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"cancer detection": models, code, and papers

Two-Dimensional ARMA Modeling for Breast Cancer Detection and Classification

Jun 19, 2009
Nidhal Bouaynaya, Jerzy Zielinski, Dan Schonfeld

We propose a new model-based computer-aided diagnosis (CAD) system for tumor detection and classification (cancerous v.s. benign) in breast images. Specifically, we show that (x-ray, ultrasound and MRI) images can be accurately modeled by two-dimensional autoregressive-moving average (ARMA) random fields. We derive a two-stage Yule-Walker Least-Squares estimates of the model parameters, which are subsequently used as the basis for statistical inference and biophysical interpretation of the breast image. We use a k-means classifier to segment the breast image into three regions: healthy tissue, benign tumor, and cancerous tumor. Our simulation results on ultrasound breast images illustrate the power of the proposed approach.

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Deep Learning and Conditional Random Fields-based Depth Estimation and Topographical Reconstruction from Conventional Endoscopy

Nov 27, 2017
Faisal Mahmood, Nicholas J. Durr

Colorectal cancer is the fourth leading cause of cancer deaths worldwide and the second leading cause in the United States. The risk of colorectal cancer can be mitigated by the identification and removal of premalignant lesions through optical colonoscopy. Unfortunately, conventional colonoscopy misses more than 20% of the polyps that should be removed, due in part to poor contrast of lesion topography. Imaging tissue topography during a colonoscopy is difficult because of the size constraints of the endoscope and the deforming mucosa. Most existing methods make geometric assumptions or incorporate a priori information, which limits accuracy and sensitivity. In this paper, we present a method that avoids these restrictions, using a joint deep convolutional neural network-conditional random field (CNN-CRF) framework. Estimated depth is used to reconstruct the topography of the surface of the colon from a single image. We train the unary and pairwise potential functions of a CRF in a CNN on synthetic data, generated by developing an endoscope camera model and rendering over 100,000 images of an anatomically-realistic colon. We validate our approach with real endoscopy images from a porcine colon, transferred to a synthetic-like domain, with ground truth from registered computed tomography measurements. The CNN-CRF approach estimates depths with a relative error of 0.152 for synthetic endoscopy images and 0.242 for real endoscopy images. We show that the estimated depth maps can be used for reconstructing the topography of the mucosa from conventional colonoscopy images. This approach can easily be integrated into existing endoscopy systems and provides a foundation for improving computer-aided detection algorithms for detection, segmentation and classification of lesions.

* 10 pages, 10 figures 
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Disease Detection from Lung X-ray Images based on Hybrid Deep Learning

Mar 02, 2020
Subrato Bharati, Prajoy Podder

Lung Disease can be considered as the second most common type of disease for men and women. Many people die of lung disease such as lung cancer, Asthma, CPD (Chronic pulmonary disease) etc. in every year. Early detection of lung cancer can lessen the probability of deaths. In this paper, a chest X ray image dataset has been used in order to diagnosis properly and analysis the lung disease. For binary classification, some important is selected. The criteria include precision, recall, F beta score and accuracy. The fusion of AI and cancer diagnosis are acquiring huge interest as a cancer diagnostic tool. In recent days, deep learning based AI for example Convolutional neural network (CNN) can be successfully applied for disease classification and prediction. This paper mainly focuses the performance of Vanilla neural network, CNN, fusion of CNN and Visual Geometry group based neural network (VGG), fusion of CNN, VGG, STN and finally Capsule network. Normally basic CNN has poor performance for rotated, tilted or other abnormal image orientation. As a result, hybrid systems have been exhibited in order to enhance the accuracy with the maintenance of less training time. All models have been implemented in two groups of data sets: full dataset and sample dataset. Therefore, a comparative analysis has been developed in this paper. Some visualization of the attributes of the dataset has also been showed in this paper

* 20 figures 
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Epithelium segmentation using deep learning in H&E-stained prostate specimens with immunohistochemistry as reference standard

Aug 17, 2018
Wouter Bulten, Péter Bándi, Jeffrey Hoven, Rob van de Loo, Johannes Lotz, Nick Weiss, Jeroen van der Laak, Bram van Ginneken, Christina Hulsbergen-van de Kaa, Geert Litjens

Prostate cancer (PCa) is graded by pathologists by examining the architectural pattern of cancerous epithelial tissue on hematoxylin and eosin (H&E) stained slides. Given the importance of gland morphology, automatically differentiating between glandular epithelial tissue and other tissues is an important prerequisite for the development of automated methods for detecting PCa. We propose a new method, using deep learning, for automatically segmenting epithelial tissue in digitized prostatectomy slides. We employed immunohistochemistry (IHC) to render the ground truth less subjective and more precise compared to manual outlining on H&E slides, especially in areas with high-grade and poorly differentiated PCa. Our dataset consisted of 102 tissue blocks, including both low and high grade PCa. From each block a single new section was cut, stained with H&E, scanned, restained using P63 and CK8/18 to highlight the epithelial structure, and scanned again. The H&E slides were co-registered to the IHC slides. On a subset of the IHC slides we applied color deconvolution, corrected stain errors manually, and trained a U-Net to perform segmentation of epithelial structures. Whole-slide segmentation masks generated by the IHC U-Net were used to train a second U-Net on H&E. Our system makes precise cell-level segmentations and segments both intact glands as well as individual (tumor) epithelial cells. We achieved an F1-score of 0.895 on a hold-out test set and 0.827 on an external reference set from a different center. We envision this segmentation as being the first part of a fully automated prostate cancer detection and grading pipeline.

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Automated image segmentation for detecting cell spreading for metastasizing assessments of cancer development

Jan 01, 2018
Sholpan Kauanova, Ivan Vorobjev, Alex Pappachen James

The automated segmentation of cells in microscopic images is an open research problem that has important implications for studies of the developmental and cancer processes based on in vitro models. In this paper, we present the approach for segmentation of the DIC images of cultured cells using G-neighbor smoothing followed by Kauwahara filtering and local standard deviation approach for boundary detection. NIH FIJI/ImageJ tools are used to create the ground truth dataset. The results of this work indicate that detection of cell boundaries using segmentation approach even in the case of realistic measurement conditions is a challenging problem.

* 2017 International Conference on Advances in Computing, Communications and Informatics (ICACCI), Udupi, 2017, pp. 2382-2387 
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Multi-class Semantic Segmentation of Skin Lesions via Fully Convolutional Networks

Nov 28, 2017
Manu Goyal, Moi Hoon Yap

Early detection of skin cancer, particularly melanoma, is crucial to enable advanced treatment. Due to the rapid growth of skin cancers, there is a growing need of computerized analysis for skin lesions. These processes including detection, classification, and segmentation. There are three main types of skin lesions in common that are benign nevi, melanoma, and seborrhoeic keratoses which have huge intra-class variations in terms of color, size, place and appearance for each class and high inter-class visual similarities in dermoscopic images. The majority of current research is focusing on melanoma segmentation, but it is also very important to segment the seborrhoeic keratoses and benign nevi lesions as these regions potentially indicate the pre-cancer stage. We propose a multiclass semantic segmentation for these three classes from publicly available ISBI-2017 challenge dataset which consists of 2750 dermoscopic images. We propose an end-to-end solution using fully convolutional networks (FCNs) for multi-class semantic segmentation, which will automatically segment the melanoma, keratoses and benign lesions. To overcome the issue of data deficiency, we propose a transfer learning approach which uses both partial transfer learning and full transfer learning to train FCNs for multi-class semantic segmentation of skin lesions. The results are presented in Dice Similarity Coefficient (Dice) to compare the performance of the deep learning segmentation methods on the dataset with 5-fold cross-validation. The results showed that the two-tier level transfer learning FCN-8s achieved the overall best result with Dice score of 0.785 in a benign category, 0.653 in melanoma segmentation, and 0.557 in seborrhoeic keratoses.

* Submitted to IEEE JBHI Special Issue on Skin Lesion Image Analysis for Melanoma Detection 
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Stochastic functional analysis with applications to robust machine learning

Oct 04, 2021
Julio Enrique Castrillon-Candas, Dingning Liu, Mark Kon

It is well-known that machine learning protocols typically under-utilize information on the probability distributions of feature vectors and related data, and instead directly compute regression or classification functions of feature vectors. In this paper we introduce a set of novel features for identifying underlying stochastic behavior of input data using the Karhunen-Lo\'{e}ve (KL) expansion, where classification is treated as detection of anomalies from a (nominal) signal class. These features are constructed from the recent Functional Data Analysis (FDA) theory for anomaly detection. The related signal decomposition is an exact hierarchical tensor product expansion with known optimality properties for approximating stochastic processes (random fields) with finite dimensional function spaces. In principle these primary low dimensional spaces can capture most of the stochastic behavior of `underlying signals' in a given nominal class, and can reject signals in alternative classes as stochastic anomalies. Using a hierarchical finite dimensional KL expansion of the nominal class, a series of orthogonal nested subspaces is constructed for detecting anomalous signal components. Projection coefficients of input data in these subspaces are then used to train an ML classifier. However, due to the split of the signal into nominal and anomalous projection components, clearer separation surfaces of the classes arise. In fact we show that with a sufficiently accurate estimation of the covariance structure of the nominal class, a sharp classification can be obtained. We carefully formulate this concept and demonstrate it on a number of high-dimensional datasets in cancer diagnostics. This method leads to a significant increase in precision and accuracy over the current top benchmarks for the Global Cancer Map (GCM) gene expression network dataset.

