An open‐source, expert‐designed decision tree application to support accurate diagnosis of myeloid malignancies
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ABSTRACT:
SUBMITTER: Coats T
PROVIDER: S-EPMC9175663 | biostudies-literature | 2021 Mar
REPOSITORIES: biostudies-literature
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Project description:The expansion of machine learning to high-stakes application domains such as medicine, finance, and criminal justice, where making informed decisions requires clear understanding of the model, has increased the interest in interpretable machine learning. The widely used Classification and Regression Trees (CART) have played a major role in health sciences, due to their simple and intuitive explanation of predictions. Ensemble methods like gradient boosting can improve the accuracy of decision trees, but at the expense of the interpretability of the generated model. Additive models, such as those produced by gradient boosting, and full interaction models, such as CART, have been investigated largely in isolation. We show that these models exist along a spectrum, revealing previously unseen connections between these approaches. This paper introduces a rigorous formalization for the additive tree, an empirically validated learning technique for creating a single decision tree, and shows that this method can produce models equivalent to CART or gradient boosted stumps at the extremes by varying a single parameter. Although the additive tree is designed primarily to provide both the model interpretability and predictive performance needed for high-stakes applications like medicine, it also can produce decision trees represented by hybrid models between CART and boosted stumps that can outperform either of these approaches.
| S-EPMC6778203 | biostudies-literature
Project description:BackgroundMoving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements."ObjectiveWe aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse).MethodsAcceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite.ResultsWe used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build.ConclusionsAutomated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization.
| S-EPMC5924365 | biostudies-literature
Project description: Not available
| S-EPMC1629446 | biostudies-literature
Project description:Heat poses an urgent threat to public health in cities, as the urban heat island (UHI) effect can amplify exposures, contributing to high heat-related mortality and morbidity. Urban trees have the potential to mitigate heat by providing substantial cooling, as well as co-benefits such as reductions in energy consumption. The City of Boston has attempted to expand its urban canopy, yet maintenance costs and high tree mortality have hindered successful canopy expansion. Here, we present an interactive web application called Right Place, Right Tree-Boston that aims to support informed decision-making for planting new trees. To highlight priority regions for canopy expansion, we developed a Boston-specific Heat Vulnerability Index (HVI) and present this alongside maps of summer daytime land surface temperatures. We also provide information about tree pests and diseases, suitability of species for various conditions, land ownership, maintenance tips, and alternatives to tree planting. This web application is designed to support decision-making at multiple spatial scales, to assist city officials as well as residents who are interested in expanding or maintaining Boston's urban forest.
| S-EPMC7544061 | biostudies-literature
Project description:For supporting clinical decision-making in audiology, Common Audiological Functional Parameters (CAFPAs) were suggested as an interpretable intermediate representation of audiological information taken from various diagnostic sources within a clinical decision-support system (CDSS). Ten different CAFPAs were proposed to represent specific functional aspects of the human auditory system, namely hearing threshold, supra-threshold deficits, binaural hearing, neural processing, cognitive abilities, and a socio-economic component. CAFPAs were established as a viable basis for deriving audiological findings and treatment recommendations, and it has been demonstrated that model-predicted CAFPAs, with machine learning models trained on expert-labeled patient cases, are sufficiently accurate to be included in a CDSS, but it requires further validation by experts. The present study aimed to validate model-predicted CAFPAs based on previously unlabeled cases from the same data set. Here, we ask to which extent domain experts agree with the model-predicted CAFPAs and whether potential disagreement can be understood in terms of patient characteristics. To these aims, an expert survey was designed and applied to two highly-experienced audiology specialists. They were asked to evaluate model-predicted CAFPAs and estimate audiological findings of the given audiological information about the patients that they were presented with simultaneously. The results revealed strong relative agreement between the two experts and importantly between experts and the prediction for all CAFPAs, except for the neural processing and binaural hearing-related ones. It turned out, however, that experts tend to score CAFPAs in a larger value range, but, on average, across patients with smaller scores as compared with the machine learning models. For the hearing threshold-associated CAFPA in frequencies smaller than 0.75 kHz and the cognitive CAFPA, not only the relative agreement but also the absolute agreement between machine and experts was very high. For those CAFPAs with an average difference between the model- and expert-estimated values, patient characteristics were predictive of the disagreement. The findings are discussed in terms of how they can help toward further improvement of model-predicted CAFPAs to be incorporated in a CDSS for audiology.
