scholarly journals DeepPhospho: Accelerate DIA phosphoproteome profiling by Deep Learning

2021 ◽  
Author(s):  
Wenqing Shui ◽  
Ronghui Lou ◽  
Weizhen Liu ◽  
Rongjie Li ◽  
Shanshan Li ◽  
...  
Keyword(s):  
Neural Network ◽  
Data Mining ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Learning Models ◽  
Spectral Library ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
User Access ◽  
Egf Signaling

Abstract Phosphoproteomics integrating data-independent acquisition (DIA) has enabled deep phosphoproteome profiling with improved quantification reproducibility and accuracy compared to data-dependent acquisition (DDA)-based phosphoproteomics. DIA data mining heavily relies on a spectral library that in most cases is built on DDA analysis of the same sample. Construction of this project-specific DDA library impairs the analytical throughput, limits the proteome coverage, and increases the sample size for DIA phosphoproteomics. Herein we introduce a novel deep neural network, DeepPhospho, which conceptually differs from previous deep learning models to achieve accurate predictions of LC-MS/MS data for phosphopeptides. By leveraging in silico libraries generated by DeepPhospho, we established a new DIA workflow for phosphoproteome profiling which involves DIA data acquisition and data mining with DeepPhospho predicted libraries, thus circumventing the need of DDA library construction. Our DeepPhospho-empowered workflow substantially expanded the phosphoproteome coverage while maintaining high quantification performance, which led to the discovery of more signaling pathways and regulated kinases in an EGF signaling study than the DDA library-based approach. DeepPhospho is provided as a web server to facilitate user access to predictions and library generation.

scholarly journals DeepPhospho accelerates DIA phosphoproteome profiling through in silico library generation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ronghui Lou ◽  
Weizhen Liu ◽  
Rongjie Li ◽  
Shanshan Li ◽  
Xuming He ◽  
...  
Keyword(s):  
Data Mining ◽  
In Silico ◽  
Deep Neural Network ◽  
Learning Models ◽  
Spectral Library ◽  
Proteome Coverage ◽  
Data Independent Acquisition ◽  
User Access ◽  
Model Training ◽  
Egf Signaling

AbstractPhosphoproteomics integrating data-independent acquisition (DIA) enables deep phosphoproteome profiling with improved quantification reproducibility and accuracy compared to data-dependent acquisition (DDA)-based phosphoproteomics. DIA data mining heavily relies on a spectral library that in most cases is built on DDA analysis of the same sample. Construction of this project-specific DDA library impairs the analytical throughput, limits the proteome coverage, and increases the sample size for DIA phosphoproteomics. Herein we introduce a deep neural network, DeepPhospho, which conceptually differs from previous deep learning models to achieve accurate predictions of LC-MS/MS data for phosphopeptides. By leveraging in silico libraries generated by DeepPhospho, we establish a DIA workflow for phosphoproteome profiling which involves DIA data acquisition and data mining with DeepPhospho predicted libraries, thus circumventing the need of DDA library construction. Our DeepPhospho-empowered workflow substantially expands the phosphoproteome coverage while maintaining high quantification performance, which leads to the discovery of more signaling pathways and regulated kinases in an EGF signaling study than the DDA library-based approach. DeepPhospho is provided as a web server as well as an offline app to facilitate user access to model training, predictions and library generation.

scholarly journals Anomaly Detection Using Deep Neural Network for IoT Architecture

2021 ◽  
Vol 11 (15) ◽  
pp. 7050
Author(s):  
Zeeshan Ahmad ◽  
Adnan Shahid Khan ◽  
Kashif Nisar ◽  
Iram Haider ◽  
Rosilah Hassan ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Anomaly Detection ◽  
Deep Neural Network ◽  
Detection System ◽  
Traffic Monitoring ◽  
Detection Accuracy ◽  
Learning Models ◽  
Prime Concern ◽  
Entry Points

The revolutionary idea of the internet of things (IoT) architecture has gained enormous popularity over the last decade, resulting in an exponential growth in the IoT networks, connected devices, and the data processed therein. Since IoT devices generate and exchange sensitive data over the traditional internet, security has become a prime concern due to the generation of zero-day cyberattacks. A network-based intrusion detection system (NIDS) can provide the much-needed efficient security solution to the IoT network by protecting the network entry points through constant network traffic monitoring. Recent NIDS have a high false alarm rate (FAR) in detecting the anomalies, including the novel and zero-day anomalies. This paper proposes an efficient anomaly detection mechanism using mutual information (MI), considering a deep neural network (DNN) for an IoT network. A comparative analysis of different deep-learning models such as DNN, Convolutional Neural Network, Recurrent Neural Network, and its different variants, such as Gated Recurrent Unit and Long Short-term Memory is performed considering the IoT-Botnet 2020 dataset. Experimental results show the improvement of 0.57–2.6% in terms of the model’s accuracy, while at the same time reducing the FAR by 0.23–7.98% to show the effectiveness of the DNN-based NIDS model compared to the well-known deep learning models. It was also observed that using only the 16–35 best numerical features selected using MI instead of 80 features of the dataset result in almost negligible degradation in the model’s performance but helped in decreasing the overall model’s complexity. In addition, the overall accuracy of the DL-based models is further improved by almost 0.99–3.45% in terms of the detection accuracy considering only the top five categorical and numerical features.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

