Brain Informatics最新文献

{"title":"Assisted neuroscience knowledge extraction via machine learning applied to neural reconstruction metadata on NeuroMorpho.Org.","authors":"Kayvan Bijari, Yasmeen Zoubi, Giorgio A Ascoli","doi":"10.1186/s40708-022-00174-4","DOIUrl":"10.1186/s40708-022-00174-4","url":null,"abstract":"<p><p>The amount of unstructured text produced daily in scholarly journals is enormous. Systematically identifying, sorting, and structuring information from such a volume of data is increasingly challenging for researchers even in delimited domains. Named entity recognition is a fundamental natural language processing tool that can be trained to annotate, structure, and extract information from scientific articles. Here, we harness state-of-the-art machine learning techniques and develop a smart neuroscience metadata suggestion system accessible by both humans through a user-friendly graphical interface and machines via Application Programming Interface. We demonstrate a practical application to the public repository of neural reconstructions, NeuroMorpho.Org, thus expanding the existing web-based metadata management system currently in use. Quantitative analysis indicates that the suggestion system reduces personnel labor by at least 50%. Moreover, our results show that larger training datasets with the same software architecture are unlikely to further improve performance without ad-hoc heuristics due to intrinsic ambiguities in neuroscience nomenclature. All components of this project are released open source for community enhancement and extensions to additional applications.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":"9 1","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2022-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9640520/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9093389","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hemodynamic functional connectivity optimization of frequency EEG microstates enables attention LSTM framework to classify distinct temporal cortical communications of different cognitive tasks.","authors":"Swati Agrawal,&nbsp;Vijayakumar Chinnadurai,&nbsp;Rinku Sharma","doi":"10.1186/s40708-022-00173-5","DOIUrl":"10.1186/s40708-022-00173-5","url":null,"abstract":"<p><p>Temporal analysis of global cortical communication of cognitive tasks in coarse EEG information is still challenging due to the underlying complex neural mechanisms. This study proposes an attention-based time-series deep learning framework that processes fMRI functional connectivity optimized quasi-stable frequency microstates for classifying distinct temporal cortical communications of the cognitive task. Seventy volunteers were subjected to visual target detection tasks, and their electroencephalogram (EEG) and functional MRI (fMRI) were acquired simultaneously. At first, the acquired EEG information was preprocessed and bandpass to delta, theta, alpha, beta, and gamma bands and then subjected to quasi-stable frequency-microstate estimation. Subsequently, time-series elicitation of each frequency microstates is optimized with graph theory measures of simultaneously eliciting fMRI functional connectivity between frontal, parietal, and temporal cortices. The distinct neural mechanisms associated with each optimized frequency-microstate were analyzed using microstate-informed fMRI. Finally, these optimized, quasi-stable frequency microstates were employed to train and validate the attention-based Long Short-Term Memory (LSTM) time-series architecture for classifying distinct temporal cortical communications of the target from other cognitive tasks. The temporal, sliding input sampling windows were chosen between 180 to 750 ms/segment based on the stability of transition probabilities of the optimized microstates. The results revealed 12 distinct frequency microstates capable of deciphering target detections' temporal cortical communications from other task engagements. Particularly, fMRI functional connectivity measures of target engagement were observed significantly correlated with the right-diagonal delta (r = 0.31), anterior-posterior theta (r = 0.35), left-right theta (r = - 0.32), alpha (r = - 0.31) microstates. Further, neuro-vascular information of microstate-informed fMRI analysis revealed the association of delta/theta and alpha/beta microstates with cortical communications and local neural processing, respectively. The classification accuracies of the attention-based LSTM were higher than the traditional LSTM architectures, particularly the frameworks that sampled the EEG data with a temporal width of 300 ms/segment. In conclusion, the study demonstrates reliable temporal classifications of global cortical communication of distinct tasks using an attention-based LSTM utilizing fMRI functional connectivity optimized quasi-stable frequency microstates.