Our understanding of the changes in functional brain organization in autism is 17 hampered by the extensive heterogeneity that characterizes this neurodevelopmental disorder. 18 Data driven clustering offers a straightforward way to decompose this heterogeneity into 19 subtypes of distinguishable connectivity types and promises an unbiased framework to 20 investigate behavioural symptoms and causative genetic factors. Yet the robustness and 21 generalizability of these imaging subtypes is unknown. Here, we show that unsupervised 22 functional connectivity subtypes are moderately associated with the clinical diagnosis of autism, 23 and that these associations generalize to independent replication data. We found that subtypes 24 identified robust patterns of functional connectivity, but that a discrete assignment of individuals 25 to these subtypes was not supported by the data. Our results support the use of data driven 26 subtyping as a data dimensionality reduction technique, rather than to establish clinical 27 categories. 28 29 Introduction 30 Autism spectrum disorder (ASD) is a prevalent neurodevelopmental condition of impaired social 31 communication and restrictive behaviour, diagnosed in about 1% of children (Lai et al., 2014; Baio 32 et al. , 2018), that is associated with extensive heterogeneity of behavioural symptoms and neuro-33 biological endophenotypes (Jacob et al., 2019; Lombardo et al., 2019). Functional magnetic reso-34 nance imaging (fMRI) has emerged as a promising technology to identify potential biomarkers of 35 functional connectivity (FC) in ASD and other psychiatric disorders (Castellanos et al., 2013). ever, efforts to characterize the functional brain organization in ASD have so far largely focused 37 on case-control comparisons, thus ignoring the presumed heterogeneity of FC alterations (Nunes 38 et al., 2019; Hahamy et al., 2015). 39 Data driven cluster analysis has long been proposed as a solution to decompose the hetero-40 1 of 23 Manuscript submitted to eLife geneity of behavioural symptoms in ASD into distinct subtypes (Eaves et al., 1994; Beglinger and 41 Smith, 2001), but these subtypes have proven difficult to distinguish in clinical practice (Lord et al., 42 2012) and were recently abandoned in favour of the broader concept of an autism spectrum (Amer-43 ican Psychiatric Association. and DSM-5 Task Force., 2013). The lack of progress towards repro-44 ducible, brain based biomarkers of ASD (Lombardo et al., 2019) has renewed interest in clustering 45 methods to decompose the heterogeneity of brain alterations into distinct subtypes that are hy-46 pothesized to underlie the multitude of behavioural symptoms. 48 neurobiological heterogeneity in ASD and relate it to behavioural symptoms (Hong et al., 2019). 49 Early work on subcortical volume alterations in ASD distinguished four subtypes, but did not find 50 significant differences of behavioural symptoms between them (Hrdlicka et al., 2005). A more re-51 cent multi-modal analysis distinguished th...