A Similarity-Based Object Classification Using Deep Neural Networks

2019 ◽  
pp. 197-219
Author(s):  
Parvathi R. ◽  
Pattabiraman V.
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Search Algorithm ◽  
Random Projection ◽  
Learning Networks ◽  
Learning Models ◽  
External Conditions ◽  
And Training

This chapter proposes a hybrid method for classification of the objects based on deep neural network and a similarity-based search algorithm. The objects are pre-processed with external conditions. After pre-processing and training different deep learning networks with the object dataset, the authors compare the results to find the best model to improve the accuracy of the results based on the features of object images extracted from the feature vector layer of a neural network. RPFOREST (random projection forest) model is used to predict the approximate nearest images. ResNet50, InceptionV3, InceptionV4, and DenseNet169 models are trained with this dataset. A proposal for adaptive finetuning of the deep learning models by determining the number of layers required for finetuning with the help of the RPForest model is given, and this experiment is conducted using the Xception model.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

scholarly journals Evaluating Deep Learning models for predicting ALK-5 inhibition

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0246126
Author(s):  
Gabriel Z. Espinoza ◽  
Rafaela M. Angelo ◽  
Patricia R. Oliveira ◽  
Kathia M. Honorio
Keyword(s):  
Neural Network ◽  
Biological Activity ◽  
Deep Learning ◽  
Deep Neural Network ◽  
External Validation ◽  
Machine Learning Techniques ◽  
Coefficient Of Determination ◽  
Support Vector ◽  
Learning Models ◽  
Alk 5

Computational methods have been widely used in drug design. The recent developments in machine learning techniques and the ever-growing chemical and biological databases are fertile ground for discoveries in this area. In this study, we evaluated the performance of Deep Learning models in comparison to Random Forest, and Support Vector Regression for predicting the biological activity (pIC50) of ALK-5 inhibitors as candidates to treat cancer. The generalization power of the models was assessed by internal and external validation procedures. A deep neural network model obtained the best performance in this comparative study, achieving a coefficient of determination of 0.658 on the external validation set with mean square error and mean absolute error of 0.373 and 0.450, respectively. Additionally, the relevance of the chemical descriptors for the prediction of biological activity was estimated using Permutation Importance. We can conclude that the forecast model obtained by the deep neural network is suitable for the problem and can be employed to predict the biological activity of new ALK-5 inhibitors.

scholarly journals Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jiarui Feng ◽  
Heming Zhang ◽  
Fuhai Li
Keyword(s):  
Neural Network ◽  
Survival Analysis ◽  
Deep Learning ◽  
Survival Time ◽  
Signaling Pathways ◽  
Cancer Patients ◽  
Deep Neural Network ◽  
Survival Prediction ◽  
Omics Data ◽  
Learning Models

Abstract Background Survival analysis is an important part of cancer studies. In addition to the existing Cox proportional hazards model, deep learning models have recently been proposed in survival prediction, which directly integrates multi-omics data of a large number of genes using the fully connected dense deep neural network layers, which are hard to interpret. On the other hand, cancer signaling pathways are important and interpretable concepts that define the signaling cascades regulating cancer development and drug resistance. Thus, it is important to investigate potential associations between patient survival and individual signaling pathways, which can help domain experts to understand deep learning models making specific predictions. Results In this exploratory study, we proposed to investigate the relevance and influence of a set of core cancer signaling pathways in the survival analysis of cancer patients. Specifically, we built a simplified and partially biologically meaningful deep neural network, DeepSigSurvNet, for survival prediction. In the model, the gene expression and copy number data of 1967 genes from 46 major signaling pathways were integrated in the model. We applied the model to four types of cancer and investigated the influence of the 46 signaling pathways in the cancers. Interestingly, the interpretable analysis identified the distinct patterns of these signaling pathways, which are helpful in understanding the relevance of signaling pathways in terms of their application to the prediction of cancer patients’ survival time. These highly relevant signaling pathways, when combined with other essential signaling pathways inhibitors, can be novel targets for drug and drug combination prediction to improve cancer patients’ survival time. Conclusion The proposed DeepSigSurvNet model can facilitate the understanding of the implications of signaling pathways on cancer patients’ survival by integrating multi-omics data and clinical factors.

