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"cancer detection": models, code, and papers

Multi Scale Curriculum CNN for Context-Aware Breast MRI Malignancy Classification

Jun 17, 2019
Christoph Haarburger, Michael Baumgartner, Daniel Truhn, Mirjam Broeckmann, Hannah Schneider, Simone Schrading, Christiane Kuhl, Dorit Merhof

Classification of malignancy for breast cancer and other cancer types is usually tackled as an object detection problem: Individual lesions are first localized and then classified with respect to malignancy. However, the drawback of this approach is that abstract features incorporating several lesions and areas that are not labelled as a lesion but contain global medically relevant information are thus disregarded: especially for dynamic contrast-enhanced breast MRI, criteria such as background parenchymal enhancement and location within the breast are important for diagnosis and cannot be captured by object detection approaches properly. In this work, we propose a 3D CNN and a multi scale curriculum learning strategy to classify malignancy globally based on an MRI of the whole breast. Thus, the global context of the whole breast rather than individual lesions is taken into account. Our proposed approach does not rely on lesion segmentations, which renders the annotation of training data much more effective than in current object detection approaches. Achieving an AUROC of 0.89, we compare the performance of our approach to Mask R-CNN and Retina U-Net as well as a radiologist. Our performance is on par with approaches that, in contrast to our method, rely on pixelwise segmentations of lesions.

* Accepted to MICCAI 2019 
  
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A Deep Learning Study on Osteosarcoma Detection from Histological Images

Nov 02, 2020
D M Anisuzzaman, Hosein Barzekar, Ling Tong, Jake Luo, Zeyun Yu

In the U.S, 5-10\% of new pediatric cases of cancer are primary bone tumors. The most common type of primary malignant bone tumor is osteosarcoma. The intention of the present work is to improve the detection and diagnosis of osteosarcoma using computer-aided detection (CAD) and diagnosis (CADx). Such tools as convolutional neural networks (CNNs) can significantly decrease the surgeon's workload and make a better prognosis of patient conditions. CNNs need to be trained on a large amount of data in order to achieve a more trustworthy performance. In this study, transfer learning techniques, pre-trained CNNs, are adapted to a public dataset on osteosarcoma histological images to detect necrotic images from non-necrotic and healthy tissues. First, the dataset was preprocessed, and different classifications are applied. Then, Transfer learning models including VGG19 and Inception V3 are used and trained on Whole Slide Images (WSI) with no patches, to improve the accuracy of the outputs. Finally, the models are applied to different classification problems, including binary and multi-class classifiers. Experimental results show that the accuracy of the VGG19 has the highest, 96\%, performance amongst all binary classes and multiclass classification. Our fine-tuned model demonstrates state-of-the-art performance on detecting malignancy of Osteosarcoma based on histologic images.

  
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Whole-Sample Mapping of Cancerous and Benign Tissue Properties

Jul 23, 2019
Lydia Neary-Zajiczek, Clara Essmann, Neil Clancy, Aiman Haider, Elena Miranda, Michael Shaw, Amir Gander, Brian Davidson, Delmiro Fernandez-Reyes, Vijay Pawar, Danail Stoyanov

Structural and mechanical differences between cancerous and healthy tissue give rise to variations in macroscopic properties such as visual appearance and elastic modulus that show promise as signatures for early cancer detection. Atomic force microscopy (AFM) has been used to measure significant differences in stiffness between cancerous and healthy cells owing to its high force sensitivity and spatial resolution, however due to absorption and scattering of light, it is often challenging to accurately locate where AFM measurements have been made on a bulk tissue sample. In this paper we describe an image registration method that localizes AFM elastic stiffness measurements with high-resolution images of haematoxylin and eosin (H\&E)-stained tissue to within 1.5 microns. Color RGB images are segmented into three structure types (lumen, cells and stroma) by a neural network classifier trained on ground-truth pixel data obtained through k-means clustering in HSV color space. Using the localized stiffness maps and corresponding structural information, a whole-sample stiffness map is generated with a region matching and interpolation algorithm that associates similar structures with measured stiffness values. We present results showing significant differences in stiffness between healthy and cancerous liver tissue and discuss potential applications of this technique.

