Brain Informatics最新文献

{"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}

{"title":"Machine learning-based ABA treatment recommendation and personalization for autism spectrum disorder: an exploratory study.","authors":"Manu Kohli,&nbsp;Arpan Kumar Kar,&nbsp;Anjali Bangalore,&nbsp;Prathosh Ap","doi":"10.1186/s40708-022-00164-6","DOIUrl":"10.1186/s40708-022-00164-6","url":null,"abstract":"<p><p>Autism spectrum is a brain development condition that impairs an individual's capacity to communicate socially and manifests through strict routines and obsessive-compulsive behavior. Applied behavior analysis (ABA) is the gold-standard treatment for autism spectrum disorder (ASD). However, as the number of ASD cases increases, there is a substantial shortage of licensed ABA practitioners, limiting the timely formulation, revision, and implementation of treatment plans and goals. Additionally, the subjectivity of the clinician and a lack of data-driven decision-making affect treatment quality. We address these obstacles by applying two machine learning algorithms to recommend and personalize ABA treatment goals for 29 study participants with ASD. The patient similarity and collaborative filtering methods predicted ABA treatment with an average accuracy of 81-84%, with a normalized discounted cumulative gain of 79-81% (NDCG) compared to clinician-prepared ABA treatment recommendations. Additionally, we assess the two models' treatment efficacy (TE) by measuring the percentage of recommended treatment goals mastered by the study participants. The proposed treatment recommendation and personalization strategy are generalizable to other intervention methods in addition to ABA and for other brain disorders. This study was registered as a clinical trial on November 5, 2020 with trial registration number CTRI/2020/11/028933.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"16"},"PeriodicalIF":0.0,"publicationDate":"2022-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9311349/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40634512","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":"Classifying oscillatory brain activity associated with Indian Rasas using network metrics.","authors":"Pankaj Pandey,&nbsp;Richa Tripathi,&nbsp;Krishna Prasad Miyapuram","doi":"10.1186/s40708-022-00163-7","DOIUrl":"https://doi.org/10.1186/s40708-022-00163-7","url":null,"abstract":"<p><p>Neural signatures for the western classification of emotions have been widely discussed in the literature. The ancient Indian treatise on performing arts known as Natyashastra categorizes emotions into nine classes, known as Rasas. Rasa-as opposed to a pure emotion-is defined as a superposition of certain transitory, dominant, and temperamental emotional states. Although Rasas have been widely discussed in the text, dedicated brain imaging studies have not been conducted in their research. Our study examines the neural oscillations, recorded through electroencephalography (EEG) imaging, that are elicited while experiencing emotional states corresponding to Rasas. We identify differences among them using network-based functional connectivity metrics in five different frequency bands. Further, Random Forest models are trained on the extracted network features, and we present our findings based on classifier predictions. We observe slow (delta) and fast brain waves (beta and gamma) exhibited the maximum discriminating features between Rasas, whereas alpha and theta bands showed fewer distinguishable pairs. Out of nine Rasas, Sringaram (love), Bibhatsam (odious), and Bhayanakam (terror) were distinguishable from other Rasas the most across frequency bands. On the scale of most network metrics, Raudram (rage) and Sringaram are on the extremes, which also resulted in their good classification accuracy of 95%. This is reminiscent of the circumplex model where anger and contentment/happiness are on extremes on the pleasant scale. Interestingly, our results are consistent with the previous studies which highlight the significant role of higher frequency oscillations in the classification of emotions, in contrast to the alpha band that has shows non-significant differences across emotions. This research contributes to one of the first attempts to investigate the neural correlates of Rasas. Therefore, the results of this study can potentially guide the explorations into the entrainment of brain oscillations between performers and viewers, which can further lead to better performances and viewer experience.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"15"},"PeriodicalIF":0.0,"publicationDate":"2022-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9287523/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40608028","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":"Efficient emotion recognition using hyperdimensional computing with combinatorial channel encoding and cellular automata.","authors":"Alisha Menon, Anirudh Natarajan, Reva Agashe, Daniel Sun, Melvin Aristio, Harrison Liew, Yakun Sophia Shao, Jan M Rabaey","doi":"10.1186/s40708-022-00162-8","DOIUrl":"10.1186/s40708-022-00162-8","url":null,"abstract":"<p><p>In this paper, a hardware-optimized approach to emotion recognition based on the efficient brain-inspired hyperdimensional computing (HDC) paradigm is proposed. Emotion recognition provides valuable information for human-computer interactions; however, the large number of input channels (> 200) and modalities (> 3 ) involved in emotion recognition are significantly expensive from a memory perspective. To address this, methods for memory reduction and optimization are proposed, including a novel approach that takes advantage of the combinatorial nature of the encoding process, and an elementary cellular automaton. HDC with early sensor fusion is implemented alongside the proposed techniques achieving two-class multi-modal classification accuracies of > 76% for valence and > 73% for arousal on the multi-modal AMIGOS and DEAP data sets, almost always better than state of the art. The required vector storage is seamlessly reduced by 98% and the frequency of vector requests by at least 1/5. The results demonstrate the potential of efficient hyperdimensional computing for low-power, multi-channeled emotion recognition tasks.