scholarly journals Identifying Genomic Islands with Deep Neural Networks

2019 ◽  
Author(s):  
Rida Assaf ◽  
Fangfang Xia ◽  
Rick Stevens
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Intrinsic Value ◽  
Genomic Islands ◽  
Rapid Spread ◽  
Different Types ◽  
Single Method ◽  
Deep Learning Model ◽  
Different Sources

AbstractBackgroundHorizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, often classified by the content of their cargo genes or their means of integration and mobility. Various computational methods have been devised to detect different types of GIs, but no single method currently is capable of detecting all GIs.ResultsWe propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools.ConclusionsWe used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was retrained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.

scholarly journals Identifying genomic islands with deep neural networks

BMC Genomics ◽  
2021 ◽  
Vol 22 (S3) ◽  
Author(s):  
Rida Assaf ◽  
Fangfang Xia ◽  
Rick Stevens
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Intrinsic Value ◽  
Genomic Islands ◽  
Rapid Spread ◽  
Different Types ◽  
Single Method ◽  
Deep Learning Model ◽  
Different Sources

Abstract Background Horizontal gene transfer is the main source of adaptability for bacteria, through which genes are obtained from different sources including bacteria, archaea, viruses, and eukaryotes. This process promotes the rapid spread of genetic information across lineages, typically in the form of clusters of genes referred to as genomic islands (GIs). Different types of GIs exist, and are often classified by the content of their cargo genes or their means of integration and mobility. While various computational methods have been devised to detect different types of GIs, no single method is capable of detecting all types. Results We propose a method, which we call Shutter Island, that uses a deep learning model (Inception V3, widely used in computer vision) to detect genomic islands. The intrinsic value of deep learning methods lies in their ability to generalize. Via a technique called transfer learning, the model is pre-trained on a large generic dataset and then re-trained on images that we generate to represent genomic fragments. We demonstrate that this image-based approach generalizes better than the existing tools. Conclusions We used a deep neural network and an image-based approach to detect the most out of the correct GI predictions made by other tools, in addition to making novel GI predictions. The fact that the deep neural network was re-trained on only a limited number of GI datasets and then successfully generalized indicates that this approach could be applied to other problems in the field where data is still lacking or hard to curate.

scholarly journals Proactive Congestion Avoidance for Distributed Deep Learning

Sensors ◽  
2020 ◽  
Vol 21 (1) ◽  
pp. 174
Author(s):  
Minkoo Kang ◽  
Gyeongsik Yang ◽  
Yeonho Yoo ◽  
Chuck Yoo
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Queue Length ◽  
Deep Neural Network ◽  
Congestion Avoidance ◽  
Model Parameters ◽  
Neural Network Training ◽  
Network Congestion ◽  
Network Training ◽  
Deep Learning Model

This paper presents “Proactive Congestion Notification” (PCN), a congestion-avoidance technique for distributed deep learning (DDL). DDL is widely used to scale out and accelerate deep neural network training. In DDL, each worker trains a copy of the deep learning model with different training inputs and synchronizes the model gradients at the end of each iteration. However, it is well known that the network communication for synchronizing model parameters is the main bottleneck in DDL. Our key observation is that the DDL architecture makes each worker generate burst traffic every iteration, which causes network congestion and in turn degrades the throughput of DDL traffic. Based on this observation, the key idea behind PCN is to prevent potential congestion by proactively regulating the switch queue length before DDL burst traffic arrives at the switch, which prepares the switches for handling incoming DDL bursts. In our evaluation, PCN improves the throughput of DDL traffic by 72% on average.

scholarly journals Diabetes Prediction Using Enhanced SVM and Deep Neural Network Learning Techniques

2021 ◽  
Vol 16 (4) ◽  
pp. 1-20
Author(s):  
P. Nagaraj ◽  
P. Deepalakshmi
Keyword(s):  
Neural Network ◽  
Support Vector Machine ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Learning Model ◽  
Support Vector ◽  
Neural Network Learning ◽  
Learning Techniques ◽  
Diabetes Prediction ◽  
Deep Learning Model

