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"cancer detection": models, code, and papers

Decision Support System for Detection and Classification of Skin Cancer using CNN

Dec 09, 2019
Rishu Garg, Saumil Maheshwari, Anupam Shukla

Skin Cancer is one of the most deathful of all the cancers. It is bound to spread to different parts of the body on the off chance that it is not analyzed and treated at the beginning time. It is mostly because of the abnormal growth of skin cells, often develops when the body is exposed to sunlight. The Detection Furthermore, the characterization of skin malignant growth in the beginning time is a costly and challenging procedure. It is classified where it develops and its cell type. High Precision and recall are required for the classification of lesions. The paper aims to use MNIST HAM-10000 dataset containing dermoscopy images. The objective is to propose a system that detects skin cancer and classifies it in different classes by using the Convolution Neural Network. The diagnosing methodology uses Image processing and deep learning model. The dermoscopy image of skin cancer taken, undergone various techniques to remove the noise and picture resolution. The image count is also increased by using various image augmentation techniques. In the end, the Transfer Learning method is used to increase the classification accuracy of the images further. Our CNN model gave a weighted average Precision of 0.88, a weighted Recall average of 0.74, and a weighted f1-score of 0.77. The transfer learning approach applied using ResNet model yielded an accuracy of 90.51%

* 9 pages, 3 figures, 5 tables 

Whole-Slide Mitosis Detection in H&E Breast Histology Using PHH3 as a Reference to Train Distilled Stain-Invariant Convolutional Networks

Aug 17, 2018
David Tellez, Maschenka Balkenhol, Irene Otte-Holler, Rob van de Loo, Rob Vogels, Peter Bult, Carla Wauters, Willem Vreuls, Suzanne Mol, Nico Karssemeijer, Geert Litjens, Jeroen van der Laak, Francesco Ciompi

Manual counting of mitotic tumor cells in tissue sections constitutes one of the strongest prognostic markers for breast cancer. This procedure, however, is time-consuming and error-prone. We developed a method to automatically detect mitotic figures in breast cancer tissue sections based on convolutional neural networks (CNNs). Application of CNNs to hematoxylin and eosin (H&E) stained histological tissue sections is hampered by: (1) noisy and expensive reference standards established by pathologists, (2) lack of generalization due to staining variation across laboratories, and (3) high computational requirements needed to process gigapixel whole-slide images (WSIs). In this paper, we present a method to train and evaluate CNNs to specifically solve these issues in the context of mitosis detection in breast cancer WSIs. First, by combining image analysis of mitotic activity in phosphohistone-H3 (PHH3) restained slides and registration, we built a reference standard for mitosis detection in entire H&E WSIs requiring minimal manual annotation effort. Second, we designed a data augmentation strategy that creates diverse and realistic H&E stain variations by modifying the hematoxylin and eosin color channels directly. Using it during training combined with network ensembling resulted in a stain invariant mitosis detector. Third, we applied knowledge distillation to reduce the computational requirements of the mitosis detection ensemble with a negligible loss of performance. The system was trained in a single-center cohort and evaluated in an independent multicenter cohort from The Cancer Genome Atlas on the three tasks of the Tumor Proliferation Assessment Challenge (TUPAC). We obtained a performance within the top-3 best methods for most of the tasks of the challenge.

* Accepted to appear in IEEE Transactions on Medical Imaging 

Y-Net: A deep Convolutional Neural Network for Polyp Detection

Jun 05, 2018
Ahmed Mohammed, Sule Yildirim, Ivar Farup, Marius Pedersen, Øistein Hovde

Colorectal polyps are important precursors to colon cancer, the third most common cause of cancer mortality for both men and women. It is a disease where early detection is of crucial importance. Colonoscopy is commonly used for early detection of cancer and precancerous pathology. It is a demanding procedure requiring significant amount of time from specialized physicians and nurses, in addition to a significant miss-rates of polyps by specialists. Automated polyp detection in colonoscopy videos has been demonstrated to be a promising way to handle this problem. {However, polyps detection is a challenging problem due to the availability of limited amount of training data and large appearance variations of polyps. To handle this problem, we propose a novel deep learning method Y-Net that consists of two encoder networks with a decoder network. Our proposed Y-Net method} relies on efficient use of pre-trained and un-trained models with novel sum-skip-concatenation operations. Each of the encoders are trained with encoder specific learning rate along the decoder. Compared with the previous methods employing hand-crafted features or 2-D/3-D convolutional neural network, our approach outperforms state-of-the-art methods for polyp detection with 7.3% F1-score and 13% recall improvement.

