Deep Learning with Neuroimaging and Genomics in Alzheimer's Disease.
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ABSTRACT:
SUBMITTER: Lin E
PROVIDER: S-EPMC8347529 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Deep learning, a state-of-the-art machine learning approach, has shown outstanding performance over traditional machine learning in identifying intricate structures in complex high-dimensional data, especially in the domain of computer vision. The application of deep learning to early detection and automated classification of Alzheimer's disease (AD) has recently gained considerable attention, as rapid progress in neuroimaging techniques has generated large-scale multimodal neuroimaging data. A systematic review of publications using deep learning approaches and neuroimaging data for diagnostic classification of AD was performed. A PubMed and Google Scholar search was used to identify deep learning papers on AD published between January 2013 and July 2018. These papers were reviewed, evaluated, and classified by algorithm and neuroimaging type, and the findings were summarized. Of 16 studies meeting full inclusion criteria, 4 used a combination of deep learning and traditional machine learning approaches, and 12 used only deep learning approaches. The combination of traditional machine learning for classification and stacked auto-encoder (SAE) for feature selection produced accuracies of up to 98.8% for AD classification and 83.7% for prediction of conversion from mild cognitive impairment (MCI), a prodromal stage of AD, to AD. Deep learning approaches, such as convolutional neural network (CNN) or recurrent neural network (RNN), that use neuroimaging data without pre-processing for feature selection have yielded accuracies of up to 96.0% for AD classification and 84.2% for MCI conversion prediction. The best classification performance was obtained when multimodal neuroimaging and fluid biomarkers were combined. Deep learning approaches continue to improve in performance and appear to hold promise for diagnostic classification of AD using multimodal neuroimaging data. AD research that uses deep learning is still evolving, improving performance by incorporating additional hybrid data types, such as-omics data, increasing transparency with explainable approaches that add knowledge of specific disease-related features and mechanisms.
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Project description:Abnormal tau inclusions are hallmarks of Alzheimer's disease and predictors of clinical decline. Several tau PET tracers are available for neurodegenerative disease research, opening avenues for molecular diagnosis in vivo. However, few have been approved for clinical use. Understanding the neurobiological basis of PET signal validation remains problematic because it requires a large-scale, voxel-to-voxel correlation between PET and (immuno) histological signals. Large dimensionality of whole human brains, tissue deformation impacting co-registration, and computing requirements to process terabytes of information preclude proper validation. We developed a computational pipeline to identify and segment particles of interest in billion-pixel digital pathology images to generate quantitative, 3D density maps. The proposed convolutional neural network for immunohistochemistry samples, IHCNet, is at the pipeline's core. We have successfully processed and immunostained over 500 slides from two whole human brains with three phospho-tau antibodies (AT100, AT8, and MC1), spanning several terabytes of images. Our artificial neural network estimated tau inclusion from brain images, which performs with ROC AUC of 0.87, 0.85, and 0.91 for AT100, AT8, and MC1, respectively. Introspection studies further assessed the ability of our trained model to learn tau-related features. We present an end-to-end pipeline to create terabytes-large 3D tau inclusion density maps co-registered to MRI as a means to facilitate validation of PET tracers.
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Project description:Alzheimer's disease (AD) is a remarkable challenge for healthcare in the 21st century. Since 2017, deep learning models with transfer learning approaches have been gaining recognition in AD detection, and progression prediction by using neuroimaging biomarkers. This paper presents a systematic review of the current state of early AD detection by using deep learning models with transfer learning and neuroimaging biomarkers. Five databases were used and the results before screening report 215 studies published between 2010 and 2020. After screening, 13 studies met the inclusion criteria. We noted that the maximum accuracy achieved to date for AD classification is 98.20% by using the combination of 3D convolutional networks and local transfer learning, and that for the prognostic prediction of AD is 87.78% by using pre-trained 3D convolutional network-based architectures. The results show that transfer learning helps researchers in developing a more accurate system for the early diagnosis of AD. However, there is a need to consider some points in future research, such as improving the accuracy of the prognostic prediction of AD, exploring additional biomarkers such as tau-PET and amyloid-PET to understand highly discriminative feature representation to separate similar brain patterns, managing the size of the datasets due to the limited availability.
