Natural language generation for electronic health records.
Ontology highlight
ABSTRACT:
SUBMITTER: Lee SH
PROVIDER: S-EPMC6345174 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe prognosis, diagnosis, and treatment of many genetic disorders and familial diseases significantly improve if the family history (FH) of a patient is known. Such information is often written in the free text of clinical notes.ObjectiveThe aim of this study is to develop automated methods that enable access to FH data through natural language processing.MethodsWe performed information extraction by using transformers to extract disease mentions from notes. We also experimented with rule-based methods for extracting family member (FM) information from text and coreference resolution techniques. We evaluated different transfer learning strategies to improve the annotation of diseases. We provided a thorough error analysis of the contributing factors that affect such information extraction systems.ResultsOur experiments showed that the combination of domain-adaptive pretraining and intermediate-task pretraining achieved an F1 score of 81.63% for the extraction of diseases and FMs from notes when it was tested on a public shared task data set from the National Natural Language Processing Clinical Challenges (N2C2), providing a statistically significant improvement over the baseline (P<.001). In comparison, in the 2019 N2C2/Open Health Natural Language Processing Shared Task, the median F1 score of all 17 participating teams was 76.59%.ConclusionsOur approach, which leverages a state-of-the-art named entity recognition model for disease mention detection coupled with a hybrid method for FM mention detection, achieved an effectiveness that was close to that of the top 3 systems participating in the 2019 N2C2 FH extraction challenge, with only the top system convincingly outperforming our approach in terms of precision.
| S-EPMC8092929 | biostudies-literature
Project description:ObjectiveTo address thyroid cancer overdiagnosis, we aim to develop a natural language processing (NLP) algorithm to determine the appropriateness of thyroid ultrasounds (TUS).Patients and methodsBetween 2017 and 2021, we identified 18,000 TUS patients at Mayo Clinic and selected 628 for chart review to create a ground truth dataset based on consensus. We developed a rule-based NLP pipeline to identify TUS as appropriate TUS (aTUS) or inappropriate TUS (iTUS) using patients' clinical notes and additional meta information. In addition, we designed an abbreviated NLP pipeline (aNLP) solely focusing on labels from TUS order requisitions to facilitate deployment at other health care systems. Our dataset was split into a training set of 468 (75%) and a test set of 160 (25%), using the former for rule development and the latter for performance evaluation.ResultsThere were 449 (95.9%) patients identified as aTUS and 19 (4.06%) as iTUS in the training set; there are 155 (96.88%) patients identified as aTUS and 5 (3.12%) were iTUS in the test set. In the training set, the pipeline achieved a sensitivity of 0.99, specificity of 0.95, and positive predictive value of 1.0 for detecting aTUS. The testing cohort revealed a sensitivity of 0.96, specificity of 0.80, and positive predictive value of 0.99. Similar performance metrics were observed in the aNLP pipeline.ConclusionThe NLP models can accurately identify the appropriateness of a thyroid ultrasound from clinical documentation and order requisition information, a critical initial step toward evaluating the drivers and outcomes of TUS use and subsequent thyroid cancer overdiagnosis.