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2022-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554110/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33500442","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning methods for the study of cybersickness: a systematic review.","authors":"Alexander Hui Xiang Yang,&nbsp;Nikola Kasabov,&nbsp;Yusuf Ozgur Cakmak","doi":"10.1186/s40708-022-00172-6","DOIUrl":"https://doi.org/10.1186/s40708-022-00172-6","url":null,"abstract":"<p><p>This systematic review offers a world-first critical analysis of machine learning methods and systems, along with future directions for the study of cybersickness induced by virtual reality (VR). VR is becoming increasingly popular and is an important part of current advances in human training, therapies, entertainment, and access to the metaverse. Usage of this technology is limited by cybersickness, a common debilitating condition experienced upon VR immersion. Cybersickness is accompanied by a mix of symptoms including nausea, dizziness, fatigue and oculomotor disturbances. Machine learning can be used to identify cybersickness and is a step towards overcoming these physiological limitations. Practical implementation of this is possible with optimised data collection from wearable devices and appropriate algorithms that incorporate advanced machine learning approaches. The present systematic review focuses on 26 selected studies. These concern machine learning of biometric and neuro-physiological signals obtained from wearable devices for the automatic identification of cybersickness. The methods, data processing and machine learning architecture, as well as suggestions for future exploration on detection and prediction of cybersickness are explored. A wide range of immersion environments, participant activity, features and machine learning architectures were identified. Although models for cybersickness detection have been developed, literature still lacks a model for the prediction of first-instance events. Future research is pointed towards goal-oriented data selection and labelling, as well as the use of brain-inspired spiking neural network models to achieve better accuracy and understanding of complex spatio-temporal brain processes related to cybersickness.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2022-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9548085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33514229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Early detection of Alzheimer's disease using neuropsychological tests: a predict-diagnose approach using neural networks.","authors":"Devarshi Mukherji,&nbsp;Manibrata Mukherji,&nbsp;Nivedita Mukherji","doi":"10.1186/s40708-022-00169-1","DOIUrl":"https://doi.org/10.1186/s40708-022-00169-1","url":null,"abstract":"<p><p>Alzheimer's disease (AD) is a slowly progressing disease for which there is no known therapeutic cure at present. Ongoing research around the world is actively engaged in the quest for identifying markers that can help predict the future cognitive state of individuals so that measures can be taken to prevent the onset or arrest the progression of the disease. Researchers are interested in both biological and neuropsychological markers that can serve as good predictors of the future cognitive state of individuals. The goal of this study is to identify non-invasive, inexpensive markers and develop neural network models that learn the relationship between those markers and the future cognitive state. To that end, we use the renowned Alzheimer's Disease Neuroimaging Initiative (ADNI) data for a handful of neuropsychological tests to train Recurrent Neural Network (RNN) models to predict future neuropsychological test results and Multi-Level Perceptron (MLP) models to diagnose the future cognitive states of trial participants based on those predicted results. The results demonstrate that the predicted cognitive states match the actual cognitive states of ADNI test subjects with a high level of accuracy. Therefore, this novel two-step technique can serve as an effective tool for the prediction of Alzheimer's disease progression. The reliance of the results on inexpensive, non-invasive tests implies that this technique can be used in countries around the world including those with limited financial resources.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2022-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9515292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40375591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"^RNeuMark: A Riemannian EEG Analysis Framework for Neuromarketing.","authors":"Kostas Georgiadis, Fotis P Kalaganis, Vangelis P Oikonomou, Spiros Nikolopoulos, Nikos A Laskaris, Ioannis Kompatsiaris","doi":"10.1186/s40708-022-00171-7","DOIUrl":"10.1186/s40708-022-00171-7","url":null,"abstract":"<p><p>Neuromarketing exploits neuroimaging techniques so as to reinforce the predictive power of conventional marketing tools, like questionnaires and focus groups. Electroencephalography (EEG) is the most commonly encountered neuroimaging technique due to its non-invasiveness, low-cost, and its very recent embedding in wearable devices. The transcription of brainwave patterns to consumer attitude is supported by various signal descriptors, while the quest for profitable novel ways is still an open research question. Here, we suggest the use of sample covariance matrices as alternative descriptors, that encapsulate the coordinated neural activity from distinct brain areas, and the adoption of Riemannian geometry for their handling. We first establish the suitability of Riemannian approach for neuromarketing-related problems and then suggest a relevant decoding scheme for predicting consumers' choices (e.g., willing to buy or not a specific product). Since the decision-making process involves the concurrent interaction of various cognitive processes and consequently of distinct brain rhythms, the proposed decoder takes the form of an ensemble classifier that builds upon a multi-view perspective, with each view dedicated to a specific frequency band. Adopting a standard machine learning procedure, and using a set of trials (training data) in conjunction with the associated behavior labels (\"buy\"/ \"not buy\"), we train a battery of classifiers accordingly. Each classifier is designed to operate in the space recovered from the inter-trial distances of SCMs and to cast a rhythm-depended decision that is eventually combined with the predictions of the rest ones. The demonstration and evaluation of the proposed approach are performed in 2 neuromarketing-related datasets of different nature. The first is employed to showcase the potential of the suggested descriptor, while the second to showcase the decoder's superiority against popular alternatives in the field.