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Gallos IK, Lehmberg D, Dietrich F, Siettos C. Data-driven modelling of brain activity using neural networks, diffusion maps, and the Koopman operator. CHAOS (WOODBURY, N.Y.) 2024; 34:013151. [PMID: 38285718 DOI: 10.1063/5.0157881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/22/2023] [Indexed: 01/31/2024]
Abstract
We propose a machine-learning approach to construct reduced-order models (ROMs) to predict the long-term out-of-sample dynamics of brain activity (and in general, high-dimensional time series), focusing mainly on task-dependent high-dimensional fMRI time series. Our approach is a three stage one. First, we exploit manifold learning and, in particular, diffusion maps (DMs) to discover a set of variables that parametrize the latent space on which the emergent high-dimensional fMRI time series evolve. Then, we construct ROMs on the embedded manifold via two techniques: Feedforward Neural Networks (FNNs) and the Koopman operator. Finally, for predicting the out-of-sample long-term dynamics of brain activity in the ambient fMRI space, we solve the pre-image problem, i.e., the construction of a map from the low-dimensional manifold to the original high-dimensional (ambient) space by coupling DMs with Geometric Harmonics (GH) when using FNNs and the Koopman modes per se. For our illustrations, we have assessed the performance of the two proposed schemes using two benchmark fMRI time series: (i) a simplistic five-dimensional model of stochastic discrete-time equations used just for a "transparent" illustration of the approach, thus knowing a priori what one expects to get, and (ii) a real fMRI dataset with recordings during a visuomotor task. We show that the proposed Koopman operator approach provides, for any practical purposes, equivalent results to the FNN-GH approach, thus bypassing the need to train a non-linear map and to use GH to extrapolate predictions in the ambient space; one can use instead the low-frequency truncation of the DMs function space of L2-integrable functions to predict the entire list of coordinate functions in the ambient space and to solve the pre-image problem.
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Affiliation(s)
- Ioannis K Gallos
- Institute of Communication and Computer Systems, National Technical University of Athens, Zografos Campus, 15780 Athens, Greece
| | - Daniel Lehmberg
- School of Computation, Information and Technology, Technical University of Munich, Munich 80333, Germany
| | - Felix Dietrich
- School of Computation, Information and Technology, Technical University of Munich, Munich 80333, Germany
| | - Constantinos Siettos
- Dipartimento di Matematica e Applicazioni "Renato Caccioppoli," Universitá degli Studi di Napoli Federico II, Naples 80125, Italy
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Gallos IK, Tryfonopoulos D, Shani G, Amditis A, Haick H, Dionysiou DD. Advancing Colorectal Cancer Diagnosis with AI-Powered Breathomics: Navigating Challenges and Future Directions. Diagnostics (Basel) 2023; 13:3673. [PMID: 38132257 PMCID: PMC10743128 DOI: 10.3390/diagnostics13243673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
Early detection of colorectal cancer is crucial for improving outcomes and reducing mortality. While there is strong evidence of effectiveness, currently adopted screening methods present several shortcomings which negatively impact the detection of early stage carcinogenesis, including low uptake due to patient discomfort. As a result, developing novel, non-invasive alternatives is an important research priority. Recent advancements in the field of breathomics, the study of breath composition and analysis, have paved the way for new avenues for non-invasive cancer detection and effective monitoring. Harnessing the utility of Volatile Organic Compounds in exhaled breath, breathomics has the potential to disrupt colorectal cancer screening practices. Our goal is to outline key research efforts in this area focusing on machine learning methods used for the analysis of breathomics data, highlight challenges involved in artificial intelligence application in this context, and suggest possible future directions which are currently considered within the framework of the European project ONCOSCREEN.
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Affiliation(s)
- Ioannis K. Gallos
- Institute of Communication and Computer Systems, National Technical University of Athens, Zografos Campus, 15780 Athens, Greece; (D.T.); (A.A.)
| | - Dimitrios Tryfonopoulos
- Institute of Communication and Computer Systems, National Technical University of Athens, Zografos Campus, 15780 Athens, Greece; (D.T.); (A.A.)
| | - Gidi Shani
- Laboratory for Nanomaterial-Based Devices, Technion—Israel Institute of Technology, Haifa 3200003, Israel; (G.S.); (H.H.)
| | - Angelos Amditis
- Institute of Communication and Computer Systems, National Technical University of Athens, Zografos Campus, 15780 Athens, Greece; (D.T.); (A.A.)
| | - Hossam Haick
- Laboratory for Nanomaterial-Based Devices, Technion—Israel Institute of Technology, Haifa 3200003, Israel; (G.S.); (H.H.)
| | - Dimitra D. Dionysiou
- Institute of Communication and Computer Systems, National Technical University of Athens, Zografos Campus, 15780 Athens, Greece; (D.T.); (A.A.)
