scholarly journals Reconstructing lost BOLD signal in individual participants using deep machine learning

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuxiang Yan ◽  
Louisa Dahmani ◽  
Jianxun Ren ◽  
Lunhao Shen ◽  
Xiaolong Peng ◽  
...  

Abstract Signal loss in blood oxygen level-dependent (BOLD) functional neuroimaging is common and can lead to misinterpretation of findings. Here, we reconstructed compromised fMRI signal using deep machine learning. We trained a model to learn principles governing BOLD activity in one dataset and reconstruct artificially compromised regions in an independent dataset, frame by frame. Intriguingly, BOLD time series extracted from reconstructed frames are correlated with the original time series, even though the frames do not independently carry any temporal information. Moreover, reconstructed functional connectivity maps exhibit good correspondence with the original connectivity maps, indicating that the model recovers functional relationships among brain regions. We replicated this result in two healthy datasets and in patients whose scans suffered signal loss due to intracortical electrodes. Critically, the reconstructions capture individual-specific information. Deep machine learning thus presents a unique opportunity to reconstruct compromised BOLD signal while capturing features of an individual’s own functional brain organization.

2019 ◽  
Author(s):  
Yuxiang Yan ◽  
Louisa Dahmani ◽  
Lunhao Shen ◽  
Xiaolong Peng ◽  
Danhong Wang ◽  
...  

AbstractThe blood oxygen level-dependent (BOLD) signal in functional neuroimaging suffers from magnetic susceptibility artifacts and interference from metal implants. The resulting signal loss hampers functional neuroimaging studies and can lead to misinterpretation of findings. Here, we reconstructed compromised BOLD signal using deep machine learning. We trained a deep learning model to learn principles governing BOLD activity in one dataset and reconstructed artificially-compromised regions in another dataset, frame by frame. Strikingly, BOLD time series extracted from reconstructed frames were correlated with the original time series, even though the frames did not independently carry information about BOLD fluctuations through time. Moreover, reconstructed functional connectivity (FC) maps exhibited good correspondence with the original FC maps, indicating that the deep learning model recovered functional relationships among brain regions. We replicated this result in patients whose scans suffered signal loss due to intracortical electrodes. Critically, the reconstructions captured individual-specific information rather than group information learned during training. Deep machine learning thus presents a unique opportunity to reconstruct compromised BOLD signal while capturing features of an individual’s own functional brain organization.


Author(s):  
Nick Ward

After stroke, there is little restitution of neural tissue, but reorganization of surviving neural networks appears to be important for recovery of function. Non-invasive techniques such as functional magnetic resonance imaging and magnetoencephalography allow some aspects of this brain reorganization to be studied. For example, early after stroke there appears to be an upregulation in task-related activity, which diminishes with time and recovery. Those with the most complete recovery tend to have the most ‘normal’ activation pattern, and those with less complete recovery tend to rely on additional brain regions. This reorganization is functionally relevant. Advances in functional neuroimaging allow the study of alterations in connections between brain regions. Understanding how brain organization is related to anatomical damage, as well as impairment and recovery that can take place over weeks and months following stroke opens the way for functional brain imaging to become a clinically useful tool in rehabilitation.


2020 ◽  
Vol 10 (11) ◽  
pp. 777
Author(s):  
Nicholas John Simos ◽  
Stavros I. Dimitriadis ◽  
Eleftherios Kavroulakis ◽  
Georgios C. Manikis ◽  
George Bertsias ◽  
...  

Neuropsychiatric systemic lupus erythematosus (NPSLE) is an autoimmune entity comprised of heterogenous syndromes affecting both the peripheral and central nervous system. Research on the pathophysiological substrate of NPSLE manifestations, including functional neuroimaging studies, is extremely limited. The present study examined person-specific patterns of whole-brain functional connectivity in NPSLE patients (n = 44) and age-matched healthy control participants (n = 39). Static functional connectivity graphs were calculated comprised of connection strengths between 90 brain regions. These connections were subsequently filtered through rigorous surrogate analysis, a technique borrowed from physics, novel to neuroimaging. Next, global as well as nodal network metrics were estimated for each individual functional brain network and were input to a robust machine learning algorithm consisting of a random forest feature selection and nested cross-validation strategy. The proposed pipeline is data-driven in its entirety, and several tests were performed in order to ensure model robustness. The best-fitting model utilizing nodal graph metrics for 11 brain regions was associated with 73.5% accuracy (74.5% sensitivity and 73% specificity) in discriminating NPSLE from healthy individuals with adequate statistical power. Closer inspection of graph metric values suggested an increased role within the functional brain network in NSPLE (indicated by higher nodal degree, local efficiency, betweenness centrality, or eigenvalue efficiency) as compared to healthy controls for seven brain regions and a reduced role for four areas. These findings corroborate earlier work regarding hemodynamic disturbances in these brain regions in NPSLE. The validity of the results is further supported by significant associations of certain selected graph metrics with accumulated organ damage incurred by lupus, with visuomotor performance and mental flexibility scores obtained independently from NPSLE patients.