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Automatic calcium scoring in low-dose chest CT using deep neural networks with dilated convolutions

Feb 01, 2018
Nikolas Lessmann, Bram van Ginneken, Majd Zreik, Pim A. de Jong, Bob D. de Vos, Max A. Viergever, Ivana Išgum

Heavy smokers undergoing screening with low-dose chest CT are affected by cardiovascular disease as much as by lung cancer. Low-dose chest CT scans acquired in screening enable quantification of atherosclerotic calcifications and thus enable identification of subjects at increased cardiovascular risk. This paper presents a method for automatic detection of coronary artery, thoracic aorta and cardiac valve calcifications in low-dose chest CT using two consecutive convolutional neural networks. The first network identifies and labels potential calcifications according to their anatomical location and the second network identifies true calcifications among the detected candidates. This method was trained and evaluated on a set of 1744 CT scans from the National Lung Screening Trial. To determine whether any reconstruction or only images reconstructed with soft tissue filters can be used for calcification detection, we evaluated the method on soft and medium/sharp filter reconstructions separately. On soft filter reconstructions, the method achieved F1 scores of 0.89, 0.89, 0.67, and 0.55 for coronary artery, thoracic aorta, aortic valve and mitral valve calcifications, respectively. On sharp filter reconstructions, the F1 scores were 0.84, 0.81, 0.64, and 0.66, respectively. Linearly weighted kappa coefficients for risk category assignment based on per subject coronary artery calcium were 0.91 and 0.90 for soft and sharp filter reconstructions, respectively. These results demonstrate that the presented method enables reliable automatic cardiovascular risk assessment in all low-dose chest CT scans acquired for lung cancer screening.

* IEEE Transactions on Medical Imaging 37(2), pp 615-625, 2018 
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DeepCervix: A Deep Learning-based Framework for the Classification of Cervical Cells Using Hybrid Deep Feature Fusion Techniques

Feb 24, 2021
Md Mamunur Rahaman, Chen Li, Yudong Yao, Frank Kulwa, Xiangchen Wu, Xiaoyan Li, Qian Wang

Cervical cancer, one of the most common fatal cancers among women, can be prevented by regular screening to detect any precancerous lesions at early stages and treat them. Pap smear test is a widely performed screening technique for early detection of cervical cancer, whereas this manual screening method suffers from high false-positive results because of human errors. To improve the manual screening practice, machine learning (ML) and deep learning (DL) based computer-aided diagnostic (CAD) systems have been investigated widely to classify cervical pap cells. Most of the existing researches require pre-segmented images to obtain good classification results, whereas accurate cervical cell segmentation is challenging because of cell clustering. Some studies rely on handcrafted features, which cannot guarantee the classification stage's optimality. Moreover, DL provides poor performance for a multiclass classification task when there is an uneven distribution of data, which is prevalent in the cervical cell dataset. This investigation has addressed those limitations by proposing DeepCervix, a hybrid deep feature fusion (HDFF) technique based on DL to classify the cervical cells accurately. Our proposed method uses various DL models to capture more potential information to enhance classification performance. Our proposed HDFF method is tested on the publicly available SIPAKMED dataset and compared the performance with base DL models and the LF method. For the SIPAKMED dataset, we have obtained the state-of-the-art classification accuracy of 99.85%, 99.38%, and 99.14% for 2-class, 3-class, and 5-class classification. Moreover, our method is tested on the Herlev dataset and achieves an accuracy of 98.32% for binary class and 90.32% for 7-class classification.

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GAN-based Medical Image Small Region Forgery Detection via a Two-Stage Cascade Framework

May 30, 2022
Jianyi Zhang, Xuanxi Huang, Yaqi Liu, Yuyang Han, Zixiao Xiang

Using generative adversarial network (GAN)\cite{RN90} for data enhancement of medical images is significantly helpful for many computer-aided diagnosis (CAD) tasks. A new attack called CT-GAN has emerged. It can inject or remove lung cancer lesions to CT scans. Because the tampering region may even account for less than 1\% of the original image, even state-of-the-art methods are challenging to detect the traces of such tampering. This paper proposes a cascade framework to detect GAN-based medical image small region forgery like CT-GAN. In the local detection stage, we train the detector network with small sub-images so that interference information in authentic regions will not affect the detector. We use depthwise separable convolution and residual to prevent the detector from over-fitting and enhance the ability to find forged regions through the attention mechanism. The detection results of all sub-images in the same image will be combined into a heatmap. In the global classification stage, using gray level co-occurrence matrix (GLCM) can better extract features of the heatmap. Because the shape and size of the tampered area are uncertain, we train PCA and SVM methods for classification. Our method can classify whether a CT image has been tampered and locate the tampered position. Sufficient experiments show that our method can achieve excellent performance.

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