CREATING A BIOMEDICAL ONTOLOGY INDEXED SEARCH ENGINE TO IMPROVE THE SEMANTIC RELEVANCE OF RETREIVED MEDICAL TEXT

Medical Subject Headings (MeSH) is a controlled vocabulary used by the National Library of Medicine to index medical articles, abstracts, and journals contained within the MEDLINE database. Although MeSH imposes uniformity and consistency in the indexing process, it has been proven that using MeSH indices only result in a small increase in precision over free-text indexing. Moreover, studies have shown that the use of controlled vocabularies in the indexing process is not an effective method to increase semantic relevance in information retrieval. To address the need for semantic relevance, we present an ontology-based information retrieval system for the MEDLINE collection that result in a 37.5% increase in precision when compared to free-text indexing systems. The presented system focuses on the ontology to: provide an alternative to text-representation for medical articles, finding relationships among co-occurring terms in abstracts, and to index terms that appear in text as well as discovered relationships. The presented system is then compared to existing MeSH and Free-Text information retrieval systems. This dissertation provides a proof-of-concept for an online retrieval system capable of providing increased semantic relevance when searching through medical abstracts in MEDLINE

Unsupervised linking of scientific articles to food systems taxonomies

In this thesis, a novel method for linking scientific articles to taxonomy terms in the domain of food systems research is presented. With food systems being in the center of 12 of the 17 United Nations Sustainable Development goals, there has been an ever-growing amount of scientific articles in this field. These articles are vital in understanding the complex nature of food systems and their inter-dependencies. However, finding relevant literature in this field is difficult for decision makers given the interdisciplinary nature of the field and that annotation and expert feedback is expensive. In the thesis, BERT-based models (SBERT, SPECTER and SciBERT) are adapted to the food systems area and fine-tuned for tasks such as text classification and text similarity, which represents a solution to the problem of finding relevant articles in the food systems domain. The proposed search system uses several taxonomies and data augmentation to achieve the results, which are visualized in a created website. Linking food systems research articles to taxonomy terms shows good accuracy, with models finetuned on domain data achieving better performance on classification task. The best fine-tuning strategy for SPECTER and SciBERT is the combination of domain adaptation and classification. Fine-tuning for text similarity for SBERT improves SBERT performance only slightly. The proposed method can be used in other domains than food systems

Semantic analysis for improved multi-document summarization of text

Excess amount of unstructured data is easily accessible in digital format. This information overload places too heavy a burden on society for its analysis and execution needs. Focused (i.e. topic, query, question, category, etc.) multi-document summarization is an information reduction solution which has reached a state-of-the-art that now demands the need to further explore other techniques to model human summarization activity. Such techniques have been mainly extractive and rely on distribution and complex machine learning on corpora in order to perform closely to human summaries. Overall, these techniques are still being used, and the field now needs to move toward more abstractive approaches to model human way of summarizing. A simple, inexpensive and domain-independent system architecture is created for adding semantic analysis to the summarization process. The proposed system is novel in its use of a new semantic analysis metric to better score sentences for selection into a summary. It also simplifies semantic processing of sentences to better capture more likely semantic-related information, reduce redundancy and reduce complexity. The system is evaluated against participants in the Document Understanding Conference and the later Text Analysis Conference using the performance ROUGE measures of n-gram recall between automated systems, human and baseline gold standard baseline summaries. The goal was to show that semantic analysis used for summarization can perform well, while remaining simple and inexpensive without significant loss of recall as compared to the foundational baseline system. Current results show improvement over the gold standard baseline when all factors of this work's semantic analysis technique are used in combination. These factors are the semantic cue words feature and semantic class weighting to determine sentences with important information. Also, the semantic triples clustering used to decompose natural language sentences to their most basic meaning and select the most important sentences added to this improvement. In competition against the gold standard baseline system on the standardized summarization evaluation metric ROUGE, this work outperforms the baseline system by more than ten position rankings. This work shows that semantic analysis and light-weight, open-domain techniques have potential.Ph.D., Information Studies -- Drexel University, 201

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe

Combining granularity-based topic-dependent and topic-independent evidences for opinion detection

Fouille des opinion, une sous-discipline dans la recherche d'information (IR) et la linguistique computationnelle, fait référence aux techniques de calcul pour l'extraction, la classification, la compréhension et l'évaluation des opinions exprimées par diverses sources de nouvelles en ligne, social commentaires des médias, et tout autre contenu généré par l'utilisateur. Il est également connu par de nombreux autres termes comme trouver l'opinion, la détection d'opinion, l'analyse des sentiments, la classification sentiment, de détection de polarité, etc. Définition dans le contexte plus spécifique et plus simple, fouille des opinion est la tâche de récupération des opinions contre son besoin aussi exprimé par l'utilisateur sous la forme d'une requête. Il y a de nombreux problèmes et défis liés à l'activité fouille des opinion. Dans cette thèse, nous nous concentrons sur quelques problèmes d'analyse d'opinion. L'un des défis majeurs de fouille des opinion est de trouver des opinions concernant spécifiquement le sujet donné (requête). Un document peut contenir des informations sur de nombreux sujets à la fois et il est possible qu'elle contienne opiniâtre texte sur chacun des sujet ou sur seulement quelques-uns. Par conséquent, il devient très important de choisir les segments du document pertinentes à sujet avec leurs opinions correspondantes. Nous abordons ce problème sur deux niveaux de granularité, des phrases et des passages. Dans notre première approche de niveau de phrase, nous utilisons des relations sémantiques de WordNet pour trouver cette association entre sujet et opinion. Dans notre deuxième approche pour le niveau de passage, nous utilisons plus robuste modèle de RI i.e. la language modèle de se concentrer sur ce problème. L'idée de base derrière les deux contributions pour l'association d'opinion-sujet est que si un document contient plus segments textuels (phrases ou passages) opiniâtre et pertinentes à sujet, il est plus opiniâtre qu'un document avec moins segments textuels opiniâtre et pertinentes. La plupart des approches d'apprentissage-machine basée à fouille des opinion sont dépendants du domaine i.e. leurs performances varient d'un domaine à d'autre. D'autre part, une approche indépendant de domaine ou un sujet est plus généralisée et peut maintenir son efficacité dans différents domaines. Cependant, les approches indépendant de domaine souffrent de mauvaises performances en général. C'est un grand défi dans le domaine de fouille des opinion à développer une approche qui est plus efficace et généralisé. Nos contributions de cette thèse incluent le développement d'une approche qui utilise de simples fonctions heuristiques pour trouver des documents opiniâtre. Fouille des opinion basée entité devient très populaire parmi les chercheurs de la communauté IR. Il vise à identifier les entités pertinentes pour un sujet donné et d'en extraire les opinions qui leur sont associées à partir d'un ensemble de documents textuels. Toutefois, l'identification et la détermination de la pertinence des entités est déjà une tâche difficile. Nous proposons un système qui prend en compte à la fois l'information de l'article de nouvelles en cours ainsi que des articles antérieurs pertinents afin de détecter les entités les plus importantes dans les nouvelles actuelles. En plus de cela, nous présentons également notre cadre d'analyse d'opinion et tâches relieés. Ce cadre est basée sur les évidences contents et les évidences sociales de la blogosphère pour les tâches de trouver des opinions, de prévision et d'avis de classement multidimensionnel. Cette contribution d'prématurée pose les bases pour nos travaux futurs. L'évaluation de nos méthodes comprennent l'utilisation de TREC 2006 Blog collection et de TREC Novelty track 2004 collection. La plupart des évaluations ont été réalisées dans le cadre de TREC Blog track.Opinion mining is a sub-discipline within Information Retrieval (IR) and Computational Linguistics. It refers to the computational techniques for extracting, classifying, understanding, and assessing the opinions expressed in various online sources like news articles, social media comments, and other user-generated content. It is also known by many other terms like opinion finding, opinion detection, sentiment analysis, sentiment classification, polarity detection, etc. Defining in more specific and simpler context, opinion mining is the task of retrieving opinions on an issue as expressed by the user in the form of a query. There are many problems and challenges associated with the field of opinion mining. In this thesis, we focus on some major problems of opinion mining

Advances in knowledge discovery and data mining Part II

19th Pacific-Asia Conference, PAKDD 2015, Ho Chi Minh City, Vietnam, May 19-22, 2015, Proceedings, Part II</p

University of Nebraska at Omaha 2018-2019 Course Catalog

Located in one of America’s best cities to live, work and learn, the University of Nebraska at Omaha (UNO) is Nebraska’s premier metropolitan university. With more than 15,000 students enrolled in 200-plus programs of study, UNO is recognized nationally for its online education, graduate education, military friendliness, and community engagement efforts.Founded in 1908, UNO has served learners of all backgrounds for more than 100 years and is dedicated to another century of excellence both in the classroom and in the community

University of Nebraska at Omaha 2020-2021 Course Catalog

Located in one of America’s best cities to live, work and learn, the University of Nebraska at Omaha (UNO) is Nebraska’s premier metropolitan university. With more than 15,000 students enrolled in 200-plus programs of study, UNO is recognized nationally for its online education, graduate education, military friendliness, and community engagement efforts. Founded in 1908, UNO has served learners of all backgrounds for more than 100 years and is dedicated to another century of excellence both in the classroom and in the communit