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Automatic identification of high impact articles in PubMed to support clinical decision making.

ABSTRACT: OBJECTIVES:The practice of evidence-based medicine involves integrating the latest best available evidence into patient care decisions. Yet, critical barriers exist for clinicians' retrieval of evidence that is relevant for a particular patient from primary sources such as randomized controlled trials and meta-analyses. To help address those barriers, we investigated machine learning algorithms that find clinical studies with high clinical impact from PubMed®. METHODS:Our machine learning algorithms use a variety of features including bibliometric features (e.g., citation count), social media attention, journal impact factors, and citation metadata. The algorithms were developed and evaluated with a gold standard composed of 502 high impact clinical studies that are referenced in 11 clinical evidence-based guidelines on the treatment of various diseases. We tested the following hypotheses: (1) our high impact classifier outperforms a state-of-the-art classifier based on citation metadata and citation terms, and PubMed's® relevance sort algorithm; and (2) the performance of our high impact classifier does not decrease significantly after removing proprietary features such as citation count. RESULTS:The mean top 20 precision of our high impact classifier was 34% versus 11% for the state-of-the-art classifier and 4% for PubMed's® relevance sort (p=0.009); and the performance of our high impact classifier did not decrease significantly after removing proprietary features (mean top 20 precision=34% vs. 36%; p=0.085). CONCLUSION:The high impact classifier, using features such as bibliometrics, social media attention and MEDLINE® metadata, outperformed previous approaches and is a promising alternative to identifying high impact studies for clinical decision support.

SUBMITTER: Bian J

PROVIDER: S-EPMC5583030 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Automatic identification of high impact articles in PubMed to support clinical decision making.

Bian Jiantao J Morid Mohammad Amin MA Jonnalagadda Siddhartha S Luo Gang G Del Fiol Guilherme G

Journal of biomedical informatics 20170726

<h4>Objectives</h4>The practice of evidence-based medicine involves integrating the latest best available evidence into patient care decisions. Yet, critical barriers exist for clinicians' retrieval of evidence that is relevant for a particular patient from primary sources such as randomized controlled trials and meta-analyses. To help address those barriers, we investigated machine learning algorithms that find clinical studies with high clinical impact from PubMed®.<h4>Methods</h4>Our machine ...[more]

PMID: 28756159

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Project description:BackgroundElectronic medical records are widely used in family practices across Canada and can improve health outcomes. However, recent reports indicate that physicians using electronic medical records work longer and have less direct patient contact which may contribute to burnout. Therefore, new and innovative digital tools are essential to reduce physician workloads and improve patient-physician interaction to address physician burnout. The objective of this study was to assess the efficiency and accuracy of clinical decision-making when using a new preventive care point-of-care clinical decision support system (CDSS). An estimate of the potential annual time savings was also determined. This study also assessed physician reported perceived usefulness and ease of use of the CDSS.MethodsQuantitative and qualitative data were collected during this study. Each participant evaluated two simulated patient charts and identified which preventive care metrics were due. The participants recorded their decisions and the time required to assess each chart. Participants then completed a Technology Acceptance Model survey regarding the perceived usefulness and ease of use of the CDSS, which included qualitative feedback. The amount of time saved was determined and participants' clinical decision-making accuracy was scored against current Canadian preventive care guidelines. The number of preventive care specific visits completed per year was determined using clinic billing data.ResultsThe preventive care CDSS saved an average of 195.7 s of chart review time (249.5 s vs 445.2 s; P < 0.001). A total of 1520 preventive visits were performed at Primrose and Bruyère Family Medicine Centres. Extrapolated across the organization, implementation of the new tool could save 82.6 h per year. Decision-making accuracy was not affected by the new tool (78.4% vs 80.9%, P > 0.05). Participants rated the perceived ease of use and usefulness to be very high.ConclusionsNew digital tools may reduce providers' workload without impacting clinical decision-making accuracy. Participants indicated that the preventive care CDSS was useful and easy to use. Further software development and clinical studies are required to further improve and characterize the effect this new CDSS has when implemented in clinical practice.

Project description:During the last years, the increasing number of DNA sequencing and protein mutagenesis studies has generated a large amount of variation data published in the biomedical literature. The collection of such data has been essential for the development and assessment of tools predicting the impact of protein variants at functional and structural levels. Nevertheless, the collection of manually curated data from literature is a highly time consuming and costly process that requires domain experts. In particular, the development of methods for predicting the effect of amino acid variants on protein stability relies on the thermodynamic data extracted from literature. In the past, such data were deposited in the ProTherm database, which however is no longer maintained since 2013. For facilitating the collection of protein thermodynamic data from literature, we developed the semi-automatic tool ThermoScan. ThermoScan is a text mining approach for the identification of relevant thermodynamic data on protein stability from full-text articles. The method relies on a regular expression searching for groups of words, including the most common conceptual words appearing in experimental studies on protein stability, several thermodynamic variables, and their units of measure. ThermoScan analyzes full-text articles from the PubMed Central Open Access subset and calculates an empiric score that allows the identification of manuscripts reporting thermodynamic data on protein stability. The method was optimized on a set of publications included in the ProTherm database, and tested on a new curated set of articles, manually selected for presence of thermodynamic data. The results show that ThermoScan returns accurate predictions and outperforms recently developed text-mining algorithms based on the analysis of publication abstracts. Availability: The ThermoScan server is freely accessible online at https://folding.biofold.org/thermoscan. The ThermoScan python code and the Google Chrome extension for submitting visualized PMC web pages to the ThermoScan server are available at https://github.com/biofold/ThermoScan.

