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"cancer detection": models, code, and papers

Multi-scale Regional Attention Deeplab3+: Multiple Myeloma Plasma Cells Segmentation in Microscopic Images

May 13, 2021
Afshin Bozorgpour, Reza Azad, Eman Showkatian, Alaa Sulaiman

Multiple myeloma cancer is a type of blood cancer that happens when the growth of abnormal plasma cells becomes out of control in the bone marrow. There are various ways to diagnose multiple myeloma in bone marrow such as complete blood count test (CBC) or counting myeloma plasma cell in aspirate slide images using manual visualization or through image processing technique. In this work, an automatic deep learning method for the detection and segmentation of multiple myeloma plasma cell have been explored. To this end, a two-stage deep learning method is designed. In the first stage, the nucleus detection network is utilized to extract each instance of a cell of interest. The extracted instance is then fed to the multi-scale function to generate a multi-scale representation. The objective of the multi-scale function is to capture the shape variation and reduce the effect of object scale on the cytoplasm segmentation network. The generated scales are then fed into a pyramid of cytoplasm networks to learn the segmentation map in various scales. On top of the cytoplasm segmentation network, we included a scale aggregation function to refine and generate a final prediction. The proposed approach has been evaluated on the SegPC2021 grand-challenge and ranked second on the final test phase among all teams.

* 10 pages, 5 figures, presented at ISBI2021 
  

Semi-Supervised Cervical Dysplasia Classification With Learnable Graph Convolutional Network

Apr 01, 2020
Yanglan Ou, Yuan Xue, Ye Yuan, Tao Xu, Vincent Pisztora, Jia Li, Xiaolei Huang

Cervical cancer is the second most prevalent cancer affecting women today. As the early detection of cervical carcinoma relies heavily upon screening and pre-clinical testing, digital cervicography has great potential as a primary or auxiliary screening tool, especially in low-resource regions due to its low cost and easy access. Although an automated cervical dysplasia detection system has been desirable, traditional fully-supervised training of such systems requires large amounts of annotated data which are often labor-intensive to collect. To alleviate the need for much manual annotation, we propose a novel graph convolutional network (GCN) based semi-supervised classification model that can be trained with fewer annotations. In existing GCNs, graphs are constructed with fixed features and can not be updated during the learning process. This limits their ability to exploit new features learned during graph convolution. In this paper, we propose a novel and more flexible GCN model with a feature encoder that adaptively updates the adjacency matrix during learning and demonstrate that this model design leads to improved performance. Our experimental results on a cervical dysplasia classification dataset show that the proposed framework outperforms previous methods under a semi-supervised setting, especially when the labeled samples are scarce.

* ISBI 2020 
  

Sharing Generative Models Instead of Private Data: A Simulation Study on Mammography Patch Classification

Mar 08, 2022
Zuzanna Szafranowska, Richard Osuala, Bennet Breier, Kaisar Kushibar, Karim Lekadir, Oliver Diaz

Early detection of breast cancer in mammography screening via deep-learning based computer-aided detection systems shows promising potential in improving the curability and mortality rates of breast cancer. However, many clinical centres are restricted in the amount and heterogeneity of available data to train such models to (i) achieve promising performance and to (ii) generalise well across acquisition protocols and domains. As sharing data between centres is restricted due to patient privacy concerns, we propose a potential solution: sharing trained generative models between centres as substitute for real patient data. In this work, we use three well known mammography datasets to simulate three different centres, where one centre receives the trained generator of Generative Adversarial Networks (GANs) from the two remaining centres in order to augment the size and heterogeneity of its training dataset. We evaluate the utility of this approach on mammography patch classification on the test set of the GAN-receiving centre using two different classification models, (a) a convolutional neural network and (b) a transformer neural network. Our experiments demonstrate that shared GANs notably increase the performance of both transformer and convolutional classification models and highlight this approach as a viable alternative to inter-centre data sharing.

