Methods to Facilitate the Capture, Use, and Reuse of Structured and Unstructured Clinical Data.

Electronic health records (EHRs) have great potential to improve quality of care and to support clinical and translational research. While EHRs are being increasingly implemented in U.S. hospitals and clinics, their anticipated benefits have been largely unachieved or underachieved. Among many factors, tedious documentation requirements and the lack of effective information retrieval tools to access and reuse data are two key reasons accounting for this deficiency. In this dissertation, I describe my research on developing novel methods to facilitate the capture, use, and reuse of both structured and unstructured clinical data. Specifically, I develop a framework to investigate potential issues in this research topic, with a focus on three significant challenges. The first challenge is structured data entry (SDE), which can be facilitated by four effective strategies based on my systematic review. I further propose a multi-strategy model to guide the development of future SDE applications. In the follow-up study, I focus on workflow integration and evaluate the feasibility of using EHR audit trail logs for clinical workflow analysis. The second challenge is the use of clinical narratives, which can be supported by my innovative information retrieval (IR) technique called “semantically-based query recommendation (SBQR)”. My user experiment shows that SBQR can help improve the perceived performance of a medical IR system, and may work better on search tasks with average difficulty. The third challenge involves reusing EHR data as a reference standard to benchmark the quality of other health-related information. My study assesses the readability of trial descriptions on ClinicalTrials.gov and found that trial descriptions are very hard to read, even harder than clinical notes. My dissertation has several contributions. First, it conducts pioneer studies with innovative methods to improve the capture, use, and reuse of clinical data. Second, my dissertation provides successful examples for investigators who would like to conduct interdisciplinary research in the field of health informatics. Third, the framework of my research can be a great tool to generate future research agenda in clinical documentation and EHRs. I will continue exploring innovative and effective methods to maximize the value of EHRs.PHDInformationUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/135845/1/tzuyu_1.pd

NEOREG : design and implementation of an online neonatal registration system to access, follow and analyse data of newborns with congenital cytomegalovirus infection

Today's registration of newborns with congenital cytomegalovirus (cCMV) infection is still performed on paper-based forms in Flanders, Belgium. This process has a large administrative impact. It is imortant that all screening tests are registered to have a complete idea of the impact of cCMV. Although these registrations are usable in computerised data analysis, these data are not available in a format to perform electronic processing. An online Neonatal Registry (NEOREG) System was designed and developed to access, follow and analyse the data of newborns remotely. It allows patients' diagnostic registration and treatment follow-up through a web interface and uses document forms in Portable Document Format (PDF), which incorporate all the elements from the existing forms. Forms are automatically processed to structured EHRs. Modules are included to perform statistical analysis. The design was driven by extendibility, security and usability requirements. The website load time, throughput and execution time of data analysis were evaluated in detail. The NEOREG system is able to replace the existing paper-based CMV records

Computational Approaches to Assisting Patients\u27 Medical Comprehension from Electronic Health Records

Patient-centered care has been established as a fundamental approach to improve the quality of health care in a seminal report by the Institute of Medicine published at the start of the century. Improved access to health information and demand for greater transparency contributed to its move into the mainstream. Research has also demonstrated that actively involving patients in the management of their own health can lead to better outcomes, and potentially lower costs. However, despite the efforts in many areas of medicine to embrace patient-centered care, engaging patients is still considered a challenge. One of the barriers is the lack of effective tools to help patients understand their health conditions, options and their consequences. Patient portals are now widely adopted by hospitals and other healthcare practices to provide patients with the capabilities to view their own Electronic Health Records. They are a rich resource of information for patients. However, the language in the records are generally difficult for patients without training in medicine to understand. Furthermore, the amount of information can often be overwhelming as well. In this work, we propose computational approaches to foster patient engagement from three aspects by exploiting the rich information in the medical records. First, we design a framework to automatically generate health literacy instruments to measure a patient\u27s literacy levels. This framework exploits readily available large scale corpora to generate instruments in a commonly used test format. Second, we investigate methods that can determine the readability of complex documents such as health records. We propose to rank document readability, instead of assigning a grade level or a pre-defined difficulty category. Lastly, we examine the problem of finding targeted educational materials to facilitate patient comprehension of medical notes. We study methods to formulate effective queries from specialized and long clinical narratives. In addition, we propose a neural network based method to identify medical concepts that are important to patients. The three aspects of this work address the issues of the overabundance and technical complexity of medical language in health records. We demonstrate that our approaches are effective with various experiments and evaluation metric