Project description:Involvement of many variables, uncertainty in treatment response, and inter-patient heterogeneity challenge objective decision-making in dynamic treatment regime (DTR) in oncology. Advanced machine learning analytics in conjunction with information-rich dense multi-omics data have the ability to overcome such challenges. We have developed a comprehensive artificial intelligence (AI)-based optimal decision-making framework for assisting oncologists in DTR. In this work, we demonstrate the proposed framework to Knowledge Based Response-Adaptive Radiotherapy (KBR-ART) applications by developing an interactive software tool entitled Adaptive Radiotherapy Clinical Decision Support (ARCliDS). ARCliDS is composed of two main components: Artifcial RT Environment (ARTE) and Optimal Decision Maker (ODM). ARTE is designed as a Markov decision process and modeled via supervised learning. Given a patient's pre- and during-treatment information, ARTE can estimate treatment outcomes for a selected daily dosage value (radiation fraction size). ODM is formulated using reinforcement learning and is trained on ARTE. ODM can recommend optimal daily dosage adjustments to maximize the tumor local control probability and minimize the side effects. Graph Neural Networks (GNN) are applied to exploit the inter-feature relationships for improved modeling performance and a novel double GNN architecture is designed to avoid nonphysical treatment response. Datasets of size 117 and 292 were available from two clinical trials on adaptive RT in non-small cell lung cancer (NSCLC) patients and adaptive stereotactic body RT (SBRT) in hepatocellular carcinoma (HCC) patients, respectively. For training and validation, dense data with 297 features were available for 67 NSCLC patients and 110 features for 71 HCC patients. To increase the sample size for ODM training, we applied Generative Adversarial Networks to generate 10,000 synthetic patients. The ODM was trained on the synthetic patients and validated on the original dataset. We found that, Double GNN architecture was able to correct the nonphysical dose-response trend and improve ARCliDS recommendation. The average root mean squared difference (RMSD) between ARCliDS recommendation and reported clinical decisions using double GNNs were 0.61 [0.03] Gy/frac (mean [sem]) for adaptive RT in NSCLC patients and 2.96 [0.42] Gy/frac for adaptive SBRT HCC compared to the single GNN's RMSDs of 0.97 [0.12] Gy/frac and 4.75 [0.16] Gy/frac, respectively. Overall, For NSCLC and HCC, ARCliDS with double GNNs was able to reproduce 36% and 50% of the good clinical decisions (local control and no side effects) and improve 74% and 30% of the bad clinical decisions, respectively. In conclusion, ARCliDS is the first web-based software dedicated to assist KBR-ART with multi-omics data. ARCliDS can learn from the reported clinical decisions and facilitate AI-assisted clinical decision-making for improving the outcomes in DTR.

Project description:Importance: Early mobilization, out-of-bed activity, is a component of acute stroke unit care; however, stroke patient heterogeneity requires complex decision-making. Clinically credible and applicable CPGs are needed to support and optimize the delivery of care. In this study, we are specifically exploring the role of clinical practice guidelines to support individual patient-level decision-making by stroke clinicians about early mobilization post-stroke. Methods: Our study uses a novel, two-pronged approach. (1) A review of CPGs containing recommendations for early mobilization practices published after 2015 was appraised using purposely selected items from the Appraisal of Guidelines Research and Evaluation-Recommendations Excellence (AGREE-REX) tool relevant to decision-making for clinicians. (2) A cross-sectional study involving semi-structured interviews with Australian expert stroke clinicians representing content experts and CPG target users. Every CPG was independently assessed against the AGREE-REX standard by two reviewers. Expert stroke clinicians, invited via email, were recruited between June 2019 to March 2020.The main outcomes from the review was the proportion of criteria addressed for each AGREE-REX item by individual and all CPG(s). The main cross-sectional outcomes were the distributions of stroke clinicians' responses about the utility of CPGs, specific areas of uncertainty in early mobilization decision-making, and suggested parameters for inclusion in future early mobilization CPGs. Results: In 18 identified CPGs, many did not adequately address the "Evidence" and "Applicability to Patients" AGREE-REX items. Out of 30 expert stroke clinicians (11 physicians [37%], 11 physiotherapists [37%], 8 nurses [26%]; median [IQR] years of experience, 14 [10-25]), 47% found current CPGs "too broad or vague," while 40% rely on individual clinical judgement and interpretation of the evidence to select an evidence-based choice of action. The areas of uncertainty in decision-making revealed four key suggestions: (1) more granular descriptions of patient and stroke characteristics for appropriate tailoring of decisions, (2) clear statements about when clinical flexibility is appropriate, (3) detailed description of the intervention dose, and (4) physical assessment criteria including safety parameters. Conclusions: The lack of specificity, clinical applicability, and adaptability of current CPGs to effectively respond to the heterogeneous clinical stroke context has provided a clear direction for improvement.

Dataset Information

Automatic identification of high impact articles in PubMed to support clinical decision making.

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Automatic identification of high impact articles in PubMed to support clinical decision making.

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