* 11 Pages, 3 figures 

MITOS-RCNN: A Novel Approach to Mitotic Figure Detection in Breast Cancer Histopathology Images using Region Based Convolutional Neural Networks

Jul 04, 2018
Siddhant Rao

Studies estimate that there will be 266,120 new cases of invasive breast cancer and 40,920 breast cancer induced deaths in the year of 2018 alone. Despite the pervasiveness of this affliction, the current process to obtain an accurate breast cancer prognosis is tedious and time consuming, requiring a trained pathologist to manually examine histopathological images in order to identify the features that characterize various cancer severity levels. We propose MITOS-RCNN: a novel region based convolutional neural network (RCNN) geared for small object detection to accurately grade one of the three factors that characterize tumor belligerence described by the Nottingham Grading System: mitotic count. Other computational approaches to mitotic figure counting and detection do not demonstrate ample recall or precision to be clinically viable. Our models outperformed all previous participants in the ICPR 2012 challenge, the AMIDA 2013 challenge and the MITOS-ATYPIA-14 challenge along with recently published works. Our model achieved an F-measure score of 0.955, a 6.11% improvement in accuracy from the most accurate of the previously proposed models.

* Submitted to Elsevier Medical Image Analysis journal. 17 pages. 3 tables. 4 figures 

Gastric Cancer Detection from X-ray Images Using Effective Data Augmentation and Hard Boundary Box Training

Aug 18, 2021
Hideaki Okamoto, Takakiyo Nomura, Kazuhito Nabeshima, Jun Hashimoto, Hitoshi Iyatomi

X-ray examination is suitable for screening of gastric cancer. Compared to endoscopy, which can only be performed by doctors, X-ray imaging can also be performed by radiographers, and thus, can treat more patients. However, the diagnostic accuracy of gastric radiographs is as low as 85%. To address this problem, highly accurate and quantitative automated diagnosis using machine learning needs to be performed. This paper proposes a diagnostic support method for detecting gastric cancer sites from X-ray images with high accuracy. The two new technical proposal of the method are (1) stochastic functional gastric image augmentation (sfGAIA), and (2) hard boundary box training (HBBT). The former is a probabilistic enhancement of gastric folds in X-ray images based on medical knowledge, whereas the latter is a recursive retraining technique to reduce false positives. We use 4,724 gastric radiographs of 145 patients in clinical practice and evaluate the cancer detection performance of the method in a patient-based five-group cross-validation. The proposed sfGAIA and HBBT significantly enhance the performance of the EfficientDet-D7 network by 5.9% in terms of the F1-score, and our screening method reaches a practical screening capability for gastric cancer (F1: 57.8%, recall: 90.2%, precision: 42.5%).

* 9 pages, 6 figures 

Colorectal Polyp Detection in Real-world Scenario: Design and Experiment Study

Jan 11, 2021
Xinzi Sun, Dechun Wang, Chenxi Zhang, Pengfei Zhang, Zinan Xiong, Yu Cao, Benyuan Liu, Xiaowei Liu, Shuijiao Chen

Colorectal polyps are abnormal tissues growing on the intima of the colon or rectum with a high risk of developing into colorectal cancer, the third leading cause of cancer death worldwide. Early detection and removal of colon polyps via colonoscopy have proved to be an effective approach to prevent colorectal cancer. Recently, various CNN-based computer-aided systems have been developed to help physicians detect polyps. However, these systems do not perform well in real-world colonoscopy operations due to the significant difference between images in a real colonoscopy and those in the public datasets. Unlike the well-chosen clear images with obvious polyps in the public datasets, images from a colonoscopy are often blurry and contain various artifacts such as fluid, debris, bubbles, reflection, specularity, contrast, saturation, and medical instruments, with a wide variety of polyps of different sizes, shapes, and textures. All these factors pose a significant challenge to effective polyp detection in a colonoscopy. To this end, we collect a private dataset that contains 7,313 images from 224 complete colonoscopy procedures. This dataset represents realistic operation scenarios and thus can be used to better train the models and evaluate a system's performance in practice. We propose an integrated system architecture to address the unique challenges for polyp detection. Extensive experiments results show that our system can effectively detect polyps in a colonoscopy with excellent performance in real time.

* 8 pages 

Oral cancer detection and interpretation: Deep multiple instance learning versus conventional deep single instance learning

Feb 03, 2022
Nadezhda Koriakina, Nataša Sladoje, Vladimir Bašić, Joakim Lindblad

The current medical standard for setting an oral cancer (OC) diagnosis is histological examination of a tissue sample from the oral cavity. This process is time consuming and more invasive than an alternative approach of acquiring a brush sample followed by cytological analysis. Skilled cytotechnologists are able to detect changes due to malignancy, however, to introduce this approach into clinical routine is associated with challenges such as a lack of experts and labour-intensive work. To design a trustworthy OC detection system that would assist cytotechnologists, we are interested in AI-based methods that reliably can detect cancer given only per-patient labels (minimizing annotation bias), and also provide information on which cells are most relevant for the diagnosis (enabling supervision and understanding). We, therefore, perform a comparison of a conventional single instance learning (SIL) approach and a modern multiple instance learning (MIL) method suitable for OC detection and interpretation, utilizing three different neural network architectures. To facilitate systematic evaluation of the considered approaches, we introduce a synthetic PAP-QMNIST dataset, that serves as a model of OC data, while offering access to per-instance ground truth. Our study indicates that on PAP-QMNIST, the SIL performs better, on average, than the MIL approach. Performance at the bag level on real-world cytological data is similar for both methods, yet the single instance approach performs better on average. Visual examination by cytotechnologist indicates that the methods manage to identify cells which deviate from normality, including malignant cells as well as those suspicious for dysplasia. We share the code as open source at


