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Trends in Cell Biology Jul 2023Modern drug discovery approaches often use high-content imaging to systematically study the effect on cells of large libraries of chemical compounds. By automatically... (Review)
Review
Modern drug discovery approaches often use high-content imaging to systematically study the effect on cells of large libraries of chemical compounds. By automatically screening thousands or millions of images to identify specific drug-induced cellular phenotypes, for example, altered cellular morphology, these approaches can reveal 'hit' compounds offering therapeutic promise. In the past few years, artificial intelligence (AI) methods based on deep learning (DL) [a family of machine learning (ML) techniques] have disrupted virtually all image analysis tasks, from image classification to segmentation. These powerful methods also promise to impact drug discovery by accelerating the identification of effective drugs and their modes of action. In this review, we highlight applications and adaptations of ML, especially DL methods for cell-based phenotypic drug discovery (PDD).
Topics: Artificial Intelligence; Deep Learning; Drug Discovery; Machine Learning; Phenotype
PubMed: 36623998
DOI: 10.1016/j.tcb.2022.11.011 -
The Analyst Oct 2021Electrochemical sensors and biosensors have been successfully used in a wide range of applications, but systematic optimization and nonlinear relationships have been... (Review)
Review
Electrochemical sensors and biosensors have been successfully used in a wide range of applications, but systematic optimization and nonlinear relationships have been compromised for electrode fabrication and data analysis. Machine learning and experimental designs are chemometric tools that have been proved to be useful in method development and data analysis. This minireview summarizes recent applications of machine learning and experimental designs in electroanalytical chemistry. First, experimental designs, , full factorial, central composite, and Box-Behnken are discussed as systematic approaches to optimize electrode fabrication to consider the effects from individual variables and their interactions. Then, the principles of machine learning algorithms, including linear and logistic regressions, neural network, and support vector machine, are introduced. These machine learning models have been implemented to extract complex relationships between chemical structures and their electrochemical properties and to analyze complicated electrochemical data to improve calibration and analyte classification, such as in electronic tongues. Lastly, the future of machine learning and experimental designs in electrochemical sensors is outlined. These chemometric strategies will accelerate the development and enhance the performance of electrochemical devices for point-of-care diagnostics and commercialization.
Topics: Algorithms; Biosensing Techniques; Machine Learning; Neural Networks, Computer; Support Vector Machine
PubMed: 34585185
DOI: 10.1039/d1an01148k -
Environmental Science and Pollution... Sep 2023The sustainability of the earth depends on renewable energy. Forecasting the output of renewable energy has a big impact on how we operate and manage our power networks.... (Review)
Review
The sustainability of the earth depends on renewable energy. Forecasting the output of renewable energy has a big impact on how we operate and manage our power networks. Accurate forecasting of renewable energy generation is crucial to ensuring grid dependability and permanence and reducing the risk and cost of the energy market and infrastructure. Although there are several approaches to forecasting solar radiation on a global scale, the two most common ones are machine learning algorithms and cloud pictures combined with physical models. The objective is to present a summary of machine learning-based techniques for solar irradiation forecasting in this context. Renewable energy is being used more and more in the world's energy grid. Numerous strategies, including hybrids, physical models, statistical approaches, and artificial intelligence techniques, have been developed to anticipate the use of renewable energy. This paper examines methods for forecasting renewable energy based on deep learning and machine learning. Review and analysis of deep learning and machine learning forecasts for renewable energy come first. The second paragraph describes metaheuristic optimization techniques for renewable energy. The third topic was the open issue of projecting renewable energy. I will wrap up with a few potential future job objectives.
Topics: Artificial Intelligence; Deep Learning; Machine Learning; Renewable Energy; Algorithms; Forecasting
PubMed: 37552450
DOI: 10.1007/s11356-023-29064-w -
Scientific Reports Sep 2022The analytic procedures incorporated to facilitate the delivery of projects are often referred to as project analytics. Existing techniques focus on retrospective...