* Accepted at MICCAI2019 
  
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Segmentation for Classification of Screening Pancreatic Neuroendocrine Tumors

Apr 04, 2020
Zhuotun Zhu, Yongyi Lu, Wei Shen, Elliot K. Fishman, Alan L. Yuille

This work presents comprehensive results to detect in the early stage the pancreatic neuroendocrine tumors (PNETs), a group of endocrine tumors arising in the pancreas, which are the second common type of pancreatic cancer, by checking the abdominal CT scans. To the best of our knowledge, this task has not been studied before as a computational task. To provide radiologists with tumor locations, we adopt a segmentation framework to classify CT volumes by checking if at least a sufficient number of voxels is segmented as tumors. To quantitatively analyze our method, we collect and voxelwisely label a new abdominal CT dataset containing $376$ cases with both arterial and venous phases available for each case, in which $228$ cases were diagnosed with PNETs while the remaining $148$ cases are normal, which is currently the largest dataset for PNETs to the best of our knowledge. In order to incorporate rich knowledge of radiologists to our framework, we annotate dilated pancreatic duct as well, which is regarded as the sign of high risk for pancreatic cancer. Quantitatively, our approach outperforms state-of-the-art segmentation networks and achieves a sensitivity of $89.47\%$ at a specificity of $81.08\%$, which indicates a potential direction to achieve a clinical impact related to cancer diagnosis by earlier tumor detection.

  
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Deep Learning for Skin Lesion Classification

Mar 13, 2017
P. Mirunalini, Aravindan Chandrabose, Vignesh Gokul, S. M. Jaisakthi

Melanoma, a malignant form of skin cancer is very threatening to life. Diagnosis of melanoma at an earlier stage is highly needed as it has a very high cure rate. Benign and malignant forms of skin cancer can be detected by analyzing the lesions present on the surface of the skin using dermoscopic images. In this work, an automated skin lesion detection system has been developed which learns the representation of the image using Google's pretrained CNN model known as Inception-v3 \cite{cnn}. After obtaining the representation vector for our input dermoscopic images we have trained two layer feed forward neural network to classify the images as malignant or benign. The system also classifies the images based on the cause of the cancer either due to melanocytic or non-melanocytic cells using a different neural network. These classification tasks are part of the challenge organized by International Skin Imaging Collaboration (ISIC) 2017. Our system learns to classify the images based on the model built using the training images given in the challenge and the experimental results were evaluated using validation and test sets. Our system has achieved an overall accuracy of 65.8\% for the validation set.

* 3 pages with 3 figures 
  
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An Efficient Approach for Polyps Detection in Endoscopic Videos Based on Faster R-CNN

Sep 04, 2018
Xi Mo, Ke Tao, Quan Wang, Guanghui Wang

Polyp has long been considered as one of the major etiologies to colorectal cancer which is a fatal disease around the world, thus early detection and recognition of polyps plays a crucial role in clinical routines. Accurate diagnoses of polyps through endoscopes operated by physicians becomes a challenging task not only due to the varying expertise of physicians, but also the inherent nature of endoscopic inspections. To facilitate this process, computer-aid techniques that emphasize fully-conventional image processing and novel machine learning enhanced approaches have been dedicatedly designed for polyp detection in endoscopic videos or images. Among all proposed algorithms, deep learning based methods take the lead in terms of multiple metrics in evolutions for algorithmic performance. In this work, a highly effective model, namely the faster region-based convolutional neural network (Faster R-CNN) is implemented for polyp detection. In comparison with the reported results of the state-of-the-art approaches on polyps detection, extensive experiments demonstrate that the Faster R-CNN achieves very competing results, and it is an efficient approach for clinical practice.