2018 ◽  
Vol 30 (4) ◽  
pp. 514-525 ◽  
Author(s):  
Sara B. Pillay ◽  
William L. Gross ◽  
William W. Graves ◽  
Colin Humphries ◽  
Diane S. Book ◽  
...  

Understanding the neural basis of recovery from stroke is a major research goal. Many functional neuroimaging studies have identified changes in brain activity in people with aphasia, but it is unclear whether these changes truly support successful performance or merely reflect increased task difficulty. We addressed this problem by examining differences in brain activity associated with correct and incorrect responses on an overt reading task. On the basis of previous proposals that semantic retrieval can assist pronunciation of written words, we hypothesized that recruitment of semantic areas would be greater on successful trials. Participants were 21 patients with left-hemisphere stroke with phonologic retrieval deficits. They read words aloud during an event-related fMRI paradigm. BOLD signals obtained during correct and incorrect trials were contrasted to highlight brain activity specific to successful trials. Successful word reading was associated with higher BOLD signal in the left angular gyrus. In contrast, BOLD signal in bilateral posterior inferior frontal cortex, SMA, and anterior cingulate cortex was greater on incorrect trials. These data show for the first time the brain regions where neural activity is correlated specifically with successful performance in people with aphasia. The angular gyrus is a key node in the semantic network, consistent with the hypothesis that additional recruitment of the semantic system contributes to successful word production when phonologic retrieval is impaired. Higher activity in other brain regions during incorrect trials likely reflects secondary engagement of attention, working memory, and error monitoring processes when phonologic retrieval is unsuccessful.


2020 ◽  
Vol 117 (31) ◽  
pp. 18788-18798 ◽  
Author(s):  
Siyuan Liu ◽  
Jakob Seidlitz ◽  
Jonathan D. Blumenthal ◽  
Liv S. Clasen ◽  
Armin Raznahan

Humans display reproducible sex differences in cognition and behavior, which may partly reflect intrinsic sex differences in regional brain organization. However, the consistency, causes and consequences of sex differences in the human brain are poorly characterized and hotly debated. In contrast, recent studies in mice—a major model organism for studying neurobiological sex differences—have established: 1) highly consistent sex biases in regional gray matter volume (GMV) involving the cortex and classical subcortical foci, 2) a preponderance of regional GMV sex differences in brain circuits for social and reproductive behavior, and 3) a spatial coupling between regional GMV sex biases and brain expression of sex chromosome genes in adulthood. Here, we directly test translatability of rodent findings to humans. First, using two independent structural-neuroimaging datasets (n> 2,000), we find that the spatial map of sex-biased GMV in humans is highly reproducible (r> 0.8 within and across cohorts). Relative GMV is female biased in prefrontal and superior parietal cortices, and male biased in ventral occipitotemporal, and distributed subcortical regions. Second, through systematic comparison with functional neuroimaging meta-analyses, we establish a statistically significant concentration of human GMV sex differences within brain regions that subserve face processing. Finally, by imaging-transcriptomic analyses, we show that GMV sex differences in human adulthood are specifically and significantly coupled to regional expression of sex-chromosome (vs. autosomal) genes and enriched for distinct cell-type signatures. These findings establish conserved aspects of sex-biased brain development in humans and mice, and shed light on the consistency, candidate causes, and potential functional corollaries of sex-biased brain anatomy in humans.