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Choi H, Tak SH, Lee D. Nursing students' learning flow, self-efficacy and satisfaction in virtual clinical simulation and clinical case seminar. BMC Nurs 2023; 22:454. [PMID: 38041090 PMCID: PMC10693023 DOI: 10.1186/s12912-023-01621-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 11/23/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Virtual clinical simulations and clinical case seminar become widely utilized to address these constraints and help nursing students acquire clinical competencies as the limitations on practicum opportunities have been intensified by the COVID-19 pandemic. The purpose of this study was to examine learning flow, self-efficacy and satisfaction in virtual clinical simulation and clinical case seminar among nursing students. METHODS A descriptive cross-sectional study was used. Forty-two junior nursing students completed survey questionnaires after participating in computer-based virtual clinical simulation and clinical case seminar, which aimed at acquiring knowledge and care skills in geriatric nursing. RESULTS Significant differences in two methods were found in learning flow which included challenge-skill balance (t = -2.24, p < .05) and action-awareness merge (t = -3.32, p < .01). There was no significant difference in learning self-efficacy (t=-1.52, p = .137) and learning satisfaction (t=-0.92, p = .365). CONCLUSIONS When there's a mismatch between the perceived challenge and the students' skill levels, it can hinder the learning process. Therefore, instructors should evaluate the clinical skill levels of their students and make necessary adjustments to the difficulty levels of simulation and clinical case seminar accordingly.
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Affiliation(s)
- Hyein Choi
- College of Nursing, Seoul National University, 103 Daehak-ro, Jongno-gu Seoul, 03080, Republic of Korea
| | - Sunghee H Tak
- College of Nursing, Seoul National University, 103 Daehak-ro, Jongno-gu Seoul, 03080, Republic of Korea.
- Research Institute of Nursing Science, College of Nursing, Seoul National University, 103 Daehak-ro, Jongno-gu Seoul, Republic of Korea.
| | - Dayeon Lee
- College of Nursing, Seoul National University, 103 Daehak-ro, Jongno-gu Seoul, 03080, Republic of Korea
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Porter A, Fei S, Damme KSF, Nusslock R, Gratton C, Mittal VA. A meta-analysis and systematic review of single vs. multimodal neuroimaging techniques in the classification of psychosis. Mol Psychiatry 2023; 28:3278-3292. [PMID: 37563277 PMCID: PMC10618094 DOI: 10.1038/s41380-023-02195-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Psychotic disorders are characterized by structural and functional abnormalities in brain networks. Neuroimaging techniques map and characterize such abnormalities using unique features (e.g., structural integrity, coactivation). However, it is unclear if a specific method, or a combination of modalities, is particularly effective in identifying differences in brain networks of someone with a psychotic disorder. METHODS A systematic meta-analysis evaluated machine learning classification of schizophrenia spectrum disorders in comparison to healthy control participants using various neuroimaging modalities (i.e., T1-weighted imaging (T1), diffusion tensor imaging (DTI), resting state functional connectivity (rs-FC), or some combination (multimodal)). Criteria for manuscript inclusion included whole-brain analyses and cross-validation to provide a complete picture regarding the predictive ability of large-scale brain systems in psychosis. For this meta-analysis, we searched Ovid MEDLINE, PubMed, PsychInfo, Google Scholar, and Web of Science published between inception and March 13th 2023. Prediction results were averaged for studies using the same dataset, but parallel analyses were run that included studies with pooled sample across many datasets. We assessed bias through funnel plot asymmetry. A bivariate regression model determined whether differences in imaging modality, demographics, and preprocessing methods moderated classification. Separate models were run for studies with internal prediction (via cross-validation) and external prediction. RESULTS 93 studies were identified for quantitative review (30 T1, 9 DTI, 40 rs-FC, and 14 multimodal). As a whole, all modalities reliably differentiated those with schizophrenia spectrum disorders from controls (OR = 2.64 (95%CI = 2.33 to 2.95)). However, classification was relatively similar across modalities: no differences were seen across modalities in the classification of independent internal data, and a small advantage was seen for rs-FC studies relative to T1 studies in classification in external datasets. We found large amounts of heterogeneity across results resulting in significant signs of bias in funnel plots and Egger's tests. Results remained similar, however, when studies were restricted to those with less heterogeneity, with continued small advantages for rs-FC relative to structural measures. Notably, in all cases, no significant differences were seen between multimodal and unimodal approaches, with rs-FC and unimodal studies reporting largely overlapping classification performance. Differences in demographics and analysis or denoising were not associated with changes in classification scores. CONCLUSIONS The results of this study suggest that neuroimaging approaches have promise in the classification of psychosis. Interestingly, at present most modalities perform similarly in the classification of psychosis, with slight advantages for rs-FC relative to structural modalities in some specific cases. Notably, results differed substantially across studies, with suggestions of biased effect sizes, particularly highlighting the need for more studies using external prediction and large sample sizes. Adopting more rigorous and systematized standards will add significant value toward understanding and treating this critical population.
