We propose a novel framework to estimate intensive care unit patients' health risk continuously with anomaly-encoded patient data. This framework consists of two modules. In the first module, we use Gaussian process models to learn change trend and day-night circulation in temporal patient data and annotate abnormal data. Such models provide dynamically adaptable bedside patient monitoring instead of conventional threshold-based monitoring. In the second module, we use the abnormal data together with the learned Gaussian models to estimate patients' risk level by predicting their in-hospital mortality and remaining length of stay in ICU ward. We show that prediction models with anomaly-encoded data have better performance than those with raw patient measurements, and they are comparable with state-of-art prediction models.