Disease progression modeling (DPM) of Alzheimer's disease (AD) aims at revealing long term pathological trajectories from short term clinical data. Along with the ability of providing a data-driven description of the natural evolution of the pathology, DPM has the potential of representing a valuable clinical instrument for automatic diagnosis, by explicitly describing the biomarker transition from normal to pathological stages along the disease time axis. In this work we reformulated DPM within a probabilistic setting to quantify the diagnostic uncertainty of individual disease severity in an hypothetical clinical scenario, with respect to missing measurements, biomarkers, and follow-up information. We show that the staging provided by the model on 582 amyloid positive testing individuals has high face validity with respect to the clinical diagnosis. Using follow-up measurements largely reduces the prediction uncertainties, while the transition from normal to pathological stages is mostly associated with the increase of brain hypo-metabolism, temporal atrophy, and worsening of clinical scores. The proposed formulation of DPM provides a statistical reference for the accurate probabilistic assessment of the pathological stage of de-novo individuals, and represents a valuable instrument for quantifying the variability and the diagnostic value of biomarkers across disease stages.