Methods and systems for event prediction include encoding a multivariate time series and a multi-type event sequence using respective transformers and an aggregation network to generate a feature vector. Event prediction is performed using the feature vector to identify a next event to occur within a system. A corrective action is performed responsive to the next event to prevent or mitigate an effect of the next event. The predicted next event can be used in a healthcare context to support decision making by medical professionals with respect to the treatment of a patient. The encoding may include machine learning models to implement the transformers and the aggregation network using deep learning.