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"cancer detection": models, code, and papers

Classification of Histopathology Images of Lung Cancer Using Convolutional Neural Network (CNN)

Dec 27, 2021
Neha Baranwal, Preethi Doravari, Renu Kachhoria

Cancer is the uncontrollable cell division of abnormal cells inside the human body, which can spread to other body organs. It is one of the non-communicable diseases (NCDs) and NCDs accounts for 71% of total deaths worldwide whereas lung cancer is the second most diagnosed cancer after female breast cancer. Cancer survival rate of lung cancer is only 19%. There are various methods for the diagnosis of lung cancer, such as X-ray, CT scan, PET-CT scan, bronchoscopy and biopsy. However, to know the subtype of lung cancer based on the tissue type H and E staining is widely used, where the staining is done on the tissue aspirated from a biopsy. Studies have reported that the type of histology is associated with prognosis and treatment in lung cancer. Therefore, early and accurate detection of lung cancer histology is an urgent need and as its treatment is dependent on the type of histology, molecular profile and stage of the disease, it is most essential to analyse the histopathology images of lung cancer. Hence, to speed up the vital process of diagnosis of lung cancer and reduce the burden on pathologists, Deep learning techniques are used. These techniques have shown improved efficacy in the analysis of histopathology slides of cancer. Several studies reported the importance of convolution neural networks (CNN) in the classification of histopathological pictures of various cancer types such as brain, skin, breast, lung, colorectal cancer. In this study tri-category classification of lung cancer images (normal, adenocarcinoma and squamous cell carcinoma) are carried out by using ResNet 50, VGG-19, Inception_ResNet_V2 and DenseNet for the feature extraction and triplet loss to guide the CNN such that it increases inter-cluster distance and reduces intra-cluster distance.


Detection of Microcalcification in Mammograms Using Wavelet Transform and Fuzzy Shell Clustering

Feb 10, 2010
T. Balakumaran, I. L. A. Vennila, C. Gowri Shankar

Microcalcifications in mammogram have been mainly targeted as a reliable earliest sign of breast cancer and their early detection is vital to improve its prognosis. Since their size is very small and may be easily overlooked by the examining radiologist, computer-based detection output can assist the radiologist to improve the diagnostic accuracy. In this paper, we have proposed an algorithm for detecting microcalcification in mammogram. The proposed microcalcification detection algorithm involves mammogram quality enhancement using multirresolution analysis based on the dyadic wavelet transform and microcalcification detection by fuzzy shell clustering. It may be possible to detect nodular components such as microcalcification accurately by introducing shape information. The effectiveness of the proposed algorithm for microcalcification detection is confirmed by experimental results.

* International Journal of Computer Science and Information Security, IJCSIS, Vol. 7, No. 1, pp. 121-125, January 2010, USA 
* IEEE format, International Journal of Computer Science and Information Security, IJCSIS January 2010, ISSN 1947 5500, 

Ovarian Cancer Detection based on Dimensionality Reduction Techniques and Genetic Algorithm

May 04, 2021
Ahmed Farag Seddik, Hassan Mostafa Ahmed

In this research, we have two serum SELDI (surface-enhanced laser desorption and ionization) mass spectra (MS) datasets to be used to select features amongst them to identify proteomic cancerous serums from normal serums. Features selection techniques have been applied and classification techniques have been applied as well. Amongst the features selection techniques we have chosen to evaluate the performance of PCA (Principal Component Analysis ) and GA (Genetic algorithm), and amongst the classification techniques we have chosen the LDA (Linear Discriminant Analysis) and Neural networks so as to evaluate the ability of the selected features in identifying the cancerous patterns. Results were obtained for two combinations of features selection techniques and classification techniques, the first one was PCA+(t-test) technique for features selection and LDA for accuracy tracking yielded an accuracy of 93.0233 % , the other one was genetic algorithm and neural network yielded an accuracy of 100%. So, we conclude that GA is more efficient for features selection and hence for cancerous patterns detection than PCA technique.