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9481797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40362969","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epilepsy seizure prediction with few-shot learning method.","authors":"Jamal Nazari,&nbsp;Ali Motie Nasrabadi,&nbsp;Mohammad Bagher Menhaj,&nbsp;Somayeh Raiesdana","doi":"10.1186/s40708-022-00170-8","DOIUrl":"https://doi.org/10.1186/s40708-022-00170-8","url":null,"abstract":"<p><p>Epileptic seizures prediction and timely alarms allow the patient to take effective and preventive actions. In this paper, a convolutional neural network (CNN) is proposed to diagnose the preictal period. Our goal is for those epileptic patients in whom seizures occur late and it is very challenging to record the preictal signal for them. In the previous works, generalized methods were inevitably used for this group of patients which were not very accurate. Our approach to solve this problem is to provide a few-shot learning method. This method, having the previous knowledge, is trained with only a small number of samples, learns new tasks and reduces the efforts to collect more data. Evaluation results for three patients from the CHB-MIT database, for a 10-min seizure prediction horizon (SPH) and a 20-min seizure occurrence period (SOP), averaged sensitivity of 95.70% and a false prediction rate (FPR) of 0.057/h and for the 5-min prediction horizon and the 25-min seizure occurrence period averaged sensitivity of 98.52% and a false prediction rate of (FPR) of 0.045/h. The proposed few-shot learning method, based on previous knowledge gained from the generalizable method, is regulated with a few new patient samples for the patient. Our results show that the accuracy obtained in this method is higher than the generalizable methods.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2022-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9481757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40362974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A multi-expert ensemble system for predicting Alzheimer transition using clinical features.","authors":"Mario Merone,&nbsp;Sebastian Luca D'Addario,&nbsp;Pierandrea Mirino,&nbsp;Francesca Bertino,&nbsp;Cecilia Guariglia,&nbsp;Rossella Ventura,&nbsp;Adriano Capirchio,&nbsp;Gianluca Baldassarre,&nbsp;Massimo Silvetti,&nbsp;Daniele Caligiore","doi":"10.1186/s40708-022-00168-2","DOIUrl":"https://doi.org/10.1186/s40708-022-00168-2","url":null,"abstract":"<p><p>Alzheimer's disease (AD) diagnosis often requires invasive examinations (e.g., liquor analyses), expensive tools (e.g., brain imaging) and highly specialized personnel. The diagnosis commonly is established when the disorder has already caused severe brain damage, and the clinical signs begin to be apparent. Instead, accessible and low-cost approaches for early identification of subjects at high risk for developing AD years before they show overt symptoms are fundamental to provide a critical time window for more effective clinical management, treatment, and care planning. This article proposes an ensemble-based machine learning algorithm for predicting AD development within 9 years from first overt signs and using just five clinical features that are easily detectable with neuropsychological tests. The validation of the system involved both healthy individuals and mild cognitive impairment (MCI) patients drawn from the ADNI open dataset, at variance with previous studies that considered only MCI. The system shows higher levels of balanced accuracy, negative predictive value, and specificity than other similar solutions. These results represent a further important step to build a preventive fast-screening machine-learning-based tool to be used as a part of routine healthcare screenings.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"20"},"PeriodicalIF":0.0,"publicationDate":"2022-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9440971/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40346448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ABOT: an open-source online benchmarking tool for machine learning-based artefact detection and removal methods from neuronal signals.","authors":"Marcos Fabietti, Mufti Mahmud, Ahmad Lotfi, M Shamim Kaiser","doi":"10.1186/s40708-022-00167-3","DOIUrl":"10.1186/s40708-022-00167-3","url":null,"abstract":"<p><p>Brain signals are recorded using different techniques to aid an accurate understanding of brain function and to treat its disorders. Untargeted internal and external sources contaminate the acquired signals during the recording process. Often termed as artefacts, these contaminations cause serious hindrances in decoding the recorded signals; hence, they must be removed to facilitate unbiased decision-making for a given investigation. Due to the complex and elusive manifestation of artefacts in neuronal signals, computational