Dataset Information

Multimodal deep learning models for early detection of Alzheimer's disease stage.

ABSTRACT: Most current Alzheimer's disease (AD) and mild cognitive disorders (MCI) studies use single data modality to make predictions such as AD stages. The fusion of multiple data modalities can provide a holistic view of AD staging analysis. Thus, we use deep learning (DL) to integrally analyze imaging (magnetic resonance imaging (MRI)), genetic (single nucleotide polymorphisms (SNPs)), and clinical test data to classify patients into AD, MCI, and controls (CN). We use stacked denoising auto-encoders to extract features from clinical and genetic data, and use 3D-convolutional neural networks (CNNs) for imaging data. We also develop a novel data interpretation method to identify top-performing features learned by the deep-models with clustering and perturbation analysis. Using Alzheimer's disease neuroimaging initiative (ADNI) dataset, we demonstrate that deep models outperform shallow models, including support vector machines, decision trees, random forests, and k-nearest neighbors. In addition, we demonstrate that integrating multi-modality data outperforms single modality models in terms of accuracy, precision, recall, and meanF1 scores. Our models have identified hippocampus, amygdala brain areas, and the Rey Auditory Verbal Learning Test (RAVLT) as top distinguished features, which are consistent with the known AD literature.

SUBMITTER: Venugopalan J

PROVIDER: S-EPMC7864942 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Multimodal deep learning models for early detection of Alzheimer's disease stage.

Venugopalan Janani J Tong Li L Hassanzadeh Hamid Reza HR Wang May D MD

Scientific reports 20210205 1

Most current Alzheimer's disease (AD) and mild cognitive disorders (MCI) studies use single data modality to make predictions such as AD stages. The fusion of multiple data modalities can provide a holistic view of AD staging analysis. Thus, we use deep learning (DL) to integrally analyze imaging (magnetic resonance imaging (MRI)), genetic (single nucleotide polymorphisms (SNPs)), and clinical test data to classify patients into AD, MCI, and controls (CN). We use stacked denoising auto-encoders ...[more]

PMID: 33547343

Similar Datasets

Project description:BackgroundIdentifying individuals with mild cognitive impairment (MCI) at risk of progressing to Alzheimer's disease (AD) provides a unique opportunity for early interventions. Therefore, accurate and long-term prediction of the conversion from MCI to AD is desired but, to date, remains challenging. Here, we developed an interpretable deep learning model featuring a novel design that incorporates interaction effects and multimodality to improve the prediction accuracy and horizon for MCI-to-AD progression.MethodsThis multi-center, multi-cohort retrospective study collected structural magnetic resonance imaging (sMRI), clinical assessments, and genetic polymorphism data of 252 patients with MCI at baseline from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. Our deep learning model was cross-validated on the ADNI-1 and ADNI-2/GO cohorts and further generalized in the ongoing ADNI-3 cohort. We evaluated the model performance using the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, and F1 score.ResultsOn the cross-validation set, our model achieved superior results for predicting MCI conversion within 4 years (AUC, 0.962; accuracy, 92.92%; sensitivity, 88.89%; specificity, 95.33%) compared to all existing studies. In the independent test, our model exhibited consistent performance with an AUC of 0.939 and an accuracy of 92.86%. Integrating interaction effects and multimodal data into the model significantly increased prediction accuracy by 4.76% (P = 0.01) and 4.29% (P = 0.03), respectively. Furthermore, our model demonstrated robustness to inter-center and inter-scanner variability, while generating interpretable predictions by quantifying the contribution of multimodal biomarkers.ConclusionsThe proposed deep learning model presents a novel perspective by combining interaction effects and multimodality, leading to more accurate and longer-term predictions of AD progression, which promises to improve pre-dementia patient care.

Project description:BackgroundEnd stage renal disease (ESRD) describes the most severe stage of chronic kidney disease (CKD), when patients need dialysis or renal transplant. There is often a delay in recognizing, diagnosing, and treating the various etiologies of CKD. The objective of the present study was to employ machine learning algorithms to develop a prediction model for progression to ESRD based on a large-scale multidimensional database.MethodsThis study analyzed 10,000,000 medical insurance claims from 550,000 patient records using a commercial health insurance database. Inclusion criteria were patients over the age of 18 diagnosed with CKD Stages 1-4. We compiled 240 predictor candidates, divided into six feature groups: demographics, chronic conditions, diagnosis and procedure features, medication features, medical costs, and episode counts. We used a feature embedding method based on implementation of the Word2Vec algorithm to further capture temporal information for the three main components of the data: diagnosis, procedures, and medications. For the analysis, we used the gradient boosting tree algorithm (XGBoost implementation).ResultsThe C-statistic for the model was 0.93 [(0.916-0.943) 95% confidence interval], with a sensitivity of 0.715 and specificity of 0.958. Positive Predictive Value (PPV) was 0.517, and Negative Predictive Value (NPV) was 0.981. For the top 1 percentile of patients identified by our model, the PPV was 1.0. In addition, for the top 5 percentile of patients identified by our model, the PPV was 0.71. All the results above were tested on the test data only, and the threshold used to obtain these results was 0.1. Notable features contributing to the model were chronic heart and ischemic heart disease as a comorbidity, patient age, and number of hypertensive crisis events.ConclusionsWhen a patient is approaching the threshold of ESRD risk, a warning message can be sent electronically to the physician, who will initiate a referral for a nephrology consultation to ensure an investigation to hasten the establishment of a diagnosis and initiate management and therapy when appropriate.

