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Open Access Issue
Autism Spectrum Disorder Classification with Interpretability in Children Based on Structural MRI Features Extracted Using Contrastive Variational Autoencoder
Big Data Mining and Analytics 2024, 7(3): 781-793
Published: 28 August 2024
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Autism Spectrum Disorder (ASD) is a highly disabling mental disease that brings significant impairments of social interaction ability to the patients, making early screening and intervention of ASD critical. With the development of the machine learning and neuroimaging technology, extensive research has been conducted on machine classification of ASD based on structural Magnetic Resonance Imaging (s-MRI). However, most studies involve with datasets where participants’ age are above 5 and lack interpretability. In this paper, we propose a machine learning method for ASD classification in children with age range from 0.92 to 4.83 years, based on s-MRI features extracted using Contrastive Variational AutoEncoder (CVAE). 78 s-MRIs, collected from Shenzhen Children’s Hospital, are used for training CVAE, which consists of both ASD-specific feature channel and common-shared feature channel. The ASD participants represented by ASD-specific features can be easily discriminated from Typical Control (TC) participants represented by the common-shared features. In case of degraded predictive accuracy when data size is extremely small, a transfer learning strategy is proposed here as a potential solution. Finally, we conduct neuroanatomical interpretation based on the correlation between s-MRI features extracted from CVAE and surface area of different cortical regions, which discloses potential biomarkers that could help target treatments of ASD in the future.

Open Access Issue
Multi-Task Learning for Alzheimer’s Disease Diagnosis and Mini-Mental State Examination Score Prediction
Big Data Mining and Analytics 2024, 7(3): 828-842
Published: 28 August 2024
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Downloads:17

Accurately diagnosing Alzheimer’s disease is essential for improving elderly health. Meanwhile, accurate prediction of the mini-mental state examination score also can measure cognition impairment and track the progression of Alzheimer’s disease. However, most of the existing methods perform Alzheimer’s disease diagnosis and mini-mental state examination score prediction separately and ignore the relation between these two tasks. To address this challenging problem, we propose a novel multi-task learning method, which uses feature interaction to explore the relationship between Alzheimer’s disease diagnosis and mini-mental state examination score prediction. In our proposed method, features from each task branch are firstly decoupled into candidate and non-candidate parts for interaction. Then, we propose feature sharing module to obtain shared features from candidate features and return shared features to task branches, which can promote the learning of each task. We validate the effectiveness of our proposed method on multiple datasets. In Alzheimer’s disease neuroimaging initiative 1 dataset, the accuracy in diagnosis task and the root mean squared error in prediction task of our proposed method is 87.86% and 2.5, respectively. Experimental results show that our proposed method outperforms most state-of-the-art methods. Our proposed method enables accurate Alzheimer’s disease diagnosis and mini-mental state examination score prediction. Therefore, it can be used as a reference for the clinical diagnosis of Alzheimer’s disease, and can also help doctors and patients track disease progression in a timely manner.

Open Access Issue
AI-Based Advanced Approaches and Dry Eye Disease Detection Based on Multi-Source Evidence: Cases, Applications, Issues, and Future Directions
Big Data Mining and Analytics 2024, 7(2): 445-484
Published: 22 April 2024
Abstract PDF (7.1 MB) Collect
Downloads:187

This study explores the potential of Artificial Intelligence (AI) in early screening and prognosis of Dry Eye Disease (DED), aiming to enhance the accuracy of therapeutic approaches for eye-care practitioners. Despite the promising opportunities, challenges such as diverse diagnostic evidence, complex etiology, and interdisciplinary knowledge integration impede the interpretability, reliability, and applicability of AI-based DED detection methods. The research conducts a comprehensive review of datasets, diagnostic evidence, and standards, as well as advanced algorithms in AI-based DED detection over the past five years. The DED diagnostic methods are categorized into three groups based on their relationship with AI techniques: (1) those with ground truth and/or comparable standards, (2) potential AI-based methods with significant advantages, and (3) supplementary methods for AI-based DED detection. The study proposes suggested DED detection standards, the combination of multiple diagnostic evidence, and future research directions to guide further investigations. Ultimately, the research contributes to the advancement of ophthalmic disease detection by providing insights into knowledge foundations, advanced methods, challenges, and potential future perspectives, emphasizing the significant role of AI in both academic and practical aspects of ophthalmology.

Open Access Issue
Continuous and Discrete Similarity Coefficient for Identifying Essential Proteins Using Gene Expression Data
Big Data Mining and Analytics 2023, 6(2): 185-200
Published: 26 January 2023
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Downloads:58

Essential proteins play a vital role in biological processes, and the combination of gene expression profiles with Protein-Protein Interaction (PPI) networks can improve the identification of essential proteins. However, gene expression data are prone to significant fluctuations due to noise interference in topological networks. In this work, we discretized gene expression data and used the discrete similarities of the gene expression spectrum to eliminate noise fluctuation. We then proposed the Pearson Jaccard coefficient (PJC) that consisted of continuous and discrete similarities in the gene expression data. Using the graph theory as the basis, we fused the newly proposed similarity coefficient with the existing network topology prediction algorithm at each protein node to recognize essential proteins. This strategy exhibited a high recognition rate and good specificity. We validated the new similarity coefficient PJC on PPI datasets of Krogan, Gavin, and DIP of yeast species and evaluated the results by receiver operating characteristic analysis, jackknife analysis, top analysis, and accuracy analysis. Compared with that of node-based network topology centrality and fusion biological information centrality methods, the new similarity coefficient PJC showed a significantly improved prediction performance for essential proteins in DC, IC, Eigenvector centrality, subgraph centrality, betweenness centrality, closeness centrality, NC, PeC, and WDC. We also compared the PJC coefficient with other methods using the NF-PIN algorithm, which predicts proteins by constructing active PPI networks through dynamic gene expression. The experimental results proved that our newly proposed similarity coefficient PJC has superior advantages in predicting essential proteins.

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