Text Summarization Techniques: A Brief Survey

In recent years, there has been a explosion in the amount of text data from a variety of sources. This volume of text is an invaluable source of information and knowledge which needs to be effectively summarized to be useful. In this review, the main approaches to automatic text summarization are described. We review the different processes for summarization and describe the effectiveness and shortcomings of the different methods.Comment: Some of references format have update

Assessing the Readability of Medical Documents: A Ranking Approach

BACKGROUND: The use of electronic health record (EHR) systems with patient engagement capabilities, including viewing, downloading, and transmitting health information, has recently grown tremendously. However, using these resources to engage patients in managing their own health remains challenging due to the complex and technical nature of the EHR narratives. OBJECTIVE: Our objective was to develop a machine learning-based system to assess readability levels of complex documents such as EHR notes. METHODS: We collected difficulty ratings of EHR notes and Wikipedia articles using crowdsourcing from 90 readers. We built a supervised model to assess readability based on relative orders of text difficulty using both surface text features and word embeddings. We evaluated system performance using the Kendall coefficient of concordance against human ratings. RESULTS: Our system achieved significantly higher concordance (.734) with human annotators than did a baseline using the Flesch-Kincaid Grade Level, a widely adopted readability formula (.531). The improvement was also consistent across different disease topics. This method\u27s concordance with an individual human user\u27s ratings was also higher than the concordance between different human annotators (.658). CONCLUSIONS: We explored methods to automatically assess the readability levels of clinical narratives. Our ranking-based system using simple textual features and easy-to-learn word embeddings outperformed a widely used readability formula. Our ranking-based method can predict relative difficulties of medical documents. It is not constrained to a predefined set of readability levels, a common design in many machine learning-based systems. Furthermore, the feature set does not rely on complex processing of the documents. One potential application of our readability ranking is personalization, allowing patients to better accommodate their own background knowledge

Improving Biomedical Abstractive Summarisation with Knowledge Aggregation from Citation Papers

Abstracts derived from biomedical literature possess distinct domain-specific characteristics, including specialised writing styles and biomedical terminologies, which necessitate a deep understanding of the related literature. As a result, existing language models struggle to generate technical summaries that are on par with those produced by biomedical experts, given the absence of domain-specific background knowledge. This paper aims to enhance the performance of language models in biomedical abstractive summarisation by aggregating knowledge from external papers cited within the source article. We propose a novel attention-based citation aggregation model that integrates domain-specific knowledge from citation papers, allowing neural networks to generate summaries by leveraging both the paper content and relevant knowledge from citation papers. Furthermore, we construct and release a large-scale biomedical summarisation dataset that serves as a foundation for our research. Extensive experiments demonstrate that our model outperforms state-of-the-art approaches and achieves substantial improvements in abstractive biomedical text summarisation.Comment: Accepted by EMNLP 202

