Automatic keyword assignment system for medical research articles using nearest-neighbor searches

Assigning accurate keywords to research articles is increasingly important concern. Keywords should be selected meticulously to describe the article well since keywords play an important role in matching readers with research articles in order to reach a bigger audience. So, improper selection of keywords may result in less attraction to readers which results in degradation in its audience. Hence, we designed and developed an automatic keyword assignment system (AKAS) for research articles based on k-nearest neighbor (k-NN) and threshold-nearest neighbor (t-NN) accompanied with information retrieval systems (IRS), which is a corpus-based method by utilizing IRS using the Medline dataset in PubMed. First, AKAS accepts an abstract of the research article or a particular text as a query to the IRS. Next, the IRS returns a ranked list of articles to the given query. Then, we selected a set of documents from this list using two different methods, which are k-NN and t-NN representing the first k documents and documents whose similarity is greater than the threshold value of t, respectively. To evaluate our proposed system, we conducted a set of experiments on a selected subset of 458,594 PubMed articles. Then, we performed an experiment to observe the performance of AKAS results by comparing with the original keywords assigned by authors. The results we obtained showed that our system suggests keywords more than 55% match in terms of F-score. We presented both methods we used and results of experiments, in detail

Finding Important Terms for Patients in Their Electronic Health Records: A Learning-to-Rank Approach Using Expert Annotations

BACKGROUND: Many health organizations allow patients to access their own electronic health record (EHR) notes through online patient portals as a way to enhance patient-centered care. However, EHR notes are typically long and contain abundant medical jargon that can be difficult for patients to understand. In addition, many medical terms in patients\u27 notes are not directly related to their health care needs. One way to help patients better comprehend their own notes is to reduce information overload and help them focus on medical terms that matter most to them. Interventions can then be developed by giving them targeted education to improve their EHR comprehension and the quality of care. OBJECTIVE: We aimed to develop a supervised natural language processing (NLP) system called Finding impOrtant medical Concepts most Useful to patientS (FOCUS) that automatically identifies and ranks medical terms in EHR notes based on their importance to the patients. METHODS: First, we built an expert-annotated corpus. For each EHR note, 2 physicians independently identified medical terms important to the patient. Using the physicians\u27 agreement as the gold standard, we developed and evaluated FOCUS. FOCUS first identifies candidate terms from each EHR note using MetaMap and then ranks the terms using a support vector machine-based learn-to-rank algorithm. We explored rich learning features, including distributed word representation, Unified Medical Language System semantic type, topic features, and features derived from consumer health vocabulary. We compared FOCUS with 2 strong baseline NLP systems. RESULTS: Physicians annotated 90 EHR notes and identified a mean of 9 (SD 5) important terms per note. The Cohen\u27s kappa annotation agreement was .51. The 10-fold cross-validation results show that FOCUS achieved an area under the receiver operating characteristic curve (AUC-ROC) of 0.940 for ranking candidate terms from EHR notes to identify important terms. When including term identification, the performance of FOCUS for identifying important terms from EHR notes was 0.866 AUC-ROC. Both performance scores significantly exceeded the corresponding baseline system scores (P \u3c .001). Rich learning features contributed to FOCUS\u27s performance substantially. CONCLUSIONS: FOCUS can automatically rank terms from EHR notes based on their importance to patients. It may help develop future interventions that improve quality of care

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