao Wang, Jiayin Zheng, Yanbo Shao, Zhaoqi Diao, Xinliang Fu, Yulong Chen, Jianyu Xiao, Jian You, Airu Yin, Yang Yang, Xiangcheng Qiu, Jinsheng Tao, Bo Wang, Hua Ji

The mortality of lung cancer has ranked high among cancers for many years. Early detection of lung cancer is critical for disease prevention, cure, and mortality rate reduction. However, existing detection methods on pulmonary nodules introduce an excessive number of false positive proposals in order to achieve high sensitivity, which is not practical in clinical situations. In this paper, we propose the multi-head detection and spatial squeeze-and-attention network, MHSnet, to detect pulmonary nodules, in order to aid doctors in the early diagnosis of lung cancers. Specifically, we first introduce multi-head detectors and skip connections to customize for the variety of nodules in sizes, shapes and types and capture multi-scale features. Then, we implement a spatial attention module to enable the network to focus on different regions differently inspired by how experienced clinicians screen CT images, which results in fewer false positive proposals. Lastly, we present a lightweight but effective false positive reduction module with the Linear Regression model to cut down the number of false positive proposals, without any constraints on the front network. Extensive experimental results compared with the state-of-the-art models have shown the superiority of the MHSnet in terms of the average FROC, sensitivity and especially false discovery rate (2.98% and 2.18% improvement in terms of average FROC and sensitivity, 5.62% and 28.33% decrease in terms of false discovery rate and average candidates per scan). The false positive reduction module significantly decreases the average number of candidates generated per scan by 68.11% and the false discovery rate by 13.48%, which is promising to reduce distracted proposals for the downstream tasks based on the detection results.

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Hyper-Heuristic Algorithm for Finding Efficient Features in Diagnose of Lung Cancer Disease

Jan 24, 2016
Mitra Montazeri, Mahdieh Soleymani Baghshah, Ahmad Enhesari

Background: Lung cancer was known as primary cancers and the survival rate of cancer is about 15%. Early detection of lung cancer is the leading factor in survival rate. All symptoms (features) of lung cancer do not appear until the cancer spreads to other areas. It needs an accurate early detection of lung cancer, for increasing the survival rate. For accurate detection, it need characterizes efficient features and delete redundancy features among all features. Feature selection is the problem of selecting informative features among all features. Materials and Methods: Lung cancer database consist of 32 patient records with 57 features. This database collected by Hong and Youngand indexed in the University of California Irvine repository. Experimental contents include the extracted from the clinical data and X-ray data, etc. The data described 3 types of pathological lung cancers and all features are taking an integer value 0-3. In our study, new method is proposed for identify efficient features of lung cancer. It is based on Hyper-Heuristic. Results: We obtained an accuracy of 80.63% using reduced 11 feature set. The proposed method compare to the accuracy of 5 machine learning feature selections. The accuracy of these 5 methods are 60.94, 57.81, 68.75, 60.94 and 68.75. Conclusions: The proposed method has better performance with the highest level of accuracy. Therefore, the proposed model is recommended for identifying an efficient symptom of Disease. These finding are very important in health research, particularly in allocation of medical resources for patients who predicted as high-risks

* J. Basic Appl. Sci. Res, 2013. 3(10): p. 134-140 
* Published in the Journal of Basic and Applied Scientific Research, 2013 
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A Smartphone based Application for Skin Cancer Classification Using Deep Learning with Clinical Images and Lesion Information

Apr 28, 2021
Breno Krohling, Pedro B. C. Castro, Andre G. C. Pacheco, Renato A. Krohling

Over the last decades, the incidence of skin cancer, melanoma and non-melanoma, has increased at a continuous rate. In particular for melanoma, the deadliest type of skin cancer, early detection is important to increase patient prognosis. Recently, deep neural networks (DNNs) have become viable to deal with skin cancer detection. In this work, we present a smartphone-based application to assist on skin cancer detection. This application is based on a Convolutional Neural Network(CNN) trained on clinical images and patients demographics, both collected from smartphones. Also, as skin cancer datasets are imbalanced, we present an approach, based on the mutation operator of Differential Evolution (DE) algorithm, to balance data. In this sense, beyond provides a flexible tool to assist doctors on skin cancer screening phase, the method obtains promising results with a balanced accuracy of 85% and a recall of 96%.

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Robust breast cancer detection in mammography and digital breast tomosynthesis using annotation-efficient deep learning approach

Dec 27, 2019
William Lotter, Abdul Rahman Diab, Bryan Haslam, Jiye G. Kim, Giorgia Grisot, Eric Wu, Kevin Wu, Jorge Onieva Onieva, Jerrold L. Boxerman, Meiyun Wang, Mack Bandler, Gopal Vijayaraghavan, A. Gregory Sorensen

Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.

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Out of distribution detection for skin and malaria images

Nov 02, 2021
Muhammad Zaida, Shafaqat Ali, Mohsen Ali, Sarfaraz Hussein, Asma Saadia, Waqas Sultani

Deep neural networks have shown promising results in disease detection and classification using medical image data. However, they still suffer from the challenges of handling real-world scenarios especially reliably detecting out-of-distribution (OoD) samples. We propose an approach to robustly classify OoD samples in skin and malaria images without the need to access labeled OoD samples during training. Specifically, we use metric learning along with logistic regression to force the deep networks to learn much rich class representative features. To guide the learning process against the OoD examples, we generate ID similar-looking examples by either removing class-specific salient regions in the image or permuting image parts and distancing them away from in-distribution samples. During inference time, the K-reciprocal nearest neighbor is employed to detect out-of-distribution samples. For skin cancer OoD detection, we employ two standard benchmark skin cancer ISIC datasets as ID, and six different datasets with varying difficulty levels were taken as out of distribution. For malaria OoD detection, we use the BBBC041 malaria dataset as ID and five different challenging datasets as out of distribution. We achieved state-of-the-art results, improving 5% and 4% in [email protected]% over the previous state-of-the-art for skin cancer and malaria OoD detection respectively.

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