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"cancer detection": models, code, and papers

LNDb: A Lung Nodule Database on Computed Tomography

Nov 25, 2019
João Pedrosa, Guilherme Aresta, Carlos Ferreira, Márcio Rodrigues, Patrícia Leitão, André Silva Carvalho, João Rebelo, Eduardo Negrão, Isabel Ramos, António Cunha, Aurélio Campilho

Lung cancer is the deadliest type of cancer worldwide and late detection is the major factor for the low survival rate of patients. Low dose computed tomography has been suggested as a potential screening tool but manual screening is costly, time-consuming and prone to variability. This has fueled the development of automatic methods for the detection, segmentation and characterisation of pulmonary nodules but its application to clinical routine is challenging. In this study, a new database for the development and testing of pulmonary nodule computer-aided strategies is presented which intends to complement current databases by giving additional focus to radiologist variability and local clinical reality. State-of-the-art nodule detection, segmentation and characterization methods are tested and compared to manual annotations as well as collaborative strategies combining multiple radiologists and radiologists and computer-aided systems. It is shown that state-of-the-art methodologies can determine a patient's follow-up recommendation as accurately as a radiologist, though the nodule detection method used shows decreased performance in this database.

  
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Prediction of Malignant & Benign Breast Cancer: A Data Mining Approach in Healthcare Applications

Feb 23, 2019
Vivek Kumar, Brojo Kishore Mishra, Manuel Mazzara, Dang N. H. Thanh, Abhishek Verma

As much as data science is playing a pivotal role everywhere, healthcare also finds it prominent application. Breast Cancer is the top rated type of cancer amongst women; which took away 627,000 lives alone. This high mortality rate due to breast cancer does need attention, for early detection so that prevention can be done in time. As a potential contributor to state-of-art technology development, data mining finds a multi-fold application in predicting Brest cancer. This work focuses on different classification techniques implementation for data mining in predicting malignant and benign breast cancer. Breast Cancer Wisconsin data set from the UCI repository has been used as experimental dataset while attribute clump thickness being used as an evaluation class. The performances of these twelve algorithms: Ada Boost M 1, Decision Table, J Rip, Lazy IBK, Logistics Regression, Multiclass Classifier, Multilayer Perceptron, Naive Bayes, Random forest and Random Tree are analyzed on this data set. Keywords- Data Mining, Classification Techniques, UCI repository, Breast Cancer, Classification Algorithms

* 8 Pages, 2 Figures, 4 Tables. Conference- Advances in Data Science and Management - Proceedings of ICDSM 2019 To be published with- Springer, Lecture Notes on Data Engineering and Communications Technologies series 
  
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2D View Aggregation for Lymph Node Detection Using a Shallow Hierarchy of Linear Classifiers

Aug 14, 2014
Ari Seff, Le Lu, Kevin M. Cherry, Holger Roth, Jiamin Liu, Shijun Wang, Joanne Hoffman, Evrim B. Turkbey, Ronald M. Summers

Enlarged lymph nodes (LNs) can provide important information for cancer diagnosis, staging, and measuring treatment reactions, making automated detection a highly sought goal. In this paper, we propose a new algorithm representation of decomposing the LN detection problem into a set of 2D object detection subtasks on sampled CT slices, largely alleviating the curse of dimensionality issue. Our 2D detection can be effectively formulated as linear classification on a single image feature type of Histogram of Oriented Gradients (HOG), covering a moderate field-of-view of 45 by 45 voxels. We exploit both simple pooling and sparse linear fusion schemes to aggregate these 2D detection scores for the final 3D LN detection. In this manner, detection is more tractable and does not need to perform perfectly at instance level (as weak hypotheses) since our aggregation process will robustly harness collective information for LN detection. Two datasets (90 patients with 389 mediastinal LNs and 86 patients with 595 abdominal LNs) are used for validation. Cross-validation demonstrates 78.0% sensitivity at 6 false positives/volume (FP/vol.) (86.1% at 10 FP/vol.) and 73.1% sensitivity at 6 FP/vol. (87.2% at 10 FP/vol.), for the mediastinal and abdominal datasets respectively. Our results compare favorably to previous state-of-the-art methods.