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Affiliation(s)
- Alexis Porter
- Department of Psychology, Northwestern University, Evanston, IL, USA.
| | - Sihan Fei
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Katherine S F Damme
- Department of Psychology, Northwestern University, Evanston, IL, USA
- Institute for Innovations in Developmental Sciences, Northwestern University, Evanston and Chicago, IL, USA
| | - Robin Nusslock
- Department of Psychology, Northwestern University, Evanston, IL, USA
| | - Caterina Gratton
- Department of Psychology, Florida State University, Tallahassee, FL, USA
| | - Vijay A Mittal
- Department of Psychology, Northwestern University, Evanston, IL, USA
- Institute for Innovations in Developmental Sciences, Northwestern University, Evanston and Chicago, IL, USA
- Department of Psychiatry, Northwestern University, Chicago, IL, USA
- Medical Social Sciences, Northwestern University, Chicago, IL, USA
- Institute for Policy Research, Northwestern University, Chicago, IL, USA
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Yin Y. Prediction and analysis of time series data based on granular computing. Front Comput Neurosci 2023; 17:1192876. [PMID: 37576071 PMCID: PMC10413556 DOI: 10.3389/fncom.2023.1192876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/06/2023] [Indexed: 08/15/2023] Open
Abstract
The advent of the Big Data era and the rapid development of the Internet of Things have led to a dramatic increase in the amount of data from various time series. How to classify, correlation rule mining and prediction of these large-sample time series data has a crucial role. However, due to the characteristics of high dimensionality, large data volume and transmission lag of sensor data, large sample time series data are affected by multiple factors and have complex characteristics such as multi-scale, non-linearity and burstiness. Traditional time series prediction methods are no longer applicable to the study of large sample time series data. Granular computing has unique advantages in dealing with continuous and complex data, and can compensate for the limitations of traditional support vector machines in dealing with large sample data. Therefore, this paper proposes to combine granular computing theory with support vector machines to achieve large-sample time series data prediction. Firstly, the definition of time series is analyzed, and the basic principles of traditional time series forecasting methods and granular computing are investigated. Secondly, in terms of predicting the trend of data changes, it is proposed to apply the fuzzy granulation algorithm to first convert the sample data into coarser granules. Then, it is combined with a support vector machine to predict the range of change of continuous time series data over a period of time. The results of the simulation experiments show that the proposed model is able to make accurate predictions of the range of data changes in future time periods. Compared with other prediction models, the proposed model reduces the complexity of the samples and improves the prediction accuracy.