| S-EPMC10947349 | biostudies-literature
Project description:BackgroundSystemic lupus erythematosus (SLE) is a rare autoimmune disorder characterized by an unpredictable course of flares and remission with diverse manifestations. Lupus nephritis, one of the major disease manifestations of SLE for organ damage and mortality, is a key component of lupus classification criteria. Accurately identifying lupus nephritis in electronic health records (EHRs) would therefore benefit large cohort observational studies and clinical trials where characterization of the patient population is critical for recruitment, study design, and analysis. Lupus nephritis can be recognized through procedure codes and structured data, such as laboratory tests. However, other critical information documenting lupus nephritis, such as histologic reports from kidney biopsies and prior medical history narratives, require sophisticated text processing to mine information from pathology reports and clinical notes. In this study, we developed algorithms to identify lupus nephritis with and without natural language processing (NLP) using EHR data from the Northwestern Medicine Enterprise Data Warehouse (NMEDW).MethodsWe developed five algorithms: a rule-based algorithm using only structured data (baseline algorithm) and four algorithms using different NLP models. The first NLP model applied simple regular expression for keywords search combined with structured data. The other three NLP models were based on regularized logistic regression and used different sets of features including positive mention of concept unique identifiers (CUIs), number of appearances of CUIs, and a mixture of three components (i.e. a curated list of CUIs, regular expression concepts, structured data) respectively. The baseline algorithm and the best performing NLP algorithm were externally validated on a dataset from Vanderbilt University Medical Center (VUMC).ResultsOur best performing NLP model incorporated features from both structured data, regular expression concepts, and mapped concept unique identifiers (CUIs) and showed improved F measure in both the NMEDW (0.41 vs 0.79) and VUMC (0.52 vs 0.93) datasets compared to the baseline lupus nephritis algorithm.ConclusionOur NLP MetaMap mixed model improved the F-measure greatly compared to the structured data only algorithm in both internal and external validation datasets. The NLP algorithms can serve as powerful tools to accurately identify lupus nephritis phenotype in EHR for clinical research and better targeted therapies.
| S-EPMC10910523 | biostudies-literature
Project description:A serious obstacle to the development of Natural Language Processing (NLP) methods in the clinical domain is the accessibility of textual data. The mental health domain is particularly challenging, partly because clinical documentation relies heavily on free text that is difficult to de-identify completely. This problem could be tackled by using artificial medical data. In this work, we present an approach to generate artificial clinical documents. We apply this approach to discharge summaries from a large mental healthcare provider and discharge summaries from an intensive care unit. We perform an extensive intrinsic evaluation where we (1) apply several measures of text preservation; (2) measure how much the model memorises training data; and (3) estimate clinical validity of the generated text based on a human evaluation task. Furthermore, we perform an extrinsic evaluation by studying the impact of using artificial text in a downstream NLP text classification task. We found that using this artificial data as training data can lead to classification results that are comparable to the original results. Additionally, using only a small amount of information from the original data to condition the generation of the artificial data is successful, which holds promise for reducing the risk of these artificial data retaining rare information from the original data. This is an important finding for our long-term goal of being able to generate artificial clinical data that can be released to the wider research community and accelerate advances in developing computational methods that use healthcare data.
| S-EPMC7224173 | biostudies-literature
Project description:There is an urgent need to monitor the mental health of large populations, especially during crises such as the COVID-19 pandemic, to timely identify the most at-risk subgroups and to design targeted prevention campaigns. We therefore developed and validated surveillance indicators related to suicidality: the monthly number of hospitalisations caused by suicide attempts and the prevalence among them of five known risks factors. They were automatically computed analysing the electronic health records of fifteen university hospitals of the Paris area, France, using natural language processing algorithms based on artificial intelligence. We evaluated the relevance of these indicators conducting a retrospective cohort study. Considering 2,911,920 records contained in a common data warehouse, we tested for changes after the pandemic outbreak in the slope of the monthly number of suicide attempts by conducting an interrupted time-series analysis. We segmented the assessment time in two sub-periods: before (August 1, 2017, to February 29, 2020) and during (March 1, 2020, to June 31, 2022) the COVID-19 pandemic. We detected 14,023 hospitalisations caused by suicide attempts. Their monthly number accelerated after the COVID-19 outbreak with an estimated trend variation reaching 3.7 (95%CI 2.1-5.3), mainly driven by an increase among girls aged 8-17 (trend variation 1.8, 95%CI 1.2-2.5). After the pandemic outbreak, acts of domestic, physical and sexual violence were more often reported (prevalence ratios: 1.3, 95%CI 1.16-1.48; 1.3, 95%CI 1.10-1.64 and 1.7, 95%CI 1.48-1.98), fewer patients died (p = 0.007) and stays were shorter (p < 0.001). Our study demonstrates that textual clinical data collected in multiple hospitals can be jointly analysed to compute timely indicators describing mental health conditions of populations. Our findings also highlight the need to better take into account the violence imposed on women, especially at early ages and in the aftermath of the COVID-19 pandemic.