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Project description:ObjectivesAlzheimer's disease (AD) is the most prevalent neurodegenerative disorder and the most common form of dementia in the elderly. Certain genes have been identified as important clinical risk factors for AD, and technological advances in genomic research, such as genome-wide association studies (GWAS), allow for analysis of polymorphisms and have been widely applied to studies of AD. However, shortcomings of GWAS include sensitivity to sample size and hereditary deletions, which result in low classification and predictive accuracy. Therefore, this paper proposes a novel deep-learning genomics approach and applies it to multitasking classification of AD progression, with the goal of identifying novel genetic biomarkers overlooked by traditional GWAS analysis.MethodsIn this study, we selected genotype data from 1461 subjects enrolled in the Alzheimer's Disease Neuroimaging Initiative, including 622 AD, 473 mild cognitive impairment (MCI), and 366 healthy control (HC) subjects. The proposed deep-learning genomics (DLG) approach consists of three steps: quality control, coding of single-nucleotide polymorphisms, and classification. The ResNet framework was used for the DLG model, and the results were compared with classifications by simple convolutional neural network structure. All data were randomly assigned to one training/validation group and one test group at a ratio of 9 : 1. And fivefold cross-validation was used.ResultsWe compared classification results from the DLG model to those from traditional GWAS analysis among the three groups. For the AD and HC groups, the accuracy, sensitivity, and specificity of classification were, respectively, 98.78 ± 1.50%, 98.39% ± 2.50%, and 99.44% ± 1.11% using the DLG model, while 71.38% ± 0.63%, 63.13% ± 2.87%, and 85.59% ± 6.66% using traditional GWAS. Similar results were obtained from the other two intergroup classifications.ConclusionThe DLG model can achieve higher accuracy and sensitivity when applied to progression of AD. More importantly, we discovered several novel genetic biomarkers of AD progression, including rs6311 and rs6313 in HTR2A, rs1354269 in NAV2, and rs690705 in RFC3. The roles of these novel loci in AD should be explored in future research.
| S-EPMC8298161 | biostudies-literature
Project description:Alzheimer's disease (AD) is mainly a neurodegenerative sickness. The primary characteristics are neuronal atrophy, amyloid deposition, and cognitive, behavioral, and psychiatric disorders. Numerous machine learning (ML) algorithms have been investigated and applied to AD identification over the past decades, emphasizing the subtle prodromal stage of mild cognitive impairment (MCI) to assess critical features that distinguish the disease's early manifestation and instruction for early detection and treatment. Identifying early MCI (EMCI) remains challenging due to the difficulty in distinguishing patients with cognitive normality from those with MCI. As a result, most classification algorithms for these two groups perform poorly. This paper proposes a hybrid Deep Learning Approach for the early detection of Alzheimer's disease. A method for early AD detection using multimodal imaging and Convolutional Neural Network with the Long Short-term memory algorithm combines magnetic resonance imaging (MRI), positron emission tomography (PET), and standard neuropsychological test scores. The proposed methodology updates the learning weights, and Adam's optimization is used to increase accuracy. The system has an unparalleled accuracy of 98.5% in classifying cognitively normal controls from EMCI. These results imply that deep neural networks may be trained to automatically discover imaging biomarkers indicative of AD and use them to identify the illness accurately.
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Project description:Deep learning offers a powerful approach for analyzing hippocampal changes in Alzheimer's disease (AD) without relying on handcrafted features. Nevertheless, an input format needs to be selected to pass the image information to the neural network, which has wide ramifications for the analysis, but has not been evaluated yet. We compare five hippocampal representations (and their respective tailored network architectures) that span from raw images to geometric representations like meshes and point clouds. We performed a thorough evaluation for the prediction of AD diagnosis and time-to-dementia prediction with experiments on an independent test dataset. In addition, we evaluated the ease of interpretability for each representation-network pair. Our results show that choosing an appropriate representation of the hippocampus for predicting Alzheimer's disease with deep learning is crucial, since it impacts performance and ease of interpretation.
