scholarly journals A robust and interpretable, end-to-end deep learning model for cytometry data

2020 ◽  
Author(s):  
Zicheng Hu ◽  
Alice Tang ◽  
Jaiveer Singh ◽  
Sanchita Bhattacharya ◽  
Atul J. Butte
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Learning Model ◽  
Deep Convolutional Neural Network ◽  
Significant Information ◽  
End To End ◽  
Deep Learning Model

AbstractCytometry technologies are essential tools for immunology research, providing high-throughput measurements of the immune cells at the single-cell level. Traditional approaches in interpreting and using cytometry measurements include manual or automated gating to identify cell subsets from the cytometry data, providing highly intuitive results but may lead to significant information loss, in that additional details in measured or correlated cell signals might be missed. In this study, we propose and test a deep convolutional neural network for analyzing cytometry data in an end-to-end fashion, allowing a direct association between raw cytometry data and the clinical outcome of interest. Using nine large CyTOF studies from the open-access ImmPort database, we demonstrated that the deep convolutional neural network model can accurately diagnose the latent cytomegalovirus (CMV) in healthy individuals, even when using highly heterogeneous data from different studies. In addition, we developed a permutation-based method for interpreting the deep convolutional neural network model and identified a CD27-CD94+ CD8+ T cell population significantly associated with latent CMV infection. Finally, we provide a tutorial for creating, training and interpreting the tailored deep learning model for cytometry data using Keras and TensorFlow (github.com/hzc363/DeepLearningCyTOF).

scholarly journals A robust and interpretable end-to-end deep learning model for cytometry data

2020 ◽  
Vol 117 (35) ◽  
pp. 21373-21380
Author(s):  
Zicheng Hu ◽  
Alice Tang ◽  
Jaiveer Singh ◽  
Sanchita Bhattacharya ◽  
Atul J. Butte
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Learning Model ◽  
Deep Convolutional Neural Network ◽  
Significant Information ◽  
End To End ◽  
Deep Learning Model

Cytometry technologies are essential tools for immunology research, providing high-throughput measurements of the immune cells at the single-cell level. Existing approaches in interpreting and using cytometry measurements include manual or automated gating to identify cell subsets from the cytometry data, providing highly intuitive results but may lead to significant information loss, in that additional details in measured or correlated cell signals might be missed. In this study, we propose and test a deep convolutional neural network for analyzing cytometry data in an end-to-end fashion, allowing a direct association between raw cytometry data and the clinical outcome of interest. Using nine large cytometry by time-of-flight mass spectrometry or mass cytometry (CyTOF) studies from the open-access ImmPort database, we demonstrated that the deep convolutional neural network model can accurately diagnose the latent cytomegalovirus (CMV) in healthy individuals, even when using highly heterogeneous data from different studies. In addition, we developed a permutation-based method for interpreting the deep convolutional neural network model. We were able to identify a CD27- CD94+ CD8+ T cell population significantly associated with latent CMV infection, confirming the findings in previous studies. Finally, we provide a tutorial for creating, training, and interpreting the tailored deep learning model for cytometry data using Keras and TensorFlow (https://github.com/hzc363/DeepLearningCyTOF).

scholarly journals Predicting Hepatocellular Carcinoma With Minimal Features From Electronic Health Records: Development of a Deep Learning Model

JMIR Cancer ◽  
10.2196/19812 ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. e19812
Author(s):  
Chia-Wei Liang ◽  
Hsuan-Chia Yang ◽  
Md Mohaimenul Islam ◽  
Phung Anh Alex Nguyen ◽  
Yi-Ting Feng ◽  
...  
Keyword(s):  
Neural Network ◽  
Hepatocellular Carcinoma ◽  
Deep Learning ◽  
Electronic Health Records ◽  
Network Model ◽  
Neural Network Model ◽  
Learning Model ◽  
Health Records ◽  
Electronic Health ◽  
Deep Learning Model

