EMR-based medical knowledge representation and inference via Markov random fields and distributed representation learning

•A general EMR-based clinical decision support system was developed.•The Markov random field was adopted for inference, and a learning algorithm for arbitrary derivable energy functions was derived.•The representation learning methods were applied to obtain the medical entity representation. Electronic medical records (EMRs) contain medical knowledge that can be used for clinical decision support (CDS). Our objective is to develop a general system that can extract and represent knowledge contained in EMRs to support three CDS tasks—test recommendation, initial diagnosis, and treatment plan recommendation—given the condition of a patient. We extracted four kinds of medical entities from records and constructed an EMR-based medical knowledge network (EMKN), in which nodes are entities and edges reflect their co-occurrence in a record. Three bipartite subgraphs (bigraphs) were extracted from the EMKN, one to support each task. One part of the bigraph was the given condition (e.g., symptoms), and the other was the condition to be inferred (e.g., diseases). Each bigraph was regarded as a Markov random field (MRF) to support the inference. We proposed three graph-based energy functions and three likelihood-based energy functions. Two of these functions are based on knowledge representation learning and can provide distributed representations of medical entities. Two EMR datasets and three metrics were utilized to evaluate the performance. As a whole, the evaluation results indicate that the proposed system outperformed the baseline methods. The distributed representation of medical entities does reflect similarity relationships with respect to knowledge level. Combining EMKN and MRF is an effective approach for general medical knowledge representation and inference. Different tasks, however, require individually designed energy functions.