* This article will be presented at MICCAI (Medical Image Computing and Computer-Assisted Intervention) 2014 
  
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Did you miss it? Automatic lung nodule detection combined with gaze information improves radiologists' screening performance

Oct 09, 2019
Guilherme Aresta, Carlos Ferreira, João Pedrosa, Teresa Araújo, João Rebelo, Eduardo Negrão, Margarida Morgado, Filipe Alves, António Cunha, Isabel Ramos, Aurélio Campilho

Early diagnosis of lung cancer via computed tomography can significantly reduce the morbidity and mortality rates associated with the pathology. However, search lung nodules is a high complexity task, which affects the success of screening programs. Whilst computer-aided detection systems can be used as second observers, they may bias radiologists and introduce significant time overheads. With this in mind, this study assesses the potential of using gaze information for integrating automatic detection systems in the clinical practice. For that purpose, 4 radiologists were asked to annotate 20 scans from a public dataset while being monitored by an eye tracker device and an automatic lung nodule detection system was developed. Our results show that radiologists follow a similar search routine and tend to have lower fixation periods in regions where finding errors occur. The overall detection sensitivity of the specialists was 0.67$\pm$0.07, whereas the system achieved 0.69. Combining the annotations of one radiologist with the automatic system significantly improves the detection performance to similar levels of two annotators. Likewise, combining the findings of radiologist with the detection algorithm only for low fixation regions still significantly improves the detection sensitivity without increasing the number of false-positives. The combination of the automatic system with the gaze information allows to mitigate possible errors of the radiologist without some of the issues usually associated with automatic detection system.

* Submitted to IEEE Transactions on Biomedical Engineering (TBME) 
  
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Automatic Pulmonary Nodule Detection in CT Scans Using Convolutional Neural Networks Based on Maximum Intensity Projection

Apr 11, 2019
Sunyi Zheng, Jiapan Guo, Xiaonan Cui, Raymond N. J. Veldhuis, Matthijs Oudkerk, Peter M. A. van Ooijen

Accurate pulmonary nodule detection in computed tomography scans is a crucial step in lung cancer screening. Computer-aided detection (CAD) systems are not routinely used by radiologists for pulmonary nodules detection in clinical practice despite their potential benefits. Maximum intensity projection (MIP) images improve the detection of pulmonary nodules in radiological evaluation with computed tomography (CT) scans. In this work, we aim to explore the feasibility of utilizing MIP images to improve the effectiveness of automatic detection of lung nodules by convolutional neural networks (CNNs). We propose a CNN based approach that takes MIP images of different slab thicknesses (5 mm, 10 mm, 15 mm) and 1mm plain multiplanar reconstruction (MPR) images as input. Such an approach augments the 2-D CT slice images with more representative spatial information that helps in the discriminating nodules from vessels through their morphologies. We use the public available LUNA16 set collected from seven academic centers to train and test our approach. Our proposed method achieves a sensitivity of 91.13% with 1 false positive per scan and a sensitivity of 94.13% with 4 false positives per scan for lung nodule detection in this dataset. Using the thick MIP images helps the detection of small pulmonary nodules (3mm-10mm) and acquires fewer false positives. Experimental results show that applying MIP images can increase the sensitivity and lower the number of false positive, which demonstrates the effectiveness and significance of the proposed maximum intensity projection based CNN framework for automatic pulmonary nodule detection in CT scans. Index Terms: Computer-aided detection (CAD), convolutional neural networks (CNNs), computed tomography scans, maximum intensity projection (MIP), pulmonary nodule detection

* Submitted to IEEE TMI 
  
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Cross-view Relation Networks for Mammogram Mass Detection

Jul 01, 2019
Jiechao Ma, Sen Liang, Xiang Li, Hongwei Li, Bjoern H Menze, Rongguo Zhang, Wei-Shi Zheng

