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Udayakumar P, Subhashini R. Connectome-based schizophrenia prediction using structural connectivity - Deep Graph Neural Network(sc-DGNN). JOURNAL OF X-RAY SCIENCE AND TECHNOLOGY 2024:XST230426. [PMID: 38820060 DOI: 10.3233/xst-230426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2024]
Abstract
Background Connectome is understanding the complex organization of the human brain's structural and functional connectivity is essential for gaining insights into cognitive processes and disorders. Objective To improve the prediction accuracy of brain disorder issues, the current study investigates dysconnected subnetworks and graph structures associated with schizophrenia. Method By using the proposed structural connectivity-deep graph neural network (sc-DGNN) model and compared with machine learning (ML) and deep learning (DL) models.This work attempts to focus on eighty-eight subjects of diffusion magnetic resonance imaging (dMRI), three classical ML, and five DL models. Result The structural connectivity-deep graph neural network (sc-DGNN) model is proposed to effectively predict dysconnectedness associated with schizophrenia and exhibits superior performance compared to traditional ML and DL (GNNs) methods in terms of accuracy, sensitivity, specificity, precision, F1-score, and Area under receiver operating characteristic (AUC). Conclusion The classification task on schizophrenia using structural connectivity matrices and experimental results showed that linear discriminant analysis (LDA) performed 72% accuracy rate in ML models and sc-DGNN performed at a 93% accuracy rate in DL models to distinguish between schizophrenia and healthy patients.
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Affiliation(s)
- P Udayakumar
- School of Computer Science Engineering and Information Systems, Vellore Institute of Technology, Vellore, Tamilnadu, India
| | - R Subhashini
- School of Computer Science Engineering and Information Systems, Vellore Institute of Technology, Vellore, Tamilnadu, India
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Nagle A, Gerrelts JP, Krause BM, Boes AD, Bruss JE, Nourski KV, Banks MI, Van Veen B. High-dimensional multivariate autoregressive model estimation of human electrophysiological data using fMRI priors. Neuroimage 2023; 277:120211. [PMID: 37385393 PMCID: PMC10528866 DOI: 10.1016/j.neuroimage.2023.120211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Multivariate autoregressive (MVAR) model estimation enables assessment of causal interactions in brain networks. However, accurately estimating MVAR models for high-dimensional electrophysiological recordings is challenging due to the extensive data requirements. Hence, the applicability of MVAR models for study of brain behavior over hundreds of recording sites has been very limited. Prior work has focused on different strategies for selecting a subset of important MVAR coefficients in the model to reduce the data requirements of conventional least-squares estimation algorithms. Here we propose incorporating prior information, such as resting state functional connectivity derived from functional magnetic resonance imaging, into MVAR model estimation using a weighted group least absolute shrinkage and selection operator (LASSO) regularization strategy. The proposed approach is shown to reduce data requirements by a factor of two relative to the recently proposed group LASSO method of Endemann et al (Neuroimage 254:119057, 2022) while resulting in models that are both more parsimonious and more accurate. The effectiveness of the method is demonstrated using simulation studies of physiologically realistic MVAR models derived from intracranial electroencephalography (iEEG) data. The robustness of the approach to deviations between the conditions under which the prior information and iEEG data is obtained is illustrated using models from data collected in different sleep stages. This approach allows accurate effective connectivity analyses over short time scales, facilitating investigations of causal interactions in the brain underlying perception and cognition during rapid transitions in behavioral state.
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Affiliation(s)
- Alliot Nagle
- Department of Electrical and Computer Engineering, University of Wisconsin, Madison, 53706, WI, USA; Department of Anesthesiology, University of Wisconsin, Madison, 53706, WI, USA
| | - Josh P Gerrelts
- Department of Electrical and Computer Engineering, University of Wisconsin, Madison, 53706, WI, USA
| | - Bryan M Krause
- Department of Anesthesiology, University of Wisconsin, Madison, 53706, WI, USA
| | - Aaron D Boes
- Department of Neurology, The University of Iowa, Iowa City, 52242, IA, USA
| | - Joel E Bruss
- Department of Neurology, The University of Iowa, Iowa City, 52242, IA, USA
| | - Kirill V Nourski
- Department of Neurosurgery, The University of Iowa, Iowa City, 52242, IA, USA; Iowa Neuroscience Institute, The University of Iowa, Iowa City, 52242, IA, USA
| | - Matthew I Banks
- Department of Anesthesiology, University of Wisconsin, Madison, 53706, WI, USA.
| | - Barry Van Veen
- Department of Electrical and Computer Engineering, University of Wisconsin, Madison, 53706, WI, USA
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van Boven MR, Henke CE, Leemhuis AG, Hoogendoorn M, van Kaam AH, Königs M, Oosterlaan J. Machine Learning Prediction Models for Neurodevelopmental Outcome After Preterm Birth: A Scoping Review and New Machine Learning Evaluation Framework. Pediatrics 2022; 150:188249. [PMID: 35670123 DOI: 10.1542/peds.2021-056052] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/25/2022] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Outcome prediction of preterm birth is important for neonatal care, yet prediction performance using conventional statistical models remains insufficient. Machine learning has a high potential for complex outcome prediction. In this scoping review, we provide an overview of the current applications of machine learning models in the prediction of neurodevelopmental outcomes in preterm infants, assess the quality of the developed models, and provide guidance for future application of machine learning models to predict neurodevelopmental outcomes of preterm infants. METHODS A systematic search was performed using PubMed. Studies were included if they reported on neurodevelopmental outcome prediction in preterm infants using predictors from the neonatal period and applying machine learning techniques. Data extraction and quality assessment were independently performed by 2 reviewers. RESULTS Fourteen studies were included, focusing mainly on very or extreme preterm infants, predicting neurodevelopmental outcome before age 3 years, and mostly assessing outcomes using the Bayley Scales of Infant Development. Predictors were most often based on MRI. The most prevalent machine learning techniques included linear regression and neural networks. None of the studies met all newly developed quality assessment criteria. Studies least prone to inflated performance showed promising results, with areas under the curve up to 0.86 for classification and R2 values up to 91% in continuous prediction. A limitation was that only 1 data source was used for the literature search. CONCLUSIONS Studies least prone to inflated prediction results are the most promising. The provided evaluation framework may contribute to improved quality of future machine learning models.
