Extracting Semantics Within Medical Documents

Abstract

In recent years there has been an increase in the generation of health care documents such as discharge summaries, and Electronic Health Records (EHRs). These documents contain a lot of actionable data buried in them. This valuable information has led to an increased scope for research on biomedical literature. However, most of the data reside in the form of free text which makes it difficult to extract useful information. The thesis develops methods to automatically extract semantics from the health care documents in an effort to check conformance of the treatment processes with standard treatment guidelines. Discharge summary is one of the major sources of information about the treatment process. A discharge summary contains information about a patient s one or more encounters with health care service providers, stored electronically to share across different stakeholders in the health care system. Text analytics over these documents has various applications and would help the caregivers to provide better health care. The main theme of the thesis is to automatically extract medical semantics from discharge summaries. We focus on semantics such as medical entities, attributes of medical entities and relationships between these entities. Further, we illustrate an application of these semantics on a Treatment Process Conformance Checking usecase. Conformance checking requires the extracted medical entities and relationships to be structured as treatment a process present in the discharge summary. We propose a workflow representation of the patient s discharge summary which is referred to as a workflow instance. The goal is to check the conformance of the workflow instance against the standard treatment plan. We validate our end-to-end pipeline from extracting semantics to conformance checking on discharge summary data of three diseases, namely, colon cancer, coronary artery disease, and brain tumor, collected from THYME corpus and MIMIC III clinical database. newline