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"cancer detection": models, code, and papers

Lung cancer screening with low-dose CT scans using a deep learning approach

Jun 01, 2019
Jason L. Causey, Yuanfang Guan, Wei Dong, Karl Walker, Jake A. Qualls, Fred Prior, Xiuzhen Huang

Lung cancer is the leading cause of cancer deaths. Early detection through low-dose computed tomography (CT) screening has been shown to significantly reduce mortality but suffers from a high false positive rate that leads to unnecessary diagnostic procedures. Quantitative image analysis coupled to deep learning techniques has the potential to reduce this false positive rate. We conducted a computational analysis of 1449 low-dose CT studies drawn from the National Lung Screening Trial (NLST) cohort. We applied to this cohort our newly developed algorithm, DeepScreener, which is based on a novel deep learning approach. The algorithm, after the training process using about 3000 CT studies, does not require lung nodule annotations to conduct cancer prediction. The algorithm uses consecutive slices and multi-task features to determine whether a nodule is likely to be cancer, and a spatial pyramid to detect nodules at different scales. We find that the algorithm can predict a patient's cancer status from a volumetric lung CT image with high accuracy (78.2%, with area under the Receiver Operating Characteristic curve (AUC) of 0.858). Our preliminary framework ranked 16th of 1972 teams (top 1%) in the Data Science Bowl 2017 (DSB2017) competition, based on the challenge datasets. We report here the application of DeepScreener on an independent NLST test set. This study indicates that the deep learning approach has the potential to significantly reduce the false positive rate in lung cancer screening with low-dose CT scans.

* 6 figures 
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Deep Learning Methods for Lung Cancer Segmentation in Whole-slide Histopathology Images -- the [email protected] Challenge 2019

Aug 21, 2020
Zhang Li, Jiehua Zhang, Tao Tan, Xichao Teng, Xiaoliang Sun, Yang Li, Lihong Liu, Yang Xiao, Byungjae Lee, Yilong Li, Qianni Zhang, Shujiao Sun, Yushan Zheng, Junyu Yan, Ni Li, Yiyu Hong, Junsu Ko, Hyun Jung, Yanling Liu, Yu-cheng Chen, Ching-wei Wang, Vladimir Yurovskiy, Pavel Maevskikh, Vahid Khanagha, Yi Jiang, Xiangjun Feng, Zhihong Liu, Daiqiang Li, Peter J. Schüffler, Qifeng Yu, Hui Chen, Yuling Tang, Geert Litjens

Accurate segmentation of lung cancer in pathology slides is a critical step in improving patient care. We proposed the [email protected] (Automatic Cancer Detection and Classification in Whole-slide Lung Histopathology) challenge for evaluating different computer-aided diagnosis (CADs) methods on the automatic diagnosis of lung cancer. The [email protected] 2019 focused on segmentation (pixel-wise detection) of cancer tissue in whole slide imaging (WSI), using an annotated dataset of 150 training images and 50 test images from 200 patients. This paper reviews this challenge and summarizes the top 10 submitted methods for lung cancer segmentation. All methods were evaluated using the false positive rate, false negative rate, and DICE coefficient (DC). The DC ranged from 0.7354$\pm$0.1149 to 0.8372$\pm$0.0858. The DC of the best method was close to the inter-observer agreement (0.8398$\pm$0.0890). All methods were based on deep learning and categorized into two groups: multi-model method and single model method. In general, multi-model methods were significantly better ($\textit{p}$<$0.01$) than single model methods, with mean DC of 0.7966 and 0.7544, respectively. Deep learning based methods could potentially help pathologists find suspicious regions for further analysis of lung cancer in WSI.

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Multi-scale Deep Learning Architecture for Nucleus Detection in Renal Cell Carcinoma Microscopy Image

Apr 28, 2021
Shiba Kuanar, Vassilis Athitsos, Dwarikanath Mahapatra, Anand Rajan

Clear cell renal cell carcinoma (ccRCC) is one of the most common forms of intratumoral heterogeneity in the study of renal cancer. ccRCC originates from the epithelial lining of proximal convoluted renal tubules. These cells undergo abnormal mutations in the presence of Ki67 protein and create a lump-like structure through cell proliferation. Manual counting of tumor cells in the tissue-affected sections is one of the strongest prognostic markers for renal cancer. However, this procedure is time-consuming and also prone to subjectivity. These assessments are based on the physical cell appearance and suffer wide intra-observer variations. Therefore, better cell nucleus detection and counting techniques can be an important biomarker for the assessment of tumor cell proliferation in routine pathological investigations. In this paper, we introduce a deep learning-based detection model for cell classification on IHC stained histology images. These images are classified into binary classes to find the presence of Ki67 protein in cancer-affected nucleus regions. Our model maps the multi-scale pyramid features and saliency information from local bounded regions and predicts the bounding box coordinates through regression. Our method validates the impact of Ki67 expression across a cohort of four hundred histology images treated with localized ccRCC and compares our results with the existing state-of-the-art nucleus detection methods. The precision and recall scores of the proposed method are computed and compared on the clinical data sets. The experimental results demonstrate that our model improves the F1 score up to 86.3% and an average area under the Precision-Recall curve as 85.73%.

