scholarly journals Briefing in Application of Machine Learning Methods in Ion Channel Prediction

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Hao Lin ◽  
Wei Chen
Keyword(s):  
Machine Learning ◽  
Ion Channels ◽  
Ion Channel ◽  
Inorganic Ions ◽  
Correct Identification ◽  
Biological Processes ◽  
Learning Methods ◽  
Channel Prediction ◽  
Machine Learning Methods ◽  
Wide Range

In cells, ion channels are one of the most important classes of membrane proteins which allow inorganic ions to move across the membrane. A wide range of biological processes are involved and regulated by the opening and closing of ion channels. Ion channels can be classified into numerous classes and different types of ion channels exhibit different functions. Thus, the correct identification of ion channels and their types using computational methods will provide in-depth insights into their function in various biological processes. In this review, we will briefly introduce and discuss the recent progress in ion channel prediction using machine learning methods.

Recent advances in predicting protein-lncRNA interactions using machine learning methods

2021 ◽  
Vol 21 ◽  
Author(s):  
Han Yu ◽  
Zi-Ang Shen ◽  
Yuan-Ke Zhou ◽  
Pu-Feng Du
Keyword(s):  
Machine Learning ◽  
Supervised Learning ◽  
Protein Interactions ◽  
Cellular Level ◽  
Future Research ◽  
Biological Processes ◽  
Learning Methods ◽  
Protein Coding ◽  
Machine Learning Methods ◽  
Non Coding Rnas

: Long non-coding RNAs (LncRNAs) are a type of RNA with little or no protein-coding ability. Their length is more than 200 nucleotides. A large number of studies have indicated that lncRNAs play a significant role in various biological processes, including chromatin organizations, epigenetic programmings, transcriptional regulations, post-transcriptional processing, and circadian mechanism at the cellular level. Since lncRNAs perform vast functions through their interactions with proteins, identifying lncRNA-protein interaction is crucial to the understandings of the lncRNA molecular functions. However, due to the high cost and time-consuming disadvantage of experimental methods, a variety of computational methods have emerged. Recently, many effective and novel machine learning methods have been developed. In general, these methods fall into two categories: semi-supervised learning methods and supervised learning methods. The latter category can be further classified into the deep learning-based method, the ensemble learning-based method, and the hybrid method. In this paper, we focused on supervised learning methods. We summarized the state-of-the-art methods in predicting lncRNA-protein interactions. Furthermore, the performance and the characteristics of different methods have also been compared in this work. Considering the limits of the existing models, we analyzed the problems and discussed future research potentials.

scholarly journals ARTIFICIAL INTELLIGENCE AND NEXT GENERATION PATHOLOGY: TOWARDS PERSONALIZED MEDICINE

2021 ◽  
Vol 65 (2) ◽  
Author(s):  
Oleksandr Dudin ◽  
◽  
Ozar Mintser ◽  
Oksana Sulaieva ◽  
◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Image Analysis ◽  
Deep Learning ◽  
Personalized Medicine ◽  
Digital Pathology ◽  
Automated Image Analysis ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Wide Range

Introduction. Over the past few decades, thanks to advances in algorithm development, the introduction of available computing power, and the management of large data sets, machine learning methods have become active in various fields of life. Among them, deep learning possesses a special place, which is used in many spheres of health care and is an integral part and prerequisite for the development of digital pathology. Objectives. The purpose of the review was to gather the data on existing image analysis technologies and machine learning tools developed for the whole-slide digital images in pathology. Methods: Analysis of the literature on machine learning methods used in pathology, staps of automated image analysis, types of neural networks, their application and capabilities in digital pathology was performed. Results. To date, a wide range of deep learning strategies have been developed, which are actively used in digital pathology, and demonstrated excellent diagnostic accuracy. In addition to diagnostic solutions, the integration of artificial intelligence into the practice of pathomorphological laboratory provides new tools for assessing the prognosis and prediction of sensitivity to different treatments. Conclusions: The synergy of artificial intelligence and digital pathology is a key tool to improve the accuracy of diagnostics, prognostication and personalized medicine facilitation

scholarly journals Deep Neural Networks Detect Suicide Risk from Textual Facebook Posts