The analytic procedures incorporated to facilitate the delivery of projects are often referred to as project analytics. Existing techniques focus on retrospective reporting and understanding the underlying relationships to make informed decisions. Although machine learning algorithms have been widely used in addressing problems within various contexts (e.g., streamlining the design of construction projects), limited studies have evaluated pre-existing machine learning methods within the delivery of construction projects. Due to this, the current research aims to contribute further to this convergence between artificial intelligence and the execution construction project through the evaluation of a specific set of machine learning algorithms. This study proposes a machine learning-based data-driven research framework for addressing problems related to project analytics. It then illustrates an example of the application of this framework. In this illustration, existing data from an open-source data repository on construction projects and cost overrun frequencies was studied in which several machine learning models (Python's Scikit-learn package) were tested and evaluated. The data consisted of 44 independent variables (from materials to labour and contracting) and one dependent variable (project cost overrun frequency), which has been categorised for processing under several machine learning models. These models include support vector machine, logistic regression, k-nearest neighbour, random forest, stacking (ensemble) model and artificial neural network. Feature selection and evaluation methods, including the Univariate feature selection, Recursive feature elimination, SelectFromModel and confusion matrix, were applied to determine the most accurate prediction model. This study also discusses the generalisability of using the proposed research framework in other research contexts within the field of project management. The proposed framework, its illustration in the context of construction projects and its potential to be adopted in different contexts will significantly contribute to project practitioners, stakeholders and academics in addressing many project-related issues.
Topics: Artificial Intelligence; Logistic Models; Machine Learning; Retrospective Studies; Support Vector Machine
PubMed: 36085353
DOI: 10.1038/s41598-022-19728-x -
Immunology and Cell Biology Jul 2017Machine learning (ML) refers to a set of automatic pattern recognition methods that have been successfully applied across various problem domains, including biomedical... (Review)
Review
Machine learning (ML) refers to a set of automatic pattern recognition methods that have been successfully applied across various problem domains, including biomedical image analysis. This review focuses on ML applications for image analysis in light microscopy experiments with typical tasks of segmenting and tracking individual cells, and modelling of reconstructed lineage trees. After describing a typical image analysis pipeline and highlighting challenges of automatic analysis (for example, variability in cell morphology, tracking in presence of clutters) this review gives a brief historical outlook of ML, followed by basic concepts and definitions required for understanding examples. This article then presents several example applications at various image processing stages, including the use of supervised learning methods for improving cell segmentation, and the application of active learning for tracking. The review concludes with remarks on parameter setting and future directions.
Topics: Animals; Cell Tracking; Humans; Image Processing, Computer-Assisted; Machine Learning; Microscopy; Supervised Machine Learning; Unsupervised Machine Learning
PubMed: 28294138
DOI: 10.1038/icb.2017.16 -
Molecules (Basel, Switzerland) Sep 2022The classification of biological neuron types and networks poses challenges to the full understanding of the human brain's organisation and functioning. In this paper,...
The classification of biological neuron types and networks poses challenges to the full understanding of the human brain's organisation and functioning. In this paper, we develop a novel objective classification model of biological neuronal morphology and electrical types and their networks, based on the attributes of neuronal communication using supervised machine learning solutions. This presents advantages compared to the existing approaches in neuroinformatics since the data related to mutual information or delay between neurons obtained from spike trains are more abundant than conventional morphological data. We constructed two open-access computational platforms of various neuronal circuits from the Blue Brain Project realistic models, named Neurpy and Neurgen. Then, we investigated how we could perform network tomography with cortical neuronal circuits for the morphological, topological and electrical classification of neurons. We extracted the simulated data of 10,000 network topology combinations with five layers, 25 morphological type (m-type) cells, and 14 electrical type (e-type) cells. We applied the data to several different classifiers (including Support Vector Machine (SVM), Decision Trees, Random Forest, and Artificial Neural Networks). We achieved accuracies of up to 70%, and the inference of biological network structures using network tomography reached up to 65% of accuracy. Objective classification of biological networks can be achieved with cascaded machine learning methods using neuron communication data. SVM methods seem to perform better amongst used techniques. Our research not only contributes to existing classification efforts but sets the road-map for future usage of brain-machine interfaces towards an in vivo objective classification of neurons as a sensing mechanism of the brain's structure.
Topics: Humans; Machine Learning; Neural Networks, Computer; Neurons; Supervised Machine Learning; Support Vector Machine
PubMed: 36234792
DOI: 10.3390/molecules27196256 -
Molecules (Basel, Switzerland) Mar 2023A deep learning-based quantitative structure-activity relationship analysis, namely the molecular image-based DeepSNAP-deep learning method, can successfully and... (Review)
Review
A deep learning-based quantitative structure-activity relationship analysis, namely the molecular image-based DeepSNAP-deep learning method, can successfully and automatically capture the spatial and temporal features in an image generated from a three-dimensional (3D) structure of a chemical compound. It allows building high-performance prediction models without extracting and selecting features because of its powerful feature discrimination capability. Deep learning (DL) is based on a neural network with multiple intermediate layers that makes it possible to solve highly complex problems and improve the prediction accuracy by increasing the number of hidden layers. However, DL models are too complex when it comes to understanding the derivation of predictions. Instead, molecular descriptor-based machine learning has clear features owing to the selection and analysis of features. However, molecular descriptor-based machine learning has some limitations in terms of prediction performance, calculation cost, feature selection, etc., while the DeepSNAP-deep learning method outperforms molecular descriptor-based machine learning due to the utilization of 3D structure information and the advanced computer processing power of DL.
