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"cancer detection": models, code, and papers

Interpretative Computer-aided Lung Cancer Diagnosis: from Radiology Analysis to Malignancy Evaluation

Feb 22, 2021
Shaohua Zheng, Zhiqiang Shen, Chenhao Peia, Wangbin Ding, Haojin Lin, Jiepeng Zheng, Lin Pan, Bin Zheng, Liqin Huang

Background and Objective:Computer-aided diagnosis (CAD) systems promote diagnosis effectiveness and alleviate pressure of radiologists. A CAD system for lung cancer diagnosis includes nodule candidate detection and nodule malignancy evaluation. Recently, deep learning-based pulmonary nodule detection has reached satisfactory performance ready for clinical application. However, deep learning-based nodule malignancy evaluation depends on heuristic inference from low-dose computed tomography volume to malignant probability, which lacks clinical cognition. Methods:In this paper, we propose a joint radiology analysis and malignancy evaluation network (R2MNet) to evaluate the pulmonary nodule malignancy via radiology characteristics analysis. Radiological features are extracted as channel descriptor to highlight specific regions of the input volume that are critical for nodule malignancy evaluation. In addition, for model explanations, we propose channel-dependent activation mapping to visualize the features and shed light on the decision process of deep neural network. Results:Experimental results on the LIDC-IDRI dataset demonstrate that the proposed method achieved area under curve of 96.27% on nodule radiology analysis and AUC of 97.52% on nodule malignancy evaluation. In addition, explanations of CDAM features proved that the shape and density of nodule regions were two critical factors that influence a nodule to be inferred as malignant, which conforms with the diagnosis cognition of experienced radiologists. Conclusion:Incorporating radiology analysis with nodule malignant evaluation, the network inference process conforms to the diagnostic procedure of radiologists and increases the confidence of evaluation results. Besides, model interpretation with CDAM features shed light on the regions which DNNs focus on when they estimate nodule malignancy probabilities.

* 11 pages, 8 figures 

Acute Lymphoblastic Leukemia Detection from Microscopic Images Using Weighted Ensemble of Convolutional Neural Networks

May 09, 2021
Chayan Mondal, Md. Kamrul Hasan, Md. Tasnim Jawad, Aishwariya Dutta, Md. Rabiul Islam, Md. Abdul Awal, Mohiuddin Ahmad

Acute Lymphoblastic Leukemia (ALL) is a blood cell cancer characterized by numerous immature lymphocytes. Even though automation in ALL prognosis is an essential aspect of cancer diagnosis, it is challenging due to the morphological correlation between malignant and normal cells. The traditional ALL classification strategy demands experienced pathologists to carefully read the cell images, which is arduous, time-consuming, and often suffers inter-observer variations. This article has automated the ALL detection task from microscopic cell images, employing deep Convolutional Neural Networks (CNNs). We explore the weighted ensemble of different deep CNNs to recommend a better ALL cell classifier. The weights for the ensemble candidate models are estimated from their corresponding metrics, such as accuracy, F1-score, AUC, and kappa values. Various data augmentations and pre-processing are incorporated for achieving a better generalization of the network. We utilize the publicly available C-NMC-2019 ALL dataset to conduct all the comprehensive experiments. Our proposed weighted ensemble model, using the kappa values of the ensemble candidates as their weights, has outputted a weighted F1-score of 88.6 %, a balanced accuracy of 86.2 %, and an AUC of 0.941 in the preliminary test set. The qualitative results displaying the gradient class activation maps confirm that the introduced model has a concentrated learned region. In contrast, the ensemble candidate models, such as Xception, VGG-16, DenseNet-121, MobileNet, and InceptionResNet-V2, separately produce coarse and scatter learned areas for most example cases. Since the proposed kappa value-based weighted ensemble yields a better result for the aimed task in this article, it can experiment in other domains of medical diagnostic applications.

