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"cancer detection": models, code, and papers

Bridging the gap between prostate radiology and pathology through machine learning

Dec 03, 2021
Indrani Bhattacharya, David S. Lim, Han Lin Aung, Xingchen Liu, Arun Seetharaman, Christian A. Kunder, Wei Shao, Simon J. C. Soerensen, Richard E. Fan, Pejman Ghanouni, Katherine J. To'o, James D. Brooks, Geoffrey A. Sonn, Mirabela Rusu

Prostate cancer is the second deadliest cancer for American men. While Magnetic Resonance Imaging (MRI) is increasingly used to guide targeted biopsies for prostate cancer diagnosis, its utility remains limited due to high rates of false positives and false negatives as well as low inter-reader agreements. Machine learning methods to detect and localize cancer on prostate MRI can help standardize radiologist interpretations. However, existing machine learning methods vary not only in model architecture, but also in the ground truth labeling strategies used for model training. In this study, we compare different labeling strategies, namely, pathology-confirmed radiologist labels, pathologist labels on whole-mount histopathology images, and lesion-level and pixel-level digital pathologist labels (previously validated deep learning algorithm on histopathology images to predict pixel-level Gleason patterns) on whole-mount histopathology images. We analyse the effects these labels have on the performance of the trained machine learning models. Our experiments show that (1) radiologist labels and models trained with them can miss cancers, or underestimate cancer extent, (2) digital pathologist labels and models trained with them have high concordance with pathologist labels, and (3) models trained with digital pathologist labels achieve the best performance in prostate cancer detection in two different cohorts with different disease distributions, irrespective of the model architecture used. Digital pathologist labels can reduce challenges associated with human annotations, including labor, time, inter- and intra-reader variability, and can help bridge the gap between prostate radiology and pathology by enabling the training of reliable machine learning models to detect and localize prostate cancer on MRI.

* Indrani Bhattacharya and David S. Lim contributed equally as first authors. Geoffrey A. Sonn and Mirabela Rusu contributed equally as senior authors 
  

Evaluate the Malignancy of Pulmonary Nodules Using the 3D Deep Leaky Noisy-or Network

Nov 22, 2017
Fangzhou Liao, Ming Liang, Zhe Li, Xiaolin Hu, Sen Song

Automatic diagnosing lung cancer from Computed Tomography (CT) scans involves two steps: detect all suspicious lesions (pulmonary nodules) and evaluate the whole-lung/pulmonary malignancy. Currently, there are many studies about the first step, but few about the second step. Since the existence of nodule does not definitely indicate cancer, and the morphology of nodule has a complicated relationship with cancer, the diagnosis of lung cancer demands careful investigations on every suspicious nodule and integration of information of all nodules. We propose a 3D deep neural network to solve this problem. The model consists of two modules. The first one is a 3D region proposal network for nodule detection, which outputs all suspicious nodules for a subject. The second one selects the top five nodules based on the detection confidence, evaluates their cancer probabilities and combines them with a leaky noisy-or gate to obtain the probability of lung cancer for the subject. The two modules share the same backbone network, a modified U-net. The over-fitting caused by the shortage of training data is alleviated by training the two modules alternately. The proposed model won the first place in the Data Science Bowl 2017 competition. The code has been made publicly available.

* 12 pages, 9 figures 
  

CSAW-M: An Ordinal Classification Dataset for Benchmarking Mammographic Masking of Cancer

Dec 02, 2021
Moein Sorkhei, Yue Liu, Hossein Azizpour, Edward Azavedo, Karin Dembrower, Dimitra Ntoula, Athanasios Zouzos, Fredrik Strand, Kevin Smith

Interval and large invasive breast cancers, which are associated with worse prognosis than other cancers, are usually detected at a late stage due to false negative assessments of screening mammograms. The missed screening-time detection is commonly caused by the tumor being obscured by its surrounding breast tissues, a phenomenon called masking. To study and benchmark mammographic masking of cancer, in this work we introduce CSAW-M, the largest public mammographic dataset, collected from over 10,000 individuals and annotated with potential masking. In contrast to the previous approaches which measure breast image density as a proxy, our dataset directly provides annotations of masking potential assessments from five specialists. We also trained deep learning models on CSAW-M to estimate the masking level and showed that the estimated masking is significantly more predictive of screening participants diagnosed with interval and large invasive cancers -- without being explicitly trained for these tasks -- than its breast density counterparts.

