Intelligent Techniques Analysis for Glycosylation Site Prediction

2021 ◽  
Vol 15 ◽  
Author(s):  
Alhassan Alkuhlani ◽  
Walaa Gad ◽  
Mohamed Roushdy ◽  
Abdel-Badeeh M. Salem
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Cell Interaction ◽  
Glycosylation Site ◽  
Machine Learning Classification ◽  
Site Prediction ◽  
Glycosylation Sites ◽  
Wide Range ◽  
Feature Extraction And Selection ◽  
Computational Intelligent

Background: Glycosylation is one of the most common post-translation modifications (PTMs) in organism cells. It plays important roles in several biological processes including cell-cell interaction, protein folding, antigen’s recognition, and immune response. In addition, glycosylation is associated with many human diseases such as cancer, diabetes and coronaviruses. The experimental techniques for identifying glycosylation sites are time-consuming, extensive laboratory work, and expensive. Therefore, computational intelligence techniques are becoming very important for glycosylation site prediction. Objective: This paper is a theoretical discussion of the technical aspects of the biotechnological (e.g., using artificial intelligence and machine learning) to digital bioinformatics research and intelligent biocomputing. The computational intelligent techniques have shown efficient results for predicting N-linked, O-linked and C-linked glycosylation sites. In the last two decades, many studies have been conducted for glycosylation site prediction using these techniques. In this paper, we analyze and compare a wide range of intelligent techniques of these studies from multiple aspects. The current challenges and difficulties facing the software developers and knowledge engineers for predicting glycosylation sites are also included. Method: The comparison between these different studies is introduced including many criteria such as databases, feature extraction and selection, machine learning classification methods, evaluation measures and the performance results. Results and conclusions: Many challenges and problems are presented. Consequently, more efforts are needed to get more accurate prediction models for the three basic types of glycosylation sites.

COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina Faizollahzadeh Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to SIR and SEIR models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

scholarly journals Predicting Tree Sap Flux and Stomatal Conductance from Drone-Recorded Surface Temperatures in a Mixed Agroforestry System—A Machine Learning Approach

2020 ◽  
Vol 12 (24) ◽  
pp. 4070
Author(s):  
Florian Ellsäßer ◽  
Alexander Röll ◽  
Joyson Ahongshangbam ◽  
Pierre-André Waite ◽  
Hendrayanto ◽  
...  
Keyword(s):  
Machine Learning ◽  
Stomatal Conductance ◽  
Prediction Models ◽  
Hydrological Cycle ◽  
Machine Learning Algorithms ◽  
Sap Flux ◽  
Plant Transpiration ◽  
Surface Temperatures ◽  
Whole Plant ◽  
Wide Range

Plant transpiration is a key element in the hydrological cycle. Widely used methods for its assessment comprise sap flux techniques for whole-plant transpiration and porometry for leaf stomatal conductance. Recently emerging approaches based on surface temperatures and a wide range of machine learning techniques offer new possibilities to quantify transpiration. The focus of this study was to predict sap flux and leaf stomatal conductance based on drone-recorded and meteorological data and compare these predictions with in-situ measured transpiration. To build the prediction models, we applied classical statistical approaches and machine learning algorithms. The field work was conducted in an oil palm agroforest in lowland Sumatra. Random forest predictions yielded the highest congruence with measured sap flux (r2 = 0.87 for trees and r2 = 0.58 for palms) and confidence intervals for intercept and slope of a Passing-Bablok regression suggest interchangeability of the methods. Differences in model performance are indicated when predicting different tree species. Predictions for stomatal conductance were less congruent for all prediction methods, likely due to spatial and temporal offsets of the measurements. Overall, the applied drone and modelling scheme predicts whole-plant transpiration with high accuracy. We conclude that there is large potential in machine learning approaches for ecological applications such as predicting transpiration.

scholarly journals Novel Type III Effectors in Pseudomonas aeruginosa

mBio ◽  
2015 ◽  
Vol 6 (2) ◽  
Author(s):  
David Burstein ◽  
Shirley Satanower ◽  
Michal Simovitch ◽  
Yana Belnik ◽  
Meital Zehavi ◽  
...  
Keyword(s):  
Machine Learning ◽  
Pseudomonas Aeruginosa ◽  
Host Cell ◽  
Type Iii Secretion ◽  
Type Iii Secretion System ◽  
Secretion System ◽  
Content Type ◽  
Machine Learning Classification ◽  
Type Iii ◽  
Wide Range