* Draft accepted as oral presentation at International Workshop on Breast Imaging (IWBI) 2022. 9 pages, 3 figures 
  

Cell nuclei classification in histopathological images using hybrid OLConvNet

Feb 21, 2022
Suvidha Tripathi, Satish Kumar Singh

Computer-aided histopathological image analysis for cancer detection is a major research challenge in the medical domain. Automatic detection and classification of nuclei for cancer diagnosis impose a lot of challenges in developing state of the art algorithms due to the heterogeneity of cell nuclei and data set variability. Recently, a multitude of classification algorithms has used complex deep learning models for their dataset. However, most of these methods are rigid and their architectural arrangement suffers from inflexibility and non-interpretability. In this research article, we have proposed a hybrid and flexible deep learning architecture OLConvNet that integrates the interpretability of traditional object-level features and generalization of deep learning features by using a shallower Convolutional Neural Network (CNN) named as $CNN_{3L}$. $CNN_{3L}$ reduces the training time by training fewer parameters and hence eliminating space constraints imposed by deeper algorithms. We used F1-score and multiclass Area Under the Curve (AUC) performance parameters to compare the results. To further strengthen the viability of our architectural approach, we tested our proposed methodology with state of the art deep learning architectures AlexNet, VGG16, VGG19, ResNet50, InceptionV3, and DenseNet121 as backbone networks. After a comprehensive analysis of classification results from all four architectures, we observed that our proposed model works well and perform better than contemporary complex algorithms.

* @article{10.1145/3345318, year = {2020},journal = {ACM Trans. Multimedia Comput. Commun. Appl.}, volume = {16}, number = {1s}, issn = {1551-6857}, articleno = {32}, numpages = {22}} 
  

Reduction of Surgical Risk Through the Evaluation of Medical Imaging Diagnostics

Mar 08, 2020
Marco A. V. M. Grinet, Nuno M. Garcia, Ana I. R. Gouveia, Jose A. F. Moutinho, Abel J. P. Gomes

Computer aided diagnosis (CAD) of Breast Cancer (BRCA) images has been an active area of research in recent years. The main goals of this research is to develop reliable automatic methods for detecting and diagnosing different types of BRCA from diagnostic images. In this paper, we present a review of the state of the art CAD methods applied to magnetic resonance (MRI) and mammography images of BRCA patients. The review aims to provide an extensive introduction to different features extracted from BRCA images through texture and statistical analysis and to categorize deep learning frameworks and data structures capable of using metadata to aggregate relevant information to assist oncologists and radiologists. We divide the existing literature according to the imaging modality and into radiomics, machine learning, or combination of both. We also emphasize the difference between each modality and methods strengths and weaknesses and analyze their performance in detecting BRCA through a quantitative comparison. We compare the results of various approaches for implementing CAD systems for the detection of BRCA. Each approachs standard workflow components are reviewed and summary tables provided. We present an extensive literature review of radiomics feature extraction techniques and machine learning methods applied in BRCA diagnosis and detection, focusing on data preparation, data structures, pre processing and post processing strategies available in the literature. There is a growing interest on radiomic feature extraction and machine learning methods for BRCA detection through histopathological images, MRI and mammography images. However, there isnt a CAD method able to combine distinct data types to provide the best diagnostic results. Employing data fusion techniques to medical images and patient data could lead to improved detection and classification results.

* 25 pages, 7 figures, Scientific grant report 
  

Automatic Lesion Boundary Segmentation in Dermoscopic Images with Ensemble Deep Learning Methods

Feb 02, 2019
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. The state-of-the-art public available datasets for skin lesions are often accompanied with a very limited amount of segmentation ground truth labeling as it is laborious and expensive. The lesion boundary segmentation is vital to locate the lesion accurately in dermoscopic images and lesion diagnosis of different skin lesion types. In this work, we propose the use of fully automated deep learning ensemble methods for accurate lesion boundary segmentation in dermoscopic images. We trained the Mask-RCNN and DeeplabV3+ methods on ISIC-2017 segmentation training dataset and evaluate the various ensemble performance of both networks on ISIC-2017 testing set, PH2 dataset. Our results showed that the proposed ensemble method segmented the skin lesions with Jaccard index of 79.58% for the ISBI 2017 test dataset. In comparison to FrCN, FCN, U-Net, and SegNet, the proposed ensemble method outperformed them by 2.48%, 7.42%, 17.95%, and 9.96% for the Jaccard index, respectively. Furthermore, the proposed ensemble method achieved a segmentation accuracy of 95.6% for some representative clinical benign cases, 90.78\% for the melanoma cases, and 91.29% for the seborrheic keratosis cases in the ISBI 2017 test dataset, exhibiting better performance than those of FrCN, FCN, U-Net, and SegNet.

