Clinical narrative analytics challenges

Precision medicine or evidence based medicine is based on the extraction of knowledge from medical records to provide individuals with the appropriate treatment in the appropriate moment according to the patient features. Despite the efforts of using clinical narratives for clinical decision support, many challenges have to be faced still today such as multilinguarity, diversity of terms and formats in different services, acronyms, negation, to name but a few. The same problems exist when one wants to analyze narratives in literature whose analysis would provide physicians and researchers with highlights. In this talk we will analyze challenges, solutions and open problems and will analyze several frameworks and tools that are able to perform NLP over free text to extract medical entities by means of Named Entity Recognition process. We will also analyze a framework we have developed to extract and validate medical terms. In particular we present two uses cases: (i) medical entities extraction of a set of infectious diseases description texts provided by MedlinePlus and (ii) scales of stroke identification in clinical narratives written in Spanish

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

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

Electronic Health Record Summarization over Heterogeneous and Irregularly Sampled Clinical Data

The increasing adoption of electronic health records (EHRs) has led to an unprecedented amount of patient health information stored in an electronic format. The ability to comb through this information is imperative, both for patient care and computational modeling. Creating a system to minimize unnecessary EHR data, automatically distill longitudinal patient information, and highlight salient parts of a patient’s record is currently an unmet need. However, summarization of EHR data is not a trivial task, as there exist many challenges with reasoning over this data. EHR data elements are most often obtained at irregular intervals as patients are more likely to receive medical care when they are ill, than when they are healthy. The presence of narrative documentation adds another layer of complexity as the notes are riddled with over-sampled text, often caused by the frequent copy-and-pasting during the documentation process. This dissertation synthesizes a set of challenges for automated EHR summarization identified in the literature and presents an array of methods for dealing with some of these challenges. We used hybrid data-driven and knowledge-based approaches to examine abundant redundancy in clinical narrative text, a data-driven approach to identify and mitigate biases in laboratory testing patterns with implications for using clinical data for research, and a probabilistic modeling approach to automatically summarize patient records and learn computational models of disease with heterogeneous data types. The dissertation also demonstrates two applications of the developed methods to important clinical questions: the questions of laboratory test overutilization and cohort selection from EHR data

Deep Learning in the Prediction of Clinically Significant Outcomes in Stroke and General Medicine Patients

Background The need for novel strategies to improve outcome prediction and the categorisation of unstructured medical data will increase as the demands on hospitals, associated with the increasing age and complexity of admitted patients, continues to rise. Stroke is a highly specialised field, in which key performance indicators and discharge planning have an important role. General medicine is a field that encompasses a wide variety of multisystem and undifferentiated illnesses. It is possible that machine learning, in particular deep learning, may be able to assist with the prediction of clinically significant outcomes both in areas with highly specialised assessment and treatment considerations (such as stroke), as well as fields with a diverse mix of medical conditions and comorbidities (such as general medicine). Method This thesis comprised of studies using machine learning to predict clinically significant outcomes in stroke and general medicine inpatients. Initially a systematic review was conducted to evaluate the existing literature regarding the prediction of one such clinically significant outcome, length of stay, in medical inpatients. Derivation and validation studies were conducted to develop models for stroke inpatients to aid with the prediction of discharge independence, survival to discharge, discharge destination and length of stay. Stroke key performance indicator-automated extraction and clinical coding categorisation were undertaken in studies employing techniques including natural language processing. Natural language processing was applied to general medicine free-text data in pilot, derivation, and validation studies in the prediction of outcomes including discharge timing. Results The systematic review identified a particular lack of prospective validation studies for machine learning models developed to aid with length of stay prediction in medical inpatients. The stroke model derivation, prospective and external validation studies demonstrated the successful use of machine learning models in the prediction of outcomes relevant to discharge planning for stroke patients. For example, an area under the receiver operator curve (AUC) of 0.85 and 0.87 was achieved for the prediction of independence at the time of discharge in the prospective and external validation datasets respectively. The automated collection of stroke key performance indicators and the application of natural language processing to stroke clinical coding also demonstrated performance as high as an AUC of 0.95-1.00 in key performance indicator classification tasks. The general medicine pilot, derivation, prospective and external validation studies demonstrated the development and success of artificial neural networks in the prediction of discharge within the next 48 hours (AUC 0.78 and 0.74 in the prospective and external validation datasets respectively). Conclusions Machine learning models (including deep learning) can successfully predict clinically significant outcomes in stroke and general medicine patients.Thesis (Ph.D.) -- University of Adelaide, Adelaide Medical School, 202

Patient Safety and Quality: An Evidence-Based Handbook for Nurses

Compiles peer-reviewed research and literature reviews on issues regarding patient safety and quality of care, ranging from evidence-based practice, patient-centered care, and nurses' working conditions to critical opportunities and tools for improvement