2020 ◽  
Author(s):  
Yaakov Ophir ◽  
Refael Tikochinski ◽  
Christa Asterhan ◽  
Itay Sisso ◽  
Roi Reichart
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Suicide Risk ◽  
Mental Health Research ◽  
Learning Methods ◽  
Psychosocial Risks ◽  
Machine Learning Methods ◽  
Task Model ◽  
Wide Range ◽  
Objective Detection

Background: Detection of suicide risk is a highly prioritized, yet complicated task. In fact, five decades of suicide research produced predictions that were only marginally better than chance (AUCs = 0.56 – 0.58). Advanced machine learning methods open up new opportunities for progress in mental health research. In the present study, Artificial Neural Network (ANN) models were constructed to predict externally valid suicide risk from everyday language of social media users. Method: The dataset included 83,292 postings authored by 1,002 authenticated, active Facebook users, alongside clinically valid psychosocial information about the users. Results: Using Deep Contextualized Word Embeddings (CWEs) for text representation, two models were constructed: A Single Task Model (STM), to predict suicide risk from Facebook postings directly (Facebook texts → suicide) and a Multi-Task Model (MTM), which included hierarchical, multilayered sets of theory-driven risk factors (Facebook texts → personality traits → psychosocial risks → psychiatric disorders → suicide). Compared with the STM predictions (.606 ≤ AUC ≤ .608), the MTM produced improved prediction accuracy (.690 ≤ AUC ≤ .759), with substantially larger effect sizes (.701 ≤ d ≤ .994). Subsequent content analyses suggest that predictions did not rely on explicit suicide-related themes, but on a wide range of content. Conclusions: Advanced machine learning methods can improve our ability to predict suicide risk from everyday social media activities. The knowledge generated by this research may eventually lead to the development of more accurate and objective detection tools and get individuals the help they need in time.

scholarly journals Deep Neural Networks Detect Suicide Risk from Textual Facebook Posts

2020 ◽  
Author(s):  
Yaakov Ophir ◽  
Refael Tikochinski ◽  
Christa Asterhan ◽  
Itay Sisso ◽  
Roi Reichart
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Suicide Risk ◽  
Mental Health Research ◽  
Learning Methods ◽  
Psychosocial Risks ◽  
Machine Learning Methods ◽  
Task Model ◽  
Wide Range ◽  
Objective Detection

Background: Detection of suicide risk is a highly prioritized, yet complicated task. In fact, five decades of suicide research produced predictions that were only marginally better than chance (AUCs = 0.56 – 0.58). Advanced machine learning methods open up new opportunities for progress in mental health research. In the present study, Artificial Neural Network (ANN) models were constructed to predict externally valid suicide risk from everyday language of social media users. Method: The dataset included 83,292 postings authored by 1,002 authenticated, active Facebook users, alongside clinically valid psychosocial information about the users. Results: Using Deep Contextualized Word Embeddings (CWEs) for text representation, two models were constructed: A Single Task Model (STM), to predict suicide risk from Facebook postings directly (Facebook texts → suicide) and a Multi-Task Model (MTM), which included hierarchical, multilayered sets of theory-driven risk factors (Facebook texts → personality traits → psychosocial risks → psychiatric disorders → suicide). Compared with the STM predictions (.606 ≤ AUC ≤ .608), the MTM produced improved prediction accuracy (.690 ≤ AUC ≤ .759), with substantially larger effect sizes (.701 ≤ d ≤ .994). Subsequent content analyses suggest that predictions did not rely on explicit suicide-related themes, but on a wide range of content. Conclusions: Advanced machine learning methods can improve our ability to predict suicide risk from everyday social media activities. The knowledge generated by this research may eventually lead to the development of more accurate and objective detection tools and get individuals the help they need in time.