| S-EPMC10955903 | biostudies-literature
Project description:ObjectivesTo develop classification algorithms that accurately identify axial SpA (axSpA) patients in electronic health records, and compare the performance of algorithms incorporating free-text data against approaches using only International Classification of Diseases (ICD) codes.MethodsAn enriched cohort of 7853 eligible patients was created from electronic health records of two large hospitals using automated searches (⩾1 ICD codes combined with simple text searches). Key disease concepts from free-text data were extracted using NLP and combined with ICD codes to develop algorithms. We created both supervised regression-based algorithms-on a training set of 127 axSpA cases and 423 non-cases-and unsupervised algorithms to identify patients with high probability of having axSpA from the enriched cohort. Their performance was compared against classifications using ICD codes only.ResultsNLP extracted four disease concepts of high predictive value: ankylosing spondylitis, sacroiliitis, HLA-B27 and spondylitis. The unsupervised algorithm, incorporating both the NLP concept and ICD code for AS, identified the greatest number of patients. By setting the probability threshold to attain 80% positive predictive value, it identified 1509 axSpA patients (mean age 53 years, 71% male). Sensitivity was 0.78, specificity 0.94 and area under the curve 0.93. The two supervised algorithms performed similarly but identified fewer patients. All three outperformed traditional approaches using ICD codes alone (area under the curve 0.80-0.87).ConclusionAlgorithms incorporating free-text data can accurately identify axSpA patients in electronic health records. Large cohorts identified using these novel methods offer exciting opportunities for future clinical research.
| S-EPMC7850056 | biostudies-literature
Project description:BackgroundMulti-center electronic health records (EHR) can support quality improvement initiatives and comparative effectiveness research in stroke care. However, limitations of EHR-based research include challenges in abstracting key clinical variables from non-structured data at scale. This is further compounded by missing data. Here we develop a natural language processing (NLP) model that automatically reads EHR notes to determine the NIH stroke scale (NIHSS) score of patients with acute stroke.MethodsThe study included notes from acute stroke patients (>= 18 years) admitted to the Massachusetts General Hospital (MGH) (2015-2022). The MGH data were divided into training (70%) and hold-out test (30%) sets. A two-stage model was developed to predict the admission NIHSS. A linear model with the least absolute shrinkage and selection operator (LASSO) was trained within the training set. For notes in the test set where the NIHSS was documented, the scores were extracted using regular expressions (stage 1), for notes where NIHSS was not documented, LASSO was used for prediction (stage 2). The reference standard for NIHSS was obtained from Get With The Guidelines Stroke Registry. The two-stage model was tested on the hold-out test set and validated in the MIMIC-III dataset (Medical Information Mart for Intensive Care-MIMIC III 2001-2012) v1.4, using root mean squared error (RMSE) and Spearman correlation (SC).ResultsWe included 4,163 patients (MGH = 3,876; MIMIC = 287); average age of 69 [SD 15] years; 53% male, and 72% white. 90% patients had ischemic stroke and 10% hemorrhagic stroke. The two-stage model achieved a RMSE [95% CI] of 3.13 [2.86-3.41] (SC = 0.90 [0.88-0. 91]) in the MGH hold-out test set and 2.01 [1.58-2.38] (SC = 0.96 [0.94-0.97]) in the MIMIC validation set.ConclusionsThe automatic NLP-based model can enable large-scale stroke severity phenotyping from EHR and therefore support real-world quality improvement and comparative effectiveness studies in stroke.