techniques serve as powerful tools for their detection and removal. Machine learning (ML) based methods have been successfully applied in this task. Due to ML's popularity, many articles are published every year, making it challenging to find, compare and select the most appropriate method for a given experiment. To this end, this paper presents ABOT (Artefact removal Benchmarking Online Tool) as an online benchmarking tool which allows users to compare existing ML-driven artefact detection and removal methods from the literature. The characteristics and related information about the existing methods have been compiled as a knowledgebase (KB) and presented through a user-friendly interface with interactive plots and tables for users to search it using several criteria. Key characteristics extracted from over 120 articles from the literature have been used in the KB to help compare the specific ML models. To comply with the FAIR (Findable, Accessible, Interoperable and Reusable) principle, the source code and documentation of the toolbox have been made available via an open-access repository.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"19"},"PeriodicalIF":0.0,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9437165/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40336979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SmaRT2P: a software for generating and processing smart line recording trajectories for population two-photon calcium imaging.","authors":"Monica Moroni,&nbsp;Marco Brondi,&nbsp;Tommaso Fellin,&nbsp;Stefano Panzeri","doi":"10.1186/s40708-022-00166-4","DOIUrl":"https://doi.org/10.1186/s40708-022-00166-4","url":null,"abstract":"<p><p>Two-photon fluorescence calcium imaging allows recording the activity of large neural populations with subcellular spatial resolution, but it is typically characterized by low signal-to-noise ratio (SNR) and poor accuracy in detecting single or few action potentials when large number of neurons are imaged. We recently showed that implementing a smart line scanning approach using trajectories that optimally sample the regions of interest increases both the SNR fluorescence signals and the accuracy of single spike detection in population imaging in vivo. However, smart line scanning requires highly specialised software to design recording trajectories, interface with acquisition hardware, and efficiently process acquired data. Furthermore, smart line scanning needs optimized strategies to cope with movement artefacts and neuropil contamination. Here, we develop and validate SmaRT2P, an open-source, user-friendly and easy-to-interface Matlab-based software environment to perform optimized smart line scanning in two-photon calcium imaging experiments. SmaRT2P is designed to interface with popular acquisition software (e.g., ScanImage) and implements novel strategies to detect motion artefacts, estimate neuropil contamination, and minimize their impact on functional signals extracted from neuronal population imaging. SmaRT2P is structured in a modular way to allow flexibility in the processing pipeline, requiring minimal user intervention in parameter setting. The use of SmaRT2P for smart line scanning has the potential to facilitate the functional investigation of large neuronal populations with increased SNR and accuracy in detecting the discharge of single and few action potentials.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"18"},"PeriodicalIF":0.0,"publicationDate":"2022-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9352634/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40585110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A robust framework to investigate the reliability and stability of explainable artificial intelligence markers of Mild Cognitive Impairment and Alzheimer's Disease.","authors":"Angela Lombardi, Domenico Diacono, Nicola Amoroso, Przemysław Biecek, Alfonso Monaco, Loredana Bellantuono, Ester Pantaleo, Giancarlo Logroscino, Roberto De Blasi, Sabina Tangaro, Roberto Bellotti","doi":"10.1186/s40708-022-00165-5","DOIUrl":"10.1186/s40708-022-00165-5","url":null,"abstract":"<p><p>In clinical practice, several standardized neuropsychological tests have been designed to assess and monitor the neurocognitive status of patients with neurodegenerative diseases such as Alzheimer's disease. Important research efforts have been devoted so far to the development of multivariate machine learning models that combine the different test indexes to predict the diagnosis and prognosis of cognitive decline with remarkable results. However, less attention has been devoted to the explainability of these models. In this work, we present a robust framework to (i) perform a threefold classification between healthy control subjects, individuals with cognitive impairment, and subjects with dementia using different cognitive indexes and (ii) analyze the variability of the explainability SHAP values associated with the decisions taken by the predictive models. We demonstrate that the SHAP values can accurately characterize how each index affects a patient's cognitive status. Furthermore, we show that a longitudinal analysis of SHAP values can provide effective information on Alzheimer's disease progression.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"17"},"PeriodicalIF":0.0,"publicationDate":"2022-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9325942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40556054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}