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Affiliation(s)
- Yushan Yin
- School of Electro-Mechanical Engineering, Xidian University, Xi’an, China
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Gonzalez-Castillo J, Fernandez IS, Lam KC, Handwerker DA, Pereira F, Bandettini PA. Manifold learning for fMRI time-varying functional connectivity. Front Hum Neurosci 2023; 17:1134012. [PMID: 37497043 PMCID: PMC10366614 DOI: 10.3389/fnhum.2023.1134012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 06/21/2023] [Indexed: 07/28/2023] Open
Abstract
Whole-brain functional connectivity (FC) measured with functional MRI (fMRI) evolves over time in meaningful ways at temporal scales going from years (e.g., development) to seconds [e.g., within-scan time-varying FC (tvFC)]. Yet, our ability to explore tvFC is severely constrained by its large dimensionality (several thousands). To overcome this difficulty, researchers often seek to generate low dimensional representations (e.g., 2D and 3D scatter plots) hoping those will retain important aspects of the data (e.g., relationships to behavior and disease progression). Limited prior empirical work suggests that manifold learning techniques (MLTs)-namely those seeking to infer a low dimensional non-linear surface (i.e., the manifold) where most of the data lies-are good candidates for accomplishing this task. Here we explore this possibility in detail. First, we discuss why one should expect tvFC data to lie on a low dimensional manifold. Second, we estimate what is the intrinsic dimension (ID; i.e., minimum number of latent dimensions) of tvFC data manifolds. Third, we describe the inner workings of three state-of-the-art MLTs: Laplacian Eigenmaps (LEs), T-distributed Stochastic Neighbor Embedding (T-SNE), and Uniform Manifold Approximation and Projection (UMAP). For each method, we empirically evaluate its ability to generate neuro-biologically meaningful representations of tvFC data, as well as their robustness against hyper-parameter selection. Our results show that tvFC data has an ID that ranges between 4 and 26, and that ID varies significantly between rest and task states. We also show how all three methods can effectively capture subject identity and task being performed: UMAP and T-SNE can capture these two levels of detail concurrently, but LE could only capture one at a time. We observed substantial variability in embedding quality across MLTs, and within-MLT as a function of hyper-parameter selection. To help alleviate this issue, we provide heuristics that can inform future studies. Finally, we also demonstrate the importance of feature normalization when combining data across subjects and the role that temporal autocorrelation plays in the application of MLTs to tvFC data. Overall, we conclude that while MLTs can be useful to generate summary views of labeled tvFC data, their application to unlabeled data such as resting-state remains challenging.
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Affiliation(s)
- Javier Gonzalez-Castillo
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, United States
| | - Isabel S. Fernandez
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, United States
| | - Ka Chun Lam
- Machine Learning Group, National Institute of Mental Health, Bethesda, MD, United States
| | - Daniel A. Handwerker
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, United States
| | - Francisco Pereira
- Machine Learning Group, National Institute of Mental Health, Bethesda, MD, United States
| | - Peter A. Bandettini
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD, United States
- Functional Magnetic Resonance Imaging (FMRI) Core, National Institute of Mental Health, Bethesda, MD, United States
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Gonzalez-Castillo J, Fernandez I, Lam KC, Handwerker DA, Pereira F, Bandettini PA. Manifold Learning for fMRI time-varying FC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.14.523992. [PMID: 36789436 PMCID: PMC9928030 DOI: 10.1101/2023.01.14.523992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Whole-brain functional connectivity ( FC ) measured with functional MRI (fMRI) evolve over time in meaningful ways at temporal scales going from years (e.g., development) to seconds (e.g., within-scan time-varying FC ( tvFC )). Yet, our ability to explore tvFC is severely constrained by its large dimensionality (several thousands). To overcome this difficulty, researchers seek to generate low dimensional representations (e.g., 2D and 3D scatter plots) expected to retain its most informative aspects (e.g., relationships to behavior, disease progression). Limited prior empirical work suggests that manifold learning techniques ( MLTs )-namely those seeking to infer a low dimensional non-linear surface (i.e., the manifold) where most of the data lies-are good candidates for accomplishing this task. Here we explore this possibility in detail. First, we discuss why one should expect tv FC data to lie on a low dimensional manifold. Second, we estimate what is the intrinsic dimension (i.e., minimum number of latent dimensions; ID ) of tvFC data manifolds. Third, we describe the inner workings of three state-of-the-art MLTs : Laplacian Eigenmaps ( LE ), T-distributed Stochastic Neighbor Embedding ( T-SNE ), and Uniform Manifold Approximation and Projection ( UMAP ). For each method, we empirically evaluate its ability to generate neuro-biologically meaningful representations of tvFC data, as well as their robustness against hyper-parameter selection. Our results show that tvFC data has an ID that ranges between 4 and 26, and that ID varies significantly between rest and task states. We also show how all three methods can effectively capture subject identity and task being performed: UMAP and T-SNE can capture these two levels of detail concurrently, but L E could only capture one at a time. We observed substantial variability in embedding quality across MLTs , and within- MLT as a function of hyper-parameter selection. To help alleviate this issue, we provide heuristics that can inform future studies. Finally, we also demonstrate the importance of feature normalization when combining data across subjects and the role that temporal autocorrelation plays in the application of MLTs to tvFC data. Overall, we conclude that while MLTs can be useful to generate summary views of labeled tvFC data, their application to unlabeled data such as resting-state remains challenging.