scholarly journals Rosetta Custom Score Functions Accurately Predict ΔΔG of Mutations at Protein-Protein Interfaces Using Machine Learning

2020 ◽  
Author(s):  
Sumant Shringari ◽  
Sam Giannakoulias ◽  
John J. Ferrie ◽  
E. James Petersson
Keyword(s):  
Machine Learning ◽  
Biological Processes ◽  
Learning Methods ◽  
Score Functions ◽  
Machine Learning Methods ◽  
Protein Interfaces ◽  
Therapeutic Molecules ◽  
First Time

Protein-protein interfaces play essential roles in a variety of biological processes and many therapeutic molecules are targeted at these interfaces. However, accurate predictions of the effects of interfacial mutations to identify “hotspots” have remained elusive despite the myriad of modeling and machine learning methods tested. Here, for the first time, we demonstrate that nonlinear reweighting of energy terms from Rosetta, through the use of machine learning, exhibits improved predictability of ΔΔG values associated with interfacial mutations.

Machine learning methods in prediction of protein palmitoylation sites: A brief review

2020 ◽  
Vol 26 ◽  
Author(s):  
Yanwen Li ◽  
Feng Pu ◽  
Jingru Wang ◽  
Zhiguo Zhou ◽  
Chunhua Zhang ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Mechanism ◽  
Computational Methods ◽  
Experimental Studies ◽  
Biological Processes ◽  
Biological Mechanism ◽  
Lipid Modification ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Protein Palmitoylation

: Protein palmitoylation is a fundamental and reversible post-translational lipid modification that involves a series of biological processes. Although a large number of experimental studies have explored the molecular mechanism behind the palmitoylation process, the computational methods has attracted much attention for its good performance in predicting palmitoylation sites compared with expensive and time-consuming biochemical experiments. The prediction of protein palmitoylation sites is helpful to reveal its biological mechanism. Therefore, the research on the application of machine learning methods to predict palmitoylation sites has become a hot topic in bioinformatics and promoted the development in related fields. In this review, we briefly introduced the recent development in predicting protein palmitoylation sites by using machine learning-based methods and discussed their benefits and drawbacks. The perspective of machine learning-based methods in predicting palmitoylation sites was also provided. We hope the review could provide a guide in related fields.

scholarly journals Application of network link prediction in drug discovery

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Khushnood Abbas ◽  
Alireza Abbasi ◽  
Shi Dong ◽  
Ling Niu ◽  
Laihang Yu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Link Prediction ◽  
Machine Learning Algorithms ◽  
Machine Learning Techniques ◽  
Biomedical Data ◽  
Learning Approaches ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Wide Range

Abstract Background Technological and research advances have produced large volumes of biomedical data. When represented as a network (graph), these data become useful for modeling entities and interactions in biological and similar complex systems. In the field of network biology and network medicine, there is a particular interest in predicting results from drug–drug, drug–disease, and protein–protein interactions to advance the speed of drug discovery. Existing data and modern computational methods allow to identify potentially beneficial and harmful interactions, and therefore, narrow drug trials ahead of actual clinical trials. Such automated data-driven investigation relies on machine learning techniques. However, traditional machine learning approaches require extensive preprocessing of the data that makes them impractical for large datasets. This study presents wide range of machine learning methods for predicting outcomes from biomedical interactions and evaluates the performance of the traditional methods with more recent network-based approaches. Results We applied a wide range of 32 different network-based machine learning models to five commonly available biomedical datasets, and evaluated their performance based on three important evaluations metrics namely AUROC, AUPR, and F1-score. We achieved this by converting link prediction problem as binary classification problem. In order to achieve this we have considered the existing links as positive example and randomly sampled negative examples from non-existant set. After experimental evaluation we found that Prone, ACT and $$LRW_5$$ L R W 5 are the top 3 best performers on all five datasets. Conclusions This work presents a comparative evaluation of network-based machine learning algorithms for predicting network links, with applications in the prediction of drug-target and drug–drug interactions, and applied well known network-based machine learning methods. Our work is helpful in guiding researchers in the appropriate selection of machine learning methods for pharmaceutical tasks.

Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein–protein interactions using machine learning methods

2016 ◽  
Vol 12 (3) ◽  
pp. 778-785 ◽  
Author(s):  
A. Srivastava ◽  
G. Mazzocco ◽  
A. Kel ◽  
L. S. Wyrwicz ◽  
D. Plewczynski
Keyword(s):  
Machine Learning ◽  
Protein Interactions ◽  
Computational Prediction ◽  
Vital Role ◽  
Biological Processes ◽  
Interacting Proteins ◽  
Protein Protein Interactions ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
P Protein

Protein–protein interactions (PPIs) play a vital role in most biological processes.

scholarly journals A unified machine learning approach to time series forecasting applied to demand at emergency departments

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Michaela A.C. Vollmer ◽  
Ben Glampson ◽  
Thomas Mellan ◽  
Swapnil Mishra ◽  
Luca Mercuri ◽  
...  
Keyword(s):  
Machine Learning ◽  
Emergency Departments ◽  
Linear Models ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
Wide Range ◽  
The Future

Abstract Background There were 25.6 million attendances at Emergency Departments (EDs) in England in 2019 corresponding to an increase of 12 million attendances over the past ten years. The steadily rising demand at EDs creates a constant challenge to provide adequate quality of care while maintaining standards and productivity. Managing hospital demand effectively requires an adequate knowledge of the future rate of admission. We develop a novel predictive framework to understand the temporal dynamics of hospital demand. Methods We compare and combine state-of-the-art forecasting methods to predict hospital demand 1, 3 or 7 days into the future. In particular, our analysis compares machine learning algorithms to more traditional linear models as measured in a mean absolute error (MAE) and we consider two different hyperparameter tuning methods, enabling a faster deployment of our models without compromising performance. We believe our framework can readily be used to forecast a wide range of policy relevant indicators. Results We find that linear models often outperform machine learning methods and that the quality of our predictions for any of the forecasting horizons of 1, 3 or 7 days are comparable as measured in MAE. Our approach is able to predict attendances at these emergency departments one day in advance up to a mean absolute error of ±14 and ±10 patients corresponding to a mean absolute percentage error of 6.8% and 8.6% respectively. Conclusions Simple linear methods like generalized linear models are often better or at least as good as ensemble learning methods like the gradient boosting or random forest algorithm. However, though sophisticated machine learning methods are not necessarily better than linear models, they improve the diversity of model predictions so that stacked predictions can be more robust than any single model including the best performing one.

scholarly journals Machine Learning for Social Science: An Agnostic Approach

2021 ◽  
Vol 24 (1) ◽  
Author(s):  
Justin Grimmer ◽  
Margaret E. Roberts ◽  
Brandon M. Stewart
Keyword(s):  
Social Sciences ◽  
Machine Learning ◽  
Social Science ◽  
Scientific Data ◽  
Annual Review ◽  
Publication Date ◽  
Learning Methods ◽  
Machine Learning Methods ◽  
The Social ◽  
Wide Range

Social scientists are now in an era of data abundance, and machine learning tools are increasingly used to extract meaning from data sets both massive and small. We explain how the inclusion of machine learning in the social sciences requires us to rethink not only applications of machine learning methods but also best practices in the social sciences. In contrast to the traditional tasks for machine learning in computer science and statistics, when machine learning is applied to social scientific data, it is used to discover new concepts, measure the prevalence of those concepts, assess causal effects, and make predictions. The abundance of data and resources facilitates the move away from a deductive social science to a more sequential, interactive, and ultimately inductive approach to inference. We explain how an agnostic approach to machine learning methods focused on the social science tasks facilitates progress across a wide range of questions. Expected final online publication date for the Annual Review of Political Science, Volume 24 is May 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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