ABSTRACT Pseudomonas aeruginosa is a Gram-negative, opportunistic pathogen that causes chronic and acute infections in immunocompromised patients. Most P. aeruginosa strains encode an active type III secretion system (T3SS), utilized by the bacteria to deliver effector proteins from the bacterial cell directly into the cytoplasm of the host cell. Four T3SS effectors have been discovered and extensively studied in P. aeruginosa: ExoT, ExoS, ExoU, and ExoY. This is especially intriguing in light of P. aeruginosa's ability to infect a wide range of hosts. We therefore hypothesized that additional T3SS effectors that have not yet been discovered are encoded in the genome of P. aeruginosa. Here, we applied a machine learning classification algorithm to identify novel P. aeruginosa effectors. In this approach, various types of data are integrated to differentiate effectors from the rest of the open reading frames of the bacterial genome. Due to the lack of a sufficient learning set of positive effectors, our machine learning algorithm integrated genomic information from another Pseudomonas species and utilized dozens of features accounting for various aspects of the effector coding genes and their products. Twelve top-ranking predictions were experimentally tested for T3SS-specific translocation, leading to the discovery of two novel T3SS effectors. We demonstrate that these effectors are not part of the injection structural complex and report initial efforts toward their characterization. IMPORTANCE Pseudomonas aeruginosa uses a type III secretion system (T3SS) to secrete toxic proteins, termed effectors, directly into the cytoplasm of the host cell. The activation of this secretion system is correlated with disease severity and patient death. Compared with many other T3SS-utilizing pathogenic bacteria, P. aeruginosa has a fairly limited arsenal of effectors that have been identified. This is in sharp contrast with the wide range of hosts that this bacterium can infect. The discovery of two novel effectors described here is an important step toward better understanding of the virulence and host evasion mechanisms adopted by this versatile pathogen and may provide novel approaches to treat P. aeruginosa infections.

scholarly journals Comparison Decision Tree and Logistic Regression Machine Learning Classification Algorithms to determine Covid-19

SinkrOn ◽  
2022 ◽  
Vol 7 (1) ◽  
pp. 59-65
Author(s):  
Artika Arista
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Decision Tree ◽  
Cross Validation ◽  
Performance Testing ◽  
Signs And Symptoms ◽  
Classification Algorithms ◽  
Machine Learning Classification ◽  
Wide Range ◽  
Testing Performance

Many people today are unsure whether they have COVID-19. The frequent fever, dry cough, and sore throat are all signs and symptoms of COVID-19. If a person has signs or symptoms of coronavirus disease 2019 (COVID-19), he/she should see the doctor or go to a clinic as soon as possible. As a result, it's vital to learn and comprehend the fundamental differences. COVID-19 can cause a wide range of symptoms. The experiments were carried out using two Machine Learning Classification Algorithms, namely Decision Tree (DT) and Logistic Regression (LR). Both algorithms were written and analyzed using the Python program in Jupyter Notebook 6.4.5. From the results obtained in the experiments of covid symptoms dataset, on average, the DT model has obtained the best cross-validation average and the testing performance average compared to the LR machine learning models. For cross-validation results, the DT model has achieved an accuracy of 98.0%. For performance testing, the DT model has achieved an accuracy of 98.0%. The LR has obtained the second-best result on the average of cross-validation performance and the testing results. For cross-validation results, the LR model has achieved an accuracy of 96.0%. For performance testing, the LR model has achieved an accuracy of 97.0%. Consequently, the DT for the COVID-19 symptoms dataset is outperforming the LR for cross-validation and testing results.

scholarly journals Interpretable machine learning in damage detection using Shapley Additive Explanations

2021 ◽  
Author(s):  
Artur Movsessian ◽  
David Garcia Cava ◽  
Dmitri Tcherniak
Keyword(s):  
Machine Learning ◽  
Damage Detection ◽  
Wind Turbine ◽  
Prediction Models ◽  
Turbine Blades ◽  
Wind Turbine Blades ◽  
Lumped Mass ◽  
Damage Indices ◽  
Wide Range ◽  
The Difference