Background Hepatocellular carcinoma (HCC), usually known as hepatoma, is the third leading cause of cancer mortality globally. Early detection of HCC helps in its treatment and increases survival rates. Objective The aim of this study is to develop a deep learning model, using the trend and severity of each medical event from the electronic health record to accurately predict the patients who will be diagnosed with HCC in 1 year. Methods Patients with HCC were screened out from the National Health Insurance Research Database of Taiwan between 1999 and 2013. To be included, the patients with HCC had to register as patients with cancer in the catastrophic illness file and had to be diagnosed as a patient with HCC in an inpatient admission. The control cases (non-HCC patients) were randomly sampled from the same database. We used age, gender, diagnosis code, drug code, and time information as the input variables of a convolution neural network model to predict those patients with HCC. We also inspected the highly weighted variables in the model and compared them to their odds ratio at HCC to understand how the predictive model works Results We included 47,945 individuals, 9553 of whom were patients with HCC. The area under the receiver operating curve (AUROC) of the model for predicting HCC risk 1 year in advance was 0.94 (95% CI 0.937-0.943), with a sensitivity of 0.869 and a specificity 0.865. The AUROC for predicting HCC patients 7 days, 6 months, 1 year, 2 years, and 3 years early were 0.96, 0.94, 0.94, 0.91, and 0.91, respectively. Conclusions The findings of this study show that the convolutional neural network model has immense potential to predict the risk of HCC 1 year in advance with minimal features available in the electronic health records.

scholarly journals A Novel Deep Convolutional Neural Network for Tuberculosis Detection

2021 ◽  
Vol 9 (VI) ◽  
pp. 1135-1139
Author(s):  
Syed Farhan Hyder Abidi
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Mycobacterium Tuberculosis ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Learning Model ◽  
Deep Convolutional Neural Network ◽  
Deep Learning Model

India accounts for the world’s largest number of cases in TB, with 2.8 million cases annually, and accounts for more than a quarter of the global TB burden. Tuberculosis (TB) is caused by the bacterium (Mycobacterium tuberculosis) which most commonly affects the lungs. TB is transmitted from person to person through the air. When people with TB cough, sneeze or spit, the germs are propelled into the air. This paper showcases a methodology which uses a Deep Learning Model (dCNN) for the detection of Tuberculosis in the lungs. The accuracy obtained by the methods for the model is desirable and dependable, which is increasingly productive in contrast to the accuracy shown by other neural networks.

scholarly journals Multi- class classification of breast cancer abnormalities using Deep Convolutional Neural Network (CNN)

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256500
Author(s):  
Maleika Heenaye-Mamode Khan ◽  
Nazmeen Boodoo-Jahangeer ◽  
Wasiimah Dullull ◽  
Shaista Nathire ◽  
Xiaohong Gao ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Neural Network ◽  
Deep Learning ◽  
Early Detection ◽  
Convolutional Neural Network ◽  
Learning Model ◽  
Learning Rate ◽  
Deep Convolutional Neural Network ◽  
Deep Learning Model

The real cause of breast cancer is very challenging to determine and therefore early detection of the disease is necessary for reducing the death rate due to risks of breast cancer. Early detection of cancer boosts increasing the survival chance up to 8%. Primarily, breast images emanating from mammograms, X-Rays or MRI are analyzed by radiologists to detect abnormalities. However, even experienced radiologists face problems in identifying features like micro-calcifications, lumps and masses, leading to high false positive and high false negative. Recent advancement in image processing and deep learning create some hopes in devising more enhanced applications that can be used for the early detection of breast cancer. In this work, we have developed a Deep Convolutional Neural Network (CNN) to segment and classify the various types of breast abnormalities, such as calcifications, masses, asymmetry and carcinomas, unlike existing research work, which mainly classified the cancer into benign and malignant, leading to improved disease management. Firstly, a transfer learning was carried out on our dataset using the pre-trained model ResNet50. Along similar lines, we have developed an enhanced deep learning model, in which learning rate is considered as one of the most important attributes while training the neural network. The learning rate is set adaptively in our proposed model based on changes in error curves during the learning process involved. The proposed deep learning model has achieved a performance of 88% in the classification of these four types of breast cancer abnormalities such as, masses, calcifications, carcinomas and asymmetry mammograms.

On The Effect Of Decomposition Granularity On DeTraC For COVID-19 Detection Using Chest X-Ray Images

2021 ◽  
Author(s):  
Nicole P. Mugova ◽  
Mohammed M. Abdelsamea ◽  
Mohamed M. Gaber
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Learning Model ◽  
Deep Convolutional Neural Network ◽  
Experimental Results ◽  
Number Of Clusters ◽  
X Ray ◽  
Chest X Ray ◽  
Deep Learning Model