Author(s):  
Nick S. Ward

After stroke, there is little restitution of neural tissue, but reorganization of surviving neural networks appears to be important for recovery of function. Non-invasive techniques such as functional magnetic resonance imaging and magnetoencephalography allow some aspects of this brain reorganization to be studied in humans. For example, early after stroke there appears to be an upregulation in task-related activity which diminishes with time, but more particularly with recovery. Those with the most complete recovery tend to have the most ‘normal’ activation patter, and those with less complete recovery tend to rely on additional brain regions. Disruption of activity in these additional regions can impair performance in stroke patients suggesting that these new patterns of brain activity can support what recovered function there is. In other words, this reorganization is functionally relevant. Advances in functional neuroimaging now allow the study of alterations in connections between brain regions. Understanding how brain organization is related to anatomical damage, as well as impairment and recovery that can take place over weeks and months following stroke opens the way for functional brain imaging to become a clinically useful tool in rehabilitation, particularly in our ability to predict outcomes and response to novel therapies. Understanding the dynamic process of systems level reorganization will allow greater understanding of the mechanisms of recovery and potentially improve our ability to deliver effective restorative therapy.


2020 ◽  
Author(s):  
Pathikkumar Patel ◽  
Bhargav Lad ◽  
Jinan Fiaidhi

During the last few years, RNN models have been extensively used and they have proven to be better for sequence and text data. RNNs have achieved state-of-the-art performance levels in several applications such as text classification, sequence to sequence modelling and time series forecasting. In this article we will review different Machine Learning and Deep Learning based approaches for text data and look at the results obtained from these methods. This work also explores the use of transfer learning in NLP and how it affects the performance of models on a specific application of sentiment analysis.


2020 ◽  
Author(s):  
Hsiao-Ko Chang ◽  
Hui-Chih Wang ◽  
Chih-Fen Huang ◽  
Feipei Lai

BACKGROUND In most of Taiwan’s medical institutions, congestion is a serious problem for emergency departments. Due to a lack of beds, patients spend more time in emergency retention zones, which make it difficult to detect cardiac arrest (CA). OBJECTIVE We seek to develop a Drug Early Warning System Model (DEWSM), it included drug injections and vital signs as this research important features. We use it to predict cardiac arrest in emergency departments via drug classification and medical expert suggestion. METHODS We propose this new model for detecting cardiac arrest via drug classification and by using a sliding window; we apply learning-based algorithms to time-series data for a DEWSM. By treating drug features as a dynamic time-series factor for cardiopulmonary resuscitation (CPR) patients, we increase sensitivity, reduce false alarm rates and mortality, and increase the model’s accuracy. To evaluate the proposed model, we use the area under the receiver operating characteristic curve (AUROC). RESULTS Four important findings are as follows: (1) We identify the most important drug predictors: bits (intravenous therapy), and replenishers and regulators of water and electrolytes (fluid and electrolyte supplement). The best AUROC of bits is 85%, it means the medical expert suggest the drug features: bits, it will affect the vital signs, and then the evaluate this model correctly classified patients with CPR reach 85%; that of replenishers and regulators of water and electrolytes is 86%. These two features are the most influential of the drug features in the task. (2) We verify feature selection, in which accounting for drugs improve the accuracy: In Task 1, the best AUROC of vital signs is 77%, and that of all features is 86%. In Task 2, the best AUROC of all features is 85%, which demonstrates that thus accounting for the drugs significantly affects prediction. (3) We use a better model: For traditional machine learning, this study adds a new AI technology: the long short-term memory (LSTM) model with the best time-series accuracy, comparable to the traditional random forest (RF) model; the two AUROC measures are 85%. It can be seen that the use of new AI technology will achieve better results, currently comparable to the accuracy of traditional common RF, and the LSTM model can be adjusted in the future to obtain better results. (4) We determine whether the event can be predicted beforehand: The best classifier is still an RF model, in which the observational starting time is 4 hours before the CPR event. Although the accuracy is impaired, the predictive accuracy still reaches 70%. Therefore, we believe that CPR events can be predicted four hours before the event. CONCLUSIONS This paper uses a sliding window to account for dynamic time-series data consisting of the patient’s vital signs and drug injections. The National Early Warning Score (NEWS) only focuses on the score of vital signs, and does not include factors related to drug injections. In this study, the experimental results of adding the drug injections are better than only vital signs. In a comparison with NEWS, we improve predictive accuracy via feature selection, which includes drugs as features. In addition, we use traditional machine learning methods and deep learning (using LSTM method as the main processing time series data) as the basis for comparison of this research. The proposed DEWSM, which offers 4-hour predictions, is better than the NEWS in the literature. This also confirms that the doctor’s heuristic rules are consistent with the results found by machine learning algorithms.


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