Acute kidney injury (AKI) is a complex disorder for which currently there is no accepted definition. Having a uniform standard for diagnosing and classifying AKI would enhance our ability to manage these patients. Future clinical and translational research in AKI will require collaborative networks of investigators drawn from various disciplines, dissemination of information via multidisciplinary joint conferences and publications, and improved translation of knowledge from pre-clinical research. We describe an initiative to develop uniform standards for defining and classifying AKI and to establish a forum for multidisciplinary interaction to improve care for patients with or at risk for AKI. Members representing key societies in critical care and nephrology along with additional experts in adult and pediatric AKI participated in a two day conference in Amsterdam, The Netherlands, in September 2005 and were assigned to one of three workgroups. Each group's discussions formed the basis for draft recommendations that were later refined and improved during discussion with the larger group. Dissenting opinions were also noted. The final draft recommendations were circulated to all participants and subsequently agreed upon as the consensus recommendations for this report. Participating societies endorsed the recommendations and agreed to help disseminate the results. The term AKI is proposed to represent the entire spectrum of acute renal failure. Diagnostic criteria for AKI are proposed based on acute alterations in serum creatinine or urine output. A staging system for AKI which reflects quantitative changes in serum creatinine and urine output has been developed. We describe the formation of a multidisciplinary collaborative network focused on AKI. We have proposed uniform standards for diagnosing and classifying AKI which will need to be validated in future studies. The Acute Kidney Injury Network offers a mechanism for proceeding with efforts to improve patient outcomes.

Acute Kidney Injury Network: report of an initiative to improve outcomes in acute kidney injury

Clinical information extraction applications: A literature review.

A systematic literature review on obesity: Understanding the causes & consequences of obesity and reviewing various machine learning approaches used to predict obesity.

Background: Clinical narratives represent the main form of communication within healthcare providing a personalized account of patient history and assessments, offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. Objective: The main aim of this study is to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigate the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. Methods: Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multi-faceted interface, to perform a literature search against MEDLINE. We identified a total of 110 relevant studies and extracted information about the text data used to support machine learning, the NLP tasks supported and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation and any relevant statistics. Results: The vast majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable due to sensitive nature of data considered. Beside the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The vast majority of studies focused on the task of text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management and surveillance. Conclusions: We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which does not require data annotation.

/pdf/clinical-text-data-in-machine-learning-systematic-review-2dxod9n6lm.pdf

Clinical Text Data in Machine Learning: Systematic Review.

With the widespread adoption of electronic health records (EHRs), large repositories of structured and unstructured patient data are becoming available to conduct observational studies. Finding patients with specific conditions or outcomes, known as phenotyping, is one of the most fundamental research problems encountered when using these new EHR data. Phenotyping forms the basis of translational research, comparative effectiveness studies, clinical decision support, and population health analyses using routinely collected EHR data. We review the evolution of electronic phenotyping, from the early rule-based methods to the cutting edge of supervised and unsupervised machine learning models. We aim to cover the most influential papers in commensurate detail, with a focus on both methodology and implementation. Finally, future research directions are explored.

Advances in Electronic Phenotyping: From Rule-Based Definitions to Machine Learning Models.

Acute Kidney Injury Incidence in Noncritically Ill Hospitalized Children, Adolescents, and Young Adults: A Retrospective Observational Study

Objective: The objective of this study is to develop an algorithm to accurately identify children with severe early onset childhood obesity (ages 1–5.99 years) using structured and unstructured data from the electronic health record (EHR). Introduction: Childhood obesity increases risk factors for cardiovascular morbidity and vascular disease. Accurate definition of a high precision phenotype through a standardize tool is critical to the success of large-scale genomic studies and validating rare monogenic variants causing severe early onset obesity. Data and Methods: Rule based and machine learning based algorithms were developed using structured and unstructured data from two EHR databases from Boston Children’s Hospital (BCH) and Cincinnati Children’s Hospital and Medical Center (CCHMC). Exclusion criteria including medications or comorbid diagnoses were defined. Machine learning algorithms were developed using cross-site training and testing in addition to experimenting with natural language processing features. Results: Precision was emphasized for a high fidelity cohort. The rule-based algorithm performed the best overall, 0.895 (CCHMC) and 0.770 (BCH). The best feature set for machine learning employed Unified Medical Language System (UMLS) concept unique identifiers (CUIs), ICD-9 codes, and RxNorm codes. Conclusions: Detecting severe early childhood obesity is essential for the intervention potential in children at the highest long-term risk of developing comorbidities related to obesity and excluding patients with underlying pathological and non-syndromic causes of obesity assists in developing a high-precision cohort for genetic study. Further such phenotyping efforts inform future practical application in health care environments utilizing clinical decision support.

/pdf/developing-an-algorithm-to-detect-early-childhood-obesity-in-4ig1sgwpzn.pdf

Developing an algorithm to detect early childhood obesity in two tertiary pediatric medical centers

Acute kidney injury (AKI) is common in pediatric inpatients and is associated with increased morbidity, mortality, and length of stay. Its early identification can reduce severity. To create and validate an electronic health record (EHR)-based AKI screening tool, we generated temporally distinct development and validation cohorts using retrospective data from our tertiary care children’s hospital, including children aged 28 days through 21 years with sufficient serum creatinine measurements to determine AKI status. AKI was defined as 1.5-fold or 0.3 mg/dl increase in serum creatinine. Age, medication exposures, platelet count, red blood cell distribution width, serum phosphorus, serum transaminases, hypotension (ICU only), and pH (ICU only) were included in AKI risk prediction models. For ICU patients, 791/1,332 (59%) of the development cohort and 470/866 (54%) of the validation cohort had AKI. In external validation, the ICU prediction model had a c-statistic=0.74 (95% confidence interval 0.71–0.77). For non-ICU patients, 722/2,337 (31%) of the development cohort and 469/1,474 (32%) of the validation cohort had AKI, and the prediction model had a c-statistic=0.69 (95% confidence interval 0.66–0.72). AKI screening can be performed using EHR data. The AKI screening tool can be incorporated into EHR systems to identify high-risk patients without serum creatinine data, enabling targeted laboratory testing, early AKI identification, and modification of care.

/pdf/electronic-health-record-based-predictive-models-for-acute-30pa221mxz.pdf

Electronic health record-based predictive models for acute kidney injury screening in pediatric inpatients

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Acute Kidney Injury Incidence in Noncritically Ill Hospitalized Children, Adolescents, and Young Adults: A Retrospective Observational Study

Developing an algorithm to detect early childhood obesity in two tertiary pediatric medical centers

Electronic health record-based predictive models for acute kidney injury screening in pediatric inpatients