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"cancer detection": models, code, and papers

ESFPNet: efficient deep learning architecture for real-time lesion segmentation in autofluorescence bronchoscopic video

Jul 15, 2022
Qi Chang, Danish Ahmad, Jennifer Toth, Rebecca Bascom, William E. Higgins

Lung cancer tends to be detected at an advanced stage, resulting in a high patient mortality rate. Thus, recent research has focused on early disease detection. Lung cancer generally first appears as lesions developing within the bronchial epithelium of the airway walls. Bronchoscopy is the procedure of choice for effective noninvasive bronchial lesion detection. In particular, autofluorescence bronchoscopy (AFB) discriminates the autofluorescence properties of normal and diseased tissue, whereby lesions appear reddish brown in AFB video frames, while normal tissue appears green. Because recent studies show AFB's ability for high lesion sensitivity, it has become a potentially pivotal method during the standard bronchoscopic airway exam for early-stage lung cancer detection. Unfortunately, manual inspection of AFB video is extremely tedious and error-prone, while limited effort has been expended toward potentially more robust automatic AFB lesion detection and segmentation. We propose a real-time deep learning architecture ESFPNet for robust detection and segmentation of bronchial lesions from an AFB video stream. The architecture features an encoder structure that exploits pretrained Mix Transformer (MiT) encoders and a stage-wise feature pyramid (ESFP) decoder structure. Results from AFB videos derived from lung cancer patient airway exams indicate that our approach gives mean Dice index and IOU values of 0.782 and 0.658, respectively, while having a processing throughput of 27 frames/sec. These values are superior to results achieved by other competing architectures that use Mix transformers or CNN-based encoders. Moreover, the superior performance on the ETIS-LaribPolypDB dataset demonstrates its potential applicability to other domains.

* Summary to SPIE 2023 

Semi-supervised multi-task learning for lung cancer diagnosis

May 04, 2018
Naji Khosravan, Ulas Bagci

Early detection of lung nodules is of great importance in lung cancer screening. Existing research recognizes the critical role played by CAD systems in early detection and diagnosis of lung nodules. However, many CAD systems, which are used as cancer detection tools, produce a lot of false positives (FP) and require a further FP reduction step. Furthermore, guidelines for early diagnosis and treatment of lung cancer are consist of different shape and volume measurements of abnormalities. Segmentation is at the heart of our understanding of nodules morphology making it a major area of interest within the field of computer aided diagnosis systems. This study set out to test the hypothesis that joint learning of false positive (FP) nodule reduction and nodule segmentation can improve the computer aided diagnosis (CAD) systems' performance on both tasks. To support this hypothesis we propose a 3D deep multi-task CNN to tackle these two problems jointly. We tested our system on LUNA16 dataset and achieved an average dice similarity coefficient (DSC) of 91% as segmentation accuracy and a score of nearly 92% for FP reduction. As a proof of our hypothesis, we showed improvements of segmentation and FP reduction tasks over two baselines. Our results support that joint training of these two tasks through a multi-task learning approach improves system performance on both. We also showed that a semi-supervised approach can be used to overcome the limitation of lack of labeled data for the 3D segmentation task.

* Accepted for publication at IEEE EMBC (40th International Engineering in Medicine and Biology Conference) 

Two-Stage Convolutional Neural Network Architecture for Lung Nodule Detection

May 09, 2019
Haichao Cao, Hong Liu, Enmin Song, Guangzhi Ma, Xiangyang Xu, Renchao Jin, Tengying Liu, Chih-Cheng Hung

Early detection of lung cancer is an effective way to improve the survival rate of patients. It is a critical step to have accurate detection of lung nodules in computed tomography (CT) images for the diagnosis of lung cancer. However, due to the heterogeneity of the lung nodules and the complexity of the surrounding environment, robust nodule detection has been a challenging task. In this study, we propose a two-stage convolutional neural network (TSCNN) architecture for lung nodule detection. The CNN architecture in the first stage is based on the improved UNet segmentation network to establish an initial detection of lung nodules. Simultaneously, in order to obtain a high recall rate without introducing excessive false positive nodules, we propose a novel sampling strategy, and use the offline hard mining idea for training and prediction according to the proposed cascaded prediction method. The CNN architecture in the second stage is based on the proposed dual pooling structure, which is built into three 3D CNN classification networks for false positive reduction. Since the network training requires a significant amount of training data, we adopt a data augmentation method based on random mask. Furthermore, we have improved the generalization ability of the false positive reduction model by means of ensemble learning. The proposed method has been experimentally verified on the LUNA dataset. Experimental results show that the proposed TSCNN architecture can obtain competitive detection performance.