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Project description:Deep learning methods have recently made notable advances in the tasks of classification and representation learning. These tasks are important for brain imaging and neuroscience discovery, making the methods attractive for porting to a neuroimager's toolbox. Success of these methods is, in part, explained by the flexibility of deep learning models. However, this flexibility makes the process of porting to new areas a difficult parameter optimization problem. In this work we demonstrate our results (and feasible parameter ranges) in application of deep learning methods to structural and functional brain imaging data. These methods include deep belief networks and their building block the restricted Boltzmann machine. We also describe a novel constraint-based approach to visualizing high dimensional data. We use it to analyze the effect of parameter choices on data transformations. Our results show that deep learning methods are able to learn physiologically important representations and detect latent relations in neuroimaging data.
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Project description:BackgroundAlzheimer's is a degenerative dementing disorder that starts with a mild memory impairment and progresses to a total loss of mental and physical faculties. The sooner the diagnosis is made, the better for the patient, as preventive actions and treatment can be started. Although tests such as the Mini-Mental State Tests Examination are usually used for early identification, diagnosis relies on magnetic resonance imaging (MRI) brain analysis.MethodsPublic initiatives such as the OASIS (Open Access Series of Imaging Studies) collection provide neuroimaging datasets openly available for research purposes. In this work, a new method based on deep learning and image processing techniques for MRI-based Alzheimer's diagnosis is proposed and compared with previous literature works.ResultsOur method achieves a balance accuracy (BAC) up to 0.93 for image-based automated diagnosis of the disease, and a BAC of 0.88 for the establishment of the disease stage (healthy tissue, very mild and severe stage).ConclusionsResults obtained surpassed the state-of-the-art proposals using the OASIS collection. This demonstrates that deep learning-based strategies are an effective tool for building a robust solution for Alzheimer's-assisted diagnosis based on MRI data.
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Project description:With increasing life expectancy in developed countries, the incidence of Alzheimer's disease (AD) and its socioeconomic impact are growing. Increasing knowledge of the mechanisms of AD facilitates the development of treatment strategies aimed at slowing down or preventing neuronal death. AD treatment trials using clinical outcome measures require long observation times and large patient samples. There is increasing evidence that neuroimaging and cerebrospinal fluid and blood biomarkers may provide information that may reduce sample sizes and observation periods. The Alzheimer's Disease Neuroimaging Initiative will help identify clinical, neuroimaging, and biomarker outcome measures that provide the highest power for measurement of longitudinal changes and for prediction of transitions.
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Project description:The application of deep learning (DL) models to neuroimaging data poses several challenges, due to the high dimensionality, low sample size, and complex temporo-spatial dependency structure of these data. Even further, DL models often act as black boxes, impeding insight into the association of cognitive state and brain activity. To approach these challenges, we introduce the DeepLight framework, which utilizes long short-term memory (LSTM) based DL models to analyze whole-brain functional Magnetic Resonance Imaging (fMRI) data. To decode a cognitive state (e.g., seeing the image of a house), DeepLight separates an fMRI volume into a sequence of axial brain slices, which is then sequentially processed by an LSTM. To maintain interpretability, DeepLight adapts the layer-wise relevance propagation (LRP) technique. Thereby, decomposing its decoding decision into the contributions of the single input voxels to this decision. Importantly, the decomposition is performed on the level of single fMRI volumes, enabling DeepLight to study the associations between cognitive state and brain activity on several levels of data granularity, from the level of the group down to the level of single time points. To demonstrate the versatility of DeepLight, we apply it to a large fMRI dataset of the Human Connectome Project. We show that DeepLight outperforms conventional approaches of uni- and multivariate fMRI analysis in decoding the cognitive states and in identifying the physiologically appropriate brain regions associated with these states. We further demonstrate DeepLight's ability to study the fine-grained temporo-spatial variability of brain activity over sequences of single fMRI samples.
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