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Samantaray T, Saini J, Pal PK, Gupta CN. Brain connectivity for subtypes of parkinson's disease using structural MRI. Biomed Phys Eng Express 2024; 10:025012. [PMID: 38224618 DOI: 10.1088/2057-1976/ad1e77] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
Objective. Delineating Parkinson's disease (PD) into distinct subtypes is a major challenge. Most studies use clinical symptoms to label PD subtypes while our work uses an imaging-based data-mining approach to subtype PD. Our study comprises two major objectives - firstly, subtyping Parkinson's patients based on grey matter information from structural magnetic resonance imaging scans of human brains; secondly, comparative structural brain connectivity analysis of PD subtypes derived from the former step.Approach. Source-based-morphometry decomposition was performed on 131 Parkinson's patients and 78 healthy controls from PPMI dataset, to derive at components (regions) with significance in disease and high effect size. The loading coefficients of significant components were thresholded for arriving at subtypes. Further, regional grey matter maps of subtype-specific subjects were separately parcellated and employed for construction of subtype-specific association matrices using Pearson correlation. These association matrices were binarized using sparsity threshold and leveraged for structural brain connectivity analysis using network metrics.Main results. Two distinct Parkinson's subtypes (namely A and B) were detected employing loadings of two components satisfying the selection criteria, and a third subtype (AB) was detected, common to these two components. Subtype A subjects were highly weighted in inferior, middle and superior frontal gyri while subtype B subjects in inferior, middle and superior temporal gyri. Network metrics analyses through permutation test revealed significant inter-subtype differences (p < 0.05) in clustering coefficient, local efficiency, participation coefficient and betweenness centrality. Moreover, hubs were obtained using betweenness centrality and mean network degree.Significance. MRI-based data-driven subtypes show frontal and temporal lobes playing a key role in PD. Graph theory-driven brain network analyses could untangle subtype-specific differences in structural brain connections showing differential network architecture. Replication of these initial results in other Parkinson's datasets may be explored in future. Clinical Relevance- Investigating structural brain connections in Parkinson's disease may provide subtype-specific treatment.
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Affiliation(s)
- Tanmayee Samantaray
- Neural Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India
| | - Jitender Saini
- Department of Neuroimaging and Interventional Radiology, National Institute of Mental Health and Neurosciences, Bengaluru, 560029, India
| | - Pramod Kumar Pal
- Department of Neurology, National Institute of Mental Health & Neuro Sciences, Bengaluru, 560029, India
| | - Cota Navin Gupta
- Neural Engineering Lab, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, 781039, India
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Tas NP, Kaya O, Macin G, Tasci B, Dogan S, Tuncer T. ASNET: A Novel AI Framework for Accurate Ankylosing Spondylitis Diagnosis from MRI. Biomedicines 2023; 11:2441. [PMID: 37760882 PMCID: PMC10525210 DOI: 10.3390/biomedicines11092441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 08/24/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Ankylosing spondylitis (AS) is a chronic, painful, progressive disease usually seen in the spine. Traditional diagnostic methods have limitations in detecting the early stages of AS. The early diagnosis of AS can improve patients' quality of life. This study aims to diagnose AS with a pre-trained hybrid model using magnetic resonance imaging (MRI). MATERIALS AND METHODS In this research, we collected a new MRI dataset comprising three cases. Furthermore, we introduced a novel deep feature engineering model. Within this model, we utilized three renowned pretrained convolutional neural networks (CNNs): DenseNet201, ResNet50, and ShuffleNet. Through these pretrained CNNs, deep features were generated using the transfer learning approach. For each pretrained network, two feature vectors were generated from an MRI. Three feature selectors were employed during the feature selection phase, amplifying the number of features from 6 to 18 (calculated as 6 × 3). The k-nearest neighbors (kNN) classifier was utilized in the classification phase to determine classification results. During the information phase, the iterative majority voting (IMV) algorithm was applied to secure voted results, and our model selected the output with the highest classification accuracy. In this manner, we have introduced a self-organized deep feature engineering model. RESULTS We have applied the presented model to the collected dataset. The proposed method yielded 99.80%, 99.60%, 100%, and 99.80% results for accuracy, recall, precision, and F1-score for the collected axial images dataset. The collected coronal image dataset yielded 99.45%, 99.20%, 99.70%, and 99.45% results for accuracy, recall, precision, and F1-score, respectively. As for contrast-enhanced images, accuracy of 95.62%, recall of 80.72%, precision of 94.24%, and an F1-score of 86.96% were attained. CONCLUSIONS Based on the results, the proposed method for classifying AS disease has demonstrated successful outcomes using MRI. The model has been tested on three cases, and its consistently high classification performance across all cases underscores the model's general robustness. Furthermore, the ability to diagnose AS disease using only axial images, without the need for contrast-enhanced MRI, represents a significant advancement in both healthcare and economic terms.