* arXiv admin note: text overlap with arXiv:1711.10449 
  

Evolving the pulmonary nodules diagnosis from classical approaches to deep learning aided decision support: three decades development course and future prospect

Jan 23, 2019
Bo Liu, Wenhao Chi, Xinran Li, Peng Li, Wenhua Liang, Haiping Liu, Wei Wang, Jianxing He

Lung cancer is the commonest cause of cancer deaths worldwide, and its mortality can be reduced significantly by performing early diagnosis and screening. Since the 1960s, driven by the pressing needs to accurately and effectively interpret the massive volume of chest images generated daily, computer-assisted diagnosis of pulmonary nodule has opened up new opportunities to relax the limitation from physicians subjectivity, experiences and fatigue. It has been witnessed that significant and remarkable advances have been achieved since the 1980s, and consistent endeavors have been exerted to deal with the grand challenges on how to accurately detect the pulmonary nodules with high sensitivity at low false-positives rate as well as on how to precisely differentiate between benign and malignant nodules. The main goal of this investigation is to provide a comprehensive state-of-the-art review of the computer-assisted nodules detection and benign-malignant classification techniques developed over three decades, which have evolved from the complicated ad hoc analysis pipeline of conventional approaches to the simplified seamlessly integrated deep learning techniques. This review also identifies challenges and highlights opportunities for future work in learning models, learning algorithms and enhancement schemes for bridging current state to future prospect and satisfying future demand. As far as the authors know, it is the first review of the literature of the past thirty years development in computer-assisted diagnosis of lung nodules. We acknowledge the value of potential multidisciplinary researches that will make the computer-assisted diagnosis of pulmonary nodules enter into the main stream of clinical medicine, and raise the state-of-the-art clinical applications as well as increase both welfares of physicians and patients.

* 74 pages, 2 figures 
  

Normalization of breast MRIs using Cycle-Consistent Generative Adversarial Networks

Dec 16, 2019
Gourav Modanwal, Adithya Vellal, Maciej A. Mazurowski

Dynamic Contrast Enhanced-Magnetic Resonance Imaging (DCE-MRI) is widely used to complement ultrasound examinations and x-ray mammography during the early detection and diagnosis of breast cancer. However, images generated by various MRI scanners (e.g. GE Healthcare vs Siemens) differ both in intensity and noise distribution, preventing algorithms trained on MRIs from one scanner to generalize to data from other scanners successfully. We propose a method for image normalization to solve this problem. MRI normalization is challenging because it requires both normalizing intensity values and mapping between the noise distributions of different scanners. We utilize a cycle-consistent generative adversarial network to learn a bidirectional mapping between MRIs produced by GE Healthcare and Siemens scanners. This allows us learning the mapping between two different scanner types without matched data, which is not commonly available. To ensure the preservation of breast shape and structures within the breast, we propose two technical innovations. First, we incorporate a mutual information loss with the CycleGAN architecture to ensure that the structure of the breast is maintained. Second, we propose a modified discriminator architecture which utilizes a smaller field-of-view to ensure the preservation of finer details in the breast tissue. Quantitative and qualitative evaluations show that the second proposed method was able to consistently preserve a high level of detail in the breast structure while also performing the proper intensity normalization and noise mapping. Our results demonstrate that the proposed model can successfully learn a bidirectional mapping between MRIs produced by different vendors, potentially enabling improved accuracy of downstream computational algorithms for diagnosis and detection of breast cancer.