Diabetes, caused by the rise in level of glucose in blood, has many latest devices to identify from blood samples. Diabetes, when unnoticed, may bring many serious diseases like heart attack, kidney disease. In this way, there is a requirement for solid research and learning model’s enhancement in the field of gestational diabetes identification and analysis. SVM is one of the powerful classification models in machine learning, and similarly, Deep Neural Network is powerful under deep learning models. In this work, we applied Enhanced Support Vector Machine and Deep Learning model Deep Neural Network for diabetes prediction and screening. The proposed method uses Deep Neural Network obtaining its input from the output of Enhanced Support Vector Machine, thus having a combined efficacy. The dataset we considered includes 768 patients’ data with eight major features and a target column with result “Positive” or “Negative”. Experiment is done with Python and the outcome of our demonstration shows that the deep Learning model gives more efficiency for diabetes prediction.

scholarly journals ASD-SAENet: A Sparse Autoencoder, and Deep-Neural Network Model for Detecting Autism Spectrum Disorder (ASD) Using fMRI Data

2021 ◽  
Vol 15 ◽  
Author(s):  
Fahad Almuqhim ◽  
Fahad Saeed
Keyword(s):  
Neural Network ◽  
Autism Spectrum Disorder ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Learning Model ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Fmri Data ◽  
Sparse Autoencoder ◽  
Deep Learning Model

Autism spectrum disorder (ASD) is a heterogenous neurodevelopmental disorder which is characterized by impaired communication, and limited social interactions. The shortcomings of current clinical approaches which are based exclusively on behavioral observation of symptomology, and poor understanding of the neurological mechanisms underlying ASD necessitates the identification of new biomarkers that can aid in study of brain development, and functioning, and can lead to accurate and early detection of ASD. In this paper, we developed a deep-learning model called ASD-SAENet for classifying patients with ASD from typical control subjects using fMRI data. We designed and implemented a sparse autoencoder (SAE) which results in optimized extraction of features that can be used for classification. These features are then fed into a deep neural network (DNN) which results in superior classification of fMRI brain scans more prone to ASD. Our proposed model is trained to optimize the classifier while improving extracted features based on both reconstructed data error and the classifier error. We evaluated our proposed deep-learning model using publicly available Autism Brain Imaging Data Exchange (ABIDE) dataset collected from 17 different research centers, and include more than 1,035 subjects. Our extensive experimentation demonstrate that ASD-SAENet exhibits comparable accuracy (70.8%), and superior specificity (79.1%) for the whole dataset as compared to other methods. Further, our experiments demonstrate superior results as compared to other state-of-the-art methods on 12 out of the 17 imaging centers exhibiting superior generalizability across different data acquisition sites and protocols. The implemented code is available on GitHub portal of our lab at: https://github.com/pcdslab/ASD-SAENet.

scholarly journals A Deep Neural Network for face Recognition

2019 ◽  
Vol 8 (12S) ◽  
pp. 420-423
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Face Recognition ◽  
Deep Neural Network ◽  
Facial Features ◽  
Biometric Authentication ◽  
Accuracy Rate ◽  
Learning Technique ◽  
The Face ◽  
Deep Learning Model

Face recognition is used to biometric authentication method to analyze the face extract and photographs useful to reputation formation from them, which can be usually called as a characteristic vector this is used to differentiate the organic features. In this paper to detect the suspect by extracting facial features from the captured image of the suspect from CCTV and match it with the pictures stored in the database and also to achieve an accuracy rate of 100 %, negligible loss using deep learning technique. For extracting the facial features, we are using deep learning model known as Convolutional Neural Network (CNN). It is one of the best models to extract features with the highest accuracy rate .

