scholarly journals Recent applications of deep learning and machine intelligence on in silico drug discovery: methods, tools and databases

2018 ◽  
Vol 20 (5) ◽  
pp. 1878-1912 ◽  
Author(s):  
Ahmet Sureyya Rifaioglu ◽  
Heval Atas ◽  
Maria Jesus Martin ◽  
Rengul Cetin-Atalay ◽  
Volkan Atalay ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Drug Discovery ◽  
Machine Intelligence ◽  
New Drugs ◽  
Machine Learning Techniques ◽  
The Past ◽  
Screening Experiments ◽  
Learning Techniques ◽  
Computational Drug Discovery

Abstract The identification of interactions between drugs/compounds and their targets is crucial for the development of new drugs. In vitro screening experiments (i.e. bioassays) are frequently used for this purpose; however, experimental approaches are insufficient to explore novel drug-target interactions, mainly because of feasibility problems, as they are labour intensive, costly and time consuming. A computational field known as ‘virtual screening’ (VS) has emerged in the past decades to aid experimental drug discovery studies by statistically estimating unknown bio-interactions between compounds and biological targets. These methods use the physico-chemical and structural properties of compounds and/or target proteins along with the experimentally verified bio-interaction information to generate predictive models. Lately, sophisticated machine learning techniques are applied in VS to elevate the predictive performance. The objective of this study is to examine and discuss the recent applications of machine learning techniques in VS, including deep learning, which became highly popular after giving rise to epochal developments in the fields of computer vision and natural language processing. The past 3 years have witnessed an unprecedented amount of research studies considering the application of deep learning in biomedicine, including computational drug discovery. In this review, we first describe the main instruments of VS methods, including compound and protein features (i.e. representations and descriptors), frequently used libraries and toolkits for VS, bioactivity databases and gold-standard data sets for system training and benchmarking. We subsequently review recent VS studies with a strong emphasis on deep learning applications. Finally, we discuss the present state of the field, including the current challenges and suggest future directions. We believe that this survey will provide insight to the researchers working in the field of computational drug discovery in terms of comprehending and developing novel bio-prediction methods.

Survey of Machine Learning Techniques in Drug Discovery

2019 ◽  
Vol 20 (3) ◽  
pp. 185-193 ◽  
Author(s):  
Natalie Stephenson ◽  
Emily Shane ◽  
Jessica Chase ◽  
Jason Rowland ◽  
David Ries ◽  
...  
Keyword(s):  
Machine Learning ◽  
Drug Discovery ◽  
Large Scale ◽  
State Of The Art ◽  
New Drugs ◽  
Machine Learning Techniques ◽  
Current Status ◽  
Learning Techniques ◽  
Pharmaceutical Industries ◽  
Current Stage

Background:Drug discovery, which is the process of discovering new candidate medications, is very important for pharmaceutical industries. At its current stage, discovering new drugs is still a very expensive and time-consuming process, requiring Phases I, II and III for clinical trials. Recently, machine learning techniques in Artificial Intelligence (AI), especially the deep learning techniques which allow a computational model to generate multiple layers, have been widely applied and achieved state-of-the-art performance in different fields, such as speech recognition, image classification, bioinformatics, etc. One very important application of these AI techniques is in the field of drug discovery.Methods:We did a large-scale literature search on existing scientific websites (e.g, ScienceDirect, Arxiv) and startup companies to understand current status of machine learning techniques in drug discovery.Results:Our experiments demonstrated that there are different patterns in machine learning fields and drug discovery fields. For example, keywords like prediction, brain, discovery, and treatment are usually in drug discovery fields. Also, the total number of papers published in drug discovery fields with machine learning techniques is increasing every year.Conclusion:The main focus of this survey is to understand the current status of machine learning techniques in the drug discovery field within both academic and industrial settings, and discuss its potential future applications. Several interesting patterns for machine learning techniques in drug discovery fields are discussed in this survey.

scholarly journals Recent Development of Artificial Intelligence Applied in Echocardiography: A Review (Preprint)

2019 ◽  
Author(s):  
Lu Liu ◽  
Ahmed Elazab ◽  
Baiying Lei ◽  
Tianfu Wang
Keyword(s):  
Artificial Intelligence ◽  
Machine Learning ◽  
Deep Learning ◽  
Cardiovascular Diseases ◽  
Disease Diagnosis ◽  
Machine Learning Techniques ◽  
Tissue Segmentation ◽  
The Past ◽  
Learning Techniques ◽  
The Future

BACKGROUND Echocardiography has a pivotal role in the diagnosis and management of cardiovascular diseases since it is real-time, cost-effective, and non-invasive. The development of artificial intelligence (AI) techniques have led to more intelligent and automatic computer-aided diagnosis (CAD) systems in echocardiography over the past few years. Automatic CAD mainly includes classification, detection of anatomical structures, tissue segmentation, and disease diagnosis, which are mainly completed by machine learning techniques and the recent developed deep learning techniques. OBJECTIVE This review aims to provide a guide for researchers and clinicians on relevant aspects of AI, machine learning, and deep learning. In addition, we review the recent applications of these methods in echocardiography and identify how echocardiography could incorporate AI in the future. METHODS This paper first summarizes the overview of machine learning and deep learning. Second, it reviews current use of AI in echocardiography by searching literature in the main databases for the past 10 years and finally discusses potential limitations and challenges in the future. RESULTS AI has showed promising improvements in analysis and interpretation of echocardiography to a new stage in the fields of standard views detection, automated analysis of chamber size and function, and assessment of cardiovascular diseases. CONCLUSIONS Compared with machine learning, deep learning methods have achieved state-of-the-art performance across different applications in echocardiography. Although there are challenges such as the required large dataset, AI can provide satisfactory results by devising various strategies. We believe AI has the potential to improve accuracy of diagnosis, reduce time consumption, and decrease the load of cardiologists.

