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"cancer detection": models, code, and papers

Transfer Learning by Cascaded Network to identify and classify lung nodules for cancer detection

Sep 24, 2020
Shah B. Shrey, Lukman Hakim, Muthusubash Kavitha, Hae Won Kim, Takio Kurita

Lung cancer is one of the most deadly diseases in the world. Detecting such tumors at an early stage can be a tedious task. Existing deep learning architecture for lung nodule identification used complex architecture with large number of parameters. This study developed a cascaded architecture which can accurately segment and classify the benign or malignant lung nodules on computed tomography (CT) images. The main contribution of this study is to introduce a segmentation network where the first stage trained on a public data set can help to recognize the images which included a nodule from any data set by means of transfer learning. And the segmentation of a nodule improves the second stage to classify the nodules into benign and malignant. The proposed architecture outperformed the conventional methods with an area under curve value of 95.67\%. The experimental results showed that the classification accuracy of 97.96\% of our proposed architecture outperformed other simple and complex architectures in classifying lung nodules for lung cancer detection.


Debiasing pipeline improves deep learning model generalization for X-ray based lung nodule detection

Jan 24, 2022
Michael Horry, Subrata Chakraborty, Biswajeet Pradhan, Manoranjan Paul, Jing Zhu, Hui Wen Loh, Prabal Datta Barua, U. Rajendra Arharya

Lung cancer is the leading cause of cancer death worldwide and a good prognosis depends on early diagnosis. Unfortunately, screening programs for the early diagnosis of lung cancer are uncommon. This is in-part due to the at-risk groups being located in rural areas far from medical facilities. Reaching these populations would require a scaled approach that combines mobility, low cost, speed, accuracy, and privacy. We can resolve these issues by combining the chest X-ray imaging mode with a federated deep-learning approach, provided that the federated model is trained on homogenous data to ensure that no single data source can adversely bias the model at any point in time. In this study we show that an image pre-processing pipeline that homogenizes and debiases chest X-ray images can improve both internal classification and external generalization, paving the way for a low-cost and accessible deep learning-based clinical system for lung cancer screening. An evolutionary pruning mechanism is used to train a nodule detection deep learning model on the most informative images from a publicly available lung nodule X-ray dataset. Histogram equalization is used to remove systematic differences in image brightness and contrast. Model training is performed using all combinations of lung field segmentation, close cropping, and rib suppression operators. We show that this pre-processing pipeline results in deep learning models that successfully generalize an independent lung nodule dataset using ablation studies to assess the contribution of each operator in this pipeline. In stripping chest X-ray images of known confounding variables by lung field segmentation, along with suppression of signal noise from the bone structure we can train a highly accurate deep learning lung nodule detection algorithm with outstanding generalization accuracy of 89% to nodule samples in unseen data.

* 32 pages, 17 figures, 4 tables 

Cancer Detection with Multiple Radiologists via Soft Multiple Instance Logistic Regression and $L_1$ Regularization

Dec 09, 2014
Inna Stainvas, Alexandra Manevitch, Isaac Leichter

This paper deals with the multiple annotation problem in medical application of cancer detection in digital images. The main assumption is that though images are labeled by many experts, the number of images read by the same expert is not large. Thus differing with the existing work on modeling each expert and ground truth simultaneously, the multi annotation information is used in a soft manner. The multiple labels from different experts are used to estimate the probability of the findings to be marked as malignant. The learning algorithm minimizes the Kullback Leibler (KL) divergence between the modeled probabilities and desired ones constraining the model to be compact. The probabilities are modeled by logit regression and multiple instance learning concept is used by us. Experiments on a real-life computer aided diagnosis (CAD) problem for CXR CAD lung cancer detection demonstrate that the proposed algorithm leads to similar results as learning with a binary RVMMIL classifier or a mixture of binary RVMMIL models per annotator. However, this model achieves a smaller complexity and is more preferable in practice.

* 20 pages, report 

Computer-aided diagnosis of lung carcinoma using deep learning - a pilot study

Mar 14, 2018
Zhang Li, Zheyu Hu, Jiaolong Xu, Tao Tan, Hui Chen, Zhi Duan, Ping Liu, Jun Tang, Guoping Cai, Quchang Ouyang, Yuling Tang, Geert Litjens, Qiang Li

Aim: Early detection and correct diagnosis of lung cancer are the most important steps in improving patient outcome. This study aims to assess which deep learning models perform best in lung cancer diagnosis. Methods: Non-small cell lung carcinoma and small cell lung carcinoma biopsy specimens were consecutively obtained and stained. The specimen slides were diagnosed by two experienced pathologists (over 20 years). Several deep learning models were trained to discriminate cancer and non-cancer biopsies. Result: Deep learning models give reasonable AUC from 0.8810 to 0.9119. Conclusion: The deep learning analysis could help to speed up the detection process for the whole-slide image (WSI) and keep the comparable detection rate with human observer.


