Formal nursing terminology systems: a means to an end

In response to the need to support diverse and complex information requirements, nursing has developed a number of different terminology systems. The two main kinds of systems that have emerged are enumerative systems and combinatorial systems, although some systems have characteristics of both approaches. Differences in the structure and content of terminology systems, while useful at a local level, prevent effective wider communication, information sharing, integration of record systems, and comparison of nursing elements of healthcare information at a more global level. Formal nursing terminology systems present an alternative approach. This paper describes a number of recent initiatives and explains how these emerging approaches may help to augment existing nursing terminology systems and overcome their limitations through mediation. The development of formal nursing terminology systems is not an end in itself and there remains a great deal of work to be done before success can be claimed. This paper presents an overview of the key issues outstanding and provides recommendations for a way forward

Automation of a problem list using natural language processing

BACKGROUND: The medical problem list is an important part of the electronic medical record in development in our institution. To serve the functions it is designed for, the problem list has to be as accurate and timely as possible. However, the current problem list is usually incomplete and inaccurate, and is often totally unused. To alleviate this issue, we are building an environment where the problem list can be easily and effectively maintained. METHODS: For this project, 80 medical problems were selected for their frequency of use in our future clinical field of evaluation (cardiovascular). We have developed an Automated Problem List system composed of two main components: a background and a foreground application. The background application uses Natural Language Processing (NLP) to harvest potential problem list entries from the list of 80 targeted problems detected in the multiple free-text electronic documents available in our electronic medical record. These proposed medical problems drive the foreground application designed for management of the problem list. Within this application, the extracted problems are proposed to the physicians for addition to the official problem list. RESULTS: The set of 80 targeted medical problems selected for this project covered about 5% of all possible diagnoses coded in ICD-9-CM in our study population (cardiovascular adult inpatients), but about 64% of all instances of these coded diagnoses. The system contains algorithms to detect first document sections, then sentences within these sections, and finally potential problems within the sentences. The initial evaluation of the section and sentence detection algorithms demonstrated a sensitivity and positive predictive value of 100% when detecting sections, and a sensitivity of 89% and a positive predictive value of 94% when detecting sentences. CONCLUSION: The global aim of our project is to automate the process of creating and maintaining a problem list for hospitalized patients and thereby help to guarantee the timeliness, accuracy and completeness of this information

Improving Syntactic Parsing of Clinical Text Using Domain Knowledge

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 caused by Prepositional Phrase (PP) attachment and coordination using semantic information. Our evaluation showed that clinical treebanks greatly improved the performance of existing parsers. The Berkeley parser achieved the best F-1 score of 86.39% on the MiPACQ treebank. For PP attachment, our proposed methods improved the accuracies of PP attachment by 2.35% on the MiPACQ corpus and 1.77% on the I2b2 corpus. For coordination, our method achieved a precision of 94.9% and a precision of 90.3% for the MiPACQ and i2b2 corpus, respectively. To further demonstrate the effectiveness of the improved parsing approaches, we applied outputs of our parsers to two external NLP tasks: semantic role labeling and temporal relation extraction. The experimental results showed that performance of both tasks’ was improved by using the parse tree information from our optimized parsers, with an improvement of 3.26% in F-measure for semantic role labelling and an improvement of 1.5% in F-measure for temporal relation extraction

Doctor of Philosophy

dissertationPublic health surveillance systems are crucial for the timely detection and response to public health threats. Since the terrorist attacks of September 11, 2001, and the release of anthrax in the following month, there has been a heightened interest in public health surveillance. The years immediately following these attacks were met with increased awareness and funding from the federal government which has significantly strengthened the United States surveillance capabilities; however, despite these improvements, there are substantial challenges faced by today's public health surveillance systems. Problems with the current surveillance systems include: a) lack of leveraging unstructured public health data for surveillance purposes; and b) lack of information integration and the ability to leverage resources, applications or other surveillance efforts due to systems being built on a centralized model. This research addresses these problems by focusing on the development and evaluation of new informatics methods to improve the public health surveillance. To address the problems above, we first identified a current public surveillance workflow which is affected by the problems described and has the opportunity for enhancement through current informatics techniques. The 122 Mortality Surveillance for Pneumonia and Influenza was chosen as the primary use case for this dissertation work. The second step involved demonstrating the feasibility of using unstructured public health data, in this case death certificates. For this we created and evaluated a pipeline iv composed of a detection rule and natural language processor, for the coding of death certificates and the identification of pneumonia and influenza cases. The second problem was addressed by presenting the rationale of creating a federated model by leveraging grid technology concepts and tools for the sharing and epidemiological analyses of public health data. As a case study of this approach, a secured virtual organization was created where users are able to access two grid data services, using death certificates from the Utah Department of Health, and two analytical grid services, MetaMap and R. A scientific workflow was created using the published services to replicate the mortality surveillance workflow. To validate these approaches, and provide proofs-of-concepts, a series of real-world scenarios were conducted

Automatic Population of Structured Reports from Narrative Pathology Reports

There are a number of advantages for the use of structured pathology reports: they can ensure the accuracy and completeness of pathology reporting; it is easier for the referring doctors to glean pertinent information from them. The goal of this thesis is to extract pertinent information from free-text pathology reports and automatically populate structured reports for cancer diseases and identify the commonalities and differences in processing principles to obtain maximum accuracy. Three pathology corpora were annotated with entities and relationships between the entities in this study, namely the melanoma corpus, the colorectal cancer corpus and the lymphoma corpus. A supervised machine-learning based-approach, utilising conditional random fields learners, was developed to recognise medical entities from the corpora. By feature engineering, the best feature configurations were attained, which boosted the F-scores significantly from 4.2% to 6.8% on the training sets. Without proper negation and uncertainty detection, the quality of the structured reports will be diminished. The negation and uncertainty detection modules were built to handle this problem. The modules obtained overall F-scores ranging from 76.6% to 91.0% on the test sets. A relation extraction system was presented to extract four relations from the lymphoma corpus. The system achieved very good performance on the training set, with 100% F-score obtained by the rule-based module and 97.2% F-score attained by the support vector machines classifier. Rule-based approaches were used to generate the structured outputs and populate them to predefined templates. The rule-based system attained over 97% F-scores on the training sets. A pipeline system was implemented with an assembly of all the components described above. It achieved promising results in the end-to-end evaluations, with 86.5%, 84.2% and 78.9% F-scores on the melanoma, colorectal cancer and lymphoma test sets respectively

Geometric Model Checking of Continuous Space

Topological Spatial Model Checking is a recent paradigm where model checking techniques are developed for the topological interpretation of Modal Logic. The Spatial Logic of Closure Spaces, SLCS, extends Modal Logic with reachability connectives that, in turn, can be used for expressing interesting spatial properties, such as "being near to" or "being surrounded by". SLCS constitutes the kernel of a solid logical framework for reasoning about discrete space, such as graphs and digital images, interpreted as quasi discrete closure spaces. Following a recently developed geometric semantics of Modal Logic, we propose an interpretation of SLCS in continuous space, admitting a geometric spatial model checking procedure, by resorting to models based on polyhedra. Such representations of space are increasingly relevant in many domains of application, due to recent developments of 3D scanning and visualisation techniques that exploit mesh processing. We introduce PolyLogicA, a geometric spatial model checker for SLCS formulas on polyhedra and demonstrate feasibility of our approach on two 3D polyhedral models of realistic size. Finally, we introduce a geometric definition of bisimilarity, proving that it characterises logical equivalence

Master of Science

thesisThere is increasing competition in the field of community pharmacy practice from chain pharmacies and other providers. There is also a lack of available studies which examine pharmacists' attitudes toward marketing and the actual use of marketing in a pharmacy; there is however, literature on "how" to market. It is first necessary to examine the current practices of pharmacists with regard to marketing before the "how" can be implemented. A questionnaire was mailed to 154 independent community pharmacies in the state of Utah. Of these pharmacies, 110 responded; however, only 83 questionnaires (53.9%) were determined to be complete for analysis. The pharmacy managers were asked to provide personal information regarding their education, number of years at present position, and their self-perception of their marketing knowledge. The pharmacy managers were also asked for specific information on the pharmacies in which they work such as professional services offered and marketed, the perceived competition, prescription volume as percent of total sales and the average menthe expenditure on marketing. The pharmacists were also asked about their attitude toward different marketing tools and the frequency of use of these tools for marketing their pharmacy and professional services. Also examined were the possible effects of factors such as attitudes, perceived competition, and volume of business in a pharmacy on the extent of marketing. On the average almost 22% of the respondents perceived the various marketing tools as being "extremely effective" and another 47% felt that these tools were "effective." However, these marketing tools were used by a much lower proportion of pharmacist who thought that they were effective. Exceptions to the rule were word-of-mouth which was used by a large percentage (95.2%) and billboard advertising which was perceived as being effective by a low percentage (19.3%). The yellow pages were perceived as being "ineffective," but were used by a relatively large percentage (92.8%) of the respondents. The average monthly marketing expenditure was $181.7 ±$186.7. This skew to the left is primarily due to the fact that 30% of the pharmacist spent less than $50.00 per month on marketing. Results indicate that the attitudes of pharmacists toward marketing and perceived competition have very little apparent influence on average monthly marketing expenditures and the frequency of use of different marketing tools. Few pharmacists reported using competition surveys and analysis of pharmacy strengths and weaknesses relative to the average number of prescriptions dispensed per day and the extent of marketing. The variables examined in this study suggest that there may be very little influence on the extent of marketing from pharmacists' attitudes towards marketing, perceived competition, and volume of prescription as a percent of total sales. To better understand the marketing decisions of pharmacists in an independent computing pharmacy, factors such as cost of marketing, time required for marketing activities, the perception for the need to market, and differentiation between pharmacies based on geographical location may also be necessary