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Modelling infectious disease spreading is crucial for planning effective containment measures, as shown in the COVID-19 pandemic. The effectiveness of planned measures can also be measured regarding saved lives and economic resources. Therefore, introducing methods able to model the evolution and the impact of measures, as well as planning tailored and updated measures, is a crucial step. Existing models for spreading modelling belong to two main classes: (i) compartmental models based on ordinary differential equations and (ii) contact-based models based on a contact structure using an underlining layer to simulate diffusion. Nevertheless, none of these methods can leverage the high computational power of artificial intelligence and deep learning. We propose a novel framework for simulating and analysing disease progression for these methods. The framework is based on the multiscale simulation of the spreading based on using a multiscale contact model built on top of a diffusion model customised by the user. The evolution of the spreading, modelled as a graph with attributed nodes, is then mapped into a latent space through graph embedding. Finally, deep learning models are used in the latent space to analyse and forecast methods without running expensive computational simulations of the contact-based model.