scholarly journals Analyzing hCov genome sequences: Applying Machine Intelligence and beyond

2020 ◽  
Author(s):  
Shashata Sawmya ◽  
Arpita Saha ◽  
Sadia Tasnim ◽  
Naser Anjum ◽  
Md. Toufikuzzaman ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Deep Learning ◽  
Evolutionary History ◽  
Genetic Material ◽  
Machine Intelligence ◽  
Genome Sequences ◽  
Analysis Pipeline ◽  
Learning Techniques ◽  
The World ◽  
Novel Virus

AbstractCovid-19 pandemic, caused by the sars-cov-2 strain of coronavirus, has affected millions of people all over the world and taken thousands of lives. It is of utmost importance that the character of this deadly virus be studied and its nature be analysed. We present here an analysis pipeline comprising phylogenetic analysis on strains of this novel virus to track its evolutionary history among the countries uncovering several interesting relationships, followed by a classification exercise to identify the virulence of the strains and extraction of important features from its genetic material that are used subsequently to predict mutation at those interesting sites using deep learning techniques. In a nutshell, we have prepared an analysis pipeline for hCov genome sequences leveraging the power of machine intelligence and uncovered what remained apparently shrouded by raw data.

scholarly journals Representation Learning for Fine-Grained Change Detection

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4486
Author(s):  
Niall O’Mahony ◽  
Sean Campbell ◽  
Lenka Krpalkova ◽  
Anderson Carvalho ◽  
Joseph Walsh ◽  
...  
Keyword(s):  
Deep Learning ◽  
Change Detection ◽  
Model Calibration ◽  
State Of The Art ◽  
Representation Learning ◽  
Machine Intelligence ◽  
The State ◽  
Sensor Data ◽  
Fine Grained ◽  
Learning Techniques

Fine-grained change detection in sensor data is very challenging for artificial intelligence though it is critically important in practice. It is the process of identifying differences in the state of an object or phenomenon where the differences are class-specific and are difficult to generalise. As a result, many recent technologies that leverage big data and deep learning struggle with this task. This review focuses on the state-of-the-art methods, applications, and challenges of representation learning for fine-grained change detection. Our research focuses on methods of harnessing the latent metric space of representation learning techniques as an interim output for hybrid human-machine intelligence. We review methods for transforming and projecting embedding space such that significant changes can be communicated more effectively and a more comprehensive interpretation of underlying relationships in sensor data is facilitated. We conduct this research in our work towards developing a method for aligning the axes of latent embedding space with meaningful real-world metrics so that the reasoning behind the detection of change in relation to past observations may be revealed and adjusted. This is an important topic in many fields concerned with producing more meaningful and explainable outputs from deep learning and also for providing means for knowledge injection and model calibration in order to maintain user confidence.

scholarly journals Deep Learning-Based Sentiment Analysis of COVID-19 Vaccination Responses from Twitter Data

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Kazi Nabiul Alam ◽  
Md Shakib Khan ◽  
Abdur Rab Dhruba ◽  
Mohammad Monirujjaman Khan ◽  
Jehad F. Al-Amri ◽  
...  
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Performance Metrics ◽  
Short Term Memory ◽  
Confusion Matrix ◽  
Short Term ◽  
Learning Techniques ◽  
The World ◽  
Long Short Term Memory ◽  
Severe Anxiety

The COVID-19 pandemic has had a devastating effect on many people, creating severe anxiety, fear, and complicated feelings or emotions. After the initiation of vaccinations against coronavirus, people’s feelings have become more diverse and complex. Our aim is to understand and unravel their sentiments in this research using deep learning techniques. Social media is currently the best way to express feelings and emotions, and with the help of Twitter, one can have a better idea of what is trending and going on in people’s minds. Our motivation for this research was to understand the diverse sentiments of people regarding the vaccination process. In this research, the timeline of the collected tweets was from December 21 to July21. The tweets contained information about the most common vaccines available recently from across the world. The sentiments of people regarding vaccines of all sorts were assessed using the natural language processing (NLP) tool, Valence Aware Dictionary for sEntiment Reasoner (VADER). Initializing the polarities of the obtained sentiments into three groups (positive, negative, and neutral) helped us visualize the overall scenario; our findings included 33.96% positive, 17.55% negative, and 48.49% neutral responses. In addition, we included our analysis of the timeline of the tweets in this research, as sentiments fluctuated over time. A recurrent neural network- (RNN-) oriented architecture, including long short-term memory (LSTM) and bidirectional LSTM (Bi-LSTM), was used to assess the performance of the predictive models, with LSTM achieving an accuracy of 90.59% and Bi-LSTM achieving 90.83%. Other performance metrics such as precision,, F1-score, and a confusion matrix were also used to validate our models and findings more effectively. This study improves understanding of the public’s opinion on COVID-19 vaccines and supports the aim of eradicating coronavirus from the world.

