Abstract 2107: Seeing glycolysis on PDAC: Applying deep learning convolutional neural network model

2020 ◽  
Author(s):  
Peiling Tsou ◽  
Chang-Jiun Wu
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model

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.

scholarly journals Comparisons of different deep learning-based methods on fault diagnosis for geared system

2019 ◽  
Vol 15 (11) ◽  
pp. 155014771988816 ◽  
Author(s):  
Bing Han ◽  
Xiaohui Yang ◽  
Yafeng Ren ◽  
Wanggui Lan
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Fault Diagnosis ◽  
Convolutional Neural Network ◽  
Mechanical System ◽  
Network Model ◽  
Learning Theory ◽  
Neural Network Model ◽  
Deep Neural Network ◽  
Gear Fault

The running state of a geared transmission system affects the stability and reliability of the whole mechanical system. It will greatly reduce the maintenance cost of a mechanical system to identify the faulty state of the geared transmission system. Based on the measured gear fault vibration signals and the deep learning theory, four fault diagnosis neural network models including fast Fourier transform–deep belief network model, wavelet transform–convolutional neural network model, Hilbert-Huang transform–convolutional neural network model, and comprehensive deep neural network model are developed and trained respectively. The results show that the gear fault diagnosis method based on deep learning theory can effectively identify various gear faults under real test conditions. The comprehensive deep neural network model is the most effective one in gear fault recognition.

scholarly journals An Efficient Deep Learning Approach to Pneumonia Classification in Healthcare

2019 ◽  
Vol 2019 ◽  
pp. 1-7 ◽  
Author(s):  
Okeke Stephen ◽  
Mangal Sain ◽  
Uchenna Joseph Maduh ◽  
Do-Un Jeong
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Data Augmentation ◽  
Classification Performance ◽  
Learning Approaches ◽  
X Ray ◽  
Chest X Ray

This study proposes a convolutional neural network model trained from scratch to classify and detect the presence of pneumonia from a collection of chest X-ray image samples. Unlike other methods that rely solely on transfer learning approaches or traditional handcrafted techniques to achieve a remarkable classification performance, we constructed a convolutional neural network model from scratch to extract features from a given chest X-ray image and classify it to determine if a person is infected with pneumonia. This model could help mitigate the reliability and interpretability challenges often faced when dealing with medical imagery. Unlike other deep learning classification tasks with sufficient image repository, it is difficult to obtain a large amount of pneumonia dataset for this classification task; therefore, we deployed several data augmentation algorithms to improve the validation and classification accuracy of the CNN model and achieved remarkable validation accuracy.

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 Deep Learning–Derived High-Level Neuroimaging Features Predict Clinical Outcomes for Large Vessel Occlusion

Stroke ◽  
2020 ◽  
Vol 51 (5) ◽  
pp. 1484-1492 ◽  
Author(s):  
Hidehisa Nishi ◽  
Naoya Oishi ◽  
Akira Ishii ◽  
Isao Ono ◽  
Takenori Ogura ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Network Model ◽  
Neural Network Model ◽  
Large Vessel ◽  
Large Vessel Occlusion ◽  
Vessel Occlusion ◽  
Neuroimaging Biomarkers ◽  
High Level

Background and Purpose— For patients with large vessel occlusion, neuroimaging biomarkers that evaluate the changes in brain tissue are important for determining the indications for mechanical thrombectomy. In this study, we applied deep learning to derive imaging features from pretreatment diffusion-weighted image data and evaluated the ability of these features in predicting clinical outcomes for patients with large vessel occlusion. Methods— This multicenter retrospective study included patients with anterior circulation large vessel occlusion treated with mechanical thrombectomy between 2013 and 2018. We designed a 2-output deep learning model based on convolutional neural networks (the convolutional neural network model). This model employed encoder-decoder architecture for the ischemic lesion segmentation, which automatically extracted high-level feature maps in its middle layers, and used its information to predict the clinical outcome. Its performance was internally validated with 5-fold cross-validation, externally validated, and the results compared with those from the standard neuroimaging biomarkers Alberta Stroke Program Early CT Score and ischemic core volume. The prediction target was a good clinical outcome, defined as a modified Rankin Scale score at 90-day follow-up of 0 to 2. Results— The derivation cohort included 250 patients, and the validation cohort included 74 patients. The convolutional neural network model showed the highest area under the receiver operating characteristic curve: 0.81±0.06 compared with 0.63±0.05 and 0.64±0.05 for the Alberta Stroke Program Early CT Score and ischemic core volume models, respectively. In the external validation, the area under the curve for the convolutional neural network model was significantly superior to those for the other 2 models. Conclusions— Compared with the standard neuroimaging biomarkers, our deep learning model derived a greater amount of prognostic information from pretreatment neuroimaging data. Although a confirmatory prospective evaluation is needed, the high-level imaging features derived by deep learning may offer an effective prognostic imaging biomarker.

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