Neural Summarization of Electronic Health Records

Hospital discharge documentation is among the most essential, yet time-consuming documents written by medical practitioners. The objective of this study was to automatically generate hospital discharge summaries using neural network summarization models. We studied various data preparation and neural network training techniques that generate discharge summaries. Using nursing notes and discharge summaries from the MIMIC-III dataset, we studied the viability of the automatic generation of various sections of a discharge summary using four state-of-the-art neural network summarization models (BART, T5, Longformer and FLAN-T5). Our experiments indicated that training environments including nursing notes as the source, and discrete sections of the discharge summary as the target output (e.g. "History of Present Illness") improve language model efficiency and text quality. According to our findings, the fine-tuned BART model improved its ROUGE F1 score by 43.6% against its standard off-the-shelf version. We also found that fine-tuning the baseline BART model with other setups caused different degrees of improvement (up to 80% relative improvement). We also observed that a fine-tuned T5 generally achieves higher ROUGE F1 scores than other fine-tuned models and a fine-tuned FLAN-T5 achieves the highest ROUGE score overall, i.e., 45.6. For majority of the fine-tuned language models, summarizing discharge summary report sections separately outperformed the summarization the entire report quantitatively. On the other hand, fine-tuning language models that were previously instruction fine-tuned showed better performance in summarizing entire reports. This study concludes that a focused dataset designed for the automatic generation of discharge summaries by a language model can produce coherent Discharge Summary sections

Doctor of Philosophy

dissertationThe problem of information transfer between healthcare sectors and across the continuum of care was examined using a mixed methods approach. These methods include qualitative interviews, retrospective case reviews and an informatic gap analysis. Findings and conclusions are reported for each study. Qualitative interviews were conducted with 16 healthcare representatives from 4 disciplines (medicine, pharmacy, nursing, and social work) and 3 healthcare sectors (hospital, skilled nursing care and community care). Three key themes from a Joint Cognitive Systems theoretical model were used to examine qualitative findings. Agreement on cross-sector care goals is neither defined nor made explicit and in some instances working at cross purposes. Care goals and information paradigms change as patients move from hospitalbased crisis stabilization, diagnosis and treatment to a postdischarge care to home or skilled nursing recovery, function restoration, or end of life support. Control of the transfer process is variable across institutions with little feedback and feed-forward. Lack of knowledge, competency and information tracking threatens sector interdependencies with suspicion and distrust. Sixty-three patients discharged between 2006 and 2008 from hospitals to skilled nursing facilities were randomly selected and reviewed. Most notably missing are discharge summaries (30%), nursing assessments or notes (17%), and social work documents (25%). Advanced directives or living wills necessary for end of life support were present in only 6% of the cases. The presence of information on activities of daily living (ADLs), other disabling conditions, and nutrition was associated with positive outcomes at the 0.001, 0.04 and 0.08levels. Consistent geriatric information transfer across the continuum is needed for relevant care management. An interoperability gap analysis conducted on the LINC (Linking Information Necessary for Care) transfer form determined its interoperability to be the semantic level 0. Detailed Clinical Models representing care management processes are challenged by the lack of consensus in terminology standards across sectors. Construction of information transfer solutions compliant with the Centers of Medicare and Medicaid Services (CMS) Stage 2 meaningful use criteria must address syntactic and semantic standards, map sector terminologies within care management processes, and account for the lack of standard terminologies in allied health domains

GP perspectives on hospital discharge letters : an interview and focus group study

Background: Written discharge communication following inpatient or outpatient clinic discharge is essential for communicating information to the GP, but GPs’ opinions on discharge communication are seldom sought. Patients are sometimes copied into this communication, but the reasons for this variation, and the resultant effects, remain unclear. Aim: To explore GP perspectives on how discharge letters can be improved in order to enhance patient outcomes. Design & setting: The study used narrative interviews with 26 GPs from 13 GP practices within the West Midlands, England. Method: Interviews were transcribed and data were analysed using corpus linguistics (CL) techniques. Results Elements pivotal to a successful letter were: diagnosis, appropriate follow-up plan, medication changes and reasons, clinical summary, investigations and/or procedures and outcomes, and what information has been given to the patient. GPs supported patients receiving discharge letters and expounded a number of benefits of this practice; for example, increased patient autonomy. Nevertheless, GPs felt that if patients are to receive direct discharge letter copies, modifications such as use of lay language and avoidance of acronyms may be required to increase patient understanding. Conclusion: GPs reported that discharge letters frequently lacked content items they assessed to be important; GPs highlighted that this can have subsequent ramifications on resources and patient experiences. Templates should be devised that put discharge letter elements assessed to be important by GPs to the forefront. Future research needs to consider other perspectives on letter content, particularly those of patients

An Interoperable Clinical Cardiology Electronic Health Record System - a standards based approach for Clinical Practice and Research with Data Reuse

