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"cancer detection": models, code, and papers

A system on chip for melanoma detection using FPGA-based SVM classifier

Sep 30, 2021
Shereen Afifi, Hamid GholamHosseini, Roopak Sinha

Support Vector Machine (SVM) is a robust machine learning model that shows high accuracy with different classification problems, and is widely used for various embedded applications. However , implementation of embedded SVM classifiers is challenging, due to the inherent complicated computations required. This motivates implementing the SVM on hardware platforms for achieving high performance computing at low cost and power consumption. Melanoma is the most aggressive form of skin cancer that increases the mortality rate. We aim to develop an optimized embedded SVM classifier dedicated for a low-cost handheld device for early detection of melanoma at the primary healthcare. In this paper, we propose a hardware/software co-design for implementing the SVM classifier onto FPGA to realize melanoma detection on a chip. The implemented SVM on a recent hybrid FPGA (Zynq) platform utilizing the modern UltraFast High-Level Synthesis design methodology achieves efficient melanoma classification on chip. The hardware implementation results demonstrate classification accuracy of 97.9%, and a significant hardware acceleration rate of 21 with only 3% resources utilization and 1.69W for power consumption. These results show that the implemented system on chip meets crucial embedded system constraints of high performance and low resources utilization, power consumption, and cost, while achieving efficient classification with high classification accuracy.

* A system on chip for melanoma detection using FPGA-based SVM classifier, Microprocessors and Microsystems 65(2019) pp.57-68 
* Journal paper, 13 pages, 3 figures, 9 tables 
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Effect of Channel Geometry and Flow Rates in Hydrodynamic Focusing on Impedance Detection of Circulating Tumor Cells

Mar 08, 2022
Hassan Raji, Iraj Dehghan Hamani

Cells, other than their biological properties, have different electric and physical properties. In an impedance cytometer, cells should pass one by one in the detection region where pairs of electrodes are located. When cells are located between electrodes, the impedance changes, and this can be indicative of the presence of a cell. This is basically because the electric properties of cells are different from the medium between the electrodes which is important in determining the impedance. One of the most important aspects which influence the performance of an impedance cytometer performance is the microchannel design. In this work, in the first step, the microchannel was designed in a way to have the best detection in the impedance cytometer. In this regard, hydrodynamic focusing was selected to focus the population of cells entering from the inlet of the main channel. To find the optimal parameters of the microchannel, different geometry for the channel itself, along with flow rates and other parameters related to sheath flow were simulated. In the next step, impedance was measured in COMSOL for White blood cells, MCF7, and MDA-MB-231 breast cancer cells. The results show that by measuring the impedance of cells using the optimized channel design, CTCs can be successfully differentiated from WBCs.

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PFA-ScanNet: Pyramidal Feature Aggregation with Synergistic Learning for Breast Cancer Metastasis Analysis

May 03, 2019
Zixu Zhao, Huangjing Lin, Hao Chen, Pheng Ann Heng

Automatic detection of cancer metastasis from whole slide images (WSIs) is a crucial step for following patient staging as well as prognosis. However, recent convolutional neural network (CNN) based approaches are struggling with the trade-off between accuracy and computation cost due to the difficulty in processing large-scale gigapixel images. To address this challenge, we propose a novel deep neural network, namely Pyramidal Feature Aggregation ScanNet (PFA-ScanNet) with pyramidal feature aggregation in both top-down and bottom-up paths. The discrimination capability of our detector is increased by leveraging the merit of contextual and spatial information from multi-scale features with larger receptive fields and less parameters. We also develop an extra decoder branch to synergistically learn the semantic information along with the detector, significantly improving the performance in recognizing the metastasis. Furthermore, a high-efficiency inference mechanism is designed with dense pooling layers, which allows dense and fast scanning for gigapixel WSI analysis. Our approach achieved the state-of-the-art FROC score of 89.1% on the Camelyon16 dataset, as well as competitive kappa score of 0.905 on the Camelyon17 leaderboard. In addition, our proposed method shows leading speed advantage over the state-of-the-art methods, which makes automatic analysis of breast cancer metastasis more applicable in the clinical usage.

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SOMPS-Net : Attention based social graph framework for early detection of fake health news

Nov 22, 2021
Prasannakumaran D, Harish Srinivasan, Sowmiya Sree S, Sri Gayathri Devi I, Saikrishnan S, Vineeth Vijayaraghavan

Fake news is fabricated information that is presented as genuine, with intention to deceive the reader. Recently, the magnitude of people relying on social media for news consumption has increased significantly. Owing to this rapid increase, the adverse effects of misinformation affect a wider audience. On account of the increased vulnerability of people to such deceptive fake news, a reliable technique to detect misinformation at its early stages is imperative. Hence, the authors propose a novel graph-based framework SOcial graph with Multi-head attention and Publisher information and news Statistics Network (SOMPS-Net) comprising of two components - Social Interaction Graph (SIG) and Publisher and News Statistics (PNS). The posited model is experimented on the HealthStory dataset and generalizes across diverse medical topics including Cancer, Alzheimer's, Obstetrics, and Nutrition. SOMPS-Net significantly outperformed other state-of-the-art graph-based models experimented on HealthStory by 17.1%. Further, experiments on early detection demonstrated that SOMPS-Net predicted fake news articles with 79% certainty within just 8 hours of its broadcast. Thus the contributions of this work lay down the foundation for capturing fake health news across multiple medical topics at its early stages.

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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 
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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 
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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 
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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 
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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.

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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.

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