scholarly journals Discovering Pathway and Cell Type Signatures in Transcriptomic Compendia with Machine Learning

2019 ◽  
Vol 2 (1) ◽  
pp. 1-17
Author(s):  
Gregory P. Way ◽  
Casey S. Greene
Keyword(s):  
Machine Learning ◽  
Machine Learning Techniques ◽  
Specific Cell ◽  
Biological Processes ◽  
Learning Approaches ◽  
Cell Type ◽  
Learning Techniques ◽  
Pathway Expression ◽  
Machine Learning Applications ◽  
Computational Resources

Pathway and cell type signatures are patterns present in transcriptome data that are associated with biological processes or phenotypic consequences. These signatures result from specific cell type and pathway expression but can require large transcriptomic compendia to detect. Machine learning techniques can be powerful tools for signature discovery through their ability to provide accurate and interpretable results. In this review, we discuss various machine learning applications to extract pathway and cell type signatures from transcriptomic compendia. We focus on the biological motivations and interpretation for both supervised and unsupervised learning approaches in this setting. We consider recent advances, including deep learning, and their applications to expanding bulk and single-cell RNA data. As data and computational resources increase, there will be more opportunities for machine learning to aid in revealing biological signatures.

scholarly journals Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning

2018 ◽  
Author(s):  
Gregory P Way ◽  
Casey S Greene
Keyword(s):  
Machine Learning ◽  
Machine Learning Techniques ◽  
Specific Cell ◽  
Biological Processes ◽  
Learning Approaches ◽  
Transcriptome Data ◽  
Cell Type ◽  
Learning Techniques ◽  
Pathway Expression ◽  
Machine Learning Applications

Pathway and cell-type signatures are patterns present in transcriptome data that are associated with biological processes or phenotypic consequences. These signatures result from specific cell-type and pathway expression, but can require large transcriptomic compendia to detect. Machine learning techniques can be powerful tools in a practitioner’s toolkit for signature discovery through their ability to provide accurate and interpretable results. In the following review, we discuss various machine learning applications to extract pathway and cell-type signatures from transcriptomic compendia. We focus on the biological motivations and interpretation for both supervised and unsupervised learning approaches in this setting. We consider recent advances, including deep learning, and their applications to expanding bulk and single cell RNA data. As data and compute resources increase, opportunities for machine learning to aid in revealing biological signatures will continue to grow.

scholarly journals Discovering pathway and cell-type signatures in transcriptomic compendia with machine learning

2018 ◽  
Author(s):  
Gregory P Way ◽  
Casey S Greene
Keyword(s):  
Machine Learning ◽  
Machine Learning Techniques ◽  
Specific Cell ◽  
Biological Processes ◽  
Learning Approaches ◽  
Transcriptome Data ◽  
Cell Type ◽  
Learning Techniques ◽  
Pathway Expression ◽  
Machine Learning Applications

Pathway and cell-type signatures are patterns present in transcriptome data that are associated with biological processes or phenotypic consequences. These signatures result from specific cell-type and pathway expression, but can require large transcriptomic compendia to detect. Machine learning techniques can be powerful tools in a practitioner’s toolkit for signature discovery through their ability to provide accurate and interpretable results. In the following review, we discuss various machine learning applications to extract pathway and cell-type signatures from transcriptomic compendia. We focus on the biological motivations and interpretation for both supervised and unsupervised learning approaches in this setting. We consider recent advances, including deep learning, and their applications to expanding bulk and single cell RNA data. As data and compute resources increase, opportunities for machine learning to aid in revealing biological signatures will continue to grow.

scholarly journals Machine Learning:A Review

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Isonkobong Christopher Udousoro
Keyword(s):  
Machine Learning ◽  
Image Processing ◽  
Data Interpretation ◽  
Relevant Information ◽  
Machine Learning Techniques ◽  
Predictive Analysis ◽  
Learning Approaches ◽  
Processing Data ◽  
Learning Techniques ◽  
Machine Learning Applications

Due to the complexity of data, interpretation of pattern or extraction of information becomes difficult; therefore application of machine learning is used to teach machines how to handle data more efficiently. With the increase of datasets, various organizations now apply machine learning applications and algorithms. Many industries apply machine learning to extract relevant information for analysis purposes. Many scholars, mathematicians and programmers have carried out research and applied several machine learning approaches in order to find solution to problems. In this paper, we focus on general review of machine learning including various machine learning techniques. These techniques can be applied to different fields like image processing, data mining, predictive analysis and so on. The paper aims at reviewing machine learning techniques and algorithms. The research methodology is based on qualitative analysis where various literatures is being reviewed based  on machine learning.

scholarly journals Classification of Phonocardiography Signals Using Imbalanced Machine Learning Techniques

2020 ◽  
pp. 103-106
Author(s):  
Mustafa Berkant Selek ◽  
Sude Pehlivan ◽  
Yalcin Isler
Keyword(s):  
Machine Learning ◽  
Frequency Domain ◽  
Cardiovascular Health ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Random Forest Algorithm ◽  
Learning Techniques ◽  
Machine Learning Applications