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Affiliation(s)
- Nevsun Pihtili Tas
- Department of Physical Medicine and Rehabilitation, Health Sciences University Elazig Fethi Sekin City Hospital, Elazig 23280, Turkey;
| | - Oguz Kaya
- Department of Orthopedics and Traumatology, Elazig Fethi Sekin City Hospital, Elazig 23280, Turkey;
| | - Gulay Macin
- Department of Radiology, Beyhekim Training and Research Hospital, Konya 42060, Turkey;
| | - Burak Tasci
- Vocational School of Technical Sciences, Firat University, Elazig 23119, Turkey;
| | - Sengul Dogan
- Department of Digital Forensics Engineering, College of Technology, Firat University, Elazig 23119, Turkey
| | - Turker Tuncer
- Department of Digital Forensics Engineering, College of Technology, Firat University, Elazig 23119, Turkey
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Detection of Parkinson's disease from EEG signals using discrete wavelet transform, different entropy measures, and machine learning techniques. Sci Rep 2022; 12:22547. [PMID: 36581646 PMCID: PMC9800369 DOI: 10.1038/s41598-022-26644-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Early detection of Parkinson's disease (PD) is very important in clinical diagnosis for preventing disease development. In this study, we present efficient discrete wavelet transform (DWT)-based methods for detecting PD from health control (HC) in two cases, namely, off-and on-medication. First, the EEG signals are preprocessed to remove major artifacts before being decomposed into several EEG sub-bands (approximate and details) using DWT. The features are then extracted from the wavelet packet-derived reconstructed signals using different entropy measures, namely, log energy entropy, Shannon entropy, threshold entropy, sure entropy, and norm entropy. Several machine learning techniques are investigated to classify the resulting PD/HC features. The effects of DWT coefficients and brain regions on classification accuracy are being investigated as well. Two public datasets are used to verify the proposed methods: the SanDiego dataset (31 subjects, 93 min) and the UNM dataset (54 subjects, 54 min). The results are promising and show that four entropy measures: log energy entropy, threshold entropy, sure entropy, and modified-Shannon entropy (TShEn) lead to high classification accuracy, indicating they are good biomarkers for PD detection. With the SanDiego dataset, the classification results of off-medication PD versus HC are 99.89, 99.87, and 99.91 for accuracy, sensitivity, and specificity, respectively, using the combination of DWT + TShEn and KNN classifier. Using the same combination, the results of on-medication PD versus HC are 94.21, 93.33, and 95%. With the UNM dataset, the obtained classification accuracy is around 99.5% in both cases of off-and on-medication PD using DWT + TShEn + SVM and DWT + ThEn + KNN, respectively. The results also demonstrate the importance of all DWT coefficients and that selecting a suitable small number of EEG channels from several brain regions could improve the classification accuracy.
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Barua PD, Baygin N, Dogan S, Baygin M, Arunkumar N, Fujita H, Tuncer T, Tan RS, Palmer E, Azizan MMB, Kadri NA, Acharya UR. Automated detection of pain levels using deep feature extraction from shutter blinds-based dynamic-sized horizontal patches with facial images. Sci Rep 2022; 12:17297. [PMID: 36241674 PMCID: PMC9568538 DOI: 10.1038/s41598-022-21380-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/27/2022] [Indexed: 01/10/2023] Open
Abstract
Pain intensity classification using facial images is a challenging problem in computer vision research. This work proposed a patch and transfer learning-based model to classify various pain intensities using facial images. The input facial images were segmented into dynamic-sized horizontal patches or "shutter blinds". A lightweight deep network DarkNet19 pre-trained on ImageNet1K was used to generate deep features from the shutter blinds and the undivided resized segmented input facial image. The most discriminative features were selected from these deep features using iterative neighborhood component analysis, which were then fed to a standard shallow fine k-nearest neighbor classifier for classification using tenfold cross-validation. The proposed shutter blinds-based model was trained and tested on datasets derived from two public databases-University of Northern British Columbia-McMaster Shoulder Pain Expression Archive Database and Denver Intensity of Spontaneous Facial Action Database-which both comprised four pain intensity classes that had been labeled by human experts using validated facial action coding system methodology. Our shutter blinds-based classification model attained more than 95% overall accuracy rates on both datasets. The excellent performance suggests that the automated pain intensity classification model can be deployed to assist doctors in the non-verbal detection of pain using facial images in various situations (e.g., non-communicative patients or during surgery). This system can facilitate timely detection and management of pain.
