Doctor of Philosophy

dissertationDisease-specific ontologies, designed to structure and represent the medical knowledge about disease etiology, diagnosis, treatment, and prognosis, are essential for many advanced applications, such as predictive modeling, cohort identification, and clinical decision support. However, manually building disease-specific ontologies is very labor-intensive, especially in the process of knowledge acquisition. On the other hand, medical knowledge has been documented in a variety of biomedical knowledge resources, such as textbook, clinical guidelines, research articles, and clinical data repositories, which offers a great opportunity for an automated knowledge acquisition. In this dissertation, we aim to facilitate the large-scale development of disease-specific ontologies through automated extraction of disease-specific vocabularies from existing biomedical knowledge resources. Three separate studies presented in this dissertation explored both manual and automated vocabulary extraction. The first study addresses the question of whether disease-specific reference vocabularies derived from manual concept acquisition can achieve a near-saturated coverage (or near the greatest possible amount of disease-pertinent concepts) by using a small number of literature sources. Using a general-purpose, manual acquisition approach we developed, this study concludes that a small number of expert-curated biomedical literature resources can prove sufficient for acquiring near-saturated disease-specific vocabularies. The second and third studies introduce automated techniques for extracting disease-specific vocabularies from both MEDLINE citations (title and abstract) and a clinical data repository. In the second study, we developed and assessed a pipeline-based system which extracts disease-specific treatments from PubMed citations. The system has achieved a mean precision of 0.8 for the top 100 extracted treatment concepts. In the third study, we applied classification models to reduce irrelevant disease-concepts associations extracted from MEDLINE citations and electronic medical records. This study suggested the combination of measures of relevance from disparate sources to improve the identification of true-relevant concepts through classification and also demonstrated the generalizability of the studied classification model to new diseases. With the studies, we concluded that existing biomedical knowledge resources are valuable sources for extracting disease-concept associations, from which classification based on statistical measures of relevance could assist a semi-automated generation of disease-specific vocabularies

Data Science Methods for Nursing-Relevant Patient Outcomes and Clinical Processes The 2019 Literature Year in Review

Data science continues to be recognized and used within healthcare due to the increased availability of large data sets and advanced analytics. It can be challenging for nurse leaders to remain apprised of this rapidly changing landscape. In this article, we describe our findings from a scoping literature review of papers published in 2019 that use data science to explore, explain, and/or predict 15 phenomena of interest to nurses. Fourteen of the 15 phenomena were associated with at least one paper published in 2019. We identified the use of many contemporary data science methods (eg, natural language processing, neural networks) for many of the outcomes. We found many studies exploring Readmissions and Pressure Injuries. The topics of Artificial Intelligence/Machine Learning Acceptance, Burnout, Patient Safety, and Unit Culture were poorly represented. We hope that the studies described in this article help readers: (1) understand the breadth and depth of data science\u27s ability to improve clinical processes and patient outcomes that are relevant to nurses and (2) identify gaps in the literature that are in need of exploratio

Novel Natural Language Processing Models for Medical Terms and Symptoms Detection in Twitter

This dissertation focuses on disambiguation of language use on Twitter about drug use, consumption types of drugs, drug legalization, ontology-enhanced approaches, and prediction analysis of data-driven by developing novel NLP models. Three technical aims comprise this work: (a) leveraging pattern recognition techniques to improve the quality and quantity of crawled Twitter posts related to drug abuse; (b) using an expert-curated, domain-specific DsOn ontology model that improve knowledge extraction in the form of drug-to-symptom and drug-to-side effect relations; and (c) modeling the prediction of public perception of the drug’s legalization and the sentiment analysis of drug consumption on Twitter. We collected 7.5 million data from August 2015 to March 2016. This work leveraged a longstanding, multidisciplinary collaboration between researchers at the Population & Center for Interventions, Treatment, and Addictions Research (CITAR) in the Boonshoft School of Medicine and the Department of Computer Science and Engineering. In addition, we aimed to develop and deploy an innovative prediction analysis algorithm for eDrugTrends, capable of semi-automated processing of Twitter data to identify emerging trends in cannabis and synthetic cannabinoid use in the U.S. In addition, the study included aim four, a use case study defined by tweets content analyzing PLWH, medication patterns, and identifying keyword trends via Twitter-based, user-generated content. This case study leveraged a multidisciplinary collaboration between researchers at the Departments of Family Medicine and Population and Public Health Sciences at Wright State University’s Boonshoft School of Medicine and the Department of Computer Science and Engineering. We collected 65K data from February 2022 to July 2022 with the U.S.-based HIV knowledge domain recruited via the Twitter API streaming platform. For knowledge discovery, domain knowledge plays a significant role in powering many intelligent frameworks, such as data analysis, information retrieval, and pattern recognition. Recent NLP and semantic web advances have contributed to extending the domain knowledge of medical terms. These techniques required a bag of seeds for medical knowledge discovery. Various initiate seeds create irrelevant data to the noise and negatively impact the prediction analysis performance. The methodology of aim one, PatRDis classifier, applied for noisy and ambiguous issues, and aim two, DsOn Ontology model, applied for semantic parsing and enriching the online medical to classify the data for HIV care medications engagement and symptom detection from Twitter. By applying the methodology of aims 2 and 3, we solved the challenges of ambiguity and explored more than 1500 cannabis and cannabinoid slang terms. Sentiments measured preceding the election, such as states with high levels of positive sentiment preceding the election who were engaged in enhancing their legalization status. we also used the same dataset for prediction analysis for marijuana legalization and consumption trend analysis (Ohio public polling data). In Aim 4, we applied three experiments, ensemble-learning, the RNN-LSM, the NNBERT-CNN models, and five techniques to determine the tweets associated with medication adherence and HIV symptoms. The long short-term memory (LSTM) model and the CNN for sentence classification produce accurate results and have been recently used in NLP tasks. CNN models use convolutional layers and maximum pooling or max-overtime pooling layers to extract higher-level features, while LSTM models can capture long-term dependencies between word sequences hence are better used for text classification. We propose attention-based RNN, MLP, and CNN deep learning models that capitalize on the advantages of LSTM and BERT techniques with an additional attention mechanism. We trained the model using NNBERT to evaluate the proposed model\u27s performance. The test results showed that the proposed models produce more accurate classification results, and BERT obtained higher recall and F1 scores than MLP or LSTM models. In addition, We developed an intelligent tool capable of automated processing of Twitter data to identify emerging trends in HIV disease, HIV symptoms, and medication adherence

Identifying Outcomes of Care from Medical Records to Improve Doctor-Patient Communication

Between appointments, healthcare providers have limited interaction with their patients, but patients have similar patterns of care. Medications have common side effects; injuries have an expected healing time; and so on. By modeling patient interventions with outcomes, healthcare systems can equip providers with better feedback. In this work, we present a pipeline for analyzing medical records according to an ontology directed at allowing closed-loop feedback between medical encounters. Working with medical data from multiple domains, we use a combination of data processing, machine learning, and clinical expertise to extract knowledge from patient records. While our current focus is on technique, the ultimate goal of this research is to inform development of a system using these models to provide knowledge-driven clinical decision-making

Reflections on the nature of measurement in language-based automated assessments of patients' mental state and cognitive function

Modern advances in computational language processing methods have enabled new approaches to the measurement of mental processes. However, the field has primarily focused on model accuracy in predicting performance on a task or a diagnostic category. Instead the field should be more focused on determining which computational analyses align best with the targeted neurocognitive/psychological functions that we want to assess. In this paper we reflect on two decades of experience with the application of language-based assessment to patients' mental state and cognitive function by addressing the questions of what we are measuring, how it should be measured and why we are measuring the phenomena. We address the questions by advocating for a principled framework for aligning computational models to the constructs being assessed and the tasks being used, as well as defining how those constructs relate to patient clinical states. We further examine the assumptions that go into the computational models and the effects that model design decisions may have on the accuracy, bias and generalizability of models for assessing clinical states. Finally, we describe how this principled approach can further the goal of transitioning language-based computational assessments to part of clinical practice while gaining the trust of critical stakeholders

Information extraction from medication leaflets

Tese de mestrado integrado. Engenharia Informática e Computação. Faculdade de Engenharia. Universidade do Porto. 201

Reflections on the nature of measurement in language-based automated assessments of patients' mental state and cognitive function

Modern advances in computational language processing methods have enabled new approaches to the measurement of mental processes. However, the field has primarily focused on model accuracy in predicting performance on a task or a diagnostic category. Instead the field should be more focused on determining which computational analyses align best with the targeted neurocognitive/psychological functions that we want to assess. In this paper we reflect on two decades of experience with the application of language-based assessment to patients' mental state and cognitive function by addressing the questions of what we are measuring, how it should be measured and why we are measuring the phenomena. We address the questions by advocating for a principled framework for aligning computational models to the constructs being assessed and the tasks being used, as well as defining how those constructs relate to patient clinical states. We further examine the assumptions that go into the computational models and the effects that model design decisions may have on the accuracy, bias and generalizability of models for assessing clinical states. Finally, we describe how this principled approach can further the goal of transitioning language-based computational assessments to part of clinical practice while gaining the trust of critical stakeholders

Nursing-Relevant Patient Outcomes and Clinical Processes in Data Science Literature: 2019 Year in Review

Data science continues to be recognized and used within healthcare due to the increased availability of large data sets and advanced analytics. It can be challenging for nurse leaders to remain apprised of this rapidly changing landscape. In this paper, we describe our findings from a scoping literature review of papers published in 2019 that use data science to explore, explain, and/or predict 15 phenomena of interest to nurses. Fourteen of the 15 phenomena were associated with at least one paper published in 2019. We identified the use of many contemporary data science methods (e.g., natural language processing, neural networks) for many of the outcomes. We found many studies exploring Readmissions and Pressure Injuries. The topics of Artificial Intelligence/Machine Learning Acceptance, Burnout, Patient Safety, and Unit Culture were poorly represented. We hope the studies described in this paper help readers: (a) understand the breadth and depth of data science’s ability to improve clinical processes and patient outcomes that are relevant to nurses and (b) identify gaps in the literature that are in need of exploration

Information retrieval and text mining technologies for chemistry

Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.A.V. and M.K. acknowledge funding from the European Community’s Horizon 2020 Program (project reference: 654021 - OpenMinted). M.K. additionally acknowledges the Encomienda MINETAD-CNIO as part of the Plan for the Advancement of Language Technology. O.R. and J.O. thank the Foundation for Applied Medical Research (FIMA), University of Navarra (Pamplona, Spain). This work was partially funded by Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia), and FEDER (European Union), and the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER-006684). We thank Iñigo Garciá -Yoldi for useful feedback and discussions during the preparation of the manuscript.info:eu-repo/semantics/publishedVersio