An interpretable generative multimodal neuroimaging-genomics framework for decoding Alzheimer’s disease

<i>Objective.</i>Alzheimer's disease (AD) is the most prevalent form of dementia worldwide, encompassing a prodromal stage known as mild cognitive impairment (MCI), where patients may either progress to AD or remain stable. The objective of the work was to capture structural and functional modulations of brain structure and function relying on multimodal MRI data and single nucleotide polymorphisms, also in case of missing views, with the twofold goal of classifying AD patients versus healthy controls and detecting MCI converters.<i>Approach.</i>We propose a multimodal deep learning (DL)-based classification framework where a generative module employing cycle generative adversarial networks was introduced in the latent space for imputing missing data (a common issue of multimodal approaches). Explainable AI method was then used to extract input features' relevance allowing for post-hoc validation and enhancing the interpretability of the learned representations.<i>Main results.</i>Experimental results on two tasks, AD detection and MCI conversion, showed that our framework reached competitive performance in the state-of-the-art with an accuracy of0.926±0.02(CI [0.90, 0.95]) and0.711±0.01(CI [0.70, 0.72]) in the two tasks, respectively. The interpretability analysis revealed gray matter modulations in cortical and subcortical brain areas typically associated with AD. Moreover, impairments in sensory-motor and visual resting state networks along the disease continuum, as well as genetic mutations defining biological processes linked to endocytosis, amyloid-beta, and cholesterol, were identified.<i>Significance.</i>Our integrative and interpretable DL approach shows promising performance for AD detection and MCI prediction while shedding light on important biological insights.