* EMBS ISC 2013 
* 7 Pages 

Skin Cancer Detection and Tracking using Data Synthesis and Deep Learning

Dec 04, 2016
Yunzhu Li, Andre Esteva, Brett Kuprel, Rob Novoa, Justin Ko, Sebastian Thrun

Dense object detection and temporal tracking are needed across applications domains ranging from people-tracking to analysis of satellite imagery over time. The detection and tracking of malignant skin cancers and benign moles poses a particularly challenging problem due to the general uniformity of large skin patches, the fact that skin lesions vary little in their appearance, and the relatively small amount of data available. Here we introduce a novel data synthesis technique that merges images of individual skin lesions with full-body images and heavily augments them to generate significant amounts of data. We build a convolutional neural network (CNN) based system, trained on this synthetic data, and demonstrate superior performance to traditional detection and tracking techniques. Additionally, we compare our system to humans trained with simple criteria. Our system is intended for potential clinical use to augment the capabilities of healthcare providers. While domain-specific, we believe the methods invoked in this work will be useful in applying CNNs across domains that suffer from limited data availability.

* 4 pages, 5 figures, Yunzhu Li and Andre Esteva contributed equally to this work 

Unsupervised Detection of Cancerous Regions in Histology Imagery using Image-to-Image Translation

Apr 28, 2021
Dejan Stepec, Danijel Skocaj

Detection of visual anomalies refers to the problem of finding patterns in different imaging data that do not conform to the expected visual appearance and is a widely studied problem in different domains. Due to the nature of anomaly occurrences and underlying generating processes, it is hard to characterize them and obtain labeled data. Obtaining labeled data is especially difficult in biomedical applications, where only trained domain experts can provide labels, which often come in large diversity and complexity. Recently presented approaches for unsupervised detection of visual anomalies approaches omit the need for labeled data and demonstrate promising results in domains, where anomalous samples significantly deviate from the normal appearance. Despite promising results, the performance of such approaches still lags behind supervised approaches and does not provide a one-fits-all solution. In this work, we present an image-to-image translation-based framework that significantly surpasses the performance of existing unsupervised methods and approaches the performance of supervised methods in a challenging domain of cancerous region detection in histology imagery.

* CVPR 2021 CVMI workshop 

A 3D Probabilistic Deep Learning System for Detection and Diagnosis of Lung Cancer Using Low-Dose CT Scans

Feb 08, 2019
Onur Ozdemir, Rebecca L. Russell, Andrew A. Berlin

We introduce a new end-to-end computer aided detection and diagnosis system for lung cancer screening using low-dose CT scans. Our system is based on 3D convolutional neural networks and achieves state-of-the-art performance for both lung nodule detection and malignancy classification tasks on the publicly available LUNA16 and Kaggle Data Science Bowl challenges. Furthermore, we characterize model uncertainty in our system and show that we can use this to provide well-calibrated classification probabilities for nodule detection and patient malignancy diagnosis. To the best of our knowledge, model uncertainty has not been considered in the context of lung CT analysis before. These calibrated probabilities informed by model uncertainty can be used for subsequent risk-based decision making towards diagnostic interventions or disease treatments, as we demonstrate using a probability-based patient referral strategy to further improve our results.


Automatic Lesion Detection System (ALDS) for Skin Cancer Classification Using SVM and Neural Classifiers

Mar 13, 2020
Muhammad Ali Farooq, Muhammad Aatif Mobeen Azhar, Rana Hammad Raza

Technology aided platforms provide reliable tools in almost every field these days. These tools being supported by computational power are significant for applications that need sensitive and precise data analysis. One such important application in the medical field is Automatic Lesion Detection System (ALDS) for skin cancer classification. Computer aided diagnosis helps physicians and dermatologists to obtain a second opinion for proper analysis and treatment of skin cancer. Precise segmentation of the cancerous mole along with surrounding area is essential for proper analysis and diagnosis. This paper is focused towards the development of improved ALDS framework based on probabilistic approach that initially utilizes active contours and watershed merged mask for segmenting out the mole and later SVM and Neural Classifier are applied for the classification of the segmented mole. After lesion segmentation, the selected features are classified to ascertain that whether the case under consideration is melanoma or non-melanoma. The approach is tested for varying datasets and comparative analysis is performed that reflects the effectiveness of the proposed system.