$\text{O}^2$PF: Oversampling via Optimum-Path Forest for Breast Cancer Detection

Jan 14, 2021
Leandro Aparecido Passos, Danilo Samuel Jodas, Luiz C. F. Ribeiro, Thierry Pinheiro, João P. Papa

Breast cancer is among the most deadly diseases, distressing mostly women worldwide. Although traditional methods for detection have presented themselves as valid for the task, they still commonly present low accuracies and demand considerable time and effort from professionals. Therefore, a computer-aided diagnosis (CAD) system capable of providing early detection becomes hugely desirable. In the last decade, machine learning-based techniques have been of paramount importance in this context, since they are capable of extracting essential information from data and reasoning about it. However, such approaches still suffer from imbalanced data, specifically on medical issues, where the number of healthy people samples is, in general, considerably higher than the number of patients. Therefore this paper proposes the $\text{O}^2$PF, a data oversampling method based on the unsupervised Optimum-Path Forest Algorithm. Experiments conducted over the full oversampling scenario state the robustness of the model, which is compared against three well-established oversampling methods considering three breast cancer and three general-purpose tasks for medical issues datasets.

* 6 pages, 3 figures. 2020 IEEE 33rd International Symposium on Computer-Based Medical Systems (CBMS) 

Assessing domain adaptation techniques for mitosis detection in multi-scanner breast cancer histopathology images

Sep 25, 2021
Jack Breen, Kieran Zucker, Nicolas Orsi, Geoff Hall, Nishant Ravikumar

Breast cancer is the most prevalent cancer worldwide and is increasing in incidence, with over two million new cases now diagnosed each year. As part of diagnostic tumour grading, histopathologists manually count the number of dividing cells (mitotic figures) in a sample. Since the process is subjective and time-consuming, artificial intelligence (AI) methods have been developed to automate the process, however these methods often perform poorly when applied to data from outside of the original (training) domain, i.e. they do not generalise well to variations in histological background, staining protocols, or scanner types. Style transfer, a form of domain adaptation, provides the means to transform images from different domains to a shared visual appearance and have been adopted in various applications to mitigate the issue of domain shift. In this paper we train two mitosis detection models and two style transfer methods and evaluate the usefulness of the latter for improving mitosis detection performance in images digitised using different scanners. We found that the best of these models, U-Net without style transfer, achieved an F1-score of 0.693 on the MIDOG 2021 preliminary test set.


Hybrid Machine Learning Model of Extreme Learning Machine Radial basis function for Breast Cancer Detection and Diagnosis; a Multilayer Fuzzy Expert System

Oct 29, 2019
Sanaz Mojrian, Gergo Pinter, Javad Hassannataj Joloudari, Imre Felde, Narjes Nabipour, Laszlo Nadai, Amir Mosavi

Mammography is often used as the most common laboratory method for the detection of breast cancer, yet associated with the high cost and many side effects. Machine learning prediction as an alternative method has shown promising results. This paper presents a method based on a multilayer fuzzy expert system for the detection of breast cancer using an extreme learning machine (ELM) classification model integrated with radial basis function (RBF) kernel called ELM-RBF, considering the Wisconsin dataset. The performance of the proposed model is further compared with a linear-SVM model. The proposed model outperforms the linear-SVM model with RMSE, R2, MAPE equal to 0.1719, 0.9374 and 0.0539, respectively. Furthermore, both models are studied in terms of criteria of accuracy, precision, sensitivity, specificity, validation, true positive rate (TPR), and false-negative rate (FNR). The ELM-RBF model for these criteria presents better performance compared to the SVM model.