| S-EPMC10980121 | biostudies-literature
Project description:AimsThis study aimed to develop and apply natural language processing (NLP) algorithms to identify recurrent atrial fibrillation (AF) episodes following rhythm control therapy initiation using electronic health records (EHRs).Methods and resultsWe included adults with new-onset AF who initiated rhythm control therapies (ablation, cardioversion, or antiarrhythmic medication) within two US integrated healthcare delivery systems. A code-based algorithm identified potential AF recurrence using diagnosis and procedure codes. An automated NLP algorithm was developed and validated to capture AF recurrence from electrocardiograms, cardiac monitor reports, and clinical notes. Compared with the reference standard cases confirmed by physicians' adjudication, the F-scores, sensitivity, and specificity were all above 0.90 for the NLP algorithms at both sites. We applied the NLP and code-based algorithms to patients with incident AF (n = 22 970) during the 12 months after initiating rhythm control therapy. Applying the NLP algorithms, the percentages of patients with AF recurrence for sites 1 and 2 were 60.7% and 69.9% (ablation), 64.5% and 73.7% (cardioversion), and 49.6% and 55.5% (antiarrhythmic medication), respectively. In comparison, the percentages of patients with code-identified AF recurrence for sites 1 and 2 were 20.2% and 23.7% for ablation, 25.6% and 28.4% for cardioversion, and 20.0% and 27.5% for antiarrhythmic medication, respectively.ConclusionWhen compared with a code-based approach alone, this study's high-performing automated NLP method identified significantly more patients with recurrent AF. The NLP algorithms could enable efficient evaluation of treatment effectiveness of AF therapies in large populations and help develop tailored interventions.
| S-EPMC10785579 | biostudies-literature
Project description:ObjectiveSocial determinants of health (SDoH) are nonclinical dispositions that impact patient health risks and clinical outcomes. Leveraging SDoH in clinical decision-making can potentially improve diagnosis, treatment planning, and patient outcomes. Despite increased interest in capturing SDoH in electronic health records (EHRs), such information is typically locked in unstructured clinical notes. Natural language processing (NLP) is the key technology to extract SDoH information from clinical text and expand its utility in patient care and research. This article presents a systematic review of the state-of-the-art NLP approaches and tools that focus on identifying and extracting SDoH data from unstructured clinical text in EHRs.Materials and methodsA broad literature search was conducted in February 2021 using 3 scholarly databases (ACL Anthology, PubMed, and Scopus) following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. A total of 6402 publications were initially identified, and after applying the study inclusion criteria, 82 publications were selected for the final review.ResultsSmoking status (n = 27), substance use (n = 21), homelessness (n = 20), and alcohol use (n = 15) are the most frequently studied SDoH categories. Homelessness (n = 7) and other less-studied SDoH (eg, education, financial problems, social isolation and support, family problems) are mostly identified using rule-based approaches. In contrast, machine learning approaches are popular for identifying smoking status (n = 13), substance use (n = 9), and alcohol use (n = 9).ConclusionNLP offers significant potential to extract SDoH data from narrative clinical notes, which in turn can aid in the development of screening tools, risk prediction models, and clinical decision support systems.
| S-EPMC8633615 | biostudies-literature
Project description:There is an increasing interest in developing artificial intelligence (AI) systems to process and interpret electronic health records (EHRs). Natural language processing (NLP) powered by pretrained language models is the key technology for medical AI systems utilizing clinical narratives. However, there are few clinical language models, the largest of which trained in the clinical domain is comparatively small at 110 million parameters (compared with billions of parameters in the general domain). It is not clear how large clinical language models with billions of parameters can help medical AI systems utilize unstructured EHRs. In this study, we develop from scratch a large clinical language model-GatorTron-using >90 billion words of text (including >82 billion words of de-identified clinical text) and systematically evaluate it on five clinical NLP tasks including clinical concept extraction, medical relation extraction, semantic textual similarity, natural language inference (NLI), and medical question answering (MQA). We examine how (1) scaling up the number of parameters and (2) scaling up the size of the training data could benefit these NLP tasks. GatorTron models scale up the clinical language model from 110 million to 8.9 billion parameters and improve five clinical NLP tasks (e.g., 9.6% and 9.5% improvement in accuracy for NLI and MQA), which can be applied to medical AI systems to improve healthcare delivery. The GatorTron models are publicly available at: https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/models/gatortron_og .
| S-EPMC9792464 | biostudies-literature