* 29 pages, 10 figures 

Detection and classification of masses in mammographic images in a multi-kernel approach

Dec 20, 2017
Sidney Marlon Lopes de Lima, Abel Guilhermino da Silva Filho, Wellington Pinheiro dos Santos

According to the World Health Organization, breast cancer is the main cause of cancer death among adult women in the world. Although breast cancer occurs indiscriminately in countries with several degrees of social and economic development, among developing and underdevelopment countries mortality rates are still high, due to low availability of early detection technologies. From the clinical point of view, mammography is still the most effective diagnostic technology, given the wide diffusion of the use and interpretation of these images. Herein this work we propose a method to detect and classify mammographic lesions using the regions of interest of images. Our proposal consists in decomposing each image using multi-resolution wavelets. Zernike moments are extracted from each wavelet component. Using this approach we can combine both texture and shape features, which can be applied both to the detection and classification of mammary lesions. We used 355 images of fatty breast tissue of IRMA database, with 233 normal instances (no lesion), 72 benign, and 83 malignant cases. Classification was performed by using SVM and ELM networks with modified kernels, in order to optimize accuracy rates, reaching 94.11%. Considering both accuracy rates and training times, we defined the ration between average percentage accuracy and average training time in a reverse order. Our proposal was 50 times higher than the ratio obtained using the best method of the state-of-the-art. As our proposed model can combine high accuracy rate with low learning time, whenever a new data is received, our work will be able to save a lot of time, hours, in learning process in relation to the best method of the state-of-the-art.

* Computer Methods and Programs in Biomedicine, 134 (2016), 11-29 

Deep Learning-Based Automatic Detection of Poorly Positioned Mammograms to Minimize Patient Return Visits for Repeat Imaging: A Real-World Application

Sep 28, 2020
Vikash Gupta, Clayton Taylor, Sarah Bonnet, Luciano M. Prevedello, Jeffrey Hawley, Richard D White, Mona G Flores, Barbaros Selnur Erdal

Screening mammograms are a routine imaging exam performed to detect breast cancer in its early stages to reduce morbidity and mortality attributed to this disease. In order to maximize the efficacy of breast cancer screening programs, proper mammographic positioning is paramount. Proper positioning ensures adequate visualization of breast tissue and is necessary for effective breast cancer detection. Therefore, breast-imaging radiologists must assess each mammogram for the adequacy of positioning before providing a final interpretation of the examination; this often necessitates return patient visits for additional imaging. In this paper, we propose a deep learning-algorithm method that mimics and automates this decision-making process to identify poorly positioned mammograms. Our objective for this algorithm is to assist mammography technologists in recognizing inadequately positioned mammograms real-time, improve the quality of mammographic positioning and performance, and ultimately reducing repeat visits for patients with initially inadequate imaging. The proposed model showed a true positive rate for detecting correct positioning of 91.35% in the mediolateral oblique view and 95.11% in the craniocaudal view. In addition to these results, we also present an automatically generated report which can aid the mammography technologist in taking corrective measures during the patient visit.

* 12 pages, 13 figures, pre-print 

Deep Learning Based Analysis of Prostate Cancer from MP-MRI

Jun 02, 2021
Pedro C. Neto

The diagnosis of prostate cancer faces a problem with overdiagnosis that leads to damaging side effects due to unnecessary treatment. Research has shown that the use of multi-parametric magnetic resonance images to conduct biopsies can drastically help to mitigate the overdiagnosis, thus reducing the side effects on healthy patients. This study aims to investigate the use of deep learning techniques to explore computer-aid diagnosis based on MRI as input. Several diagnosis problems ranging from classification of lesions as being clinically significant or not to the detection and segmentation of lesions are addressed with deep learning based approaches. This thesis tackled two main problems regarding the diagnosis of prostate cancer. Firstly, XmasNet was used to conduct two large experiments on the classification of lesions. Secondly, detection and segmentation experiments were conducted, first on the prostate and afterward on the prostate cancer lesions. The former experiments explored the lesions through a two-dimensional space, while the latter explored models to work with three-dimensional inputs. For this task, the 3D models explored were the 3D U-Net and a pretrained 3D ResNet-18. A rigorous analysis of all these problems was conducted with a total of two networks, two cropping techniques, two resampling techniques, two crop sizes, five input sizes and data augmentations experimented for lesion classification. While for segmentation two models, two input sizes and data augmentations were experimented. However, while the binary classification of the clinical significance of lesions and the detection and segmentation of the prostate already achieve the desired results (0.870 AUC and 0.915 dice score respectively), the classification of the PIRADS score and the segmentation of lesions still have a large margin to improve (0.664 accuracy and 0.690 dice score respectively).


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 

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.


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 

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