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Affiliation(s)
- Menne R van Boven
- Departments of Neonatology.,Pediatrics, Follow-Me Program, Emma Neuroscience Group, and Amsterdam Reproduction and Development
| | - Celina E Henke
- Pediatrics, Follow-Me Program, Emma Neuroscience Group, and Amsterdam Reproduction and Development.,Psychosocial Department, Emma Children's Hospital, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Aleid G Leemhuis
- Departments of Neonatology.,Pediatrics, Follow-Me Program, Emma Neuroscience Group, and Amsterdam Reproduction and Development
| | - Mark Hoogendoorn
- Faculty of Science, Quantitative Data Analytics Group, Department Computer Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Anton H van Kaam
- Departments of Neonatology.,Pediatrics, Follow-Me Program, Emma Neuroscience Group, and Amsterdam Reproduction and Development
| | - Marsh Königs
- Pediatrics, Follow-Me Program, Emma Neuroscience Group, and Amsterdam Reproduction and Development
| | - Jaap Oosterlaan
- Pediatrics, Follow-Me Program, Emma Neuroscience Group, and Amsterdam Reproduction and Development
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Graña M, Silva M. Impact of Machine Learning Pipeline Choices in Autism Prediction From Functional Connectivity Data. Int J Neural Syst 2021; 31:2150009. [PMID: 33472548 DOI: 10.1142/s012906572150009x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Autism Spectrum Disorder (ASD) is a largely prevalent neurodevelopmental condition with a big social and economical impact affecting the entire life of families. There is an intense search for biomarkers that can be assessed as early as possible in order to initiate treatment and preparation of the family to deal with the challenges imposed by the condition. Brain imaging biomarkers have special interest. Specifically, functional connectivity data extracted from resting state functional magnetic resonance imaging (rs-fMRI) should allow to detect brain connectivity alterations. Machine learning pipelines encompass the estimation of the functional connectivity matrix from brain parcellations, feature extraction, and building classification models for ASD prediction. The works reported in the literature are very heterogeneous from the computational and methodological point of view. In this paper, we carry out a comprehensive computational exploration of the impact of the choices involved while building these machine learning pipelines. Specifically, we consider six brain parcellation definitions, five methods for functional connectivity matrix construction, six feature extraction/selection approaches, and nine classifier building algorithms. We report the prediction performance sensitivity to each of these choices, as well as the best results that are comparable with the state of the art.
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Affiliation(s)
- Manuel Graña
- Computational Intelligence Group, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Moises Silva
- Universidad Mayor de San Andres, La Paz, Bolivia
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Functional and Structural Connectome Features for Machine Learning Chemo-Brain Prediction in Women Treated for Breast Cancer with Chemotherapy. Brain Sci 2020; 10:brainsci10110851. [PMID: 33198294 PMCID: PMC7696512 DOI: 10.3390/brainsci10110851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/07/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is the leading cancer among women worldwide, and a high number of breast cancer patients are struggling with psychological and cognitive disorders. In this study, we aim to use machine learning models to discriminate between chemo-brain participants and healthy controls (HCs) using connectomes (connectivity matrices) and topological coefficients. Nineteen female post-chemotherapy breast cancer (BC) survivors and 20 female HCs were recruited for this study. Participants in both groups received resting-state functional magnetic resonance imaging (rs-fMRI) and generalized q-sampling imaging (GQI). Logistic regression (LR), decision tree classifier (CART), and xgboost (XGB) were the models we adopted for classification. In connectome analysis, LR achieved an accuracy of 79.49% with the functional connectomes and an accuracy of 71.05% with the structural connectomes. In the topological coefficient analysis, accuracies of 87.18%, 82.05%, and 83.78% were obtained by the functional global efficiency with CART, the functional global efficiency with XGB, and the structural transitivity with CART, respectively. The areas under the curves (AUCs) were 0.93, 0.94, 0.87, 0.88, and 0.84, respectively. Our study showed the discriminating ability of functional connectomes, structural connectomes, and global efficiency. We hope our findings can contribute to an understanding of the chemo brain and the establishment of a clinical system for tracking chemo brain.
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Pannek K, George JM, Boyd RN, Colditz PB, Rose SE, Fripp J. Brain microstructure and morphology of very preterm-born infants at term equivalent age: Associations with motor and cognitive outcomes at 1 and 2 years. Neuroimage 2020; 221:117163. [DOI: 10.1016/j.neuroimage.2020.117163] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 06/27/2020] [Accepted: 07/08/2020] [Indexed: 12/13/2022] Open
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Wang L, Shi Y, Suk HI, Noble A, Hamarneh G. Special issue on machine learning in medical imaging. Comput Med Imaging Graph 2019; 74:10-11. [PMID: 30908957 DOI: 10.1016/j.compmedimag.2019.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Li Wang
- Department of Radiology and BRIC, University of North Carolina at Chapel Hill, USA.
| | - Yinghuan Shi
- Department of Computer Science and Technology, Nanjing University, PR China
| | - Heung-Il Suk
- Department of Brain and Cognitive Engineering, Korea University, Republic of Korea
| | - Alison Noble
- Biomedical Engineering, University of Oxford, UK
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