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Affiliation(s)
- Prabal Datta Barua
- grid.1048.d0000 0004 0473 0844School of Business (Information System), University of Southern Queensland, Toowoomba, QLD 4350 Australia ,grid.117476.20000 0004 1936 7611Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, NSW 2007 Australia
| | - Nursena Baygin
- grid.16487.3c0000 0000 9216 0511Department of Computer Engineering, College of Engineering, Kafkas University, Kars, Turkey
| | - Sengul Dogan
- grid.411320.50000 0004 0574 1529Department of Digital Forensics Engineering, College of Technology, Firat University, Elazig, Turkey
| | - Mehmet Baygin
- grid.449062.d0000 0004 0399 2738Department of Computer Engineering, College of Engineering, Ardahan University, Ardahan, Turkey
| | - N. Arunkumar
- Rathinam College of Engineering, Coimbatore, India
| | - Hamido Fujita
- Faculty of Information Technology, HUTECH University of Technology, Ho Chi Minh City, Viet Nam ,grid.4489.10000000121678994Andalusian Research Institute in Data Science and Computational Intelligence, University of Granada, Granada, Spain ,grid.443998.b0000 0001 2172 3919Regional Research Center, Iwate Prefectural University, Iwate, Japan
| | - Turker Tuncer
- grid.411320.50000 0004 0574 1529Department of Digital Forensics Engineering, College of Technology, Firat University, Elazig, Turkey
| | - Ru-San Tan
- grid.419385.20000 0004 0620 9905Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Duke-NUS Medical School, Singapore, Singapore
| | - Elizabeth Palmer
- grid.430417.50000 0004 0640 6474Centre of Clinical Genetics, Sydney Children’s Hospitals Network, Randwick, 2031 Australia ,grid.1005.40000 0004 4902 0432School of Women’s and Children’s Health, University of New South Wales, Randwick, 2031 Australia
| | - Muhammad Mokhzaini Bin Azizan
- grid.462995.50000 0001 2218 9236Department of Electrical and Electronic Engineering, Faculty of Engineering and Built Environment, Universiti Sains Islam Malaysia (USIM), Nilai, Malaysia
| | - Nahrizul Adib Kadri
- grid.10347.310000 0001 2308 5949Department of Biomedical Engineering, Faculty of Engineering, University Malaya, 50603 Kuala Lumpur, Malaysia
| | - U. Rajendra Acharya
- grid.462630.50000 0000 9158 4937Department of Electronics and Computer Engineering, Ngee Ann Polytechnic, Singapore, 599489 Singapore ,grid.443365.30000 0004 0388 6484Department of Biomedical Engineering, School of Science and Technology, SUSS University, Singapore, Singapore ,grid.252470.60000 0000 9263 9645Department of Biomedical Informatics and Medical Engineering, Asia University, Taichung, Taiwan
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Aydemir E, Baygin M, Dogan S, Tuncer T, Barua PD, Chakraborty S, Faust O, Arunkumar N, Kaysi F, Acharya UR. Mental performance classification using fused multilevel feature generation with EEG signals. INTERNATIONAL JOURNAL OF HEALTHCARE MANAGEMENT 2022. [DOI: 10.1080/20479700.2022.2130645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Emrah Aydemir
- Department of Management Information, College of Management, Sakarya University, Sakarya, Turkey
| | - Mehmet Baygin
- Department of Computer Engineering, College of Engineering, Ardahan University, Ardahan, Turkey
| | - Sengul Dogan
- Department of Digital Forensics Engineering, College of Technology, Firat University, Elazig, Turkey
| | - Turker Tuncer
- Department of Digital Forensics Engineering, College of Technology, Firat University, Elazig, Turkey
| | - Prabal Datta Barua
- School of Management & Enterprise, University of Southern Queensland, Darling Heights, Australia
- Faculty of Engineering and Information Technology, University of Technology Sydney, Sydney, Australia
| | - Subrata Chakraborty
- School of Science and Technology, Faculty of Science, Agriculture, Business and Law, University of New England, Armidale, Australia
- Center for Advanced Modelling and Geospatial Information Systems, Faculty of Engineering and IT, University of Technology Sydney, Sydney, Australia
| | - Oliver Faust
- School of Computing, Anglia Ruskin University, Cambridge, UK
| | - N. Arunkumar
- Department of Electronics and Instrumentation, SASTRA University, Thanjavur, India
| | - Feyzi Kaysi
- Department of Electronic and Automation, Vocational School of Technical Sciences, Istanbul University-Cerrahpasa, Istanbul, Turkey
| | - U. Rajendra Acharya
- Department of Electronics and Computer Engineering, Ngee Ann Polytechnic, Singapore, Singapore
- Department of Biomedical Engineering, School of Science and Technology, SUSS University, Singapore, Singapore
- Department of Biomedical Informatics and Medical Engineering, Asia University, Taichung, Taiwan
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