scholarly journals Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning

2019 ◽  
Author(s):  
J.J. Almagro Armenteros ◽  
M. Salvatore ◽  
O. Emanuelsson ◽  
O. Winther ◽  
G. von Heijne ◽  
...  
Keyword(s):  
Machine Learning ◽  
Secretory Pathway ◽  
Plant Proteins ◽  
Learning Approaches ◽  
Machine Learning Methods ◽  
Sorting Signals ◽  
Transit Peptides ◽  
Targeting Peptide ◽  
The One ◽  
State Of Art

AbstractIn bioinformatics, machine learning methods have been used to predict features embedded in the sequences. In contrast to what is generally assumed, machine learning approaches can also provide new insights into the underlying biology. Here, we demonstrate this by presenting TargetP 2.0, a novel state of art method to identify N-terminal sorting signals, which direct proteins to the secretory pathway, mitochondria and chloroplasts or other plastids.By examining the strongest signals from the attention layer in the network, we find that the second residue in the protein, i.e. the one following the initial methionine, has a strong influence on the classification. When subsequently examining all targeting peptides, we observe that two-thirds of chloroplast and thylakoid transit peptides have an alanine in position two, but only 20% of other plant proteins. Further highlighting the importance of the second residue, we also note that in fungi and single-celled eukaryotes, less than 30% of the targeting peptides have an amino acid that allows the removal of the N-terminal methionine compared with 60% for the proteins without targeting peptide.TargetP 2.0 is available at http://www.cbs.dtu.dk/services/TargetP-2.0/index.php

scholarly journals Detecting sequence signals in targeting peptides using deep learning

2019 ◽  
Vol 2 (5) ◽  
pp. e201900429 ◽  
Author(s):  
Jose Juan Almagro Armenteros ◽  
Marco Salvatore ◽  
Olof Emanuelsson ◽  
Ole Winther ◽  
Gunnar von Heijne ◽  
...  
Keyword(s):  
Machine Learning ◽  
Secretory Pathway ◽  
State Of The Art ◽  
Plant Proteins ◽  
Learning Approaches ◽  
Machine Learning Methods ◽  
Sorting Signals ◽  
Transit Peptides ◽  
Targeting Peptide ◽  
The One

In bioinformatics, machine learning methods have been used to predict features embedded in the sequences. In contrast to what is generally assumed, machine learning approaches can also provide new insights into the underlying biology. Here, we demonstrate this by presenting TargetP 2.0, a novel state-of-the-art method to identify N-terminal sorting signals, which direct proteins to the secretory pathway, mitochondria, and chloroplasts or other plastids. By examining the strongest signals from the attention layer in the network, we find that the second residue in the protein, that is, the one following the initial methionine, has a strong influence on the classification. We observe that two-thirds of chloroplast and thylakoid transit peptides have an alanine in position 2, compared with 20% in other plant proteins. We also note that in fungi and single-celled eukaryotes, less than 30% of the targeting peptides have an amino acid that allows the removal of the N-terminal methionine compared with 60% for the proteins without targeting peptide. The importance of this feature for predictions has not been highlighted before.

scholarly journals Machine Learning Methods Applied to the Prediction of Pseudo-nitzschia spp. Blooms in the Galician Rias Baixas (NW Spain)

2021 ◽  
Vol 10 (4) ◽  
pp. 199
Author(s):  
Francisco M. Bellas Aláez ◽  
Jesus M. Torres Palenzuela ◽  
Evangelos Spyrakos ◽  
Luis González Vilas
Keyword(s):  
Machine Learning ◽  
Performance Metrics ◽  
Prediction Models ◽  
Support Vector ◽  
False Alarms ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Rías Baixas ◽  
New Algorithms

This work presents new prediction models based on recent developments in machine learning methods, such as Random Forest (RF) and AdaBoost, and compares them with more classical approaches, i.e., support vector machines (SVMs) and neural networks (NNs). The models predict Pseudo-nitzschia spp. blooms in the Galician Rias Baixas. This work builds on a previous study by the authors (doi.org/10.1016/j.pocean.2014.03.003) but uses an extended database (from 2002 to 2012) and new algorithms. Our results show that RF and AdaBoost provide better prediction results compared to SVMs and NNs, as they show improved performance metrics and a better balance between sensitivity and specificity. Classical machine learning approaches show higher sensitivities, but at a cost of lower specificity and higher percentages of false alarms (lower precision). These results seem to indicate a greater adaptation of new algorithms (RF and AdaBoost) to unbalanced datasets. Our models could be operationally implemented to establish a short-term prediction system.

scholarly journals Machine Learning for Biometrics

2012 ◽  
pp. 704-723
Author(s):  
Albert Ali Salah
Keyword(s):  
Machine Learning ◽  
Learning Approaches ◽  
Relevant Research ◽  
Robust Identification ◽  
Research Issues ◽  
Personal Traits ◽  
Machine Learning Methods ◽  
Biometric Template ◽  
Fusion Methods ◽  
Areas Of Interest

Biometrics aims at reliable and robust identification of humans from their personal traits, mainly for security and authentication purposes, but also for identifying and tracking the users of smarter applications. Frequently considered modalities are fingerprint, face, iris, palmprint and voice, but there are many other possible biometrics, including gait, ear image, retina, DNA, and even behaviours. This chapter presents a survey of machine learning methods used for biometrics applications, and identifies relevant research issues. The author focuses on three areas of interest: offline methods for biometric template construction and recognition, information fusion methods for integrating multiple biometrics to obtain robust results, and methods for dealing with temporal information. By introducing exemplary and influential machine learning approaches in the context of specific biometrics applications, the author hopes to provide the reader with the means to create novel machine learning solutions to challenging biometrics problems.

Machine Learning Approaches for Sentiment Analysis

2014 ◽  
pp. 193-208 ◽  
Author(s):  
Basant Agarwal ◽  
Namita Mittal
Keyword(s):  
Machine Learning ◽  
Sentiment Analysis ◽  
Opinion Mining ◽  
Machine Learning Algorithms ◽  
Sentiment Classification ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Knowledge Based ◽  
Semantic Orientation

Opinion Mining or Sentiment Analysis is the study that analyzes people's opinions or sentiments from the text towards entities such as products and services. It has always been important to know what other people think. With the rapid growth of availability and popularity of online review sites, blogs', forums', and social networking sites' necessity of analysing and understanding these reviews has arisen. The main approaches for sentiment analysis can be categorized into semantic orientation-based approaches, knowledge-based, and machine-learning algorithms. This chapter surveys the machine learning approaches applied to sentiment analysis-based applications. The main emphasis of this chapter is to discuss the research involved in applying machine learning methods mostly for sentiment classification at document level. Machine learning-based approaches work in the following phases, which are discussed in detail in this chapter for sentiment classification: (1) feature extraction, (2) feature weighting schemes, (3) feature selection, and (4) machine-learning methods. This chapter also discusses the standard free benchmark datasets and evaluation methods for sentiment analysis. The authors conclude the chapter with a comparative study of some state-of-the-art methods for sentiment analysis and some possible future research directions in opinion mining and sentiment analysis.

Machine Learning Approaches for Sentiment Analysis

Big Data ◽  
2016 ◽  
pp. 1917-1933
Author(s):  
Basant Agarwal ◽  
Namita Mittal
Keyword(s):  
Machine Learning ◽  
Sentiment Analysis ◽  
Opinion Mining ◽  
Machine Learning Algorithms ◽  
Sentiment Classification ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Knowledge Based ◽  
Semantic Orientation

Opinion Mining or Sentiment Analysis is the study that analyzes people's opinions or sentiments from the text towards entities such as products and services. It has always been important to know what other people think. With the rapid growth of availability and popularity of online review sites, blogs', forums', and social networking sites' necessity of analysing and understanding these reviews has arisen. The main approaches for sentiment analysis can be categorized into semantic orientation-based approaches, knowledge-based, and machine-learning algorithms. This chapter surveys the machine learning approaches applied to sentiment analysis-based applications. The main emphasis of this chapter is to discuss the research involved in applying machine learning methods mostly for sentiment classification at document level. Machine learning-based approaches work in the following phases, which are discussed in detail in this chapter for sentiment classification: (1) feature extraction, (2) feature weighting schemes, (3) feature selection, and (4) machine-learning methods. This chapter also discusses the standard free benchmark datasets and evaluation methods for sentiment analysis. The authors conclude the chapter with a comparative study of some state-of-the-art methods for sentiment analysis and some possible future research directions in opinion mining and sentiment analysis.

The Usage Analysis of Machine Learning Methods for Intrusion Detection in Software-Defined Networks

2021 ◽  
pp. 959-975
Author(s):  
Derya Yiltas-Kaplan
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Intrusion Detection ◽  
Network Architectures ◽  
Software Defined Networks ◽  
Learning Approaches ◽  
Advantages And Disadvantages ◽  
Machine Learning Methods ◽  
Network Problems ◽  
Usage Analysis

This chapter focuses on the process of the machine learning with considering the architecture of software-defined networks (SDNs) and their security mechanisms. In general, machine learning has been studied widely in traditional network problems, but recently there have been a limited number of studies in the literature that connect SDN security and machine learning approaches. The main reason of this situation is that the structure of SDN has emerged newly and become different from the traditional networks. These structural variances are also summarized and compared in this chapter. After the main properties of the network architectures, several intrusion detection studies on SDN are introduced and analyzed according to their advantages and disadvantages. Upon this schedule, this chapter also aims to be the first organized guide that presents the referenced studies on the SDN security and artificial intelligence together.

