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Radiology Radiology

Ultrasound-based internal carotid artery plaque characterization using deep learning paradigm on a supercomputer: a cardiovascular disease/stroke risk assessment system.

In The international journal of cardiovascular imaging

Visual or manual characterization and classification of atherosclerotic plaque lesions are tedious, error-prone, and time-consuming. The purpose of this study is to develop and design an automated carotid plaque characterization and classification system into binary classes, namely symptomatic and asymptomatic types via the deep learning (DL) framework implemented on a supercomputer. We hypothesize that on ultrasound images, symptomatic carotid plaques have (a) a low grayscale median because of a histologically large lipid core and relatively little collagen and calcium, and (b) a higher chaotic (heterogeneous) grayscale distribution due to the composition. The methodology consisted of building a DL model of Artificial Intelligence (called Atheromatic 2.0, AtheroPoint, CA, USA) that used a classic convolution neural network consisting of 13 layers and implemented on a supercomputer. The DL model used a cross-validation protocol for estimating the classification accuracy (ACC) and area-under-the-curve (AUC). A sample of 346 carotid ultrasound-based delineated plaques were used (196 symptomatic and 150 asymptomatic, mean age 69.9 ± 7.8 years, with 39% females). This was augmented using geometric transformation yielding 2312 plaques (1191 symptomatic and 1120 asymptomatic plaques). K10 (90% training and 10% testing) cross-validation DL protocol was implemented and showed an (i) accuracy and (ii) AUC without and with augmentation of 86.17%, 0.86 (p-value < 0.0001), and 89.7%, 0.91 (p-value < 0.0001), respectively. The DL characterization system consisted of validation of the two hypotheses: (a) mean feature strength (MFS) and (b) Mandelbrot's fractal dimension (FD) for measuring chaotic behavior. We demonstrated that both MFS and FD were higher in symptomatic plaques compared to asymptomatic plaques by 64.15 ± 0.73% (p-value < 0.0001) and 6 ± 0.13% (p-value < 0.0001), respectively. The benchmarking results show that DL with augmentation (ACC: 89.7%, AUC: 0.91 (p-value < 0.0001)) is superior to previously published machine learning (ACC: 83.7%) by 6.0%. The Atheromatic runs the test patient in < 2 s. Deep learning can be a useful tool for carotid ultrasound-based characterization and classification of symptomatic and asymptomatic plaques.

Saba Luca, Sanagala Skandha S, Gupta Suneet K, Koppula Vijaya K, Johri Amer M, Sharma Aditya M, Kolluri Raghu, Bhatt Deepak L, Nicolaides Andrew, Suri Jasjit S

2021-Jan-09

Accuracy, And speed, Artificial intelligence, Asymptomatic, Atherosclerosis, Carotid plaque, Deep learning, Machine learning, Performance, Supercomputer, Symptomatic, Ultrasound

Surgery Surgery

LASSO-Based Machine Learning Algorithm for Prediction of Lymph Node Metastasis in T1 Colorectal Cancer.

In Cancer research and treatment : official journal of Korean Cancer Association

Purpose : The role of tumor-infiltrating lymphocytes (TILs) in predicting lymph node metastasis (LNM) in patients with T1 colorectal cancer (CRC) remains unclear. Furthermore, clinical utility of a machine learning-based approach has not been widely studied.

Materials and Methods : Immunohistochemistry for TILs against CD3, CD8, and forkhead box P3 in both center and invasive margin of the tumor were performed using surgically resected T1 CRC slides. Three-hundred-and-sixteen patients were enrolled and categorized into training (n=221) and validation (n=95) sets via random sampling. Using clinicopathologic variables including TILs, the least absolute shrinkage and selection operator (LASSO) regression model was applied for variable selection and predictive signature building in the training set. The predictive accuracy of our model and the Japanese criteria were compared using area under the receiver operating characteristic (AUROC), net reclassification improvement (NRI)/integrated discrimination improvement (IDI), and decision curve analysis (DCA) in the validation set.