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Affiliation(s)
| | - Isabel Fernandez
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD
| | - Ka Chun Lam
- Machine Learning Group, National Institute of Mental Health, Bethesda, MD
| | - Daniel A Handwerker
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD
| | - Francisco Pereira
- Machine Learning Group, National Institute of Mental Health, Bethesda, MD
| | - Peter A Bandettini
- Section on Functional Imaging Methods, National Institute of Mental Health, Bethesda, MD,Machine Learning Group, National Institute of Mental Health, Bethesda, MD,FMRI Core, National Institute of Mental Health, Bethesda, MD
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Cheng N, Guo M, Yan F, Guo Z, Meng J, Ning K, Zhang Y, Duan Z, Han Y, Wang C. Application of machine learning in predicting aggressive behaviors from hospitalized patients with schizophrenia. Front Psychiatry 2023; 14:1016586. [PMID: 37020730 PMCID: PMC10067917 DOI: 10.3389/fpsyt.2023.1016586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
Objective To establish a predictive model of aggressive behaviors from hospitalized patients with schizophrenia through applying multiple machine learning algorithms, to provide a reference for accurately predicting and preventing of the occurrence of aggressive behaviors. Methods The cluster sampling method was used to select patients with schizophrenia who were hospitalized in our hospital from July 2019 to August 2021 as the survey objects, and they were divided into an aggressive behavior group (611 cases) and a non-aggressive behavior group (1,426 cases) according to whether they experienced obvious aggressive behaviors during hospitalization. Self-administered General Condition Questionnaire, Insight and Treatment Attitude Questionnaire (ITAQ), Family APGAR (Adaptation, Partnership, Growth, Affection, Resolve) Questionnaire (APGAR), Social Support Rating Scale Questionnaire (SSRS) and Family Burden Scale of Disease Questionnaire (FBS) were used for the survey. The Multi-layer Perceptron, Lasso, Support Vector Machine and Random Forest algorithms were used to build a predictive model for the occurrence of aggressive behaviors from hospitalized patients with schizophrenia and to evaluate its predictive effect. Nomogram was used to build a clinical application tool. Results The area under the receiver operating characteristic curve (AUC) values of the Multi-Layer Perceptron, Lasso, Support Vector Machine, and Random Forest were 0.904 (95% CI: 0.877-0.926), 0.901 (95% CI: 0.874-0.923), 0.902 (95% CI: 0.876-0.924), and 0.955 (95% CI: 0.935-0.970), where the AUCs of the Random Forest and the remaining three models were statistically different (p < 0.0001), and the remaining three models were not statistically different in pair comparisons (p > 0.5). Conclusion Machine learning models can fairly predict aggressive behaviors in hospitalized patients with schizophrenia, among which Random Forest has the best predictive effect and has some value in clinical application.
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Affiliation(s)
- Nuo Cheng
- Department of Clinical Medicine, Zhengzhou University, Zhengzhou, Henan, China
| | - Meihao Guo
- Department of Infection Prevention and Control, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Fang Yan
- Department of Infection Prevention and Control, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Zhengjun Guo
- Henan Mental Disease Prevention and Control Center, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Jun Meng
- Editorial Department of Journal of Clinical Psychosomatic Diseases, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Kui Ning
- Department of Medical Administration, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Yanping Zhang
- Department of Medicine, Zhengzhou University, Zhengzhou, Henan, China
| | - Zitian Duan
- The Seventh Psychiatric Department, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Yong Han
- Henan Key Laboratory of Biological Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- *Correspondence: Han Yong,
| | - Changhong Wang
- Department of Clinical Psychiatry, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
- Wang Changhong,
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Zhang P, He Z, Mao Y, Sun R, Qu Y, Chen L, Ma P, Yin S, Yin T, Zeng F. Aberrant resting-state functional connectivity and topological properties of the subcortical network in functional dyspepsia patients. Front Mol Neurosci 2022; 15:1001557. [PMCID: PMC9606653 DOI: 10.3389/fnmol.2022.1001557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Functional dyspepsia (FD) is a disorder of gut-brain interaction. Previous studies have demonstrated a wide range of abnormalities in functional brain activity and connectivity patterns in FD. However, the connectivity pattern of the subcortical network (SCN), which is a hub of visceral information transmission and processing, remains unclear in FD patients. The study compared the resting-state functional connectivity (rsFC) and the global and nodal topological properties of SCN between 109 FD patients and 98 healthy controls, and then explored the correlations between the connectivity metrics and clinical symptoms in FD patients. The results demonstrated that FD patients manifested the increased rsFC in seventeen edges among the SCN, decreased small-worldness and local efficiency in SCN, as well as increased nodal efficiency and nodal degree centrality in the anterior thalamus than healthy controls (p < 0.05, false discovery rate corrected). Moreover, the rsFC of the right anterior thalamus-left nucleus accumbens edge was significantly correlated with the NDSI scores (r = 0.255, p = 0.008, uncorrected) and NDLQI scores (r = −0.241, p = 0.013, uncorrected), the nodal efficiency of right anterior thalamus was significantly correlated with NDLQI scores (r = 0.204, p = 0.036, uncorrected) in FD patients. This study indicated the abnormal rsFC pattern, as well as global and nodal topological properties of the SCN, especially the bilateral anterior thalamus in FD patients, which enhanced our understanding of the central pathophysiology of FD and will lay the foundation for the objective diagnosis of FD and the development of new therapies.