* 35th Conference on Neural Information Processing Systems (NeurIPS 2021) Track on Datasets and Benchmarks 
  

Automated detection of oral pre-cancerous tongue lesions using deep learning for early diagnosis of oral cavity cancer

Sep 18, 2019
Mohammed Zubair M. Shamim, Sadatullah Syed, Mohammad Shiblee, Mohammed Usman, Syed Ali

Discovering oral cavity cancer (OCC) at an early stage is an effective way to increase patient survival rate. However, current initial screening process is done manually and is expensive for the average individual, especially in developing countries worldwide. This problem is further compounded due to the lack of specialists in such areas. Automating the initial screening process using artificial intelligence (AI) to detect pre-cancerous lesions can prove to be an effective and inexpensive technique that would allow patients to be triaged accordingly to receive appropriate clinical management. In this study, we have applied and evaluated the efficacy of six deep convolutional neural network (DCNN) models using transfer learning, for identifying pre-cancerous tongue lesions directly using a small data set of clinically annotated photographic images to diagnose early signs of OCC. DCNN model based on Vgg19 architecture was able to differentiate between benign and pre-cancerous tongue lesions with a mean classification accuracy of 0.98, sensitivity 0.89 and specificity 0.97. Additionally, the ResNet50 DCNN model was able to distinguish between five types of tongue lesions i.e. hairy tongue, fissured tongue, geographic tongue, strawberry tongue and oral hairy leukoplakia with a mean classification accuracy of 0.97. Preliminary results using an (AI+Physician) ensemble model demonstrate that an automated initial screening process of tongue lesions using DCNNs can achieve near-human level classification performance for diagnosing early signs of OCC in patients.

* 25 pages, 10 figures 
  

Medico Multimedia Task at MediaEval 2020: Automatic Polyp Segmentation

Dec 30, 2020
Debesh Jha, Steven A. Hicks, Krister Emanuelsen, Håvard Johansen, Dag Johansen, Thomas de Lange, Michael A. Riegler, Pål Halvorsen

Colorectal cancer is the third most common cause of cancer worldwide. According to Global cancer statistics 2018, the incidence of colorectal cancer is increasing in both developing and developed countries. Early detection of colon anomalies such as polyps is important for cancer prevention, and automatic polyp segmentation can play a crucial role for this. Regardless of the recent advancement in early detection and treatment options, the estimated polyp miss rate is still around 20\%. Support via an automated computer-aided diagnosis system could be one of the potential solutions for the overlooked polyps. Such detection systems can help low-cost design solutions and save doctors time, which they could for example use to perform more patient examinations. In this paper, we introduce the 2020 Medico challenge, provide some information on related work and the dataset, describe the task and evaluation metrics, and discuss the necessity of organizing the Medico challenge.

* MediaEval 2020 
  

Recent advances in deep learning applied to skin cancer detection

Dec 06, 2019
Andre G. C. Pacheco, Renato A. Krohling

Skin cancer is a major public health problem around the world. Its early detection is very important to increase patient prognostics. However, the lack of qualified professionals and medical instruments are significant issues in this field. In this context, over the past few years, deep learning models applied to automated skin cancer detection have become a trend. In this paper, we present an overview of the recent advances reported in this field as well as a discussion about the challenges and opportunities for improvement in the current models. In addition, we also present some important aspects regarding the use of these models in smartphones and indicate future directions we believe the field will take.

* Paper accepted in the Retrospectives Workshop @ NeurIPS 2019 
  

BCNet: A Deep Convolutional Neural Network for Breast Cancer Grading

Jul 11, 2021
Pouya Hallaj Zavareh, Atefeh Safayari, Hamidreza Bolhasani

Breast cancer has become one of the most prevalent cancers by which people all over the world are affected and is posed serious threats to human beings, in a particular woman. In order to provide effective treatment or prevention of this cancer, disease diagnosis in the early stages would be of high importance. There have been various methods to detect this disorder in which using images have to play a dominant role. Deep learning has been recently adopted widely in different areas of science, especially medicine. In breast cancer detection problems, some diverse deep learning techniques have been developed on different datasets and resulted in good accuracy. In this article, we aimed to present a deep neural network model to classify histopathological images from the Databiox image dataset as the first application on this image database. Our proposed model named BCNet has taken advantage of the transfer learning approach in which VGG16 is selected from available pertained models as a feature extractor. Furthermore, to address the problem of insufficient data, we employed the data augmentation technique to expand the input dataset. All implementations in this research, ranging from pre-processing actions to depicting the diagram of the model architecture, have been carried out using tf.keras API. As a consequence of the proposed model execution, the significant validation accuracy of 88% and evaluation accuracy of 72% obtained.

