Contrastive and Transfer Learning for Aligned Multimodal Neuroimaging Classification of Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) assessment remains challenging because behavioural instruments are partly observer-dependent and neuroimaging data are heterogeneous. This paper presents FAA (Fuse After Aligned), which is a multimodal classification framework that combines transfer learning for structural MRI (sMRI) representation learning with a contrastive objective for the pre-fusion alignment of sMRI and resting-state functional MRI-derived functional connectivity (FC) features. Evaluation was restricted to the single-site ABIDE-I New York University subset comprising 75 participants with ASD and 98 typically developing controls. Under the reported five-fold internal cross-validation protocol, FAA achieved a mean accuracy of 92.6% compared with 87.4% for naive fusion and 90.9% for the sMRI-only baseline. Ablation analyses indicate that adding the contrastive objective is associated with improved classification performance and that ResNet-18 outperforms the evaluated ViT-16 configurations in this small-sample setting. These findings support the methodological value of pre-fusion feature alignment within the evaluated cohort. The framework offers a robust, computationally efficient, and clinically viable approach for objective ASD diagnosis with strong potential for generalisation to multi-site neuroimaging applications.