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Affiliation(s)
- Pan Zhang
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhaoxuan He
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yangke Mao
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ruirui Sun
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuzhu Qu
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li Chen
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Peihong Ma
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- School of Acupuncture-Moxibustion and Tuina, Beijing University of Chinese Medicine, Beijing, China
| | - Shuai Yin
- First Affiliated Hospital, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Tao Yin
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Tao Yin,
| | - Fang Zeng
- Acupuncture and Tuina School, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Brain Science Research Center, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Fang Zeng,
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10
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Plechawska-Wójcik M, Karczmarek P, Krukow P, Kaczorowska M, Tokovarov M, Jonak K. Recognition of Electroencephalography-Related Features of Neuronal Network Organization in Patients With Schizophrenia Using the Generalized Choquet Integrals. Front Neuroinform 2022; 15:744355. [PMID: 34970131 PMCID: PMC8712566 DOI: 10.3389/fninf.2021.744355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
In this study, we focused on the verification of suitable aggregation operators enabling accurate differentiation of selected neurophysiological features extracted from resting-state electroencephalographic recordings of patients who were diagnosed with schizophrenia (SZ) or healthy controls (HC). We built the Choquet integral-based operators using traditional classification results as an input to the procedure of establishing the fuzzy measure densities. The dataset applied in the study was a collection of variables characterizing the organization of the neural networks computed using the minimum spanning tree (MST) algorithms obtained from signal-spaced functional connectivity indicators and calculated separately for predefined frequency bands using classical linear Granger causality (GC) measure. In the series of numerical experiments, we reported the results of classification obtained using numerous generalizations of the Choquet integral and other aggregation functions, which were tested to find the most appropriate ones. The obtained results demonstrate that the classification accuracy can be increased by 1.81% using the extended versions of the Choquet integral called in the literature, namely, generalized Choquet integral or pre-aggregation operators.
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Affiliation(s)
| | - Paweł Karczmarek
- Department of Computer Science, Lublin University of Technology, Lublin, Poland
| | - Paweł Krukow
- Department of Clinical Neuropsychiatry, Medical University of Lublin, Lublin, Poland
| | - Monika Kaczorowska
- Department of Computer Science, Lublin University of Technology, Lublin, Poland
| | - Mikhail Tokovarov
- Department of Computer Science, Lublin University of Technology, Lublin, Poland
| | - Kamil Jonak
- Department of Computer Science, Lublin University of Technology, Lublin, Poland.,Department of Clinical Neuropsychiatry, Medical University of Lublin, Lublin, Poland
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11
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Xiao G, Wang H, Shen J, Chen Z, Zhang Z, Ge X. Synergy Factorized Bilinear Network with a Dual Suppression Strategy for Brain Tumor Classification in MRI. MICROMACHINES 2021; 13:mi13010015. [PMID: 35056179 PMCID: PMC8780069 DOI: 10.3390/mi13010015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/15/2021] [Accepted: 12/20/2021] [Indexed: 12/30/2022]
Abstract
Automatic brain tumor classification is a practicable means of accelerating clinical diagnosis. Recently, deep convolutional neural network (CNN) training with MRI datasets has succeeded in computer-aided diagnostic (CAD) systems. To further improve the classification performance of CNNs, there is still a difficult path forward with regards to subtle discriminative details among brain tumors. We note that the existing methods heavily rely on data-driven convolutional models while overlooking what makes a class different from the others. Our study proposes to guide the network to find exact differences among similar tumor classes. We first present a “dual suppression encoding” block tailored to brain tumor MRIs, which diverges two paths from our network to refine global orderless information and local spatial representations. The aim is to use more valuable clues for correct classes by reducing the impact of negative global features and extending the attention of salient local parts. Then we introduce a “factorized bilinear encoding” layer for feature fusion. The aim is to generate compact and discriminative representations. Finally, the synergy between these two components forms a pipeline that learns in an end-to-end way. Extensive experiments exhibited superior classification performance in qualitative and quantitative evaluation on three datasets.