Self supervised learning improves dMMR/MSI detection from histology slides across multiple cancers

Sep 13, 2021
Charlie Saillard, Olivier Dehaene, Tanguy Marchand, Olivier Moindrot, Aurélie Kamoun, Benoit Schmauch, Simon Jegou

Microsatellite instability (MSI) is a tumor phenotype whose diagnosis largely impacts patient care in colorectal cancers (CRC), and is associated with response to immunotherapy in all solid tumors. Deep learning models detecting MSI tumors directly from H&E stained slides have shown promise in improving diagnosis of MSI patients. Prior deep learning models for MSI detection have relied on neural networks pretrained on ImageNet dataset, which does not contain any medical image. In this study, we leverage recent advances in self-supervised learning by training neural networks on histology images from the TCGA dataset using MoCo V2. We show that these networks consistently outperform their counterparts pretrained using ImageNet and obtain state-of-the-art results for MSI detection with AUCs of 0.92 and 0.83 for CRC and gastric tumors, respectively. These models generalize well on an external CRC cohort (0.97 AUC on PAIP) and improve transfer from one organ to another. Finally we show that predictive image regions exhibit meaningful histological patterns, and that the use of MoCo features highlighted more relevant patterns according to an expert pathologist.

* Accepted for poster and oral presentation at the MICCAI 2021 COMPAY Workshop (submitted the 19th of July 2021) 

Internal-transfer Weighting of Multi-task Learning for Lung Cancer Detection

Dec 16, 2019
Yiyuan Yang, Riqiang Gao, Yucheng Tang, Sanja L. Antic, Steve Deppen, Yuankai Huo, Kim L. Sandler, Pierre P. Massion, Bennett A. Landman

Recently, multi-task networks have shown to both offer additional estimation capabilities, and, perhaps more importantly, increased performance over single-task networks on a "main/primary" task. However, balancing the optimization criteria of multi-task networks across different tasks is an area of active exploration. Here, we extend a previously proposed 3D attention-based network with four additional multi-task subnetworks for the detection of lung cancer and four auxiliary tasks (diagnosis of asthma, chronic bronchitis, chronic obstructive pulmonary disease, and emphysema). We introduce and evaluate a learning policy, Periodic Focusing Learning Policy (PFLP), that alternates the dominance of tasks throughout the training. To improve performance on the primary task, we propose an Internal-Transfer Weighting (ITW) strategy to suppress the loss functions on auxiliary tasks for the final stages of training. To evaluate this approach, we examined 3386 patients (single scan per patient) from the National Lung Screening Trial (NLST) and de-identified data from the Vanderbilt Lung Screening Program, with a 2517/277/592 (scans) split for training, validation, and testing. Baseline networks include a single-task strategy and a multi-task strategy without adaptive weights (PFLP/ITW), while primary experiments are multi-task trials with either PFLP or ITW or both. On the test set for lung cancer prediction, the baseline single-task network achieved prediction AUC of 0.8080 and the multi-task baseline failed to converge (AUC 0.6720). However, applying PFLP helped multi-task network clarify and achieved test set lung cancer prediction AUC of 0.8402. Furthermore, our ITW technique boosted the PFLP enabled multi-task network and achieved an AUC of 0.8462 (McNemar test, p < 0.01).

* Accepted by Medical Imaging, SPIE2020 

Elimination of Specular reflection and Identification of ROI: The First Step in Automated Detection of Cervical Cancer using Digital Colposcopy

Aug 11, 2011
Abhishek Das, Avijit Kar, Debasis Bhattacharyya

Cervical Cancer is one of the most common forms of cancer in women worldwide. Most cases of cervical cancer can be prevented through screening programs aimed at detecting precancerous lesions. During Digital Colposcopy, Specular Reflections (SR) appear as bright spots heavily saturated with white light. These occur due to the presence of moisture on the uneven cervix surface, which act like mirrors reflecting light from the illumination source. Apart from camouflaging the actual features, the SR also affects subsequent segmentation routines and hence must be removed. Our novel technique eliminates the SR and makes the colposcopic images (cervigram) ready for segmentation algorithms. The cervix region occupies about half of the cervigram image. Other parts of the image contain irrelevant information, such as equipment, frames, text and non-cervix tissues. This irrelevant information can confuse automatic identification of the tissues within the cervix. The first step is, therefore, focusing on the cervical borders, so that we have a geometric boundary on the relevant image area. We have proposed a type of modified kmeans clustering algorithm to evaluate the region of interest.

*, 2011 
* IEEE Imaging Systems and Techniques, 2011, Print ISBN: 978-1-61284-894-5, pages 237 - 241