Kernel-based Nonlinear Manifold Learning for EEG-based Functional Connectivity Analysis and Channel Selection with Application to Alzheimer's Disease

Rajintha Gunawardena, Ptolemaios G. Sarrigiannis, Daniel J. Blackburn, Fei He

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1 Citation (Scopus)
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Dynamical, causal, and cross-frequency coupling analysis using the electroencephalogram (EEG) has gained significant attention for diagnosing and characterizing neurological disorders. Selecting important EEG channels is crucial for reducing computational complexity in implementing these methods and improving classification accuracy. In neuroscience, measures of (dis) similarity between EEG channels are often used as functional connectivity (FC) features, and important channels are selected via feature selection. Developing a generic measure of (dis) similarity is important for FC analysis and channel selection. In this study, learning of (dis) similarity information within the EEG is achieved using kernel-based nonlinear manifold learning. The focus is on FC changes and, thereby, EEG channel selection. Isomap and Gaussian Process Latent Variable Model (Isomap-GPLVM) are employed for this purpose. The resulting kernel (dis) similarity matrix is used as a novel measure of linear and nonlinear FC between EEG channels. The analysis of EEG from healthy controls (HC) and patients with mild to moderate Alzheimer's disease (AD) are presented as a case study. Classification results are compared with other commonly used FC measures. Our analysis shows significant differences in FC between bipolar channels of the occipital region and other regions (i.e. parietal, centro-parietal, and fronto-central) between AD and HC groups. Furthermore, our results indicate that FC changes between channels along the fronto-parietal region and the rest of the EEG are important in diagnosing AD. Our results and its relation to functional networks are consistent with those obtained from previous studies using fMRI, resting-state fMRI and EEG.

Original languageEnglish
Pages (from-to)140-156
Number of pages17
Early online date8 Jun 2023
Publication statusPublished - 15 Jul 2023

Bibliographical note

This is an open access article under the CC BY-NC-ND license (


The EEG data was funded by a grant from Alzheimer’s Research UK, grant
reference number ARUK-PPG20114B-25.


  • Alzheimer's disease
  • EEG
  • channel selection
  • manifold learning
  • machine learning
  • functional connectivity

ASJC Scopus subject areas

  • Neuroscience(all)


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