Covid-19 is a growing issue in society and there is a need for resources to manage the disease. This paper looks at studying the effect of class decomposition in our previously proposed deep Convolutional Neural Network, called DeTraC (Decompose, Transfer and Compose). DeTraC has the ability to robustly detect and predict Covid-19 from chest X-ray images. The experimental results showed that changing the number of clusters affected the performance of DeTraC and influenced the accuracy of the model. As the number of clusters increased, the accuracy decreased for the shallow tuning mode but increased for the deep tuning mode. This shows the importance of using suitable hyperparameter settings in order to get the best results from a deep learning model. The highest accuracy obtained, in this study, was 98.33% from the deep tuning model.

scholarly journals Predicting Hepatocellular Carcinoma With Minimal Features From Electronic Health Records: Development of a Deep Learning Model (Preprint)

2020 ◽  
Author(s):  
Chia-Wei Liang ◽  
Hsuan-Chia Yang ◽  
Md Mohaimenul Islam ◽  
Phung Anh Alex Nguyen ◽  
Yi-Ting Feng ◽  
...  
Keyword(s):  
Neural Network ◽  
Hepatocellular Carcinoma ◽  
Deep Learning ◽  
Electronic Health Records ◽  
Network Model ◽  
Neural Network Model ◽  
Learning Model ◽  
Health Records ◽  
Electronic Health ◽  
Deep Learning Model

BACKGROUND Hepatocellular carcinoma (HCC), usually known as hepatoma, is the third leading cause of cancer mortality globally. Early detection of HCC helps in its treatment and increases survival rates. OBJECTIVE The aim of this study is to develop a deep learning model, using the trend and severity of each medical event from the electronic health record to accurately predict the patients who will be diagnosed with HCC in 1 year. METHODS Patients with HCC were screened out from the National Health Insurance Research Database of Taiwan between 1999 and 2013. To be included, the patients with HCC had to register as patients with cancer in the catastrophic illness file and had to be diagnosed as a patient with HCC in an inpatient admission. The control cases (non-HCC patients) were randomly sampled from the same database. We used age, gender, diagnosis code, drug code, and time information as the input variables of a convolution neural network model to predict those patients with HCC. We also inspected the highly weighted variables in the model and compared them to their odds ratio at HCC to understand how the predictive model works RESULTS We included 47,945 individuals, 9553 of whom were patients with HCC. The area under the receiver operating curve (AUROC) of the model for predicting HCC risk 1 year in advance was 0.94 (95% CI 0.937-0.943), with a sensitivity of 0.869 and a specificity 0.865. The AUROC for predicting HCC patients 7 days, 6 months, 1 year, 2 years, and 3 years early were 0.96, 0.94, 0.94, 0.91, and 0.91, respectively. CONCLUSIONS The findings of this study show that the convolutional neural network model has immense potential to predict the risk of HCC 1 year in advance with minimal features available in the electronic health records.

Deep learning model for protein disease classification

2021 ◽  
Vol 16 ◽  
Author(s):  
Farida Alaaeldin Mostafa ◽  
Yasmine Mohamed Afify ◽  
Rasha Mohamed Ismail ◽  
Nagwa Lotfy Badr
Keyword(s):  
Neural Network ◽  
Support Vector Machine ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Protein Analysis ◽  
Kernel Functions ◽  
Support Vector ◽  
Feature Descriptors

Background: Protein sequence analysis helps in the prediction of protein functions. As the number of proteins increases, it gives the bioinformaticians a challenge to analyze and study the similarity between them. Most of the existing protein analysis methods use Support Vector Machine. Deep learning did not receive much attention regarding protein analysis as it is noted that little work focused on studying the protein diseases classification. Objective: The contribution of this paper is to present a deep learning approach that classifies protein diseases based on protein descriptors. Methods: Different protein descriptors are used and decomposed into modified feature descriptors. Uniquely, we introduce using Convolutional Neural Network model to learn and classify protein diseases. The modified feature descriptors are fed to the Convolutional Neural Network model on a dataset of 1563 protein sequences classified into 3 different disease classes: Aids, Tumor suppressor, and Proto oncogene. Results: The usage of the modified feature descriptors shows a significant increase in the performance of the Convolutional Neural Network model over Support Vector Machine using different kernel functions. One modified feature descriptor improved by 19.8%, 27.9%, 17.6%, 21.5%, 17.3%, and 22% for evaluation metrics: Area Under the Curve, Matthews Correlation Coefficient, Accuracy, F1-score, Recall, and Precision, respectively. Conclusion: Results show that the prediction of the proposed modified feature descriptors significantly surpasses that of Support Vector Machine model.

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