Currently in hospitals, several information systems manage, very often autonomously, the patient’s personal, clinical and diagnostic data. This originates a clinical information management system consisting of a myriad of independent subsystems which, although efficient in their specific purpose, make the integration of the whole system very difficult and limit the use of clinical data, especially as regards the reuse of these data for research purposes. Mainly for these reasons, the management of the Genoese ASL3 decided to commission the University of Genoa to set up a medical record system that could be easily integrated with the rest of the information system already present, but which offered solid interoperability features, and which could support the research skills of hospital health workers. My PhD work aimed to develop an electronic health record system for a cardiology ward, obtaining a prototype which is functional and usable in a hospital ward. The choice of cardiology was due to the wide availability of the staff of the cardiology department to support me in the development and in the test phase. The resulting medical record system has been designed “ab initio” to be fully integrated into the hospital information system and to exchange data with the regional health information infrastructure. In order to achieve interoperability the system is based on the Health Level Seven standards for exchanging information between medical information systems. These standards are widely deployed and allow for the exchange of information in several functional domains. Specific decision support sections for particular aspects of the clinical life were also included. The data collected by this system were the basis for examples of secondary use for the development of two models based on machine learning algorithms. The first model allows to predict mortality in patients with heart failure within 6 months from their admission, and the second is focused on the discrimination between heart failure versus chronic ischemic heart disease in the elderly population, which is the widest population section served by the cardiological ward

Overview of the ShARe/CLEF eHealth evaluation lab 2013

Discharge summaries and other free-text reports in healthcare transfer information between working shifts and geographic locations. Patients are likely to have difficulties in understanding their content, because of their medical jargon, non-standard abbreviations, and ward-specific idioms. This paper reports on an evaluation lab with an aim to support the continuum of care by developing methods and resources that make clinical reports in English easier to understand for patients, and which helps them in finding information related to their condition. This ShARe/CLEFeHealth2013 lab offered student mentoring and shared tasks: identification and normalisation of disorders (1a and 1b) and normalisation of abbreviations and acronyms (2) in clinical reports with respect to terminology standards in healthcare as well as information retrieval (3) to address questions patients may have when reading clinical reports. The focus on patients' information needs as opposed to the specialised information needs of physicians and other healthcare workers was the main feature of the lab distinguishing it from previous shared tasks. De-identied clinical reports for the three tasks were from US intensive care and originated from the MIMIC II database. Other text documents for Task 3 were from the Internet and originated from the Khresmoi project. Task 1 annotations originated from the ShARe annotations. For Tasks 2 and 3, new annotations, queries, and relevance assessments were created. 64, 56, and 55 people registered their interest in Tasks 1, 2, and 3, respectively. 34 unique teams (3 members per team on average) participated with 22, 17, 5, and 9 teams in Tasks 1a, 1b, 2 and 3, respectively. The teams were from Australia, China, France, India, Ireland, Republic of Korea, Spain, UK, and USA. Some teams developed and used additional annotations, but this strategy contributed to the system performance only in Task 2. The best systems had the F1 score of 0.75 in Task 1a; Accuracies of 0.59 and 0.72 in Tasks 1b and 2; and Precision at 10 of 0.52 in Task 3. The results demonstrate the substantial community interest and capabilities of these systems in making clinical reports easier to understand for patients. The organisers have made data and tools available for future research and development

Spanish for Emergency Room Nursing: A Task-Based Needs Analysis for a Languages for Specific Purposes Context

Language barriers in medical settings can impede access to healthcare and increase the risk of medical error for limited English proficiency (LEP) patients, especially in emergency situations (Bender et al., 2004: Martinez, 2010). Nurses who are competent in their patient’s first language can decrease the risk of these issues and care more effectively for their LEP patients (Altstaedter, 2017; Fernandez et al., 2011). However, general foreign language courses do not prepare students for communication in medical settings, and there are few language courses specifically for emergency room (ER) nurses (Amerson & Burgins, 2005; Hardin, 2015). This dissertation will present the results of a study drawing on Task-Based Language Teaching (TBLT) and Languages for Specific Purposes (LSP) to conduct a task-based needs analysis (NA) to 1) determine the Spanish language needs of primarily English-speaking emergency room nurses in the Southeastern US and 2) inform the design of a potential Spanish for ER Nursing course. This mixed-methods study included three phases of both data collection and analysis, adapted from Serafini and Torres (2015) and Malicka et al. (2019). In Phase 1, a variety of open-ended measures were used to determine tasks common in ER settings as reported by each type of participant. In Phase 2, participants rated the frequency and importance of these tasks. In Phase 3, the participants reviewed the list of tasks in follow-up interviews. Results are presented as a series of tasks performed in the ER context, ranked according to frequency and importance. This study adds to existing LSP research that has to date been limited regarding studies in non-English contexts and improves upon methodological limitations in previous studies that have used a NA. The findings of this study will inform future curricular decisions in a Spanish for ER nursing course as well as address the healthcare inequalities experienced by LEP patients