scholarly journals Complex Data Imputation by Auto-Encoders and Convolutional Neural Networks—A Case Study on Genome Gap-Filling

Computers ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 37 ◽  
Author(s):  
Luca Cappelletti ◽  
Tommaso Fontana ◽  
Guido Walter Di Donato ◽  
Lorenzo Di Tucci ◽  
Elena Casiraghi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Missing Data ◽  
State Of The Art ◽  
The State ◽  
Complex Data ◽  
Data Imputation ◽  
Genome Sequences ◽  
Missing Data Imputation ◽  
The Past ◽  
Learning Techniques

Missing data imputation has been a hot topic in the past decade, and many state-of-the-art works have been presented to propose novel, interesting solutions that have been applied in a variety of fields. In the past decade, the successful results achieved by deep learning techniques have opened the way to their application for solving difficult problems where human skill is not able to provide a reliable solution. Not surprisingly, some deep learners, mainly exploiting encoder-decoder architectures, have also been designed and applied to the task of missing data imputation. However, most of the proposed imputation techniques have not been designed to tackle “complex data”, that is high dimensional data belonging to datasets with huge cardinality and describing complex problems. Precisely, they often need critical parameters to be manually set or exploit complex architecture and/or training phases that make their computational load impracticable. In this paper, after clustering the state-of-the-art imputation techniques into three broad categories, we briefly review the most representative methods and then describe our data imputation proposals, which exploit deep learning techniques specifically designed to handle complex data. Comparative tests on genome sequences show that our deep learning imputers outperform the state-of-the-art KNN-imputation method when filling gaps in human genome sequences.

scholarly journals Existential Methods on Diabetes Detection using Machine Learning

2020 ◽  
Vol 8 (6) ◽  
pp. 3034-3039
Keyword(s):  
Diabetes Mellitus ◽  
Machine Learning ◽  
Logistic Regression ◽  
Diabetic Retinopathy ◽  
Deep Learning ◽  
Literature Review ◽  
Learning Techniques ◽  
The World ◽  
Diabetes Prediction

Nowadays, a lot of research is going on in healthcare. One of the significant diseases increased all over the world is Diabetes Mellitus (DM). In this paper, the literature review is done on diabetes prediction using Machine Learning and Deep Learning techniques. Various ML algorithms are used using PIDD (Pima Indian diabetes dataset), and improved k- means using logistic regression among all algorithms achieved the highest accuracy. DL algorithms like CNN and LMST used in diabetic retinopathy images.

scholarly journals Automated Detection of COVID-19 using Deep Learning

2021 ◽  
Vol 10 (2) ◽  
pp. , 824-830
Keyword(s):  
Public Health ◽  
Deep Learning ◽  
Global Economy ◽  
Imaging Techniques ◽  
Automated Detection ◽  
Diagnostic Tools ◽  
Radiological Imaging ◽  
Daily Lives ◽  
Learning Techniques ◽  
The World

Corona virus 2019 (COVID-2019), has first appeared in Wuhan, China in December 2019, spread around the world rapidly causing thousands of fatalities. It is caused a devastating result in our daily lives, public health, and also the global economy. It is important to sight the positive cases as early as possible therefore forestall any unfoldment of this epidemic and to quickly treat affected patients. The necessity for auxiliary diagnostic tools has increased as there aren't any accurate automated toolkits available. Recent findings obtained using radiology imaging techniques suggest that such images contain salient information about the COVID-19 virus. Coupling deep learning techniques with radiological imaging may end up within the accurate detection of this disease. This assistance will help to beat the matter of an absence of specialized physicians in the remote villages.

scholarly journals The emergence of SARS-CoV-2 by an unusual genome reconstitution

2020 ◽  
Author(s):  
Seong-Tshool Hong ◽  
Md. Mehedi Hassan ◽  
Shirina Sharmin ◽  
Jinny Hong ◽  
Hoi-Seon Lee ◽  
...  
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Pairwise Comparison ◽  
Surface Protein ◽  
Plasmodium Malariae ◽  
Spike Protein ◽  
Genome Sequences ◽  
The World ◽  
The Common ◽  
Virus Strains

Abstract SARS-CoV-2 has been spreading remarkedly fast around the world since its emergence while the origin of the virus remains ambiguous. Here, we constructed all of the original prototype genome sequences of SARS-CoV-2 by selecting the common nucleotide among the different virus strains with species. Phylogenetic analysis on the prototype sequences showed that SARS-CoV-2 was a direct descendant of Bat-CoV and was closely related to Pan-CoV, Bat-SL-CoV, and SARS-CoV. The pairwise comparison of SARS-CoV-2 with Bat-CoV showed an unusual replacement of the motif consisting of 7 amino acids within the spike protein of SARS-CoV-2. Database searches showed that the motif originated from a surface protein of Plasmodium malariae, suggesting that the SARS-CoV-2 was emerged after acquiring the motif of the malaria surface protein.

scholarly journals Diagnosis of COVID-19 using CT scan images and deep learning techniques

