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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 -
Computers in Biology and Medicine Mar 2022In the present research we tackled the classification of seven genetic cardiac diseases and control subjects by using an extensive set of machine learning algorithms...
In the present research we tackled the classification of seven genetic cardiac diseases and control subjects by using an extensive set of machine learning algorithms with their variations from simple K-nearest neighbor searching method to support vector machines. The research was based on calcium transient signals measured from induced pluripotent stem cell-derived cardiomyocytes. All in all, 55 different machine learning alternatives were used to model eight classes by applying the principle of 10-fold crossvalidation with the peak data of 1626 signals. The best classification accuracy of approximately 69% was given by random forests, which can be seen high enough here to show machine learning to be potential for the differentiation of the eight disease classes.
Topics: Algorithms; Data Science; Heart Diseases; Humans; Induced Pluripotent Stem Cells; Machine Learning; Support Vector Machine
PubMed: 34999413
DOI: 10.1016/j.compbiomed.2022.105218 -
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 -
Briefings in Bioinformatics May 2023CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9) is a popular and effective two-component technology used for... (Review)
Review
CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated protein 9) is a popular and effective two-component technology used for targeted genetic manipulation. It is currently the most versatile and accurate method of gene and genome editing, which benefits from a large variety of practical applications. For example, in biomedicine, it has been used in research related to cancer, virus infections, pathogen detection, and genetic diseases. Current CRISPR/Cas9 research is based on data-driven models for on- and off-target prediction as a cleavage may occur at non-target sequence locations. Nowadays, conventional machine learning and deep learning methods are applied on a regular basis to accurately predict on-target knockout efficacy and off-target profile of given single-guide RNAs (sgRNAs). In this paper, we present an overview and a comparative analysis of traditional machine learning and deep learning models used in CRISPR/Cas9. We highlight the key research challenges and directions associated with target activity prediction. We discuss recent advances in the sgRNA-DNA sequence encoding used in state-of-the-art on- and off-target prediction models. Furthermore, we present the most popular deep learning neural network architectures used in CRISPR/Cas9 prediction models. Finally, we summarize the existing challenges and discuss possible future investigations in the field of on- and off-target prediction. Our paper provides valuable support for academic and industrial researchers interested in the application of machine learning methods in the field of CRISPR/Cas9 genome editing.
Topics: CRISPR-Cas Systems; Deep Learning; Gene Editing; Machine Learning
PubMed: 37080758
DOI: 10.1093/bib/bbad131 -
BioEssays : News and Reviews in... Feb 2024Bioimage analysis plays a critical role in extracting information from biological images, enabling deeper insights into cellular structures and processes. The... (Review)
Review
Bioimage analysis plays a critical role in extracting information from biological images, enabling deeper insights into cellular structures and processes. The integration of machine learning and deep learning techniques has revolutionized the field, enabling the automated, reproducible, and accurate analysis of biological images. Here, we provide an overview of the history and principles of machine learning and deep learning in the context of bioimage analysis. We discuss the essential steps of the bioimage analysis workflow, emphasizing how machine learning and deep learning have improved preprocessing, segmentation, feature extraction, object tracking, and classification. We provide examples that showcase the application of machine learning and deep learning in bioimage analysis. We examine user-friendly software and tools that enable biologists to leverage these techniques without extensive computational expertise. This review is a resource for researchers seeking to incorporate machine learning and deep learning in their bioimage analysis workflows and enhance their research in this rapidly evolving field.
Topics: Deep Learning; Image Processing, Computer-Assisted; Microscopy, Fluorescence; Software; Machine Learning
PubMed: 38058114
DOI: 10.1002/bies.202300114 -
Spectrochimica Acta. Part A, Molecular... Sep 2022Raman spectroscopy, a "fingerprint" spectrum of substances, can be used to characterize various biological and chemical samples. To allow for blood classification using... (Review)
Review
Raman spectroscopy, a "fingerprint" spectrum of substances, can be used to characterize various biological and chemical samples. To allow for blood classification using single-cell Raman spectroscopy, several machine learning algorithms were implemented and compared. A single-cell laser optical tweezer Raman spectroscopy system was established to obtain the Raman spectra of red blood cells. The Boruta algorithm extracted the spectral feature frequency shift, reduced the spectral dimension, and determined the essential features that affect classification. Next, seven machine learning classification models are analyzed and compared based on the classification accuracy, precision, and recall indicators. The results show that support vector machines and artificial neural networks are the two most appropriate machine learning algorithms for single-cell Raman spectrum blood classification, and this finding provides essential guidance for future research studies.
Topics: Algorithms; Machine Learning; Neural Networks, Computer; Optical Tweezers; Spectrum Analysis, Raman; Support Vector Machine
PubMed: 35500354
DOI: 10.1016/j.saa.2022.121274 -
Computational Intelligence and... 2022Recent imaging science and technology discoveries have considered hyperspectral imagery and remote sensing. The current intelligent technologies, such as support vector... (Review)
Review
Recent imaging science and technology discoveries have considered hyperspectral imagery and remote sensing. The current intelligent technologies, such as support vector machines, sparse representations, active learning, extreme learning machines, transfer learning, and deep learning, are typically based on the learning of the machines. These techniques enrich the processing of such three-dimensional, multiple bands, and high-resolution images with their precision and fidelity. This article presents an extensive survey depicting machine-dependent technologies' contributions and deep learning on landcover classification based on hyperspectral images. The objective of this study is three-fold. First, after reading a large pool of Web of Science (WoS), Scopus, SCI, and SCIE-indexed and SCIE-related articles, we provide a novel approach for review work that is entirely systematic and aids in the inspiration of finding research gaps and developing embedded questions. Second, we emphasize contemporary advances in machine learning (ML) methods for identifying hyperspectral images, with a brief, organized overview and a thorough assessment of the literature involved. Finally, we draw the conclusions to assist researchers in expanding their understanding of the relationship between machine learning and hyperspectral images for future research.
Topics: Machine Learning; Support Vector Machine
PubMed: 35528334
DOI: 10.1155/2022/3854635