Machine learning analysis of Autism phenotype data supports a four-dimensional continuum with three overlapping subtypes

Autism Spectrum Disorder (ASD) is a heterogeneous neurodevelopmental condition defined by differences in social communication and restricted, repetitive behaviours. As diagnostic criteria have broadened, ASD is now recognised across a wider range of individuals, raising key questions about its structure: does ASD have discrete sub-types, or is it better conceptualised as a continuous, possibly multidimensional, condition? We aim to explore whether a multidimensional continuum model more accurately captures the variability within ASD. We analysed a large SPARK phenotypic dataset of medical history and diagnostic surveys (background history, SCQ, RBS-R; n=36,710 individuals). We apply and compare two traditional statistical approaches, Factor Analysis and Gaussian Mixture Models, with a modern machine learning technique, the Variational Autoencoder (VAE). VAEs reconstructed unseen test data with ~4-fold better accuracy than Factor Analysis, and ~8-fold better accuracy than Gaussian Mixture Models. We identified four stable latent factors across 100 independently trained VAEs. These four dimensions provide an individual behavioural profile that can be visualized using radar-plots, offering a compact way to compare profiles at the person level. Through further analysis, we found evidence for 3 overlapping clusters or subtypes of ASD identified within the 4D latent space. This work aims to inform new ways of modelling ASD using a VAE that will be able to discern between a continuum or a clustered output and that go beyond binary diagnosis, instead reflecting the complex range of trait profiles, with implications for personalised diagnosis and intervention.