Results : LNM was detected in 29 (13.1%) and 12 (12.6%) patients in training and validation sets, respectively. Nine variables were selected and used to generate the LASSO model. Its performance was similar in training and validation sets (AUROC, 0.795 vs. 0.765; p=0.747). In the validation set, the LASSO model showed better outcomes in predicting LNM than Japanese criteria, as measured by AUROC (0.765 vs. 0.518, p=0.003) and NRI (0.447, p=0.030)/IDI (0.121, p=0.034). DCA showed positive net benefits in using our model.

Conclusion : Our LASSO model incorporating histopathologic parameters and TILs showed superior performance compared to conventional Japanese criteria in predicting LNM in patients with T1 CRC.

Kang Jeonghyun, Choi Yoon Jung, Kim Im-Kyung, Lee Hye Sun, Kim Hogeun, Baik Seung Hyuk, Kim Nam Kyu, Lee Kang Young

2020-Dec-29

LASSO, Lymph node, Machine learning, T1 colorectal cancer, Tumor-infiltrating lymphocytes

General General

Detection of Epileptic Seizure Using Pretrained Deep Convolutional Neural Network and Transfer Learning.

In European neurology

INTRODUCTION : The diagnosis of epilepsy takes a certain process, depending entirely on the attending physician. However, the human factor may cause erroneous diagnosis in the analysis of the EEG signal. In the past 2 decades, many advanced signal processing and machine learning methods have been developed for the detection of epileptic seizures. However, many of these methods require large data sets and complex operations.

METHODS : In this study, an end-to-end machine learning model is presented for detection of epileptic seizure using the pretrained deep two-dimensional convolutional neural network (CNN) and the concept of transfer learning. The EEG signal is converted directly into visual data with a spectrogram and used directly as input data.

RESULTS : The authors analyzed the results of the training of the proposed pretrained AlexNet CNN model. Both binary and ternary classifications were performed without any extra procedure such as feature extraction. By performing data set creation from short-term spectrogram graphic images, the authors were able to achieve 100% accuracy for binary classification for epileptic seizure detection and 100% for ternary classification.

DISCUSSION/CONCLUSION : The proposed automatic identification and classification model can help in the early diagnosis of epilepsy, thus providing the opportunity for effective early treatment.

Nogay Hidir Selcuk, Adeli Hojjat

2021-Jan-08

AlexNet, Electroencephalogram, Epileptic seizure detection, Pretrained deep convolutional neural network, Spectrogram, Transfer learning

Dermatology Dermatology

Robustness of convolutional neural networks in recognition of pigmented skin lesions.

In European journal of cancer (Oxford, England : 1990)

BACKGROUND : A basic requirement for artificial intelligence (AI)-based image analysis systems, which are to be integrated into clinical practice, is a high robustness. Minor changes in how those images are acquired, for example, during routine skin cancer screening, should not change the diagnosis of such assistance systems.

OBJECTIVE : To quantify to what extent minor image perturbations affect the convolutional neural network (CNN)-mediated skin lesion classification and to evaluate three possible solutions for this problem (additional data augmentation, test-time augmentation, anti-aliasing).

METHODS : We trained three commonly used CNN architectures to differentiate between dermoscopic melanoma and nevus images. Subsequently, their performance and susceptibility to minor changes ('brittleness') was tested on two distinct test sets with multiple images per lesion. For the first set, image changes, such as rotations or zooms, were generated artificially. The second set contained natural changes that stemmed from multiple photographs taken of the same lesions.

RESULTS : All architectures exhibited brittleness on the artificial and natural test set. The three reviewed methods were able to decrease brittleness to varying degrees while still maintaining performance. The observed improvement was greater for the artificial than for the natural test set, where enhancements were minor.

CONCLUSIONS : Minor image changes, relatively inconspicuous for humans, can have an effect on the robustness of CNNs differentiating skin lesions. By the methods tested here, this effect can be reduced, but not fully eliminated. Thus, further research to sustain the performance of AI classifiers is needed to facilitate the translation of such systems into the clinic.