  

Machine Learning Approaches to Predict Breast Cancer: Bangladesh Perspective

Jun 30, 2022
Taminul Islam, Arindom Kundu, Nazmul Islam Khan, Choyon Chandra Bonik, Flora Akter, Md Jihadul Islam

Nowadays, Breast cancer has risen to become one of the most prominent causes of death in recent years. Among all malignancies, this is the most frequent and the major cause of death for women globally. Manually diagnosing this disease requires a good amount of time and expertise. Breast cancer detection is time-consuming, and the spread of the disease can be reduced by developing machine-based breast cancer predictions. In Machine learning, the system can learn from prior instances and find hard-to-detect patterns from noisy or complicated data sets using various statistical, probabilistic, and optimization approaches. This work compares several machine learning algorithm's classification accuracy, precision, sensitivity, and specificity on a newly collected dataset. In this work Decision tree, Random Forest, Logistic Regression, Naive Bayes, and XGBoost, these five machine learning approaches have been implemented to get the best performance on our dataset. This study focuses on finding the best algorithm that can forecast breast cancer with maximum accuracy in terms of its classes. This work evaluated the quality of each algorithm's data classification in terms of efficiency and effectiveness. And also compared with other published work on this domain. After implementing the model, this study achieved the best model accuracy, 94% on Random Forest and XGBoost.

* 15 pages, 9 figures, accepted for publication as a book chapter to 2nd International Conference on Ubiquitous Computing and Intelligent Information Systems 
  

Evolution-based Fine-tuning of CNNs for Prostate Cancer Detection

Nov 04, 2019
Khashayar Namdar, Isha Gujrathi, Masoom A. Haider, Farzad Khalvati

Convolutional Neural Networks (CNNs) have been used for automated detection of prostate cancer where Area Under Receiver Operating Characteristic (ROC) curve (AUC) is usually used as the performance metric. Given that AUC is not differentiable, common practice is to train the CNN using a loss functions based on other performance metrics such as cross entropy and monitoring AUC to select the best model. In this work, we propose to fine-tune a trained CNN for prostate cancer detection using a Genetic Algorithm to achieve a higher AUC. Our dataset contained 6-channel Diffusion-Weighted MRI slices of prostate. On a cohort of 2,955 training, 1,417 validation, and 1,334 test slices, we reached test AUC of 0.773; a 9.3% improvement compared to the base CNN model.

* Accepted for the 33rd Conference on Neural Information Processing Systems (NeurIPS 2019), Medical Imaging Meets NEURIPS Workshop 
  

Automated Skin Lesion Classification Using Ensemble of Deep Neural Networks in ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection Challenge

Jan 30, 2019
Md Ashraful Alam Milton

In this paper, we studied extensively on different deep learning based methods to detect melanoma and skin lesion cancers. Melanoma, a form of malignant skin cancer is very threatening to health. Proper diagnosis of melanoma at an earlier stage is crucial for the success rate of complete cure. Dermoscopic images with Benign and malignant forms of skin cancer can be analyzed by computer vision system to streamline the process of skin cancer detection. In this study, we experimented with various neural networks which employ recent deep learning based models like PNASNet-5-Large, InceptionResNetV2, SENet154, InceptionV4. Dermoscopic images are properly processed and augmented before feeding them into the network. We tested our methods on International Skin Imaging Collaboration (ISIC) 2018 challenge dataset. Our system has achieved best validation score of 0.76 for PNASNet-5-Large model. Further improvement and optimization of the proposed methods with a bigger training dataset and carefully chosen hyper-parameter could improve the performances. The code available for download at https://github.com/miltonbd/ISIC_2018_classification

* ISIC 2018 
  
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