Cardiovascular diseases, which involve heart and blood vessel dysfunctions, cause a higher number of deaths than any other disease in the world. Throughout history, many approaches have been developed to analyze cardiovascular health by diagnosing such conditions. One of the methodologies is recording and analyzing heart sounds to distinguish normal and abnormal functioning of the heart, which is called Phonocardiography. With the emergence of machine learning applications in healthcare, this process can be automated via the extraction of various features from phonocardiography signals and performing classification with several machine learning algorithms. Many studies have been conducted to extract time and frequency domain features from the phonocardiography signals by segmenting them first into individual heart cycles, and then by classifying them using different machine learning and deep learning approaches. In this study, various time and frequency domain features have been extracted using the complete signal rather than just segments of it. Random Forest algorithm was found to be the most successful algorithm in terms of accuracy as well as recall and precision.

scholarly journals Machine Learning Frameworks in Cancer Detection

2021 ◽  
Vol 297 ◽  
pp. 01073
Author(s):  
Sabyasachi Pramanik ◽  
K. Martin Sagayam ◽  
Om Prakash Jena
Keyword(s):  
Machine Learning ◽  
Prediction Models ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Cancer Development ◽  
Support Vector ◽  
Learning Approaches ◽  
Learning Techniques ◽  
Fact Finding ◽  
Risk Of Cancer

Cancer has been described as a diverse illness with several distinct subtypes that may occur simultaneously. As a result, early detection and forecast of cancer types have graced essentially in cancer fact-finding methods since they may help to improve the clinical treatment of cancer survivors. The significance of categorizing cancer suffers into higher or lower-threat categories has prompted numerous fact-finding associates from the bioscience and genomics field to investigate the utilization of machine learning (ML) algorithms in cancer diagnosis and treatment. Because of this, these methods have been used with the goal of simulating the development and treatment of malignant diseases in humans. Furthermore, the capacity of machine learning techniques to identify important characteristics from complicated datasets demonstrates the significance of these technologies. These technologies include Bayesian networks and artificial neural networks, along with a number of other approaches. Decision Trees and Support Vector Machines which have already been extensively used in cancer research for the creation of predictive models, also lead to accurate decision making. The application of machine learning techniques may undoubtedly enhance our knowledge of cancer development; nevertheless, a sufficient degree of validation is required before these approaches can be considered for use in daily clinical practice. An overview of current machine learning approaches utilized in the simulation of cancer development is presented in this paper. All of the supervised machine learning approaches described here, along with a variety of input characteristics and data samples, are used to build the prediction models. In light of the increasing trend towards the use of machine learning methods in biomedical research, we offer the most current papers that have used these approaches to predict risk of cancer or patient outcomes in order to better understand cancer.

scholarly journals Machine learning for metagenomics: methods and tools

Metagenomics ◽  
2017 ◽  
Vol 1 (1) ◽  
Author(s):  
Hayssam Soueidan ◽  
Macha Nikolski
Keyword(s):  
Machine Learning ◽  
Gene Prediction ◽  
Full Range ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Unified Framework ◽  
Comparative Metagenomics ◽  
Learning Techniques ◽  
Ngs Data ◽  
Modern Machine

AbstractOwing to the complexity and variability of metagenomic studies, modern machine learning approaches have seen increased usage to answer a variety of question encompassing the full range of metagenomic NGS data analysis.We review here the contribution of machine learning techniques for the field of metagenomics, by presenting known successful approaches in a unified framework. This review focuses on five important metagenomic problems:OTU-clustering, binning, taxonomic proffiing and assignment, comparative metagenomics and gene prediction. For each of these problems, we identify the most prominent methods, summarize the machine learning approaches used and put them into perspective of similar methods.We conclude our review looking further ahead at the challenge posed by the analysis of interactions within microbial communities and different environments, in a field one could call “integrative metagenomics”.

Analysis of Kinase Inhibitors and Druggability of Kinase-Targets Using Machine Learning Techniques

2012 ◽  
pp. 155-165
Author(s):  
S. Prasanthi ◽  
S.Durga Bhavani ◽  
T. Sobha Rani ◽  
Raju S. Bapi
Keyword(s):  
Machine Learning ◽  
Decision Tree ◽  
Kinase Inhibitors ◽  
Kinase Inhibitor ◽  
Classification Problem ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Decision Tree Classifier ◽  
Data Set ◽  
Learning Techniques