Project description:BACKGROUND: High-throughput profiling of human tissues typically yield as results the gene lists comprised of a mix of relevant molecular entities with multiple false positives that obstruct the translation of such results into mechanistic hypotheses. From general probabilistic considerations, gene lists distilled for the mechanistically relevant components can be far more useful for subsequent experimental design or data interpretation. RESULTS: The input candidate gene lists were processed into different tiers of evidence consistency established by enrichment analysis across subsets of the same experiments and across different experiments and platforms. The cut-offs were established empirically through ontological and semantic enrichment; resultant shortened gene list was re-expanded by Ingenuity Pathway Assistant tool. The resulting sub-networks provided the basis for generating mechanistic hypotheses that were partially validated by literature search. This approach differs from previous consistency-based studies in that the cut-off on the Receiver Operating Characteristic of the true-false separation process is optimized by flexible selection of the consistency building procedure. The gene list distilled by this analytic technique and its network representation were termed Compact Disease Model (CDM). Here we present the CDM signature for the study of early-stage Alzheimer's disease. The integrated analysis of this gene signature allowed us to identify the protein traffic vesicles as prominent players in the pathogenesis of Alzheimer's. Considering the distances and complexity of protein trafficking in neurons, it is plausible that spontaneous protein misfolding along with a shortage of growth stimulation result in neurodegeneration. Several potentially overlapping scenarios of early-stage Alzheimer pathogenesis have been discussed, with an emphasis on the protective effects of AT-1 mediated antihypertensive response on cytoskeleton remodeling, along with neuronal activation of oncogenes, luteinizing hormone signaling and insulin-related growth regulation, forming a pleiotropic model of its early stages. Alignment with emerging literature confirmed many predictions derived from early-stage Alzheimer's disease' CDM. CONCLUSIONS: A flexible approach for high-throughput data analysis, the Compact Disease Model generation, allows extraction of meaningful, mechanism-centered gene sets compatible with instant translation of the results into testable hypotheses.

Project description:ObjectivesTo employ different automated convolutional neural network (CNN)-based transfer learning (TL) methods for both binary and multiclass classification of Alzheimer's disease (AD) using brain MRI.MethodsHerein, we applied three popular pre-trained CNN models (ResNet101, Xception, and InceptionV3) using a fine-tuned approach of TL on 3D T1-weighted brain MRI from a subset of ADNI dataset (n = 305 subjects). To evaluate power of TL, the aforementioned networks were also trained from scratch for performance comparison. Initially, Unet network segmentedthe MRI scans into characteristic components of gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). The proposed networks were trained and tested over the pre-processed and augmented segmented and whole images for both binary (NC/AD + progressive mild cognitive impairment (pMCI)+stable MCI (sMCI)) and 4-class (AD/pMCI/sMCI/NC) classification. Also, two independent test sets from the OASIS (n = 30) and AIBL (n = 60) datasets were used to externally assess the performance of the proposed algorithms.ResultsThe proposed TL-based CNN models achieved better performance compared to the training CNN models from scratch. On the ADNI test set, InceptionV3-TL achieved the highest accuracy of 93.75% and AUC of 92.0% for binary classification, as well as the highest accuracy of 93.75% and AUC of 96.0% for multiclass classification of AD on the whole images. On the OASIS test set, InceptionV3-TL outperformed two other models by achieving 93.33% accuracy with 93.0% AUC in binary classification of AD on the whole images. On the AIBL test set, InceptionV3-TL also outperformed two other models in both binary and multiclass classification tasks on the whole MR images and achieved accuracy/AUC of 93.33%/95.0% and 90.0%/93.0%, respectively. The GM segment as input provided the highest performance in both binary and multiclass classification of AD, as compared to the WM and CSF segments.ConclusionThis study demonstrates the potential of applying deep TL approach for automated detection and classification of AD using brain MRI with high accuracy and robustness across internal and external test data, suggesting that these models can possibly be used as a supportive tool to assist clinicians in creating objective opinion and correct diagnosis.Advances in knowledgeWe used CNN-based TL approaches and the augmentation techniques to overcome the insufficient data problem. Our study provides evidence that deep TL algorithms can be used for both binary and multiclass classification of AD with high accuracy.

Dataset Information

Multimodal deep learning models for early detection of Alzheimer's disease stage.

Publications

Multimodal deep learning models for early detection of Alzheimer's disease stage.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets