Bioinformatics Commons^™

Design And Architecture Of An Ontology-Driven Dialogue System For Hpv Vaccine Counseling, Amith Faheem Muhammad

Dissertations & Theses (Open Access)

Speech and conversational technologies are increasingly being used by consumers, with the inevitability that one day they will be integrated in health care. Where this technology could be of service is in patient-provider communication, specifically for communicating the risks and benefits of vaccines. Human papillomavirus (HPV) vaccine, in particular, is a vaccine that inoculates individuals from certain HPV viruses responsible for adulthood cancers - cervical, head and neck cancers, etc. My research focuses on the architecture and development of speech-enabled conversational agent that relies on series of consumer-centric health ontologies and the technology that utilizes these ontologies. Ontologies are computable …

Ontology-Based Clinical Information Extraction Using Snomed Ct, Jun Li

Dissertations & Theses (Open Access)

Extracting and encoding clinical information captured in unstructured clinical documents with standard medical terminologies is vital to enable secondary use of clinical data from practice. SNOMED CT is the most comprehensive medical ontology with broad types of concepts and detailed relationships and it has been widely used for many clinical applications. However, few studies have investigated the use of SNOMED CT in clinical information extraction.

In this dissertation research, we developed a fine-grained information model based on the SNOMED CT and built novel information extraction systems to recognize clinical entities and identify their relations, as well as to encode them …

Improving Syntactic Parsing Of Clinical Text Using Domain Knowledge, Min Jiang

Dissertations & Theses (Open Access)

Syntactic parsing is one of the fundamental tasks of Natural Language Processing (NLP). However, few studies have explored syntactic parsing in the medical domain. This dissertation systematically investigated different methods to improve the performance of syntactic parsing of clinical text, including (1) Constructing two clinical treebanks of discharge summaries and progress notes by developing annotation guidelines that handle missing elements in clinical sentences; (2) Retraining four state-of-the-art parsers, including the Stanford parser, Berkeley parser, Charniak parser, and Bikel parser, using clinical treebanks, and comparing their performance to identify better parsing approaches; and (3) Developing new methods to reduce syntactic ambiguity …

Biomedical Language Understanding And Extraction (Blue-Text): A Minimal Syntactic, Semantic Method, Parsa Mirhaji

Dissertations & Theses (Open Access)

Clinical text understanding (CTU) is of interest to health informatics because critical clinical information frequently represented as unconstrained text in electronic health records are extensively used by human experts to guide clinical practice, decision making, and to document delivery of care, but are largely unusable by information systems for queries and computations. Recent initiatives advocating for translational research call for generation of technologies that can integrate structured clinical data with unstructured data, provide a unified interface to all data, and contextualize clinical information for reuse in multidisciplinary and collaborative environment envisioned by CTSA program. This implies that technologies for the …