Report-Guided Automatic Lesion Annotation for Deep Learning-Based Prostate Cancer Detection in bpMRI

Dec 09, 2021
Joeran S. Bosma, Anindo Saha, Matin Hosseinzadeh, Ilse Slootweg, Maarten de Rooij, Henkjan Huisman

Deep learning-based diagnostic performance increases with more annotated data, but manual annotation is a bottleneck in most fields. Experts evaluate diagnostic images during clinical routine, and write their findings in reports. Automatic annotation based on clinical reports could overcome the manual labelling bottleneck. We hypothesise that dense annotations for detection tasks can be generated using model predictions, guided by sparse information from these reports. To demonstrate efficacy, we generated clinically significant prostate cancer (csPCa) annotations, guided by the number of clinically significant findings in the radiology reports. We included 7,756 prostate MRI examinations, of which 3,050 were manually annotated and 4,706 were automatically annotated. We evaluated the automatic annotation quality on the manually annotated subset: our score extraction correctly identified the number of csPCa lesions for $99.3\%$ of the reports and our csPCa segmentation model correctly localised $83.8 \pm 1.1\%$ of the lesions. We evaluated prostate cancer detection performance on 300 exams from an external centre with histopathology-confirmed ground truth. Augmenting the training set with automatically labelled exams improved patient-based diagnostic area under the receiver operating characteristic curve from $88.1\pm 1.1\%$ to $89.8\pm 1.0\%$ ($P = 1.2 \cdot 10^{-4}$) and improved lesion-based sensitivity at one false positive per case from $79.2 \pm 2.8\%$ to $85.4 \pm 1.9\%$ ($P<10^{-4}$), with $mean \pm std.$ over 15 independent runs. This improved performance demonstrates the feasibility of our report-guided automatic annotations. Source code is made publicly available at Best csPCa detection algorithm is made available at


Unsupervised Learning of Deep-Learned Features from Breast Cancer Images

Jun 21, 2020
Sanghoon Lee, Colton Farley, Simon Shim, Yanjun Zhao, Wookjin Choi, Wook-Sung Yoo

Detecting cancer manually in whole slide images requires significant time and effort on the laborious process. Recent advances in whole slide image analysis have stimulated the growth and development of machine learning-based approaches that improve the efficiency and effectiveness in the diagnosis of cancer diseases. In this paper, we propose an unsupervised learning approach for detecting cancer in breast invasive carcinoma (BRCA) whole slide images. The proposed method is fully automated and does not require human involvement during the unsupervised learning procedure. We demonstrate the effectiveness of the proposed approach for cancer detection in BRCA and show how the machine can choose the most appropriate clusters during the unsupervised learning procedure. Moreover, we present a prototype application that enables users to select relevant groups mapping all regions related to the groups in whole slide images.

* 7 pages for IEEE BIBE 

End-to-end Prostate Cancer Detection in bpMRI via 3D CNNs: Effect of Attention Mechanisms, Clinical Priori and Decoupled False Positive Reduction

Jan 18, 2021
Anindo Saha, Matin Hosseinzadeh, Henkjan Huisman

We present a novel multi-stage 3D computer-aided detection and diagnosis (CAD) model for automated localization of clinically significant prostate cancer (csPCa) in bi-parametric MR imaging (bpMRI). State-of-the-art attention mechanisms drive its detection network, which aims to accurately discriminate csPCa lesions from indolent cancer and the wide range of benign pathology that can afflict the prostate gland. In parallel, a decoupled residual classifier is used to achieve consistent false positive reduction, without sacrificing high detection sensitivity or computational efficiency. Furthermore, a probabilistic anatomical prior, which captures the spatial prevalence of csPCa and its zonal distinction, is computed and encoded into the CNN architecture to guide model generalization with domain-specific clinical knowledge. For 486 institutional testing scans, the 3D CAD system achieves $83.69\pm5.22\%$ and $93.19\pm2.96\%$ detection sensitivity at 0.50 and 1.46 false positive(s) per patient, respectively, along with $0.882$ AUROC in patient-based diagnosis $-$significantly outperforming four baseline architectures (USEResNet, UNet++, nnU-Net, Attention U-Net). For 296 external testing scans, the ensembled CAD system shares moderate agreement with a consensus of expert radiologists ($76.69\%$; $kappa=0.511$) and independent pathologists ($81.08\%$; $kappa=0.559$); demonstrating a strong ability to localize histologically-confirmed malignancies and generalize beyond the radiologically-estimated annotations of the 1950 training-validation cases used in this study.

* Under Review at MedIA: Medical Image Analysis. This manuscript incorporates and expands upon our 2020 Medical Imaging Meets NeurIPS Workshop paper (arXiv:2011.00263)