Proficiency-aware systems

In an increasingly digital world, technological developments such as data-driven algorithms and context-aware applications create opportunities for novel human-computer interaction (HCI). We argue that these systems have the latent potential to stimulate users and encourage personal growth. However, users increasingly rely on the intelligence of interactive systems. Thus, it remains a challenge to design for proficiency awareness, essentially demanding increased user attention whilst preserving user engagement. Designing and implementing systems that allow users to become aware of their own proficiency and encourage them to recognize learning benefits is the primary goal of this research. In this thesis, we introduce the concept of proficiency-aware systems as one solution. In our definition, proficiency-aware systems use estimates of the user's proficiency to tailor the interaction in a domain and facilitate a reflective understanding for this proficiency. We envision that proficiency-aware systems leverage collected data for learning benefit. Here, we see self-reflection as a key for users to become aware of necessary efforts to advance their proficiency. A key challenge for proficiency-aware systems is the fact that users often have a different self-perception of their proficiency. The benefits of personal growth and advancing one's repertoire might not necessarily be apparent to users, alienating them, and possibly leading to abandoning the system. To tackle this challenge, this work does not rely on learning strategies but rather focuses on the capabilities of interactive systems to provide users with the necessary means to reflect on their proficiency, such as showing calculated text difficulty to a newspaper editor or visualizing muscle activity to a passionate sportsperson. We first elaborate on how proficiency can be detected and quantified in the context of interactive systems using physiological sensing technologies. Through developing interaction scenarios, we demonstrate the feasibility of gaze- and electromyography-based proficiency-aware systems by utilizing machine learning algorithms that can estimate users' proficiency levels for stationary vision-dominant tasks (reading, information intake) and dynamic manual tasks (playing instruments, fitness exercises). Secondly, we show how to facilitate proficiency awareness for users, including design challenges on when and how to communicate proficiency. We complement this second part by highlighting the necessity of toolkits for sensing modalities to enable the implementation of proficiency-aware systems for a wide audience. In this thesis, we contribute a definition of proficiency-aware systems, which we illustrate by designing and implementing interactive systems. We derive technical requirements for real-time, objective proficiency assessment and identify design qualities of communicating proficiency through user reflection. We summarize our findings in a set of design and engineering guidelines for proficiency awareness in interactive systems, highlighting that proficiency feedback makes performance interpretable for the user.In einer zunehmend digitalen Welt schaffen technologische Entwicklungen - wie datengesteuerte Algorithmen und kontextabhängige Anwendungen - neuartige Interaktionsmöglichkeiten mit digitalen Geräten. Jedoch verlassen sich Nutzer oftmals auf die Intelligenz dieser Systeme, ohne dabei selbst auf eine persönliche Weiterentwicklung hinzuwirken. Wird ein solches Vorgehen angestrebt, verlangt dies seitens der Anwender eine erhöhte Aufmerksamkeit. Es ist daher herausfordernd, ein entsprechendes Design für Kompetenzbewusstsein (Proficiency Awareness) zu etablieren. Das primäre Ziel dieser Arbeit ist es, eine Methodik für das Design und die Implementierung von interaktiven Systemen aufzustellen, die Nutzer dabei unterstützen über ihre eigene Kompetenz zu reflektieren, um dadurch Lerneffekte implizit wahrnehmen können. Diese Arbeit stellt ein Konzept für fähigkeitsbewusste Systeme (proficiency-aware systems) vor, welche die Fähigkeiten von Nutzern abschätzen, die Interaktion entsprechend anpassen sowie das Bewusstsein der Nutzer über deren Fähigkeiten fördern. Hierzu sollten die Systeme gesammelte Daten von Nutzern einsetzen, um Lerneffekte sichtbar zu machen. Die Möglichkeit der Anwender zur Selbstreflexion ist hierbei als entscheidend anzusehen, um als Motivation zur Verbesserung der eigenen Fähigkeiten zu dienen. Eine zentrale Herausforderung solcher Systeme ist die Tatsache, dass Nutzer - im Vergleich zur Abschätzung des Systems - oft eine divergierende Selbstwahrnehmung ihrer Kompetenz haben. Im ersten Moment sind daher die Vorteile einer persönlichen Weiterentwicklung nicht unbedingt ersichtlich. Daher baut diese Forschungsarbeit nicht darauf auf, Nutzer über vorgegebene Lernstrategien zu unterrichten, sondern sie bedient sich der Möglichkeiten interaktiver Systeme, die Anwendern die notwendigen Hilfsmittel zur Verfügung stellen, damit diese selbst über ihre Fähigkeiten reflektieren können. Einem Zeitungseditor könnte beispielsweise die aktuelle Textschwierigkeit angezeigt werden, während einem passionierten Sportler dessen Muskelaktivität veranschaulicht wird. Zunächst wird herausgearbeitet, wie sich die Fähigkeiten der Nutzer mittels physiologischer Sensortechnologien erkennen und quantifizieren lassen. Die Evaluation von Interaktionsszenarien demonstriert die Umsetzbarkeit fähigkeitsbewusster Systeme, basierend auf der Analyse von Blickbewegungen und Muskelaktivität. Hierbei kommen Algorithmen des maschinellen Lernens zum Einsatz, die das Leistungsniveau der Anwender für verschiedene Tätigkeiten berechnen. Im Besonderen analysieren wir stationäre Aktivitäten, die hauptsächlich den Sehsinn ansprechen (Lesen, Aufnahme von Informationen), sowie dynamische Betätigungen, die die Motorik der Nutzer fordern (Spielen von Instrumenten, Fitnessübungen). Der zweite Teil zeigt auf, wie Systeme das Bewusstsein der Anwender für deren eigene Fähigkeiten fördern können, einschließlich der Designherausforderungen , wann und wie das System erkannte Fähigkeiten kommunizieren sollte. Abschließend wird die Notwendigkeit von Toolkits für Sensortechnologien hervorgehoben, um die Implementierung derartiger Systeme für ein breites Publikum zu ermöglichen. Die Forschungsarbeit beinhaltet eine Definition für fähigkeitsbewusste Systeme und veranschaulicht dieses Konzept durch den Entwurf und die Implementierung interaktiver Systeme. Ferner werden technische Anforderungen objektiver Echtzeitabschätzung von Nutzerfähigkeiten erforscht und Designqualitäten für die Kommunikation dieser Abschätzungen mittels Selbstreflexion identifiziert. Zusammengefasst sind die Erkenntnisse in einer Reihe von Design- und Entwicklungsrichtlinien für derartige Systeme. Insbesondere die Kommunikation, der vom System erkannten Kompetenz, hilft Anwendern, die eigene Leistung zu interpretieren

Evaluating the Efficacy of Communicative Reading Strategies With High-Risk First-Grade Students.

The specific aim of this project was to determine the efficacy of an integrated approach to remediation of oral language and reading. Communicative Reading Strategies (CRS) (Norris, 1985) was used with a group of twenty-one high-risk first grade students. Improvements were measured for aspects of language development that are specifically related to success in oral language use and reading. Nine children demonstrating below average performance on standardized measures assessing language and reading received intervention. A control group of 12 matched children served to control for changes as a result of maturation or general curriculum effect. The treatment group received intervention four days per week for 45 minutes each day for eight weeks during the summer. Changes in performance on both standardized reading and language measures and informal reading measures from pre-treatment to post-treatment were used to compare treatment and control groups. Additional posttesting at four months and nine months following treatment compared long term effects. The differences between gain scores for the two groups were compared at three different time intervals. Results revealed significant gains on both the standardized test and on the informal reading assessment. Results verified that CRS is an effective intervention for poor readers. Treatment subjects simultaneously improved on word recognition, reading rate, and comprehension for both measures. The treatment group again showed improvement on word analysis skills that could not be attributed to time or maturation. Although statistical differences were not found between groups on oral language measures, gains for individual subjects suggest CRS treatment positively affected language abilities

Efficacy of Communicative Reading Strategies as an Instructional Approach for Adult Low-Ability Readers.

Twelve adult low-ability readers participated in a pretest-posttest control group study investigating the efficacy of Communicative Reading Strategies (CRS) as an instructional reading approach. Six adults received CRS instruction and constituted the experimental group. The remaining six adults received skill-based instruction and served as the control group. All participants demonstrated instructional level reading skills at or below a fifth grade level and completed 40 hours of instruction. Changes in performance on measures of word recognition, comprehension, and reading rate from pretest to posttest were used to compare CRS and control groups. Results of Mann Whitney U analyses revealed that both methods of instruction were effective in improving word recognition and comprehension abilities for most subjects. For individual subjects and mean group gains, the word recognition and comprehension results favored the CRS group, although these differences did not reach a level of statistical significance. Further analyses of the reading performance of CRS subjects revealed additional findings. Scaffolding provided by CRS interactions increased both the assisted word recognition level and assisted comprehension scores for most subjects at both pretest and posttest. Furthermore, reading gains made under scaffolded conditions at pretest were highly predictive of actual unassisted reading gains demonstrated after 40 hours of instruction. Measures of reading accuracy, fluency, rate, comprehension, and story retelling ability obtained from CRS subjects after every 10 hours of instruction was not representative of actual gains demonstrated at posttest