Mammogram is the most effective imaging modality for the mass lesion detection of breast cancer at the early stage. The information from the two paired views (i.e., medio-lateral oblique and cranio-caudal) are highly relational and complementary, and this is crucial for doctors' decisions in clinical practice. However, existing mass detection methods do not consider jointly learning effective features from the two relational views. To address this issue, this paper proposes a novel mammogram mass detection framework, termed Cross-View Relation Region-based Convolutional Neural Networks (CVR-RCNN). The proposed CVR-RCNN is expected to capture the latent relation information between the corresponding mass region of interests (ROIs) from the two paired views. Evaluations on a new large-scale private dataset and a public mammogram dataset show that the proposed CVR-RCNN outperforms existing state-of-the-art mass detection methods. Meanwhile, our experimental results suggest that incorporating the relation information across two views helps to train a superior detection model, which is a promising avenue for mammogram mass detection.

  
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Transfer learning with class-weighted and focal loss function for automatic skin cancer classification

Sep 13, 2020
Duyen N. T. Le, Hieu X. Le, Lua T. Ngo, Hoan T. Ngo

Skin cancer is by far in top-3 of the world's most common cancer. Among different skin cancer types, melanoma is particularly dangerous because of its ability to metastasize. Early detection is the key to success in skin cancer treatment. However, skin cancer diagnosis is still a challenge, even for experienced dermatologists, due to strong resemblances between benign and malignant lesions. To aid dermatologists in skin cancer diagnosis, we developed a deep learning system that can effectively and automatically classify skin lesions into one of the seven classes: (1) Actinic Keratoses, (2) Basal Cell Carcinoma, (3) Benign Keratosis, (4) Dermatofibroma, (5) Melanocytic nevi, (6) Melanoma, (7) Vascular Skin Lesion. The HAM10000 dataset was used to train the system. An end-to-end deep learning process, transfer learning technique, utilizing multiple pre-trained models, combining with class-weighted and focal loss were applied for the classification process. The result was that our ensemble of modified ResNet50 models can classify skin lesions into one of the seven classes with top-1, top-2 and top-3 accuracy 93%, 97% and 99%, respectively. This deep learning system can potentially be integrated into computer-aided diagnosis systems that support dermatologists in skin cancer diagnosis.

* 7 pages, 8 figures 
  
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Towards a Computed-Aided Diagnosis System in Colonoscopy: Automatic Polyp Segmentation Using Convolution Neural Networks

Jan 15, 2021
Patrick Brandao, Odysseas Zisimopoulos, Evangelos Mazomenos, Gastone Ciuti, Jorge Bernal, Marco Visentini-Scarzanella, Arianna Menciassi, Paolo Dario, Anastasios Koulaouzidis, Alberto Arezzo, David J Hawkes, Danail Stoyanov

Early diagnosis is essential for the successful treatment of bowel cancers including colorectal cancer (CRC) and capsule endoscopic imaging with robotic actuation can be a valuable diagnostic tool when combined with automated image analysis. We present a deep learning rooted detection and segmentation framework for recognizing lesions in colonoscopy and capsule endoscopy images. We restructure established convolution architectures, such as VGG and ResNets, by converting them into fully-connected convolution networks (FCNs), fine-tune them and study their capabilities for polyp segmentation and detection. We additionally use Shape from-Shading (SfS) to recover depth and provide a richer representation of the tissue's structure in colonoscopy images. Depth is incorporated into our network models as an additional input channel to the RGB information and we demonstrate that the resulting network yields improved performance. Our networks are tested on publicly available datasets and the most accurate segmentation model achieved a mean segmentation IU of 47.78% and 56.95% on the ETIS-Larib and CVC-Colon datasets, respectively. For polyp detection, the top performing models we propose surpass the current state of the art with detection recalls superior to 90% for all datasets tested. To our knowledge, we present the first work to use FCNs for polyp segmentation in addition to proposing a novel combination of SfS and RGB that boosts performance

* Journal of Medical Robotics Research, Volume 03, No. 02, 1840002 (2018) G 
* 10 pages, 6 figures 
  
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