This paper describes a technology for predicting the aggravation of diabetic nephropathy from electronic health record (EHR). For the prediction, we used features extracted from event sequence of lab tests in EHR with a stacked convolutional autoencoder which can extract both local and global temporal information. The extracted features can be interpreted as similarities to a small number of typical sequences of lab tests, that may help us to understand the disease courses and to provide detailed health guidance. In our experiments on real-world EHRs, we confirmed that our approach performed better than baseline methods and that the extracted features were promising for understanding the disease.