Consolidated List of Requirements

This document is a consolidated catalogue of requirements for the Electronic Health Care Record (EHCR) and Electronic Health Care Record Architecture (EHCRA), gleaned largely from work done in the EU Framework III and IV programmes and CEN, but also including input from other sources including world-wide standardisation initiatives. The document brings together the relevant work done into a classified inventory of requirements to inform the on-going standardisation process as well as act as a guide to future implementation of EHCRA-based systems. It is meant as a contribution both to understanding of the standard and to the work that is being considered to improve the standard. Major features include the classification into issues affecting the Health Care Record, the EHCR, EHCR processing, EHCR interchange and the sharing of health care information and EHCR systems. The principal information sources are described briefly. It is offered as documentation that is complementary to the four documents of the ENV 13606 Parts I-IV produced by CEN Pts 26,27,28,29. The requirements identified and classified in this deliverable are referenced in other deliverables

Clinical foundations and information architecture for the implementation of a federated health record service

Clinical care increasingly requires healthcare professionals to access patient record information that may be distributed across multiple sites, held in a variety of paper and electronic formats, and represented as mixtures of narrative, structured, coded and multi-media entries. A longitudinal person-centred electronic health record (EHR) is a much-anticipated solution to this problem, but its realisation is proving to be a long and complex journey. This Thesis explores the history and evolution of clinical information systems, and establishes a set of clinical and ethico-legal requirements for a generic EHR server. A federation approach (FHR) to harmonising distributed heterogeneous electronic clinical databases is advocated as the basis for meeting these requirements. A set of information models and middleware services, needed to implement a Federated Health Record server, are then described, thereby supporting access by clinical applications to a distributed set of feeder systems holding patient record information. The overall information architecture thus defined provides a generic means of combining such feeder system data to create a virtual electronic health record. Active collaboration in a wide range of clinical contexts, across the whole of Europe, has been central to the evolution of the approach taken. A federated health record server based on this architecture has been implemented by the author and colleagues and deployed in a live clinical environment in the Department of Cardiovascular Medicine at the Whittington Hospital in North London. This implementation experience has fed back into the conceptual development of the approach and has provided "proof-of-concept" verification of its completeness and practical utility. This research has benefited from collaboration with a wide range of healthcare sites, informatics organisations and industry across Europe though several EU Health Telematics projects: GEHR, Synapses, EHCR-SupA, SynEx, Medicate and 6WINIT. The information models published here have been placed in the public domain and have substantially contributed to two generations of CEN health informatics standards, including CEN TC/251 ENV 13606

The Benefits of Voluntary Inpatient Psychiatric Hospitalization: Myth or Reality?

Throughout the United States, mentally ill persons are confined against their will in psychiatric hospitals as a result of being accused of dangerous behavior. Some are committed involuntarily by a judge after an administrative hearing during which they are afforded legal representation, a right to be present, and important due process protections, including the right to cross-examine witnesses and present one\u27s own witnesses. However, a significant number of individuals, initially confined in psychiatric institutions for allegedly posing a danger to life or safety, never see an impartial judge, lawyer, or even a family member. These mentally ill individuals are not involuntarily committed. They are committed, without any benefit of due process protections, as voluntary patients. The legal and medical implications of imposing voluntary status to a patient being admitted to a psychiatric hospital are of paramount importance. This Article focuses primarily on the specific criteria to be used in determining whether a patient\u27s admission into a psychiatric hospital is voluntary. The questions it seeks to answer include: should psychiatrists be required to administer a mental status exam? Should witnesses be present at the time the person is voluntarily admitted and what, if any, documentation should be required? Should the mental disorder diagnosis of the patient be a major factor in determining competence to give voluntary consent? Should periodic review be required to determine whether the person continues to meet the criteria for voluntary admission? This Article will make specific recommendations as to when a psychiatric hospital will be permitted to accept and treat a mentally ill person as a voluntary patient and will ask what the legal significance is of the phrase knowingly and competently as used in defining consent to hospitalization. Related to its primary focus, this Article examines the process through which a mentally ill person is voluntarily confined to a psychiatric hospital. It reviews diagnostic methods in order to help identify the existence of patient coercion. It discusses the need for a waiting period before the time the hospital assigns patient status and the time a patient signs an admission form. It also discusses the relevance of the proximity between the time a patient signs the form and his initial confinement involuntary civil commitment hearing. In particular, the Article explores whether there are certain time periods during the initial observation status of a patient in which there is more likely to be stress, anxiety, misunderstanding, coercion, or clear understanding as to the significance of the voluntary status. A further aspect of the article is an exploration of the legal issues surrounding voluntary confinement. The questions addressed in this regard include: should a legal guardian or power of attorney be permitted to voluntarily admit a person into a psychiatric facility? What are the legal implications of an advanced medical directive or living will? Should an attorney be consulted by the patient prior to any voluntary admission, and should a judge review the voluntary admission to ensure that the patient is legally competent to be voluntarily admitted? What is the relevance of a prior court determination of the patient to being found legally incompetent? Voluntary psychiatric hospitalization should be the result of a competent and informed decision arrived at within a non-coercive environment. Hospitalization based on anything less is not only involuntary, but it is an infringement of personal liberty. Because of the uncertainties surrounding voluntary patient status-uncertainties exacerbated by the absence of due process protections-the criteria and procedures of voluntary admission demand careful and thorough scrutiny. By ensuring that voluntary admission is in fact voluntary, such scrutiny is the first step in protecting a mentally ill patient\u27s personal liberty