Maron Roman C, Haggenmüller Sarah, von Kalle Christof, Utikal Jochen S, Meier Friedegund, Gellrich Frank F, Hauschild Axel, French Lars E, Schlaak Max, Ghoreschi Kamran, Kutzner Heinz, Heppt Markus V, Haferkamp Sebastian, Sondermann Wiebke, Schadendorf Dirk, Schilling Bastian, Hekler Achim, Krieghoff-Henning Eva, Kather Jakob N, Fröhling Stefan, Lipka Daniel B, Brinker Titus J

2021-Jan-07

Artificial intelligence, Deep learning, Dermatology, Machine learning, Melanoma, Neural networks, Nevus, Skin neoplasms

General General

Identification of toxicity pathway of diesel particulate matter using AOP of PPARγ inactivation leading to pulmonary fibrosis.

In Environment international

Diesel particulate matter (DPM), a major subset of urban fine particulate matter (PM2.5), raises huge concerns for human health and has therefore been classified as a group 1 carcinogen by the International Agency for Research on Cancer (IARC). However, as DPM is a complex mixture of various chemicals, understanding of DPM's toxicity mechanism remains limited. As the major exposure route of DPM is through inhalation, we herein investigated its toxicity mechanism based on the Adverse Outcome Pathway (AOP) of pulmonary fibrosis, which we previously submitted to AOPWiki as AOP ID 206 (AOP206). We first screened whether individual chemicals in DPM have the potential to exert their toxicity through AOP206 by using the ToxCast database and deep learning models approach, then confirmed this by examining whether DPM as a mixture alters the expression of the molecular initiating event (MIE) and key events (KEs) of AOP206. For identifying the activeness of the component chemicals of DPM, we used 24 ToxCast assays potentially related to AOP206 and deep learning models based on these assays, which were identified and developed in our previous study. Of the 100 individual chemicals in DPM, 34 were active in PPARγ (MIE)-related assay, of which 17 were active in one or more KEs. To further identify whether individual chemicals in DPM are related to the MIE of AOP206, we performed molecular docking simulation on PPARγ for the chemicals showing activeness. Benzo[e]pyrene, benzo[a]pyrene and other related chemicals were the most likely to bind to PPARγ. In in vitro experiments, PPARγ activity increased with exposure of the DPM mixture, and the protein expression of PPARγ (MIE), and fibronectin (AO) also tended to be increased. Overall, we have demonstrated that AOP206 can be applied to identify the toxicity pathway of DPM. Further, we suggest that applying the AOP approach using ToxCast and deep learning models is useful for identifying potential toxicity pathways of chemical mixtures, such as DPM, by determining the activity of individual chemicals.

Jeong Jaeseong, Bae Su-Yong, Choi Jinhee

2021-Jan-12

Adverse Outcome Pathway, Deep learning, Diesel particulate matter, Mixture toxicity, Molecular docking, ToxCast

General General

An enhanced approach to the robust discriminant analysis and class sparsity based embedding.

In Neural networks : the official journal of the International Neural Network Society

In recent times, feature extraction attracted much attention in machine learning and pattern recognition fields. This paper extends and improves a scheme for linear feature extraction that can be used in supervised multi-class classification problems. Inspired by recent frameworks for robust sparse LDA and Inter-class sparsity, we propose a unifying criterion able to retain the advantages of these two powerful linear discriminant methods. We introduce an iterative alternating minimization scheme in order to estimate the linear transformation and the orthogonal matrix. The linear transformation is efficiently updated via the steepest descent gradient technique. The proposed framework is generic in the sense that it allows the combination and tuning of other linear discriminant embedding methods. We used our proposed method to fine tune the linear solutions delivered by two recent linear methods: RSLDA and RDA_FSIS. Experiments have been conducted on public image datasets of different types including objects, faces, and digits. The proposed framework compared favorably with several competing methods.

Khoder A, Dornaika F

2020-Dec-30

Discriminant model, Feature extraction, Image categorization, Inter-class sparsity, Linear embedding, Supervised learning