* 13 pages, 10 figures, 3 tables 
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Artificial Neural Network Based Breast Cancer Screening: A Comprehensive Review

May 29, 2020
Subrato Bharati, Prajoy Podder, M. Rubaiyat Hossain Mondal

Breast cancer is a common fatal disease for women. Early diagnosis and detection is necessary in order to improve the prognosis of breast cancer affected people. For predicting breast cancer, several automated systems are already developed using different medical imaging modalities. This paper provides a systematic review of the literature on artificial neural network (ANN) based models for the diagnosis of breast cancer via mammography. The advantages and limitations of different ANN models including spiking neural network (SNN), deep belief network (DBN), convolutional neural network (CNN), multilayer neural network (MLNN), stacked autoencoders (SAE), and stacked de-noising autoencoders (SDAE) are described in this review. The review also shows that the studies related to breast cancer detection applied different deep learning models to a number of publicly available datasets. For comparing the performance of the models, different metrics such as accuracy, precision, recall, etc. were used in the existing studies. It is found that the best performance was achieved by residual neural network (ResNet)-50 and ResNet-101 models of CNN algorithm.

* International Journal of Computer Information Systems and Industrial Management Applications (ISSN 2150-7988), Volume 12 (2020), pp. 125-137 
* 13 pages, 8 figures 
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Deep Learning for Automated Medical Image Analysis

Mar 12, 2019
Wentao Zhu

Medical imaging is an essential tool in many areas of medical applications, used for both diagnosis and treatment. However, reading medical images and making diagnosis or treatment recommendations require specially trained medical specialists. The current practice of reading medical images is labor-intensive, time-consuming, costly, and error-prone. It would be more desirable to have a computer-aided system that can automatically make diagnosis and treatment recommendations. Recent advances in deep learning enable us to rethink the ways of clinician diagnosis based on medical images. In this thesis, we will introduce 1) mammograms for detecting breast cancers, the most frequently diagnosed solid cancer for U.S. women, 2) lung CT images for detecting lung cancers, the most frequently diagnosed malignant cancer, and 3) head and neck CT images for automated delineation of organs at risk in radiotherapy. First, we will show how to employ the adversarial concept to generate the hard examples improving mammogram mass segmentation. Second, we will demonstrate how to use the weakly labeled data for the mammogram breast cancer diagnosis by efficiently design deep learning for multi-instance learning. Third, the thesis will walk through DeepLung system which combines deep 3D ConvNets and GBM for automated lung nodule detection and classification. Fourth, we will show how to use weakly labeled data to improve existing lung nodule detection system by integrating deep learning with a probabilistic graphic model. Lastly, we will demonstrate the AnatomyNet which is thousands of times faster and more accurate than previous methods on automated anatomy segmentation.

* PhD Thesis 
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Microscopic Nuclei Classification, Segmentation and Detection with improved Deep Convolutional Neural Network (DCNN) Approaches

Nov 08, 2018
Md Zahangir Alom, Chris Yakopcic, Tarek M. Taha, Vijayan K. Asari

Due to cellular heterogeneity, cell nuclei classification, segmentation, and detection from pathological images are challenging tasks. In the last few years, Deep Convolutional Neural Networks (DCNN) approaches have been shown state-of-the-art (SOTA) performance on histopathological imaging in different studies. In this work, we have proposed different advanced DCNN models and evaluated for nuclei classification, segmentation, and detection. First, the Densely Connected Recurrent Convolutional Network (DCRN) model is used for nuclei classification. Second, Recurrent Residual U-Net (R2U-Net) is applied for nuclei segmentation. Third, the R2U-Net regression model which is named UD-Net is used for nuclei detection from pathological images. The experiments are conducted with different datasets including Routine Colon Cancer(RCC) classification and detection dataset, and Nuclei Segmentation Challenge 2018 dataset. The experimental results show that the proposed DCNN models provide superior performance compared to the existing approaches for nuclei classification, segmentation, and detection tasks. The results are evaluated with different performance metrics including precision, recall, Dice Coefficient (DC), Means Squared Errors (MSE), F1-score, and overall accuracy. We have achieved around 3.4% and 4.5% better F-1 score for nuclei classification and detection tasks compared to recently published DCNN based method. In addition, R2U-Net shows around 92.15% testing accuracy in term of DC. These improved methods will help for pathological practices for better quantitative analysis of nuclei in Whole Slide Images(WSI) which ultimately will help for better understanding of different types of cancer in clinical workflow.