Topics: Deep Learning; Quantitative Structure-Activity Relationship; Neural Networks, Computer; Machine Learning
PubMed: 36903654
DOI: 10.3390/molecules28052410 -
Progress in Biophysics and Molecular... Oct 2022Cancer is a disease which is characterised by the unusual and uncontrollable growth of body cells. This usually happens asymptomatically and gets spread to other parts... (Review)
Review
Cancer is a disease which is characterised by the unusual and uncontrollable growth of body cells. This usually happens asymptomatically and gets spread to other parts of the body. The major problem in treating cancer is that its progress is not monitored once it is diagnosed. The progress or the prognosis can be done through survival analysis. The survival analysis is the branch of statistics that deals in predicting the time of event of occurrence. In the case of cancer prognosis the event is the survival time of the patient from the onset of the disease or it can be the recurrence of the disease after undergoing a treatment. This study aims to bring out the machine learning and deep learning models involved in providing the prognosis to the cancer patients.
Topics: Deep Learning; Humans; Machine Learning; Neoplasms
PubMed: 35933043
DOI: 10.1016/j.pbiomolbio.2022.07.004 -
Mathematical Biosciences and... Aug 2022Preventive identification of mechanical parts failures has always played a crucial role in machine maintenance. Over time, as the processing cycles are repeated, the... (Review)
Review
Preventive identification of mechanical parts failures has always played a crucial role in machine maintenance. Over time, as the processing cycles are repeated, the machinery in the production system is subject to wear with a consequent loss of technical efficiency compared to optimal conditions. These conditions can, in some cases, lead to the breakage of the elements with consequent stoppage of the production process pending the replacement of the element. This situation entails a large loss of turnover on the part of the company. For this reason, it is crucial to be able to predict failures in advance to try to replace the element before its wear can cause a reduction in machine performance. Several systems have recently been developed for the preventive faults detection that use a combination of low-cost sensors and algorithms based on machine learning. In this work the different methodologies for the identification of the most common mechanical failures are examined and the most widely applied algorithms based on machine learning are analyzed: Support Vector Machine (SVM) solutions, Artificial Neural Network (ANN) algorithms, Convolutional Neural Network (CNN) model, Recurrent Neural Network (RNN) applications, and Deep Generative Systems. These topics have been described in detail and the works most appreciated by the scientific community have been reviewed to highlight the strengths in identifying faults and to outline the directions for future challenges.
Topics: Algorithms; Machine Learning; Neural Networks, Computer; Support Vector Machine
PubMed: 36124599
DOI: 10.3934/mbe.2022534 -
Robust and data-efficient generalization of self-supervised machine learning for diagnostic imaging.Nature Biomedical Engineering Jun 2023Machine-learning models for medical tasks can match or surpass the performance of clinical experts. However, in settings differing from those of the training dataset,...
Machine-learning models for medical tasks can match or surpass the performance of clinical experts. However, in settings differing from those of the training dataset, the performance of a model can deteriorate substantially. Here we report a representation-learning strategy for machine-learning models applied to medical-imaging tasks that mitigates such 'out of distribution' performance problem and that improves model robustness and training efficiency. The strategy, which we named REMEDIS (for 'Robust and Efficient Medical Imaging with Self-supervision'), combines large-scale supervised transfer learning on natural images and intermediate contrastive self-supervised learning on medical images and requires minimal task-specific customization. We show the utility of REMEDIS in a range of diagnostic-imaging tasks covering six imaging domains and 15 test datasets, and by simulating three realistic out-of-distribution scenarios. REMEDIS improved in-distribution diagnostic accuracies up to 11.5% with respect to strong supervised baseline models, and in out-of-distribution settings required only 1-33% of the data for retraining to match the performance of supervised models retrained using all available data. REMEDIS may accelerate the development lifecycle of machine-learning models for medical imaging.
Topics: Supervised Machine Learning; Machine Learning; Diagnostic Imaging
PubMed: 37291435
DOI: 10.1038/s41551-023-01049-7