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2022-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9237202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40403105","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":"Stroke recovery phenotyping through network trajectory approaches and graph neural networks.","authors":"Sanjukta Krishnagopal,&nbsp;Keith Lohse,&nbsp;Robynne Braun","doi":"10.1186/s40708-022-00160-w","DOIUrl":"https://doi.org/10.1186/s40708-022-00160-w","url":null,"abstract":"<p><p>Stroke is a leading cause of neurological injury characterized by impairments in multiple neurological domains including cognition, language, sensory and motor functions. Clinical recovery in these domains is tracked using a wide range of measures that may be continuous, ordinal, interval or categorical in nature, which can present challenges for multivariate regression approaches. This has hindered stroke researchers' ability to achieve an integrated picture of the complex time-evolving interactions among symptoms. Here, we use tools from network science and machine learning that are particularly well-suited to extracting underlying patterns in such data, and may assist in prediction of recovery patterns. To demonstrate the utility of this approach, we analyzed data from the NINDS tPA trial using the Trajectory Profile Clustering (TPC) method to identify distinct stroke recovery patterns for 11 different neurological domains at 5 discrete time points. Our analysis identified 3 distinct stroke trajectory profiles that align with clinically relevant stroke syndromes, characterized both by distinct clusters of symptoms, as well as differing degrees of symptom severity. We then validated our approach using graph neural networks to determine how well our model performed predictively for stratifying patients into these trajectory profiles at early vs. later time points post-stroke. We demonstrate that trajectory profile clustering is an effective method for identifying clinically relevant recovery subtypes in multidimensional longitudinal datasets, and for early prediction of symptom progression subtypes in individual patients. This paper is the first work introducing network trajectory approaches for stroke recovery phenotyping, and is aimed at enhancing the translation of such novel computational approaches for practical clinical application.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":" ","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2022-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9206968/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39991015","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":"ID-Seg: an infant deep learning-based segmentation framework to improve limbic structure estimates.","authors":"Yun Wang, Fateme Sadat Haghpanah, Xuzhe Zhang, Katie Santamaria, Gabriela Koch da Costa Aguiar Alves, Elizabeth Bruno, Natalie Aw, Alexis Maddocks, Cristiane S Duarte, Catherine Monk, Andrew Laine, Jonathan Posner","doi":"10.1186/s40708-022-00161-9","DOIUrl":"10.1186/s40708-022-00161-9","url":null,"abstract":"<p><p>Infant brain magnetic resonance imaging (MRI) is a promising approach for studying early neurodevelopment. However, segmenting small regions such as limbic structures is challenging due to their low inter-regional contrast and high curvature. MRI studies of the adult brain have successfully applied deep learning techniques to segment limbic structures, and similar deep learning models are being leveraged for infant studies. However, these deep learning-based infant MRI segmentation models have generally been derived from small datasets, and may suffer from generalization problems. Moreover, the accuracy of segmentations derived from these deep learning models relative to more standard Expectation-Maximization approaches has not been characterized. To address these challenges, we leveraged a large, public infant MRI dataset (n = 473) and the transfer-learning technique to first pre-train a deep convolutional neural network model on two limbic structures: amygdala and hippocampus. Then we used a leave-one-out cross-validation strategy to fine-tune the pre-trained model and evaluated it separately on two independent datasets with manual labels. We term this new approach the Infant Deep learning SEGmentation Framework (ID-Seg). ID-Seg performed well on both datasets with a mean dice similarity score (DSC) of 0.87, a mean intra-class correlation (ICC) of 0.93, and a mean average surface distance (ASD) of 0.31 mm. Compared to the Developmental Human Connectome pipeline (dHCP) pipeline, ID-Seg significantly improved segmentation accuracy. In a third infant MRI dataset (n = 50), we used ID-Seg and dHCP separately to estimate amygdala and hippocampus volumes and shapes. The estimates derived from ID-seg, relative to those from the dHCP, showed stronger associations with behavioral problems assessed in these infants at age 2. In sum, ID-Seg consistently performed well on two different datasets with an 0.87 DSC, however, multi-site testing and extension for brain regions beyond the amygdala and hippocampus are still needed.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":"3 1","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2022-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9148335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74255297","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":"Smart imaging to empower brain-wide neuroscience at single-cell levels.","authors":"Shuxia Guo, Jie Xue, Jian Liu, Xiangqiao Ye, Yichen Guo, Di Liu, Xuan Zhao, Feng Xiong, Xiaofeng Han, Hanchuan Peng","doi":"10.1186/s40708-022-00158-4","DOIUrl":"10.1186/s40708-022-00158-4","url":null,"abstract":"<p><p>A deep understanding of the neuronal connectivity and networks with detailed cell typing across brain regions is necessary to unravel the mechanisms behind the emotional and memorial functions as well as to find the treatment of brain impairment. Brain-wide imaging with single-cell resolution provides unique advantages to access morphological features of a neuron and to investigate the connectivity of neuron networks, which has led to exciting discoveries over the past years based on animal models, such as rodents. Nonetheless, high-throughput systems are in urgent demand to support studies of neural morphologies at larger scale and more detailed level, as well as to enable research on non-human primates (NHP) and human brains. The advances in artificial intelligence (AI) and computational resources bring great opportunity to 'smart' imaging systems, i.e., to automate, speed up, optimize and upgrade the imaging systems with AI and computational strategies. In this light, we review the important computational techniques that can support smart systems in brain-wide imaging at single-cell resolution.</p>","PeriodicalId":37465,"journal":{"name":"Brain Informatics","volume":"9 1","pages":"10"},"PeriodicalIF":0.0,"publicationDate":"2022-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9095808/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71427640","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}