The present invention provides methods, systems, and computer programs for inferring a patient's clinical status in the course of treatment. The method includes the steps of accessing a patient's data, such as data collected prior, during, and/or after the treatment, and identifying from the patient's data abnormal events occurring in the course of the treatment. The abnormal events are generally identified by applying a scoring system for inferring a patient's clinical status. This scoring system includes a plurality of scoring schemes applicable at different times with respect to at least one milestone event.