Abstract 12569: Analysis of Deep Learning Models for Prediction of Heart Failure Mortality

Circulation ◽  
2020 ◽  
Vol 142 (Suppl_3) ◽  
Author(s):  
Chayakrit Krittanawong ◽  
Kipp W Johnson ◽  
Usman Baber ◽  
Mehmet Aydar ◽  
Zhen Wang ◽  
...  
Keyword(s):  
Neural Network ◽  
Heart Failure ◽  
Deep Learning ◽  
Network Model ◽  
Neural Network Model ◽  
Deep Neural Network ◽  
Validation Cohort ◽  
Sensitivity Analyses ◽  
Brier Score ◽  
Learning Models

Introduction: Heart failure (HF) is a leading cause of hospitalization, morbidity and mortality. Deep learning (DL) techniques appear to show promising results in risk stratification and prognosis in several conditions in medicine. However, few methods using DL exist to help quantitatively estimate prognosis of HF. We hypothesized that deep learning (DL) techniques could prognosis of HF using simple variables. We propose application of a custom-built deep-neural-network model to identify mortality in HF patients. Methods: Custom-built deep-neural-networks were assessed using survey data from 42,147 participants from the National Health and Nutrition Examination Survey 1999-2016 (NHANES). Variables were selected using clinical judgment and stepwise backward regressions to develop prediction models. We partitioned the data into training and testing sets and repetitive experiments. We then evaluated model performance based on discrimination and calibration including the area under the receiver-operator characteristics curve (C-statistics), balanced accuracy, probability calibration with sigmoid, and the Brier score, respectively. As sensitivity analyses, we examined results limited to cases with complete clinical information available. We validated models’ performance using Mount Sinai database. Results: Of 42,147 participants with 4,060 variables, 1,491 (3.5%) had HF and HF mortality was 51.8%. In validation cohort, of 26,333 HF patients, the mortality in HF patients was 405 (1.5%). Final model using only 20 variables (age, race, gender, BMI, smoking, alcohol consumption, HTN, COPD, SBP, DBP, HR, HDL, LDL, CRP, A1C, BUN, creatinine, hemoglobin, sodium level, on statin) was tested. A state-of-the-art deep learning models achieved high accuracy for predicting mortality in HF patients with an AUC of 0.96 (95% CI: 0.95-0.99) in the first cohort and AUC of 0.93 (95% CI: 0.91-0.96) in validation cohort. Conclusions: A deep neural network model has shown to have high predictive accuracy and discriminative and calibrative power for prediction of HF mortality. Further research can delineate the clinical implications of DL in predicting HF mortality.

scholarly journals MALWARE DETECTION SYSTEM BASED ON DEEP LEARNING TECHNIQUE

2021 ◽  
Vol 1 (1) ◽  
pp. 33-44
Author(s):  
Zahraa Z. Edie ◽  
Ammar D. Jasim
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Deep Neural Network ◽  
Detection System ◽  
Learning Models ◽  
Future Evolution ◽  
Malware Classification ◽  
Learning Technique ◽  
Family Classification

In this paper, we propose a malware classification and detection framework using transfer learning based on existing Deep Learning models that have been pre-trained on massive image datasets, we applied a deep Convolutional Neural Network (CNN) based on Xception model to perform malware image classification. The Xception model is a recently developed special CNN architecture that is more powerful with less overfitting problems than the current popular CNN models such as VGG16, The experimental results on a Malimg Dataset which is comprising 9,821 samples from 26 different families ,Malware samples are represented as byteplot grayscale images and a deep neural network is trained freezing the convolutional layers of Xception model adapting the last layer to malware family classification , The performance of our approach was compared with other methods including KNN, SVM, VGG16 etc. , the Xception model can effectively be used to classify and detect  malware families and  achieve the highest validation accuracy  than all other approaches including VGG16 model which are using image-based malware, our approach does not require any features engineering, making it more effective to adapt to any future evolution in malware, and very much less time consuming than the champion’s solution.

scholarly journals An Automobile Environment Detection System Based on Deep Neural Network and its Implementation Using IoT-Enabled In-Vehicle Air Quality Sensors

2020 ◽  
Vol 12 (6) ◽  
pp. 2475 ◽  
Author(s):  
Jae-joon Chung ◽  
Hyun-Jung Kim
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Air Quality ◽  
Deep Neural Network ◽  
Short Term Memory ◽  
Detection System ◽  
Learning Models ◽  
Generative Adversarial Network ◽  
Detection Model ◽  
Adversarial Network

This paper elucidates the development of a deep learning–based driver assistant that can prevent driving accidents arising from drowsiness. As a precursor to this assistant, the relationship between the sensation of sleep depravity among drivers during long journeys and CO2 concentrations in vehicles is established. Multimodal signals are collected by the assistant using five sensors that measure the levels of CO, CO2, and particulate matter (PM), as well as the temperature and humidity. These signals are then transmitted to a server via the Internet of Things, and a deep neural network utilizes this information to analyze the air quality in the vehicle. The deep network employs long short-term memory (LSTM), skip-generative adversarial network (GAN), and variational auto-encoder (VAE) models to build an air quality anomaly detection model. The deep learning models gather data via LSTM, while the semi-supervised deep learning models collect data via GANs and VAEs. The purpose of this assistant is to provide vehicle air quality information, such as PM alerts and sleep-deprived driving alerts, to drivers in real time and thereby prevent accidents.

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