Differential Diagnosis Documentation In Emergency Medicine

Diagnosis is a central aspect of emergency medicine. Coming to the correct diagnosis impacts patient morbidity and mortality and also the healthcare expenditures. Medical decision making is driven by the path of figuring out the differential diagnosis. Once a decent Natural Language Processing (NLP) system is developed including general characterization of differential diagnose, associated with downstream testing, diagnostic error, etc., we could be able to automatically extract differential diagnoses within clinical notes, which would have a large impact on healthcare. The main purpose of our investigative study is the characterization of differential diagnosis documentation within emergency provider notes and the development of an annotated corpus that could be used for further downstream development of NLP applications. We conducted a retrospective analysis of emergency provider notes to identify, categorize, and extract information around differential diagnoses using manual annotation. We used a light annotation framework within the MATTER cycle and extracted the information from our annotations based on a random sample of 1545 medical records. We describe the demographics information and note that only 18.1% of patients were actually given a differential diagnosis by the physicians. We examined factors including age groups, race and ethnicity groups, language preferred, acuity level, and major complaints that could lead to differences in differential diagnosis rates among patients. Within the differential diagnosis groups, evidence support and probability terms are reported. We also examined cough, chest pain, shortness of breath, abdominal pain, back pain, and falling, which are the top six complaints. Still, we suffered from limitations including sample size, nature of the accuracy of annotations, etc

Named Entity Recognition in Chinese Clinical Text

Objective: Named entity recognition (NER) is one of the fundamental tasks in natural language processing (NLP). In the medical domain, there have been a number of studies on NER in English clinical notes; however, very limited NER research has been done on clinical notes written in Chinese. The goal of this study is to develop corpora, methods, and systems for NER in Chinese clinical text. Materials and methods: To study entities in Chinese clinical text, we started with building annotated clinical corpora in Chinese. We developed an NER annotation guideline in Chinese by extending the one used in the 2010 i2b2 NLP challenge. We randomly selected 400 admission notes and 400 discharge summaries from Peking Union Medical College Hospital (PUMCH) in China. For each note, four types of entities including clinical problems, procedures, labs, and medications were annotated according to the developed guideline. In addition, an annotation tool was developed to assist two MD students to annotate Chinese clinical documents. A comparison of entity distribution between Chinese and English clinical notes (646 English and 400 Chinese discharge summaries) was performed using the annotated corpora, to identify the important features for NER. In the NER study, two-thirds of the 400 notes were used for training the NER systems and one-third were used for testing. We investigated the effects of different types of features including bag-of-characters, word segmentation, part-of-speech, and section information, with different machine learning (ML) algorithms including Conditional Random Fields (CRF), Support Vector Machines (SVM), Maximum Entropy (ME), and Structural Support Vector Machines (SSVM) on the Chinese clinical NER task. All classifiers were trained on the training dataset, evaluated on the test set, and microaveraged precision, recall, and F-measure were reported. Results: Our evaluation on the independent test set showed that most types of features were beneficial to Chinese NER systems, although the improvements were limited. By combining word segmentation and section information, the system achieved the highest performance, indicating that these two types of features are complementary to each other. When the same types of optimized features were used, CRF and SSVM outperformed SVM and ME. More specifically, SSVM reached the highest performance among the four algorithms, with F-measures of 93.51% and 90.01% for admission notes and discharge summaries respectively. Conclusions: In this study, we created large annotated datasets of Chinese admission notes and discharge summaries and then systematically evaluated different types of features (e.g., syntactic, semantic, and segmentation information) and four ML algorithms including CRF, SVM, SSVM, and ME for clinical NER in Chinese. To the best of our knowledge, this is one of the earliest comprehensive effort in Chinese clinical NER research and we believe it will provide valuable insights to NLP research in Chinese clinical text. Our results suggest that both word segmentation and section information improves NER in Chinese clinical text, and SSVM, a recent sequential labelling algorithm, outperformed CRF and other classification algorithms. Our best system achieved F-measures of 90.01% and 93.52% on Chinese discharge summaries and admission notes, respectively, indicating a promising start on Chinese NLP research

DEVELOPING A CLINICAL LINGUISTIC FRAMEWORK FOR PROBLEM LIST GENERATION FROM CLINICAL TEXT

Regulatory institutions such as the Institute of Medicine and Joint Commission endorse problem lists as an effective method to facilitate transitions of care for patients. In practice, the problem list is a common model for documenting a care provider's medical reasoning with respect to a problem and its status during patient care. Although natural language processing (NLP) systems have been developed to support problem list generation, encoding many information layers - morphological, syntactic, semantic, discourse, and pragmatic - can prove computationally expensive. The contribution of each information layer for accurate problem list generation has not been formally assessed. We would expect a problem list generator that relies on natural language processing would improve its performance with the addition of rich semantic features We hypothesize that problem list generation can be approached as a two-step classification problem - problem mention status (Aim One) and patient problem status (Aim Two) classification. In Aim One, we will automatically classify the status of each problem mention using semantic features about problems described in the clinical narrative. In Aim Two, we will classify active patient problems from individual problem mentions and their statuses. We believe our proposal is significant in two ways. First, our experiments will develop and evaluate semantic features, some commonly modeled and others not in the clinical text. The annotations we use will be made openly available to other NLP researchers to encourage future research on this task and other related problems including foundational NLP algorithms (assertion classification and coreference resolution) and applied clinical applications (patient timeline and record visualization). Second, by generating and evaluating existing NLP systems, we are building an open-source problem list generator and demonstrating the performance for problem list generation using these features

Text mining patient experiences from online health communities

Social media has had an impact on how patients experience healthcare. Through online channels, patients are sharing information and their experiences with potentially large audiences all over the world. While sharing in this way may offer immediate benefits to themselves and their readership (e.g. other patients) these unprompted, self-authored accounts of illness are also an important resource for healthcare researchers. They offer unprecedented insight into understanding patients’experience of illness. Work has been undertaken through qualitative analysis in order to explore this source of data and utilising the information expressed through these media. However, the manual nature of the analysis means that scope is limited to a small proportion of the hundreds of thousands of authors who are creating content. In our research, we aim to explore utilising text mining to support traditional qualitative analysis of this data. Text mining uses a number of processes in order to extract useful facts from text and analyse patterns within – the ultimate aim is to generate new knowledge by analysing textual data en mass. We developed QuTiP – a Text Mining framework which can enable large scale qualitative analyses of patient narratives shared over social media. In this thesis, we describe QuTiP and our application of the framework to analyse the accounts of patients living with chronic lung disease. As well as a qualitative analysis, we describe our approaches to automated information extraction, term recognition and text classification in order to automatically extract relevant information from blog post data. Within the QuTiP framework, these individual automated approaches can be brought together to support further analyses of large social media datasets

Extracção de informação médica em português europeu

Doutoramento em Engenharia InformáticaThe electronic storage of medical patient data is becoming a daily experience in most of the practices and hospitals worldwide. However, much of the data available is in free-form text, a convenient way of expressing concepts and events, but especially challenging if one wants to perform automatic searches, summarization or statistical analysis. Information Extraction can relieve some of these problems by offering a semantically informed interpretation and abstraction of the texts. MedInX, the Medical Information eXtraction system presented in this document, is the first information extraction system developed to process textual clinical discharge records written in Portuguese. The main goal of the system is to improve access to the information locked up in unstructured text, and, consequently, the efficiency of the health care process, by allowing faster and reliable access to quality information on health, for both patient and health professionals. MedInX components are based on Natural Language Processing principles, and provide several mechanisms to read, process and utilize external resources, such as terminologies and ontologies, in the process of automatic mapping of free text reports onto a structured representation. However, the flexible and scalable architecture of the system, also allowed its application to the task of Named Entity Recognition on a shared evaluation contest focused on Portuguese general domain free-form texts. The evaluation of the system on a set of authentic hospital discharge letters indicates that the system performs with 95% F-measure, on the task of entity recognition, and 95% precision on the task of relation extraction. Example applications, demonstrating the use of MedInX capabilities in real applications in the hospital setting, are also presented in this document. These applications were designed to answer common clinical problems related with the automatic coding of diagnoses and other health-related conditions described in the documents, according to the international classification systems ICD-9-CM and ICF. The automatic review of the content and completeness of the documents is an example of another developed application, denominated MedInX Clinical Audit system.O armazenamento electrónico dos dados médicos do paciente é uma prática cada vez mais comum nos hospitais e clínicas médicas de todo o mundo. No entanto, a maior parte destes dados são disponibilizados sob a forma de texto livre, uma forma conveniente de expressar conceitos e termos mas particularmente desafiante quando se pretende realizar procuras, sumarização ou análise estatística de uma forma automática. As tecnologias de extracção automática de informação podem ajudar a solucionar alguns destes problemas através da interpretação semântica e da abstracção do conteúdo dos textos. O sistema de Extracção de Informação Médica apresentado neste documento, o MedInX, é o primeiro sistema desenvolvido para o processamento de cartas de alta hospitalar escritas em Português. O principal objectivo do sistema é a melhoria do acesso à informação trancada nos textos e, consequentemente, a melhoria da eficiência dos cuidados de saúde, através do acesso rápido e confiável à informação, quer relativa ao doente, quer aos profissionais de saúde. O MedInX utiliza diversas componentes, baseadas em princípios de processamento de linguagem natural, para a análise dos textos clínicos, e contém vários mecanismos para ler, processar e utilizar recursos externos, como terminologias e ontologias. Este recursos são utilizados, em particular, no mapeamento automático do texto livre para uma representação estruturada. No entanto, a arquitectura flexível e escalável do sistema permitiu, também, a sua aplicação na tarefa de Reconhecimento de Entidades Nomeadas numa avaliação conjunta relativa ao processamento de textos de domínio geral, escritos em Português. A avaliação do sistema num conjunto de cartas de alta hospitalar reais, indica que o sistema realiza a tarefa de extracção de informação com uma medida F de 95% e a tarefa de extracção de relações com uma precisão de 95%. A utilidade do sistema em aplicações reais é demonstrada através do desenvolvimento de um conjunto de projectos exemplificativos, que pretendem responder a problemas concretos e comuns em ambiente hospitalar. Estes problemas estão relacionados com a codificação automática de diagnósticos e de outras condições relacionadas com o estado de saúde do doente, seguindo as classificações internacionais, ICD-9-CM e ICF. A revisão automática do conteúdo dos documentos é outro exemplo das possíveis aplicações práticas do sistema. Esta última aplicação é representada pelo o sistema de auditoria do MedInX

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