The advancement of Electronic Health Records (EHRs) and machine learning have enabled a data-driven and personalised approach to healthcare. One step in this direction is to uncover patient sub-types with similar disease trajectories in a heterogeneous population. This is especially important in the context of mechanical ventilation in intensive care, where mortality is high and there is no consensus on treatment. In this work, we present a new approach to clustering mechanical ventilation episodes, using a multi-task combination of supervised, self-supervised and unsupervised learning techniques. Our dynamic clustering assignment is explicitly guided to reflect the phenotype, trajectory and outcomes of the patient. Experimentation on a real-world dataset is encouraging, and we hope that we could someday translate this into actionable insights in guiding future clinical research.