scholarly journals Detection and Severity Evaluation of Combined Rail Defects Using Deep Learning

Vibration ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 341-356
Author(s):  
Jessada Sresakoolchai ◽  
Sakdirat Kaewunruen
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Machine Learning Techniques ◽  
Rolling Stock ◽  
Raw Data ◽  
Learning Techniques ◽  
Combined Defects

Various techniques have been developed to detect railway defects. One of the popular techniques is machine learning. This unprecedented study applies deep learning, which is a branch of machine learning techniques, to detect and evaluate the severity of rail combined defects. The combined defects in the study are settlement and dipped joint. Features used to detect and evaluate the severity of combined defects are axle box accelerations simulated using a verified rolling stock dynamic behavior simulation called D-Track. A total of 1650 simulations are run to generate numerical data. Deep learning techniques used in the study are deep neural network (DNN), convolutional neural network (CNN), and recurrent neural network (RNN). Simulated data are used in two ways: simplified data and raw data. Simplified data are used to develop the DNN model, while raw data are used to develop the CNN and RNN model. For simplified data, features are extracted from raw data, which are the weight of rolling stock, the speed of rolling stock, and three peak and bottom accelerations from two wheels of rolling stock. In total, there are 14 features used as simplified data for developing the DNN model. For raw data, time-domain accelerations are used directly to develop the CNN and RNN models without processing and data extraction. Hyperparameter tuning is performed to ensure that the performance of each model is optimized. Grid search is used for performing hyperparameter tuning. To detect the combined defects, the study proposes two approaches. The first approach uses one model to detect settlement and dipped joint, and the second approach uses two models to detect settlement and dipped joint separately. The results show that the CNN models of both approaches provide the same accuracy of 99%, so one model is good enough to detect settlement and dipped joint. To evaluate the severity of the combined defects, the study applies classification and regression concepts. Classification is used to evaluate the severity by categorizing defects into light, medium, and severe classes, and regression is used to estimate the size of defects. From the study, the CNN model is suitable for evaluating dipped joint severity with an accuracy of 84% and mean absolute error (MAE) of 1.25 mm, and the RNN model is suitable for evaluating settlement severity with an accuracy of 99% and mean absolute error (MAE) of 1.58 mm.

scholarly journals Sentiment Analysis using various Machine Learning and Deep Learning Techniques

2021 ◽  
pp. 385-394
Author(s):  
V Umarani ◽  
A Julian ◽  
J Deepa
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Naive Bayes ◽  
Naïve Bayes ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Analysis Process ◽  
Learning Techniques

Sentiment analysis has gained a lot of attention from researchers in the last year because it has been widely applied to a variety of application domains such as business, government, education, sports, tourism, biomedicine, and telecommunication services. Sentiment analysis is an automated computational method for studying or evaluating sentiments, feelings, and emotions expressed as comments, feedbacks, or critiques. The sentiment analysis process can be automated using machine learning techniques, which analyses text patterns faster. The supervised machine learning technique is the most used mechanism for sentiment analysis. The proposed work discusses the flow of sentiment analysis process and investigates the common supervised machine learning techniques such as multinomial naive bayes, Bernoulli naive bayes, logistic regression, support vector machine, random forest, K-nearest neighbor, decision tree, and deep learning techniques such as Long Short-Term Memory and Convolution Neural Network. The work examines such learning methods using standard data set and the experimental results of sentiment analysis demonstrate the performance of various classifiers taken in terms of the precision, recall, F1-score, RoC-Curve, accuracy, running time and k fold cross validation and helps in appreciating the novelty of the several deep learning techniques and also giving the user an overview of choosing the right technique for their application.

scholarly journals Comparison of Machine Learning algorithm for COVID-19 Death Risk Prediction

2021 ◽  
Author(s):  
Praveeen Anandhanathan ◽  
Priyanka Gopalan
Keyword(s):  
Machine Learning ◽  
Learning Algorithm ◽  
Machine Learning Techniques ◽  
Support Vector ◽  
Nearest Neighbour ◽  
Decision Tree Algorithm ◽  
The Past ◽  
Random Forest Method ◽  
Learning Techniques ◽  
The World

Abstract Coronavirus disease (COVID-19) is spreading across the world. Since at first it has appeared in Wuhan, China in December 2019, it has become a serious issue across the globe. There are no accurate resources to predict and find the disease. So, by knowing the past patients’ records, it could guide the clinicians to fight against the pandemic. Therefore, for the prediction of healthiness from symptoms Machine learning techniques can be implemented. From this we are going to analyse only the symptoms which occurs in every patient. These predictions can help clinicians in the easier manner to cure the patients. Already for prediction of many of the diseases, techniques like SVM (Support vector Machine), Fuzzy k-Means Clustering, Decision Tree algorithm, Random Forest Method, ANN (Artificial Neural Network), KNN (k-Nearest Neighbour), Naïve Bayes, Linear Regression model are used. As we haven’t faced this disease before, we can’t say which technique will give the maximum accuracy. So, we are going to provide an efficient result by comparing all the such algorithms in RStudio.

scholarly journals The rise and fall of machine learning methods in biomedical research

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 2012 ◽  
Author(s):  
Hashem Koohy
Keyword(s):  
Machine Learning ◽  
Biomedical Research ◽  
Life Sciences ◽  
Biological Data ◽  
Research Note ◽  
Machine Learning Techniques ◽  
Learning Methods ◽  
The Past ◽  
Machine Learning Methods ◽  
Learning Techniques

In the era of explosion in biological data, machine learning techniques are becoming more popular in life sciences, including biology and medicine. This research note examines the rise and fall of the most commonly used machine learning techniques in life sciences over the past three decades.

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