  

WeakSTIL: Weak whole-slide image level stromal tumor infiltrating lymphocyte scores are all you need

Sep 13, 2021
Yoni Schirris, Mendel Engelaer, Andreas Panteli, Hugo Mark Horlings, Efstratios Gavves, Jonas Teuwen

We present WeakSTIL, an interpretable two-stage weak label deep learning pipeline for scoring the percentage of stromal tumor infiltrating lymphocytes (sTIL%) in H&E-stained whole-slide images (WSIs) of breast cancer tissue. The sTIL% score is a prognostic and predictive biomarker for many solid tumor types. However, due to the high labeling efforts and high intra- and interobserver variability within and between expert annotators, this biomarker is currently not used in routine clinical decision making. WeakSTIL compresses tiles of a WSI using a feature extractor pre-trained with self-supervised learning on unlabeled histopathology data and learns to predict precise sTIL% scores for each tile in the tumor bed by using a multiple instance learning regressor that only requires a weak WSI-level label. By requiring only a weak label, we overcome the large annotation efforts required to train currently existing TIL detection methods. We show that WeakSTIL is at least as good as other TIL detection methods when predicting the WSI-level sTIL% score, reaching a coefficient of determination of $0.45\pm0.15$ when compared to scores generated by an expert pathologist, and an AUC of $0.89\pm0.05$ when treating it as the clinically interesting sTIL-high vs sTIL-low classification task. Additionally, we show that the intermediate tile-level predictions of WeakSTIL are highly interpretable, which suggests that WeakSTIL pays attention to latent features related to the number of TILs and the tissue type. In the future, WeakSTIL may be used to provide consistent and interpretable sTIL% predictions to stratify breast cancer patients into targeted therapy arms.

* 8 pages, 8 figures, 1 table, 4 pages supplementary 
  

Predicting breast tumor proliferation from whole-slide images: the TUPAC16 challenge

Jul 22, 2018
Mitko Veta, Yujing J. Heng, Nikolas Stathonikos, Babak Ehteshami Bejnordi, Francisco Beca, Thomas Wollmann, Karl Rohr, Manan A. Shah, Dayong Wang, Mikael Rousson, Martin Hedlund, David Tellez, Francesco Ciompi, Erwan Zerhouni, David Lanyi, Matheus Viana, Vassili Kovalev, Vitali Liauchuk, Hady Ahmady Phoulady, Talha Qaiser, Simon Graham, Nasir Rajpoot, Erik Sjöblom, Jesper Molin, Kyunghyun Paeng, Sangheum Hwang, Sunggyun Park, Zhipeng Jia, Eric I-Chao Chang, Yan Xu, Andrew H. Beck, Paul J. van Diest, Josien P. W. Pluim

Tumor proliferation is an important biomarker indicative of the prognosis of breast cancer patients. Assessment of tumor proliferation in a clinical setting is highly subjective and labor-intensive task. Previous efforts to automate tumor proliferation assessment by image analysis only focused on mitosis detection in predefined tumor regions. However, in a real-world scenario, automatic mitosis detection should be performed in whole-slide images (WSIs) and an automatic method should be able to produce a tumor proliferation score given a WSI as input. To address this, we organized the TUmor Proliferation Assessment Challenge 2016 (TUPAC16) on prediction of tumor proliferation scores from WSIs. The challenge dataset consisted of 500 training and 321 testing breast cancer histopathology WSIs. In order to ensure fair and independent evaluation, only the ground truth for the training dataset was provided to the challenge participants. The first task of the challenge was to predict mitotic scores, i.e., to reproduce the manual method of assessing tumor proliferation by a pathologist. The second task was to predict the gene expression based PAM50 proliferation scores from the WSI. The best performing automatic method for the first task achieved a quadratic-weighted Cohen's kappa score of $\kappa$ = 0.567, 95% CI [0.464, 0.671] between the predicted scores and the ground truth. For the second task, the predictions of the top method had a Spearman's correlation coefficient of r = 0.617, 95% CI [0.581 0.651] with the ground truth. This was the first study that investigated tumor proliferation assessment from WSIs. The achieved results are promising given the difficulty of the tasks and weakly-labelled nature of the ground truth. However, further research is needed to improve the practical utility of image analysis methods for this task.

* Overview paper of the TUPAC16 challenge: http://tupac.tue-image.nl/ 
  
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