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Affiliation(s)
- Guanghua Xiao
- College of Computer and Information Engineering, Hohai University, Nanjing 211100, China; (G.X.); (J.S.); (Z.C.); (Z.Z.)
- Department of Equipment Engineering, Jiangsu Urban and Rural Construction College, Changzhou 213147, China
| | - Huibin Wang
- College of Computer and Information Engineering, Hohai University, Nanjing 211100, China; (G.X.); (J.S.); (Z.C.); (Z.Z.)
- Correspondence:
| | - Jie Shen
- College of Computer and Information Engineering, Hohai University, Nanjing 211100, China; (G.X.); (J.S.); (Z.C.); (Z.Z.)
| | - Zhe Chen
- College of Computer and Information Engineering, Hohai University, Nanjing 211100, China; (G.X.); (J.S.); (Z.C.); (Z.Z.)
| | - Zhen Zhang
- College of Computer and Information Engineering, Hohai University, Nanjing 211100, China; (G.X.); (J.S.); (Z.C.); (Z.Z.)
| | - Xiaomin Ge
- Department of Radiology, Changzhou Second People’s Hospital Affiliated to Nanjing Medical University, Changzhou 213000, China;
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12
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Zhao W, Li H, Hao Y, Hu G, Zhang Y, Frederick BDB, Cong F. An efficient functional magnetic resonance imaging data reduction strategy using neighborhood preserving embedding algorithm. Hum Brain Mapp 2021; 43:1561-1576. [PMID: 34890077 PMCID: PMC8886658 DOI: 10.1002/hbm.25742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/17/2021] [Accepted: 11/24/2021] [Indexed: 12/03/2022] Open
Abstract
High dimensionality data have become common in neuroimaging fields, especially group‐level functional magnetic resonance imaging (fMRI) datasets. fMRI connectivity analysis is a widely used, powerful technique for studying functional brain networks to probe underlying mechanisms of brain function and neuropsychological disorders. However, data‐driven technique like independent components analysis (ICA), can yield unstable and inconsistent results, confounding the true effects of interest and hindering the understanding of brain functionality and connectivity. A key contributing factor to this instability is the information loss that occurs during fMRI data reduction. Data reduction of high dimensionality fMRI data in the temporal domain to identify the important information within group datasets is necessary for such analyses and is crucial to ensure the accuracy and stability of the outputs. In this study, we describe an fMRI data reduction strategy based on an adapted neighborhood preserving embedding (NPE) algorithm. Both simulated and real data results indicate that, compared with the widely used data reduction method, principal component analysis, the NPE‐based data reduction method (a) shows superior performance on efficient data reduction, while enhancing group‐level information, (b) develops a unique stratagem for selecting components based on an adjacency graph of eigenvectors, (c) generates more reliable and reproducible brain networks under different model orders when the outputs of NPE are used for ICA, (d) is more sensitive to revealing task‐evoked activation for task fMRI, and (e) is extremely attractive and powerful for the increasingly popular fast fMRI and very large datasets.