* 31 pages, 9 figures 

Self-transfer learning via patches: A prostate cancer triage approach based on bi-parametric MRI

Jul 22, 2021
Alvaro Fernandez-Quilez, Trygve Eftestøl, Morten Goodwin, Svein Reidar Kjosavik, Ketil Oppedal

Prostate cancer (PCa) is the second most common cancer diagnosed among men worldwide. The current PCa diagnostic pathway comes at the cost of substantial overdiagnosis, leading to unnecessary treatment and further testing. Bi-parametric magnetic resonance imaging (bp-MRI) based on apparent diffusion coefficient maps (ADC) and T2-weighted (T2w) sequences has been proposed as a triage test to differentiate between clinically significant (cS) and non-clinically significant (ncS) prostate lesions. However, analysis of the sequences relies on expertise, requires specialized training, and suffers from inter-observer variability. Deep learning (DL) techniques hold promise in tasks such as classification and detection. Nevertheless, they rely on large amounts of annotated data which is not common in the medical field. In order to palliate such issues, existing works rely on transfer learning (TL) and ImageNet pre-training, which has been proven to be sub-optimal for the medical imaging domain. In this paper, we present a patch-based pre-training strategy to distinguish between cS and ncS lesions which exploit the region of interest (ROI) of the patched source domain to efficiently train a classifier in the full-slice target domain which does not require annotations by making use of transfer learning (TL). We provide a comprehensive comparison between several CNNs architectures and different settings which are presented as a baseline. Moreover, we explore cross-domain TL which exploits both MRI modalities and improves single modality results. Finally, we show how our approaches outperform the standard approaches by a considerable margin

* 13 pages. Article under review 

Deep SNP: An End-to-end Deep Neural Network with Attention-based Localization for Break-point Detection in SNP Array Genomic data

Jun 22, 2018
Hamid Eghbal-zadeh, Lukas Fischer, Niko Popitsch, Florian Kromp, Sabine Taschner-Mandl, Khaled Koutini, Teresa Gerber, Eva Bozsaky, Peter F. Ambros, Inge M. Ambros, Gerhard Widmer, Bernhard A. Moser

Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming manual curation. As deep-learning methods outperformed classical state-of-the-art algorithms in various domains and have also been successfully applied to life science problems including medicine and biology, we here propose Deep SNP, a novel Deep Neural Network to learn from genomic data. Specifically, we used a manually curated dataset from 12 genomic single nucleotide polymorphism array (SNPa) profiles as truth-set and aimed at predicting the presence or absence of genomic breakpoints, an indicator of structural chromosomal variations, in windows of 40,000 probes. We compare our results with well-known neural network models as well as Rawcopy though this tool is designed to predict breakpoints and in addition genomic segments with high sensitivity. We show, that Deep SNP is capable of successfully predicting the presence or absence of a breakpoint in large genomic windows and outperforms state-of-the-art neural network models. Qualitative examples suggest that integration of a localization unit may enable breakpoint detection and prediction of genomic segments, even if the breakpoint coordinates were not provided for network training. These results warrant further evaluation of DeepSNP for breakpoint localization and subsequent calling of genomic segments.

* Accepted at the Joint ICML and IJCAI 2018 Workshop on Computational Biology 

Transferability of Deep Learning Algorithms for Malignancy Detection in Confocal Laser Endomicroscopy Images from Different Anatomical Locations of the Upper Gastrointestinal Tract

Feb 24, 2019
Marc Aubreville, Miguel Goncalves, Christian Knipfer, Nicolai Oetter, Helmut Neumann, Florian Stelzle, Christopher Bohr, Andreas Maier

Squamous Cell Carcinoma (SCC) is the most common cancer type of the epithelium and is often detected at a late stage. Besides invasive diagnosis of SCC by means of biopsy and histo-pathologic assessment, Confocal Laser Endomicroscopy (CLE) has emerged as noninvasive method that was successfully used to diagnose SCC in vivo. For interpretation of CLE images, however, extensive training is required, which limits its applicability and use in clinical practice of the method. To aid diagnosis of SCC in a broader scope, automatic detection methods have been proposed. This work compares two methods with regard to their applicability in a transfer learning sense, i.e. training on one tissue type (from one clinical team) and applying the learnt classification system to another entity (different anatomy, different clinical team). Besides a previously proposed, patch-based method based on convolutional neural networks, a novel classification method on image level (based on a pre-trained Inception V.3 network with dedicated preprocessing and interpretation of class activation maps) is proposed and evaluated. The newly presented approach improves recognition performance, yielding accuracies of 91.63% on the first data set (oral cavity) and 92.63% on a joint data set. The generalization from oral cavity to the second data set (vocal folds) lead to similar area-under-the-ROC curve values than a direct training on the vocal folds data set, indicating good generalization.


