Clinical text data in machine learning: Systematic review

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

Life Sciences Program Tasks and Bibliography for FY 1997

This document includes information on all peer reviewed projects funded by the Office of Life and Microgravity Sciences and Applications, Life Sciences Division during fiscal year 1997. This document will be published annually and made available to scientists in the space life sciences field both as a hard copy and as an interactive internet web page

Separator fluid volume requirements in multi-infusion settings

INTRODUCTION. Intravenous (IV) therapy is a widely used method for the administration of medication in hospitals worldwide. ICU and surgical patients in particular often require multiple IV catheters due to incompatibility of certain drugs and the high complexity of medical therapy. This increases discomfort by painful invasive procedures, the risk of infections and costs of medication and disposable considerably. When different drugs are administered through the same lumen, it is common ICU practice to flush with a neutral fluid between the administration of two incompatible drugs in order to optimally use infusion lumens. An important constraint for delivering multiple incompatible drugs is the volume of separator fluid that is sufficient to safely separate them. OBJECTIVES. In this pilot study we investigated whether the choice of separator fluid, solvent, or administration rate affects the separator volume required in a typical ICU infusion setting. METHODS. A standard ICU IV line (2m, 2ml, 1mm internal diameter) was filled with methylene blue (40 mg/l) solution and flushed using an infusion pump with separator fluid. Independent variables were solvent for methylene blue (NaCl 0.9% vs. glucose 5%), separator fluid (NaCl 0.9% vs. glucose 5%), and administration rate (50, 100, or 200 ml/h). Samples were collected using a fraction collector until <2% of the original drug concentration remained and were analyzed using spectrophotometry. RESULTS. We did not find a significant effect of administration rate on separator fluid volume. However, NaCl/G5% (solvent/separator fluid) required significantly less separator fluid than NaCl/NaCl (3.6 ± 0.1 ml vs. 3.9 ± 0.1 ml, p <0.05). Also, G5%/G5% required significantly less separator fluid than NaCl/NaCl (3.6 ± 0.1 ml vs. 3.9 ± 0.1 ml, p <0.05). The significant decrease in required flushing volume might be due to differences in the viscosity of the solutions. However, mean differences were small and were most likely caused by human interactions with the fluid collection setup. The average required flushing volume is 3.7 ml. CONCLUSIONS. The choice of separator fluid, solvent or administration rate had no impact on the required flushing volume in the experiment. Future research should take IV line length, diameter, volume and also drug solution volumes into account in order to provide a full account of variables affecting the required separator fluid volume

ESICM LIVES 2017 : 30th ESICM Annual Congress. September 23-27, 2017.

INTRODUCTION. Unplanned readmission to intensive care is highly undesirable in that it contributes to increased variance in care, disruption, difficulty in resource allocation and may increase length of stay and mortality particularly if subject to delays. Unlike the ICU admission from the ward, readmission prediction has received relatively little attention, perhaps in part because at the point of ICU discharge, full physiological information is systematically available to the clinician and so it is expected that readmission should be largely due to unpredictable factors. However it may be that there are multidimensional trends that are difficult for the clinician to perceive that may nevertheless be predictive of readmission. OBJECTIVES. We investigated whether machine learning (ML) techniques could be used to improve on the simple published SWIFT score [1] for the prediction of unplanned readmission to ICU within 48 hours. METHODS. We extracted systolic BP, pulse pressure, heart and respiration rate, temperature, SpO2, bilirubin, creatinine, INR, lactate, white cell count, platelet count, pH, FiO2, and total Glasgow Coma Score from ICU stays of over 2000 adult patients from our hospital electronic patient record system. We trained our own custom multidimensional / time-sensitive algorithmic ML system to predict failed discharges defined as either readmission or unexpected death within 48 hours of discharge. We used 10-fold cross validation to assess performance. We also assessed the effect of augmenting our system by transfer learning (TL) with 44,000 additional cases from the MIMIC III database. RESULTS. The SWIFT score performed relatively poorly with an AUROC of around 0.6 which our ML system trained on local data was also able to match. However when augmented with an additional dataset by TL, the AUROC for the ML system improved statistically and clinically significantly to over 0.7. CONCLUSIONS. Machine learning is able to improve on predictors based on simple multiple logistic regression. Thus there is likely to be information in the trends and in combinations of variables. A disadvantage with this technique is that ML approaches require large amounts of data for training. However, ML approaches can be improved by TL. Basing prediction models on locally derived data augmented by TL is a potentially novel approach to generating tools that customised to the institution yet can exploit the potential power of ML algorithms. REFERENCES [1] Gajic O, Malinchoc M, Comfere TB, et al. The Stability and Workload Index for Transfer score predicts unplanned intensive care unit patient readmission: initial development and validation. Crit Care Med. 2008;36(3):676–82. Grant Acknowledgement This work was internally funded