* 6 pages, 10 figures,2018 International Conference on Pattern Recognition 
  
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Comparison of different CNNs for breast tumor classification from ultrasound images

Dec 28, 2020
Jorge F. Lazo, Sara Moccia, Emanuele Frontoni, Elena De Momi

Breast cancer is one of the deadliest cancer worldwide. Timely detection could reduce mortality rates. In the clinical routine, classifying benign and malignant tumors from ultrasound (US) imaging is a crucial but challenging task. An automated method, which can deal with the variability of data is therefore needed. In this paper, we compared different Convolutional Neural Networks (CNNs) and transfer learning methods for the task of automated breast tumor classification. The architectures investigated in this study were VGG-16 and Inception V3. Two different training strategies were investigated: the first one was using pretrained models as feature extractors and the second one was to fine-tune the pre-trained models. A total of 947 images were used, 587 corresponded to US images of benign tumors and 360 with malignant tumors. 678 images were used for the training and validation process, while 269 images were used for testing the models. Accuracy and Area Under the receiver operating characteristic Curve (AUC) were used as performance metrics. The best performance was obtained by fine tuning VGG-16, with an accuracy of 0.919 and an AUC of 0.934. The obtained results open the opportunity to further investigation with a view of improving cancer detection.

  
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A fully automated framework for lung tumour detection, segmentation and analysis

Jan 04, 2018
Devesh Walawalkar

Early and correct diagnosis is a very important aspect of cancer treatment. Detection of tumour in Computed Tomography scan is a tedious and tricky task which requires expert knowledge and a lot of human working hours. As small human error is present in any work he does, it is possible that a CT scan could be misdiagnosed causing the patient to become terminal. This paper introduces a novel fully automated framework which helps to detect and segment tumour, if present in a lung CT scan series. It also provides useful analysis of the detected tumour such as its approximate volume, centre location and more. The framework provides a single click solution which analyses all CT images of a single patient series in one go. It helps to reduce the work of manually going through each CT slice and provides quicker and more accurate tumour diagnosis. It makes use of customized image processing and image segmentation methods, to detect and segment the prospective tumour region from the CT scan. It then uses a trained ensemble classifier to correctly classify the segmented region as being tumour or not. Tumour analysis further computed can then be used to determine malignity of the tumour. With an accuracy of 98.14%, the implemented framework can be used in various practical scenarios, capable of eliminating need of any expert pathologist intervention.

  
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Classification and Segmentation of Pulmonary Lesions in CT images using a combined VGG-XGBoost method, and an integrated Fuzzy Clustering-Level Set technique

Jan 04, 2021
Niloofar Akhavan Javan, Ali Jebreili, Babak Mozafari, Morteza Hosseinioun

Given that lung cancer is one of the deadliest diseases, and many die from the disease every year, early detection and diagnosis of this disease are valuable, preventing cancer from growing and spreading. So if cancer is diagnosed in the early stage, the patient's life will be saved. However, the current pulmonary disease diagnosis is made by human resources, which is time-consuming and requires a specialist in this field. Also, there is a high level of errors in human diagnosis. Our goal is to develop a system that can detect and classify lung lesions with high accuracy and segment them in CT-scan images. In the proposed method, first, features are extracted automatically from the CT-scan image; then, the extracted features are classified by Ensemble Gradient Boosting methods. Finally, if there is a lesion in the CT-scan image, using a hybrid method based on [1], including Fuzzy Clustering and Level Set, the lesion is segmented. We collected a dataset, including CT-scan images of pulmonary lesions. The target community was the patients in Mashhad. The collected samples were then tagged by a specialist. We used this dataset for training and testing our models. Finally, we were able to achieve an accuracy of 96% for this dataset. This system can help physicians to diagnose pulmonary lesions and prevent possible mistakes.

  
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