Deep learning reveals pathology-confirmed neuroimaging signatures in Alzheimer’s, vascular and Lewy body dementias

Concurrent neurodegenerative and vascular pathologies pose a diagnostic challenge in the clinical setting, with histopathology remaining the definitive modality for dementia-type diagnosis. To address this clinical challenge, we introduce a neuropathology-based, data-driven, multi-label deep-learning framework to identify and quantify in vivo biomarkers for Alzheimer's disease (AD), vascular dementia (VD) and Lewy body dementia (LBD) using antemortem T1-weighted MRI scans of 423 demented and 361 control participants from National Alzheimer's Coordinating Center and Alzheimer's Disease Neuroimaging Initiative datasets. Based on the best-performing deep-learning model, explainable heat maps were extracted to visualize disease patterns, and the novel Deep Signature of Pathology Atrophy REcognition (DeepSPARE) indices were developed, where a higher DeepSPARE score indicates more brain alterations associated with that specific pathology. A substantial discrepancy in clinical and neuropathological diagnosis was observed in the demented patients: 71% had more than one pathology, but 67% were diagnosed clinically as AD only. Based on these neuropathological diagnoses and leveraging cross-validation principles, the deep-learning model achieved the best performance, with a balanced accuracy of 0.844, 0.839 and 0.623 for AD, VD and LBD, respectively, and was used to generate the explainable deep-learning heat maps and DeepSPARE indices. The explainable deep-learning heat maps revealed distinct neuroimaging brain alteration patterns for each pathology: (i) the AD heat map highlighted bilateral hippocampal regions; (ii) the VD heat map emphasized white matter regions; and (iii) the LBD heat map exposed occipital alterations. The DeepSPARE indices were validated by examining their associations with cognitive testing and neuropathological and neuroimaging measures using linear mixed-effects models. The DeepSPARE-AD index was associated with Mini-Mental State Examination, the Trail Making Test B, memory, hippocampal volume, Braak stages, Consortium to Establish a Registry for Alzheimer's Disease (CERAD) scores and Thal phases false-discovery rate (FDR)-adjusted P < 0.05. The DeepSPARE-VD index was associated with white matter hyperintensity volume and cerebral amyloid angiopathy (FDR-adjusted P < 0.001), and the DeepSPARE-LBD index was associated with Lewy body stages (FDR-adjusted P < 0.05). The findings were replicated in an out-of-sample Alzheimer's Disease Neuroimaging Initiative dataset by testing associations with cognitive, imaging, plasma and CSF measures. CSF and plasma tau phosphorylated at threonine-181 (pTau181) were significantly associated with DeepSPARE-AD in the AD and mild cognitive impairment amyloid-β positive (AD/MCIΑβ+) group (FDR-adjusted P < 0.001), and CSF α-synuclein was associated solely with DeepSPARE-LBD (FDR-adjusted P = 0.036). Overall, these findings demonstrate the advantages of our innovative deep-learning framework in detecting antemortem neuroimaging signatures linked to different pathologies. The newly deep-learning-derived DeepSPARE indices are precise, pathology-sensitive and single-valued non-invasive neuroimaging metrics, bridging the traditional widely available in vivo T1 imaging with histopathology.