* 7 pages, 5 figures 

A Comprehensive Study of Data Augmentation Strategies for Prostate Cancer Detection in Diffusion-weighted MRI using Convolutional Neural Networks

Jun 01, 2020
Ruqian Hao, Khashayar Namdar, Lin Liu, Masoom A. Haider, Farzad Khalvati

Data augmentation refers to a group of techniques whose goal is to battle limited amount of available data to improve model generalization and push sample distribution toward the true distribution. While different augmentation strategies and their combinations have been investigated for various computer vision tasks in the context of deep learning, a specific work in the domain of medical imaging is rare and to the best of our knowledge, there has been no dedicated work on exploring the effects of various augmentation methods on the performance of deep learning models in prostate cancer detection. In this work, we have statically applied five most frequently used augmentation techniques (random rotation, horizontal flip, vertical flip, random crop, and translation) to prostate Diffusion-weighted Magnetic Resonance Imaging training dataset of 217 patients separately and evaluated the effect of each method on the accuracy of prostate cancer detection. The augmentation algorithms were applied independently to each data channel and a shallow as well as a deep Convolutional Neural Network (CNN) were trained on the five augmented sets separately. We used Area Under Receiver Operating Characteristic (ROC) curve (AUC) to evaluate the performance of the trained CNNs on a separate test set of 95 patients, using a validation set of 102 patients for finetuning. The shallow network outperformed the deep network with the best 2D slice-based AUC of 0.85 obtained by the rotation method.


Accurate Prostate Cancer Detection and Segmentation on Biparametric MRI using Non-local Mask R-CNN with Histopathological Ground Truth

Oct 28, 2020
Zhenzhen Dai, Ivan Jambor, Pekka Taimen, Milan Pantelic, Mohamed Elshaikh, Craig Rogers, Otto Ettala, Peter Boström, Hannu Aronen, Harri Merisaari, Ning Wen

Purpose: We aimed to develop deep machine learning (DL) models to improve the detection and segmentation of intraprostatic lesions (IL) on bp-MRI by using whole amount prostatectomy specimen-based delineations. We also aimed to investigate whether transfer learning and self-training would improve results with small amount labelled data. Methods: 158 patients had suspicious lesions delineated on MRI based on bp-MRI, 64 patients had ILs delineated on MRI based on whole mount prostatectomy specimen sections, 40 patients were unlabelled. A non-local Mask R-CNN was proposed to improve the segmentation accuracy. Transfer learning was investigated by fine-tuning a model trained using MRI-based delineations with prostatectomy-based delineations. Two label selection strategies were investigated in self-training. The performance of models was evaluated by 3D detection rate, dice similarity coefficient (DSC), 95 percentile Hausdrauff (95 HD, mm) and true positive ratio (TPR). Results: With prostatectomy-based delineations, the non-local Mask R-CNN with fine-tuning and self-training significantly improved all evaluation metrics. For the model with the highest detection rate and DSC, 80.5% (33/41) of lesions in all Gleason Grade Groups (GGG) were detected with DSC of 0.548[0.165], 95 HD of 5.72[3.17] and TPR of 0.613[0.193]. Among them, 94.7% (18/19) of lesions with GGG > 2 were detected with DSC of 0.604[0.135], 95 HD of 6.26[3.44] and TPR of 0.580[0.190]. Conclusion: DL models can achieve high prostate cancer detection and segmentation accuracy on bp-MRI based on annotations from histologic images. To further improve the performance, more data with annotations of both MRI and whole amount prostatectomy specimens are required.


Local image registration a comparison for bilateral registration mammography

Aug 12, 2013
José M. Celaya-Padilla, Juan Rodriguez-Rojas, Victor Trevino, José G. Gerardo Tamez-Pena

Early tumor detection is key in reducing the number of breast cancer death and screening mammography is one of the most widely available and reliable method for early detection. However, it is difficult for the radiologist to process with the same attention each case, due the large amount of images to be read. Computer aided detection (CADe) systems improve tumor detection rate; but the current efficiency of these systems is not yet adequate and the correct interpretation of CADe outputs requires expert human intervention. Computer aided diagnosis systems (CADx) are being designed to improve cancer diagnosis accuracy, but they have not been efficiently applied in breast cancer. CADx efficiency can be enhanced by considering the natural mirror symmetry between the right and left breast. The objective of this work is to evaluate co-registration algorithms for the accurate alignment of the left to right breast for CADx enhancement. A set of mammograms were artificially altered to create a ground truth set to evaluate the registration efficiency of DEMONs, and SPLINE deformable registration algorithms. The registration accuracy was evaluated using mean square errors, mutual information and correlation. The results on the 132 images proved that the SPLINE deformable registration over-perform the DEMONS on mammography images.

* 9 pages, Submitted to The 9th International Seminar on Medical Information Processing and Analysis (formerly International Seminar on Medical Image Processing and Analysis) (pending approval)