Vast majority of successful drugs or inhibitors achieve their activity by binding to, and modifying the activity of a protein leading to the concept of druggability. A target protein is druggable if it has the potential to bind the drug-like molecules. Hence kinase inhibitors need to be studied to understand the specificity of a kinase inhibitor in choosing a particular kinase target. In this paper we focus on human kinase drug target sequences since kinases are known to be potential drug targets. Also we do a preliminary analysis of kinase inhibitors in order to study the problem in the protein-ligand space in future. The identification of druggable kinases is treated as a classification problem in which druggable kinases are taken as positive data set and non-druggable kinases are chosen as negative data set. The classification problem is addressed using machine learning techniques like support vector machine (SVM) and decision tree (DT) and using sequence-specific features. One of the challenges of this classification problem is due to the unbalanced data with only 48 druggable kinases available against 509 non-drugggable kinases present at Uniprot. The accuracy of the decision tree classifier obtained is 57.65 which is not satisfactory. A two-tier architecture of decision trees is carefully designed such that recognition on the non-druggable dataset also gets improved. Thus the overall model is shown to achieve a final performance accuracy of 88.37. To the best of our knowledge, kinase druggability prediction using machine learning approaches has not been reported in literature.

Overview of Machine Learning Approaches for Wireless Communication

2021 ◽  
pp. 1579-1597
Author(s):  
Tolga Ensari ◽  
Melike Günay ◽  
Yağız Nalçakan ◽  
Eyyüp Yildiz
Keyword(s):  
Machine Learning ◽  
Wireless Communications ◽  
Smart Phones ◽  
Machine Learning Techniques ◽  
Learning Approaches ◽  
Research Areas ◽  
Learning Techniques ◽  
Recent Developments ◽  
Security And Reliability ◽  
Day By Day

Machine learning is one of the most popular research areas, and it is commonly used in wireless communications and networks. Security and fast communication are among of the key requirements for next generation wireless networks. Machine learning techniques are getting more important day-by-day since the types, amount, and structure of data is continuously changing. Recent developments in smart phones and other devices like drones, wearable devices, machines with sensors need reliable communication within internet of things (IoT) systems. For this purpose, artificial intelligence can increase the security and reliability and manage the data that is generated by the wireless systems. In this chapter, the authors investigate several machine learning techniques for wireless communications including deep learning, which represents a branch of artificial neural networks.

scholarly journals A Machine Learning View on Momentum and Reversal Trading

Algorithms ◽  
2018 ◽  
Vol 11 (11) ◽  
pp. 170 ◽  
Author(s):  
Zhixi Li ◽  
Vincent Tam
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Stock Market ◽  
Short Term Memory ◽  
Predictive Ability ◽  
Trading Strategies ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Learning Approaches ◽  
Learning Techniques

Momentum and reversal effects are important phenomena in stock markets. In academia, relevant studies have been conducted for years. Researchers have attempted to analyze these phenomena using statistical methods and to give some plausible explanations. However, those explanations are sometimes unconvincing. Furthermore, it is very difficult to transfer the findings of these studies to real-world investment trading strategies due to the lack of predictive ability. This paper represents the first attempt to adopt machine learning techniques for investigating the momentum and reversal effects occurring in any stock market. In the study, various machine learning techniques, including the Decision Tree (DT), Support Vector Machine (SVM), Multilayer Perceptron Neural Network (MLP), and Long Short-Term Memory Neural Network (LSTM) were explored and compared carefully. Several models built on these machine learning approaches were used to predict the momentum or reversal effect on the stock market of mainland China, thus allowing investors to build corresponding trading strategies. The experimental results demonstrated that these machine learning approaches, especially the SVM, are beneficial for capturing the relevant momentum and reversal effects, and possibly building profitable trading strategies. Moreover, we propose the corresponding trading strategies in terms of market states to acquire the best investment returns.

Recent Advances in Machine Learning Based Prediction of RNA-protein Interactions

2019 ◽  
Vol 26 (8) ◽  
pp. 601-619 ◽  
Author(s):  
Amit Sagar ◽  
Bin Xue
Keyword(s):  
Machine Learning ◽  
Protein Interaction ◽  
Protein Interactions ◽  
Experimental Methods ◽  
Machine Learning Techniques ◽  
Computational Techniques ◽  
Biological Processes ◽  
Complete Spectrum ◽  
Future Developments ◽  
Learning Techniques

The interactions between RNAs and proteins play critical roles in many biological processes. Therefore, characterizing these interactions becomes critical for mechanistic, biomedical, and clinical studies. Many experimental methods can be used to determine RNA-protein interactions in multiple aspects. However, due to the facts that RNA-protein interactions are tissuespecific and condition-specific, as well as these interactions are weak and frequently compete with each other, those experimental techniques can not be made full use of to discover the complete spectrum of RNA-protein interactions. To moderate these issues, continuous efforts have been devoted to developing high quality computational techniques to study the interactions between RNAs and proteins. Many important progresses have been achieved with the application of novel techniques and strategies, such as machine learning techniques. Especially, with the development and application of CLIP techniques, more and more experimental data on RNA-protein interaction under specific biological conditions are available. These CLIP data altogether provide a rich source for developing advanced machine learning predictors. In this review, recent progresses on computational predictors for RNA-protein interaction were summarized in the following aspects: dataset, prediction strategies, and input features. Possible future developments were also discussed at the end of the review.

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