Detection of Economy-Related Turkish Tweets Based on Machine Learning Approaches

2022 ◽  
pp. 171-195
Author(s):  
Jale Bektaş
Keyword(s):  
Machine Learning ◽  
Text Mining ◽  
Text Classification ◽  
Integration Method ◽  
Classification Problem ◽  
Feature Representation ◽  
Learning Approaches ◽  
Machine Learning Methods ◽  
Linguistic Approach ◽  
Turkish Language

Conducting NLP for Turkish is a lot harder than other Latin-based languages such as English. In this study, by using text mining techniques, a pre-processing frame is conducted in which TF-IDF values are calculated in accordance with a linguistic approach on 7,731 tweets shared by 13 famous economists in Turkey, retrieved from Twitter. Then, the classification results are compared with four common machine learning methods (SVM, Naive Bayes, LR, and integration LR with SVM). The features represented by the TF-IDF are experimented in different N-grams. The findings show the success of a text classification problem is relative with the feature representation methods, and the performance superiority of SVM is better compared to other ML methods with unigram feature representation. The best results are obtained via the integration method of SVM with LR with the Acc of 82.9%. These results show that these methodologies are satisfying for the Turkish language.

scholarly journals Machine Learning Methods for Precision Medicine Research Designed to Reduce Health Disparities: A Structured Tutorial

2020 ◽  
Vol 30 (Suppl 1) ◽  
pp. 217-228 ◽  
Author(s):  
Sanjay Basu ◽  
James H. Faghmous ◽  
Patrick Doupe
Keyword(s):  
Machine Learning ◽  
Health Disparities ◽  
Precision Medicine ◽  
Learning Approaches ◽  
Learning Methods ◽  
Medicine Research ◽  
Machine Learning Methods ◽  
Box Models ◽  
Precision Medicine Research ◽  
Key Terms

  Precision medicine research designed to reduce health disparities often involves studying multi-level datasets to understand how diseases manifest disproportionately in one group over another, and how scarce health care resources can be directed precisely to those most at risk for disease. In this article, we provide a structured tutorial for medical and public health research­ers on the application of machine learning methods to conduct precision medicine research designed to reduce health dispari­ties. We review key terms and concepts for understanding machine learning papers, including supervised and unsupervised learning, regularization, cross-validation, bagging, and boosting. Metrics are reviewed for evaluating machine learners and major families of learning approaches, including tree-based learning, deep learning, and ensemble learning. We highlight the advan­tages and disadvantages of different learning approaches, describe strategies for interpret­ing “black box” models, and demonstrate the application of common methods in an example dataset with open-source statistical code in R.Ethn Dis. 2020;30(Suppl 1):217-228; doi:10.18865/ed.30.S1.217

scholarly journals Method for a cloud based remaining-service-life-prediction for vehicle-gearboxes based on big-data-analysis and machine learning

2020 ◽  
Vol 84 (4) ◽  
pp. 305-314
Author(s):  
Daniel Vietze ◽  
Michael Hein ◽  
Karsten Stahl
Keyword(s):  
Machine Learning ◽  
Big Data ◽  
Service Life ◽  
Operating Time ◽  
The Other ◽  
Learning Approaches ◽  
State Of Health ◽  
Remaining Service Life ◽  
Other Hand ◽  
The One

AbstractMost vehicle-gearboxes operating today are designed for a limited service-life. On the one hand, this creates significant potential for decreasing cost and mass as well as reduction of the carbon-footprint. On the other hand, this causes a rising risk of failure with increasing operating time of the machine. Especially if a failure can result in a high economic loss, this fact creates a conflict of goals. On the one hand, the machine should only be maintained or replaced when necessary and, on the other hand, the probability of a failure increases with longer operating times. Therefore, a method is desirable, making it possible to predict the remaining service-life and state of health with as little effort as possible.Centerpiece of gearboxes are the gears. A failure of these components usually causes the whole gearbox to fail. The fatigue life analysis deals with the dimensioning of gears according to the expected loads and the required service-life. Unfortunately, there is very little possibility to validate the technical design during operation, today. Hence, the goal of this paper is to present a method, enabling the prediction of the remaining-service-life and state-of-health of gears during operation. Within this method big-data and machine-learning approaches are used. The method is designed in a way, enabling an easy transfer to other machine elements and kinds of machinery.

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