2020 ◽  
Author(s):  
Vruddhi Shah ◽  
Rinkal Keniya ◽  
Akanksha Shridharani ◽  
Manav Punjabi ◽  
Jainam Shah ◽  
...  
Keyword(s):  
Neural Network ◽  
Computed Tomography ◽  
Deep Learning ◽  
Early Diagnosis ◽  
Ct Scan ◽  
Efficient Method ◽  
Learning Models ◽  
Automated Diagnosis ◽  
Learning Techniques ◽  
The World

Early diagnosis of the coronavirus disease in 2019 (COVID-19) is essential for controlling this pandemic. COVID-19 has been spreading rapidly all over the world. There is no vaccine available for this virus yet. Fast and accurate COVID-19 screening is possible using computed tomography (CT) scan images. The deep learning techniques used in the proposed method was based on a convolutional neural network (CNN). Our manuscript focuses on differentiating the CT scan images of COVID-19 and non-COVID 19 CT using different deep learning techniques. A self developed model named CTnet-10 was designed for the COVID-19 diagnosis, having an accuracy of 82.1 %. Also, other models that we tested are DenseNet-169, VGG-16, ResNet-50, InceptionV3, and VGG-19. The VGG-19 proved to be superior with an accuracy of 94.52 % as compared to all other deep learning models. Automated diagnosis of COVID-19 from the CT scan pictures can be used by the doctors as a quick and efficient method for COVID-19 screening.

scholarly journals Quantifying Seagrass Distribution in Coastal Water with Deep Learning Models

2020 ◽  
Vol 12 (10) ◽  
pp. 1581 ◽  
Author(s):  
Daniel Perez ◽  
Kazi Islam ◽  
Victoria Hill ◽  
Richard Zimmerman ◽  
Blake Schaeffer ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Transfer Learning ◽  
Satellite Images ◽  
Support Vector ◽  
Learning Approach ◽  
Learning Models ◽  
Learning Techniques ◽  
The World ◽  
New Locations

Coastal ecosystems are critically affected by seagrass, both economically and ecologically. However, reliable seagrass distribution information is lacking in nearly all parts of the world because of the excessive costs associated with its assessment. In this paper, we develop two deep learning models for automatic seagrass distribution quantification based on 8-band satellite imagery. Specifically, we implemented a deep capsule network (DCN) and a deep convolutional neural network (CNN) to assess seagrass distribution through regression. The DCN model first determines whether seagrass is presented in the image through classification. Second, if seagrass is presented in the image, it quantifies the seagrass through regression. During training, the regression and classification modules are jointly optimized to achieve end-to-end learning. The CNN model is strictly trained for regression in seagrass and non-seagrass patches. In addition, we propose a transfer learning approach to transfer knowledge in the trained deep models at one location to perform seagrass quantification at a different location. We evaluate the proposed methods in three WorldView-2 satellite images taken from the coastal area in Florida. Experimental results show that the proposed deep DCN and CNN models performed similarly and achieved much better results than a linear regression model and a support vector machine. We also demonstrate that using transfer learning techniques for the quantification of seagrass significantly improved the results as compared to directly applying the deep models to new locations.

Impact Analysis of Machine Learning Techniques for COVID-19 Diagnosis: A Critical Review

2021 ◽  
Vol 12 (2) ◽  
pp. 510-516
Author(s):  
Anshul, Et. al.
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Severe Acute Respiratory Syndrome ◽  
Impact Analysis ◽  
Machine Learning Techniques ◽  
X Ray ◽  
Learning Techniques ◽  
The World ◽  
Almost All

COVID-19 virus belongs to the severe acute respiratory syndrome (SARS) family raised a situation of health emergency in almost all the countries of the world. Numerous machine learning and deep learning based techniques are used to diagnose COVID positive patients using different image modalities like CT SCAN, X-RAY, or CBX, etc. This paper provides the works done in COVID-19 diagnosis, the role of ML and DL based methods to solve this problem, and presents limitations with respect to COVID-19 diagnosis.

scholarly journals Complete Genome Sequence of a Tomato Brown Rugose Fruit Virus Isolated in the United States

2020 ◽  
Vol 9 (29) ◽  
Author(s):  
Bidisha Chanda ◽  
Yazmín Rivera ◽  
Schyler O. Nunziata ◽  
Marco E. Galvez ◽  
Andrea Gilliard ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Evolutionary History ◽  
The United States ◽  
Sequence Identity ◽  
Tight Cluster ◽  
The World ◽  
The U.S

ABSTRACT The complete genome sequence of a U.S. isolate of a Tomato brown rugose fruit virus (ToBRFV) (CA18-01) was obtained through Illumina and MinION sequencing. The U.S. ToBRFV isolate shared a high nucleic acid sequence identity (>99%) with known ToBRFV isolates. Phylogenetic analysis revealed a tight cluster for ToBRFV isolates throughout the world, suggesting a short evolutionary history.

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