Image Data collection and implementation of deep learning-based model in detecting Monkeypox disease using modified VGG16

Jun 04, 2022
Md Manjurul Ahsan, Muhammad Ramiz Uddin, Mithila Farjana, Ahmed Nazmus Sakib, Khondhaker Al Momin, Shahana Akter Luna

While the world is still attempting to recover from the damage caused by the broad spread of COVID-19, the Monkeypox virus poses a new threat of becoming a global pandemic. Although the Monkeypox virus itself is not deadly and contagious as COVID-19, still every day, new patients case has been reported from many nations. Therefore, it will be no surprise if the world ever faces another global pandemic due to the lack of proper precautious steps. Recently, Machine learning (ML) has demonstrated huge potential in image-based diagnoses such as cancer detection, tumor cell identification, and COVID-19 patient detection. Therefore, a similar application can be adopted to diagnose the Monkeypox-related disease as it infected the human skin, which image can be acquired and further used in diagnosing the disease. Considering this opportunity, in this work, we introduce a newly developed "Monkeypox2022" dataset that is publicly available to use and can be obtained from our shared GitHub repository. The dataset is created by collecting images from multiple open-source and online portals that do not impose any restrictions on use, even for commercial purposes, hence giving a safer path to use and disseminate such data when constructing and deploying any type of ML model. Further, we propose and evaluate a modified VGG16 model, which includes two distinct studies: Study One and Two. Our exploratory computational results indicate that our suggested model can identify Monkeypox patients with an accuracy of $97\pm1.8\%$ (AUC=97.2) and $88\pm0.8\%$ (AUC=0.867) for Study One and Two, respectively. Additionally, we explain our model's prediction and feature extraction utilizing Local Interpretable Model-Agnostic Explanations (LIME) help to a deeper insight into specific features that characterize the onset of the Monkeypox virus.


A Computer Vision Pipeline for Automated Determination of Cardiac Structure and Function and Detection of Disease by Two-Dimensional Echocardiography

Jan 12, 2018
Jeffrey Zhang, Sravani Gajjala, Pulkit Agrawal, Geoffrey H. Tison, Laura A. Hallock, Lauren Beussink-Nelson, Eugene Fan, Mandar A. Aras, ChaRandle Jordan, Kirsten E. Fleischmann, Michelle Melisko, Atif Qasim, Alexei Efros, Sanjiv J. Shah, Ruzena Bajcsy, Rahul C. Deo

Automated cardiac image interpretation has the potential to transform clinical practice in multiple ways including enabling low-cost serial assessment of cardiac function in the primary care and rural setting. We hypothesized that advances in computer vision could enable building a fully automated, scalable analysis pipeline for echocardiogram (echo) interpretation. Our approach entailed: 1) preprocessing; 2) convolutional neural networks (CNN) for view identification, image segmentation, and phasing of the cardiac cycle; 3) quantification of chamber volumes and left ventricular mass; 4) particle tracking to compute longitudinal strain; and 5) targeted disease detection. CNNs accurately identified views (e.g. 99% for apical 4-chamber) and segmented individual cardiac chambers. Cardiac structure measurements agreed with study report values (e.g. mean absolute deviations (MAD) of 7.7 mL/kg/m2 for left ventricular diastolic volume index, 2918 studies). We computed automated ejection fraction and longitudinal strain measurements (within 2 cohorts), which agreed with commercial software-derived values [for ejection fraction, MAD=5.3%, N=3101 studies; for strain, MAD=1.5% (n=197) and 1.6% (n=110)], and demonstrated applicability to serial monitoring of breast cancer patients for trastuzumab cardiotoxicity. Overall, we found that, compared to manual measurements, automated measurements had superior performance across seven internal consistency metrics with an average increase in the Spearman correlation coefficient of 0.05 (p=0.02). Finally, we developed disease detection algorithms for hypertrophic cardiomyopathy and cardiac amyloidosis, with C-statistics of 0.93 and 0.84, respectively. Our pipeline lays the groundwork for using automated interpretation to support point-of-care handheld cardiac ultrasound and large-scale analysis of the millions of echos archived within healthcare systems.

