Automating the Transformation of Free-Text Clinical Problems into SNOMED CT Expressions

An important function of the patient record is to effectively and concisely communicate patient problems. In many cases, these problems are represented as short textual summarizations and appear in various sections of the record including problem lists, diagnoses, and chief complaints. While free-text problem descriptions effectively capture the clinicians' intent, these unstructured representations are problematic for downstream analytics. We present an automated approach to converting free-text problem descriptions into structured Systematized Nomenclature of Medicine - Clinical Terms (SNOMED CT) expressions. Our methods focus on incorporating new advances in deep learning to build formal semantic representations of summary level clinical problems from text. We evaluate our methods against current approaches as well as against a large clinical corpus. We find that our methods outperform current techniques on the important relation identification sub-task of this conversion, and highlight the challenges of applying these methods to real-world clinical text.