* 18 pages, 16 figures, 3 Tables 
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No Surprises: Training Robust Lung Nodule Detection for Low-Dose CT Scans by Augmenting with Adversarial Attacks

Mar 08, 2020
Siqi Liu, Arnaud Arindra Adiyoso Setio, Florin C. Ghesu, Eli Gibson, Sasa Grbic, Bogdan Georgescu, Dorin Comaniciu

Detecting malignant pulmonary nodules at an early stage can allow medical interventions which increases the survival rate of lung cancer patients. Using computer vision techniques to detect nodules can improve the sensitivity and the speed of interpreting chest CT for lung cancer screening. Many studies have used CNNs to detect nodule candidates. Though such approaches have been shown to outperform the conventional image processing based methods regarding the detection accuracy, CNNs are also known to be limited to generalize on under-represented samples in the training set and prone to imperceptible noise perturbations. Such limitations can not be easily addressed by scaling up the dataset or the models. In this work, we propose to add adversarial synthetic nodules and adversarial attack samples to the training data to improve the generalization and the robustness of the lung nodule detection systems. In order to generate hard examples of nodules from a differentiable nodule synthesizer, we use projected gradient descent (PGD) to search the latent code within a bounded neighbourhood that would generate nodules to decrease the detector response. To make the network more robust to unanticipated noise perturbations, we use PGD to search for noise patterns that can trigger the network to give over-confident mistakes. By evaluating on two different benchmark datasets containing consensus annotations from three radiologists, we show that the proposed techniques can improve the detection performance on real CT data. To understand the limitations of both the conventional networks and the proposed augmented networks, we also perform stress-tests on the false positive reduction networks by feeding different types of artificially produced patches. We show that the augmented networks are more robust to both under-represented nodules as well as resistant to noise perturbations.

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DenseNet approach to segmentation and classification of dermatoscopic skin lesions images

Oct 09, 2021
Reza Zare, Arash Pourkazemi

At present, cancer is one of the most important health issues in the world. Because early detection and appropriate treatment in cancer are very effective in the recovery and survival of patients, image processing as a diagnostic tool can help doctors to diagnose in the first recognition of cancer. One of the most important steps in diagnosing a skin lesion is to automatically detect the border of the skin image because the accuracy of the next steps depends on it. If these subtleties are identified, they can have a great impact on the diagnosis of the disease. Therefore, there is a good opportunity to develop more accurate algorithms to analyze such images. This paper proposes an improved method for segmentation and classification for skin lesions using two architectures, the U-Net for image segmentation and the DenseNet121 for image classification which have excellent accuracy. We tested the segmentation architecture of our model on the ISIC-2018 dataset and the classification on the HAM10000 dataset. Our results show that the combination of U-Net and DenseNet121 architectures provides acceptable results in dermatoscopic image analysis compared to previous research. Another classification examined in this study is cancerous and non-cancerous samples. In this classification, cancerous and non-cancerous samples were detected in DenseNet121 network with 79.49% and 93.11% accuracy respectively.

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An Overview of Melanoma Detection in Dermoscopy Images Using Image Processing and Machine Learning

Jan 28, 2016
Nabin K. Mishra, M. Emre Celebi

The incidence of malignant melanoma continues to increase worldwide. This cancer can strike at any age; it is one of the leading causes of loss of life in young persons. Since this cancer is visible on the skin, it is potentially detectable at a very early stage when it is curable. New developments have converged to make fully automatic early melanoma detection a real possibility. First, the advent of dermoscopy has enabled a dramatic boost in clinical diagnostic ability to the point that melanoma can be detected in the clinic at the very earliest stages. The global adoption of this technology has allowed accumulation of large collections of dermoscopy images of melanomas and benign lesions validated by histopathology. The development of advanced technologies in the areas of image processing and machine learning have given us the ability to allow distinction of malignant melanoma from the many benign mimics that require no biopsy. These new technologies should allow not only earlier detection of melanoma, but also reduction of the large number of needless and costly biopsy procedures. Although some of the new systems reported for these technologies have shown promise in preliminary trials, widespread implementation must await further technical progress in accuracy and reproducibility. In this paper, we provide an overview of computerized detection of melanoma in dermoscopy images. First, we discuss the various aspects of lesion segmentation. Then, we provide a brief overview of clinical feature segmentation. Finally, we discuss the classification stage where machine learning algorithms are applied to the attributes generated from the segmented features to predict the existence of melanoma.

* 15 pages, 3 figures 
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Multiple Myeloma Cancer Cell Instance Segmentation

Sep 19, 2021
Dikshant Sagar

Images remain the largest data source in the field of healthcare. But at the same time, they are the most difficult to analyze. More than often, these images are analyzed by human experts such as pathologists and physicians. But due to considerable variation in pathology and the potential fatigue of human experts, an automated solution is much needed. The recent advancement in Deep learning could help us achieve an efficient and economical solution for the same. In this research project, we focus on developing a Deep Learning-based solution for detecting Multiple Myeloma cancer cells using an Object Detection and Instance Segmentation System. We explore multiple existing solutions and architectures for the task of Object Detection and Instance Segmentation and try to leverage them and come up with a novel architecture to achieve comparable and competitive performance on the required task. To train our model to detect and segment Multiple Myeloma cancer cells, we utilize a dataset curated by us using microscopic images of cell slides provided by Dr.Ritu Gupta(Prof., Dept. of Oncology AIIMS).

* B.Tech Thesis Paper 
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