Flood prediction based on weather parameters using deep learning

2019 ◽  
Vol 11 (4) ◽  
pp. 1766-1783 ◽  
Author(s):  
Suresh Sankaranarayanan ◽  
Malavika Prabhakar ◽  
Sreesta Satish ◽  
Prerna Jain ◽  
Anjali Ramprasad ◽  
...  
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Deep Neural Network ◽  
Rainfall Intensity ◽  
Nearest Neighbor ◽  
Support Vector ◽  
K Nearest Neighbor ◽  
Flood Prediction ◽  
Deep Learning Model

Abstract Today, India is one of the worst flood-affected countries in the world, with the recent disaster in Kerala in August 2018 being a prime example. A good amount of work has been carried out by employing Internet of Things (IoT) and machine learning (ML) techniques in the past for flood occurrence based on rainfall, humidity, temperature, water flow, water level etc. However, the challenge is that no one has attempted the possibility of occurrence of flood based on temperature and rainfall intensity. So accordingly Deep Neural Network has been employed for predicting the occurrence of flood based on temperature and rainfall intensity. In addition, a deep learning model is compared with other machine learning models (support vector machine (SVM), K-nearest neighbor (KNN) and Naïve Bayes) in terms of accuracy and error. The results indicate that the deep neural network can be efficiently used for flood forecasting with highest accuracy based on monsoon parameters only before flood occurrence.

scholarly journals Neural Twins Talk and Alternative Calculations

2021 ◽  
Vol 15 (01) ◽  
pp. 93-116
Author(s):  
Zanyar Zohourianshahzadi ◽  
Jugal K. Kalita
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Input Image ◽  
Neural Pathways ◽  
Image Captioning ◽  
Attention Model ◽  
Deep Learning Model ◽  
Previous Image

Inspired by how the human brain employs more neural pathways when increasing the focus on a subject, we introduce a novel twin cascaded attention model that outperforms a state-of-the-art image captioning model that was originally implemented using one channel of attention for the visual grounding task. Visual grounding ensures the existence of words in the caption sentence that are grounded into a particular region in the input image. After a deep learning model is trained on visual grounding task, the model employs the learned patterns regarding the visual grounding and the order of objects in the caption sentences, when generating captions. We report the results of our experiments in three image captioning tasks on the COCO dataset. The results are reported using standard image captioning metrics to show the improvements achieved by our model over the previous image captioning model. The results gathered from our experiments suggest that employing more parallel attention pathways in a deep neural network leads to higher performance. Our implementation of Neural Twins Talk (NTT) is publicly available at: https://github.com/zanyarz/NeuralTwinsTalk .

Improving Sentiment Analysis using Hybrid Deep Learning Model

2020 ◽  
Vol 13 (4) ◽  
pp. 627-640 ◽  
Author(s):  
Avinash Chandra Pandey ◽  
Dharmveer Singh Rajpoot
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Computational Cost ◽  
Extraction Process ◽  
Learning Model ◽  
Sentiment Classification ◽  
Deep Learning Model

Background: Sentiment analysis is a contextual mining of text which determines viewpoint of users with respect to some sentimental topics commonly present at social networking websites. Twitter is one of the social sites where people express their opinion about any topic in the form of tweets. These tweets can be examined using various sentiment classification methods to find the opinion of users. Traditional sentiment analysis methods use manually extracted features for opinion classification. The manual feature extraction process is a complicated task since it requires predefined sentiment lexicons. On the other hand, deep learning methods automatically extract relevant features from data hence; they provide better performance and richer representation competency than the traditional methods. Objective: The main aim of this paper is to enhance the sentiment classification accuracy and to reduce the computational cost. Method: To achieve the objective, a hybrid deep learning model, based on convolution neural network and bi-directional long-short term memory neural network has been introduced. Results: The proposed sentiment classification method achieves the highest accuracy for the most of the datasets. Further, from the statistical analysis efficacy of the proposed method has been validated. Conclusion: Sentiment classification accuracy can be improved by creating veracious hybrid models. Moreover, performance can also be enhanced by tuning the hyper parameters of deep leaning models.

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