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Affiliation(s)
- Wei Zhao
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Huanjie Li
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Yuxing Hao
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Guoqiang Hu
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Yunge Zhang
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China
| | - Blaise de B Frederick
- Brain Imaging Center, McLean Hospital, Belmont, Massachusetts, USA.,Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, USA
| | - Fengyu Cong
- School of Biomedical Engineering, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China.,School of Artificial Intelligence, Faculty of Electronic Information and Electrical Engineering, Dalian University of Technology, Dalian, China.,Key Laboratory of Integrated Circuit and Biomedical Electronic System, Liaoning Province, Dalian University of Technology, Dalian, China.,Faculty of Information Technology, University of Jyvaskyla, Jyvaskyla, Finland
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13
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Park BY, Bethlehem RAI, Paquola C, Larivière S, Rodríguez-Cruces R, Vos de Wael R, Bullmore ET, Bernhardt BC. An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization. eLife 2021; 10:e64694. [PMID: 33787489 PMCID: PMC8087442 DOI: 10.7554/elife.64694] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 03/30/2021] [Indexed: 12/13/2022] Open
Abstract
Adolescence is a critical time for the continued maturation of brain networks. Here, we assessed structural connectome development in a large longitudinal sample ranging from childhood to young adulthood. By projecting high-dimensional connectomes into compact manifold spaces, we identified a marked expansion of structural connectomes, with strongest effects in transmodal regions during adolescence. Findings reflected increased within-module connectivity together with increased segregation, indicating increasing differentiation of higher-order association networks from the rest of the brain. Projection of subcortico-cortical connectivity patterns into these manifolds showed parallel alterations in pathways centered on the caudate and thalamus. Connectome findings were contextualized via spatial transcriptome association analysis, highlighting genes enriched in cortex, thalamus, and striatum. Statistical learning of cortical and subcortical manifold features at baseline and their maturational change predicted measures of intelligence at follow-up. Our findings demonstrate that connectome manifold learning can bridge the conceptual and empirical gaps between macroscale network reconfigurations, microscale processes, and cognitive outcomes in adolescent development.
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Affiliation(s)
- Bo-yong Park
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
- Department of Data Science, Inha UniversityIncheonRepublic of Korea
| | - Richard AI Bethlehem
- Autism Research Centre, Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
- Brain Mapping Unit, Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Casey Paquola
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum JülichJülichGermany
| | - Sara Larivière
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Raul Rodríguez-Cruces
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Reinder Vos de Wael
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
| | - Edward T Bullmore
- Brain Mapping Unit, Department of Psychiatry, University of CambridgeCambridgeUnited Kingdom
| | - Boris C Bernhardt
- McConnell Brain Imaging Centre, Montreal Neurological Institute and Hospital, McGill UniversityMontrealCanada
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14
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Gallos IK, Gkiatis K, Matsopoulos GK, Siettos C. ISOMAP and machine learning algorithms for the construction of embedded functional connectivity networks of anatomically separated brain regions from resting state fMRI data of patients with Schizophrenia. AIMS Neurosci 2021; 8:295-321. [PMID: 33709030 PMCID: PMC7940114 DOI: 10.3934/neuroscience.2021016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 11/18/2022] Open
Abstract
We construct Functional Connectivity Networks (FCN) from resting state fMRI (rsfMRI) recordings towards the classification of brain activity between healthy and schizophrenic subjects using a publicly available dataset (the COBRE dataset) of 145 subjects (74 healthy controls and 71 schizophrenic subjects). First, we match the anatomy of the brain of each individual to the Desikan-Killiany brain atlas. Then, we use the conventional approach of correlating the parcellated time series to construct FCN and ISOMAP, a nonlinear manifold learning algorithm to produce low-dimensional embeddings of the correlation matrices. For the classification analysis, we computed five key local graph-theoretic measures of the FCN and used the LASSO and Random Forest (RF) algorithms for feature selection. For the classification we used standard linear Support Vector Machines. The classification performance is tested by a double cross-validation scheme (consisting of an outer and an inner loop of "Leave one out" cross-validation (LOOCV)). The standard cross-correlation methodology produced a classification rate of 73.1%, while ISOMAP resulted in 79.3%, thus providing a simpler model with a smaller number of features as chosen from LASSO and RF, namely the participation coefficient of the right thalamus and the strength of the right lingual gyrus.
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Affiliation(s)
- Ioannis K Gallos
- School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Greece
| | - Kostakis Gkiatis
- School of Electrical and Computer Engineering, National Technical University of Athens, Greece
| | - George K Matsopoulos
- School of Electrical and Computer Engineering, National Technical University of Athens, Greece
| | - Constantinos Siettos
- Dipartimento di Matematica e Applicazioni “Renato Caccioppoli”, Università degli Studi di Napoli Federico II, Italy
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