Dataset Information

Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies.

ABSTRACT: Deep neural networks (DNNs) capture complex relationships among variables, however, because they require copious samples, their potential has yet to be fully tapped for understanding relationships between gene expression and human phenotypes. Here we introduce an analysis framework, namely MD-AD (Multi-task Deep learning for Alzheimer's Disease neuropathology), which leverages an unexpected synergy between DNNs and multi-cohort settings. In these settings, true joint analysis can be stymied using conventional statistical methods, which require "harmonized" phenotypes and tend to capture cohort-level variations, obscuring subtler true disease signals. Instead, MD-AD incorporates related phenotypes sparsely measured across cohorts, and learns interactions between genes and phenotypes not discovered using linear models, identifying subtler signals than cohort-level variations which can be uniquely recapitulated in animal models and across tissues. We show that MD-AD exploits sex-specific relationships between microglial immune response and neuropathology, providing a nuanced context for the association between inflammatory genes and Alzheimer's Disease.

SUBMITTER: Beebe-Wang N

PROVIDER: S-EPMC8433314 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies.

Beebe-Wang Nicasia N Celik Safiye S Weinberger Ethan E Sturmfels Pascal P De Jager Philip L PL Mostafavi Sara S Lee Su-In SI

Nature communications 20210910 1

Deep neural networks (DNNs) capture complex relationships among variables, however, because they require copious samples, their potential has yet to be fully tapped for understanding relationships between gene expression and human phenotypes. Here we introduce an analysis framework, namely MD-AD (Multi-task Deep learning for Alzheimer's Disease neuropathology), which leverages an unexpected synergy between DNNs and multi-cohort settings. In these settings, true joint analysis can be stymied usin ...[more]

PMID: 34508095

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Project description:Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects millions of individuals worldwide, causing severe cognitive decline and memory impairment. The early and accurate diagnosis of AD is crucial for effective intervention and disease management. In recent years, deep learning techniques have shown promising results in medical image analysis, including AD diagnosis from neuroimaging data. However, the lack of interpretability in deep learning models hinders their adoption in clinical settings, where explainability is essential for gaining trust and acceptance from healthcare professionals. In this study, we propose an explainable AI (XAI)-based approach for the diagnosis of Alzheimer's disease, leveraging the power of deep transfer learning and ensemble modeling. The proposed framework aims to enhance the interpretability of deep learning models by incorporating XAI techniques, allowing clinicians to understand the decision-making process and providing valuable insights into disease diagnosis. By leveraging popular pre-trained convolutional neural networks (CNNs) such as VGG16, VGG19, DenseNet169, and DenseNet201, we conducted extensive experiments to evaluate their individual performances on a comprehensive dataset. The proposed ensembles, Ensemble-1 (VGG16 and VGG19) and Ensemble-2 (DenseNet169 and DenseNet201), demonstrated superior accuracy, precision, recall, and F1 scores compared to individual models, reaching up to 95%. In order to enhance interpretability and transparency in Alzheimer's diagnosis, we introduced a novel model achieving an impressive accuracy of 96%. This model incorporates explainable AI techniques, including saliency maps and grad-CAM (gradient-weighted class activation mapping). The integration of these techniques not only contributes to the model's exceptional accuracy but also provides clinicians and researchers with visual insights into the neural regions influencing the diagnosis. Our findings showcase the potential of combining deep transfer learning with explainable AI in the realm of Alzheimer's disease diagnosis, paving the way for more interpretable and clinically relevant AI models in healthcare.

Dataset Information

Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies.

Publications

Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer's disease neuropathologies.

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