BACKGROUND: Observational biomedical studies facilitate a new strategy for large-scale electronic health record (EHR) utilization to support precision medicine. However, data label inaccessibility is an increasingly important issue in clinical prediction, despite the use of synthetic and semisupervised learning from data. Little research has aimed to uncover the underlying graphical structure of EHRs. OBJECTIVE: A network-based generative adversarial semisupervised method is proposed. The objective is to train clinical prediction models on label-deficient EHRs to achieve comparable learning performance to supervised methods. METHODS: Three public data sets and one colorectal cancer data set gathered from the Second Affiliated Hospital of Zhejiang University were selected as benchmarks. The proposed models were trained on 5% to 25% labeled data and evaluated on classification metrics against conventional semisupervised and supervised methods. The data quality, model security, and memory scalability were also evaluated. RESULTS: The proposed method for semisupervised classification outperforms related semisupervised methods under the same setup, with the average area under the receiver operating characteristics curve (AUC) reaching 0.945, 0.673, 0.611, and 0.588 for the four data sets, respectively, followed by graph-based semisupervised learning (0.450, 0.454, 0.425, and 0.5676, respectively) and label propagation (0.475,0.344, 0.440, and 0.477, respectively). The average classification AUCs with 10% labeled data were 0.929, 0.719, 0.652, and 0.650, respectively, comparable to that of the supervised learning methods logistic regression (0.601, 0.670, 0.731, and 0.710, respectively), support vector machines (0.733, 0.720, 0.720, and 0.721, respectively), and random forests (0.982, 0.750, 0.758, and 0.740, respectively). The concerns regarding the secondary use of data and data security are alleviated by realistic data synthesis and robust privacy preservation. CONCLUSIONS: Training clinical prediction models on label-deficient EHRs is indispensable in data-driven research. The proposed method has great potential to exploit the intrinsic structure of EHRs and achieve comparable learning performance to supervised methods.