In recent years, Machine Learning (ML) techniques have gained popularity in Structural Health Monitoring (SHM). These have been particularly used for damage detection in a wide range of engineering applications such as wind turbine blades. The outcomes of previous research studies in this area have demonstrated the capabilities of ML for robust damage detection. However, the primary challenge facing ML in SHM is the lack of interpretability of the prediction models hindering the broader implementation of these techniques. For this purpose, this study integrates the novel Shapley Additive exPlanations (SHAP) method into a ML-based damage detection process as a tool for introducing interpretability and, thus, build evidence for reliable decision-making in SHM applications. The SHAP method is based on coalitional game theory and adds global and local interpretability to ML-based models by computing the marginal contribution of each feature. The contribution is used to understand the nature of damage indices (DIs). The applicability of the SHAP method is first demonstrated on a simple lumped mass-spring-damper system with simulated temperature variabilities. Later, the SHAP method has been evaluated on data from an in-operation V27 wind turbine with artificially introduced damage in one of its blades. The results show the relationship between the environmental and operational variabilities (EOVs) and their direct influence on the damage indices. This ultimately helps to understand the difference between false positives caused by EOVs and true positives resulting from damage in the structure.

scholarly journals Deep Learning Prediction of Adverse Drug Reactions in Drug Discovery Using Open TG–GATEs and FAERS Databases

2021 ◽  
Vol 1 ◽  
Author(s):  
Attayeb Mohsen ◽  
Lokesh P. Tripathi ◽  
Kenji Mizuguchi
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Adverse Drug Reactions ◽  
Predictive Models ◽  
Prediction Models ◽  
Expression Profiles ◽  
Fine Tuning ◽  
Machine Learning Techniques ◽  
Drug Reactions ◽  
Wide Range

Machine learning techniques are being increasingly used in the analysis of clinical and omics data. This increase is primarily due to the advancements in Artificial intelligence (AI) and the build-up of health-related big data. In this paper we have aimed at estimating the likelihood of adverse drug reactions or events (ADRs) in the course of drug discovery using various machine learning methods. We have also described a novel machine learning-based framework for predicting the likelihood of ADRs. Our framework combines two distinct datasets, drug-induced gene expression profiles from Open TG–GATEs (Toxicogenomics Project–Genomics Assisted Toxicity Evaluation Systems) and ADR occurrence information from FAERS (FDA [Food and Drug Administration] Adverse Events Reporting System) database, and can be applied to many different ADRs. It incorporates data filtering and cleaning as well as feature selection and hyperparameters fine tuning. Using this framework with Deep Neural Networks (DNN), we built a total of 14 predictive models with a mean validation accuracy of 89.4%, indicating that our approach successfully and consistently predicted ADRs for a wide range of drugs. As case studies, we have investigated the performances of our prediction models in the context of Duodenal ulcer and Hepatitis fulminant, highlighting mechanistic insights into those ADRs. We have generated predictive models to help to assess the likelihood of ADRs in testing novel pharmaceutical compounds. We believe that our findings offer a promising approach for ADR prediction and will be useful for researchers in drug discovery.

scholarly journals COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina Faizollahzadeh Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to SIR and SEIR models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

scholarly journals COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina F. Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

Abstract Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to susceptible-infected-recovered (SIR) and susceptible-exposed-infectious-recovered (SEIR) models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

scholarly journals COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina Faizollahzadeh Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to SIR and SEIR models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

scholarly journals COVID-19 Outbreak Prediction with Machine Learning

2020 ◽  
Author(s):  
Sina Faizollahzadeh Ardabili ◽  
Amir Mosavi ◽  
Pedram Ghamisi ◽  
Filip Ferdinand ◽  
Annamaria R. Varkonyi-Koczy ◽  
...  
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Fuzzy Inference ◽  
Control Measures ◽  
Future Research ◽  
Complex Nature ◽  
Inference System ◽  
Wide Range ◽  
Standard Models ◽  
High Level

: Several outbreak prediction models for COVID-19 are being used by officials around the world to make informed-decisions and enforce relevant control measures. Among the standard models for COVID-19 global pandemic prediction, simple epidemiological and statistical models have received more attention by authorities, and they are popular in the media. Due to a high level of uncertainty and lack of essential data, standard models have shown low accuracy for long-term prediction. Although the literature includes several attempts to address this issue, the essential generalization and robustness abilities of existing models needs to be improved. This paper presents a comparative analysis of machine learning and soft computing models to predict the COVID-19 outbreak as an alternative to SIR and SEIR models. Among a wide range of machine learning models investigated, two models showed promising results (i.e., multi-layered perceptron, MLP, and adaptive network-based fuzzy inference system, ANFIS). Based on the results reported here, and due to the highly complex nature of the COVID-19 outbreak and variation in its behavior from nation-to-nation, this study suggests machine learning as an effective tool to model the outbreak. This paper provides an initial benchmarking to demonstrate the potential of machine learning for future research. Paper further suggests that real novelty in outbreak prediction can be realized through integrating machine learning and SEIR models.

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