* 9 figures, 2 tables 

Deep learning assessment of breast terminal duct lobular unit involution: towards automated prediction of breast cancer risk

Oct 31, 2019
Suzanne C Wetstein, Allison M Onken, Christina Luffman, Gabrielle M Baker, Michael E Pyle, Kevin H Kensler, Ying Liu, Bart Bakker, Ruud Vlutters, Marinus B van Leeuwen, Laura C Collins, Stuart J Schnitt, Josien PW Pluim, Rulla M Tamimi, Yujing J Heng, Mitko Veta

Terminal ductal lobular unit (TDLU) involution is the regression of milk-producing structures in the breast. Women with less TDLU involution are more likely to develop breast cancer. A major bottleneck in studying TDLU involution in large cohort studies is the need for labor-intensive manual assessment of TDLUs. We developed a computational pathology solution to automatically capture TDLU involution measures. Whole slide images (WSIs) of benign breast biopsies were obtained from the Nurses' Health Study (NHS). A first set of 92 WSIs was annotated for TDLUs, acini and adipose tissue to train deep convolutional neural network (CNN) models for detection of acini, and segmentation of TDLUs and adipose tissue. These networks were integrated into a single computational method to capture TDLU involution measures including number of TDLUs per tissue area, median TDLU span and median number of acini per TDLU. We validated our method on 40 additional WSIs by comparing with manually acquired measures. Our CNN models detected acini with an F1 score of 0.73$\pm$0.09, and segmented TDLUs and adipose tissue with Dice scores of 0.86$\pm$0.11 and 0.86$\pm$0.04, respectively. The inter-observer ICC scores for manual assessments on 40 WSIs of number of TDLUs per tissue area, median TDLU span, and median acini count per TDLU were 0.71, 95% CI [0.51, 0.83], 0.81, 95% CI [0.67, 0.90], and 0.73, 95% CI [0.54, 0.85], respectively. Intra-observer reliability was evaluated on 10/40 WSIs with ICC scores of >0.8. Inter-observer ICC scores between automated results and the mean of the two observers were: 0.80, 95% CI [0.63, 0.90] for number of TDLUs per tissue area, 0.57, 95% CI [0.19, 0.77] for median TDLU span, and 0.80, 95% CI [0.62, 0.89] for median acini count per TDLU. TDLU involution measures evaluated by manual and automated assessment were inversely associated with age and menopausal status.


Colon Nuclei Instance Segmentation using a Probabilistic Two-Stage Detector

Mar 01, 2022
Pedro Costa, Yongpan Fu, João Nunes, Aurélio Campilho, Jaime S. Cardoso

Cancer is one of the leading causes of death in the developed world. Cancer diagnosis is performed through the microscopic analysis of a sample of suspicious tissue. This process is time consuming and error prone, but Deep Learning models could be helpful for pathologists during cancer diagnosis. We propose to change the CenterNet2 object detection model to also perform instance segmentation, which we call SegCenterNet2. We train SegCenterNet2 in the CoNIC challenge dataset and show that it performs better than Mask R-CNN in the competition metrics.


Skin Lesion Synthesis with Generative Adversarial Networks

Feb 08, 2019
Alceu Bissoto, Fábio Perez, Eduardo Valle, Sandra Avila

Skin cancer is by far the most common type of cancer. Early detection is the key to increase the chances for successful treatment significantly. Currently, Deep Neural Networks are the state-of-the-art results on automated skin cancer classification. To push the results further, we need to address the lack of annotated data, which is expensive and require much effort from specialists. To bypass this problem, we propose using Generative Adversarial Networks for generating realistic synthetic skin lesion images. To the best of our knowledge, our results are the first to show visually-appealing synthetic images that comprise clinically-meaningful information.

* Conference: ISIC Skin Image Analysis Workshop and Challenge @ MICCAI 2018