| S-EPMC9446152 | biostudies-literature
Project description:Neurons perform computations by integrating inputs from thousands of synapses-mostly in the dendritic tree-to drive action potential firing in the axon. One fruitful approach to studying this process is to record from neurons using patch-clamp electrodes, fill the recorded neurons with a substance that allows subsequent staining, reconstruct the three-dimensional architectures of the dendrites, and use the resulting functional and structural data to develop computer models of dendritic integration. Accurately producing quantitative reconstructions of dendrites is typically a tedious process taking many hours of manual inspection and measurement. Here we present ShuTu, a new software package that facilitates accurate and efficient reconstruction of dendrites imaged using bright-field microscopy. The program operates in two steps: (1) automated identification of dendritic processes, and (2) manual correction of errors in the automated reconstruction. This approach allows neurons with complex dendritic morphologies to be reconstructed rapidly and efficiently, thus facilitating the use of computer models to study dendritic structure-function relationships and the computations performed by single neurons.
| S-EPMC6834530 | biostudies-literature
Project description:BackgroundThere is today no gold standard method to accurately define the time passed since infection at HIV diagnosis. Infection timing and incidence measurement is however essential to better monitor the dynamics of local epidemics and the effect of prevention initiatives.MethodsThree methods for infection timing were evaluated using 237 serial samples from documented seroconversions and 566 cross sectional samples from newly diagnosed patients: identification of antibodies against the HIV p31 protein in INNO-LIA, SediaTM BED CEIA and SediaTM LAg-Avidity EIA. A multi-assay decision tree for infection timing was developed.ResultsClear differences in recency window between BED CEIA, LAg-Avidity EIA and p31 antibody presence were observed with a switch from recent to long term infection a median of 169.5, 108.0 and 64.5 days after collection of the pre-seroconversion sample respectively. BED showed high reliability for identification of long term infections while LAg-Avidity is highly accurate for identification of recent infections. Using BED as initial assay to identify the long term infections and LAg-Avidity as a confirmatory assay for those classified as recent infection by BED, explores the strengths of both while reduces the workload. The short recency window of p31 antibodies allows to discriminate very early from early infections based on this marker. BED recent infection results not confirmed by LAg-Avidity are considered to reflect a period more distant from the infection time. False recency predictions in this group can be minimized by elimination of patients with a CD4 count of less than 100 cells/mm3 or without no p31 antibodies. For 566 cross sectional sample the outcome of the decision tree confirmed the infection timing based on the results of all 3 markers but reduced the overall cost from 13.2 USD to 5.2 USD per sample.ConclusionsA step-wise multi assay decision tree allows accurate timing of the HIV infection at diagnosis at affordable effort and cost and can be an important new tool in studies analyzing the dynamics of local epidemics or the effects of prevention strategies.
| S-EPMC5708102 | biostudies-literature
Project description:This paper presents AVATREE, a computational modelling framework that generates Anatomically Valid Airway tree conformations and provides capabilities for simulation of broncho-constriction apparent in obstructive pulmonary conditions. Such conformations are obtained from the personalized 3D geometry generated from computed tomography (CT) data through image segmentation. The patient-specific representation of the bronchial tree structure is extended beyond the visible airway generation depth using a knowledge-based technique built from morphometric studies. Additional functionalities of AVATREE include visualization of spatial probability maps for the airway generations projected on the CT imaging data, and visualization of the airway tree based on local structure properties. Furthermore, the proposed toolbox supports the simulation of broncho-constriction apparent in pulmonary diseases, such as chronic obstructive pulmonary disease (COPD) and asthma. AVATREE is provided as an open-source toolbox in C++ and is supported by a graphical user interface integrating the modelling functionalities. It can be exploited in studies of gas flow, gas mixing, ventilation patterns and particle deposition in the pulmonary system, with the aim to improve clinical decision making.
| S-EPMC7122715 | biostudies-literature
Project description:Many questions relevant to conservation decision-making are characterized by extreme uncertainty due to lack of empirical data and complexity of the underlying ecologic processes, leading to a rapid increase in the use of structured protocols to elicit expert knowledge. Published ecologic applications often employ a modified Delphi method, where experts provide judgments anonymously and mathematical aggregation techniques are used to combine judgments. The Sheffield elicitation framework (SHELF) differs in its behavioral approach to synthesizing individual judgments into a fully specified probability distribution for an unknown quantity. We used the SHELF protocol remotely to assess extinction risk of three subterranean aquatic species that are being considered for listing under the U.S. Endangered Species Act. We provided experts an empirical threat assessment for each known locality over a video conference and recorded judgments on the probability of population persistence over four generations with online submission forms and R-shiny apps available through the SHELF package. Despite large uncertainty for all populations, there were key differences between species' risk of extirpation based on spatial variation in dominant threats, local land use and management practices, and species' microhabitat. The resulting probability distributions provided decision makers with a full picture of uncertainty that was consistent with the probabilistic nature of risk assessments. Discussion among experts during SHELF's behavioral aggregation stage clearly documented dominant threats (e.g., development, timber harvest, animal agriculture, and cave visitation) and their interactions with local cave geology and species' habitat. Our virtual implementation of the SHELF protocol demonstrated the flexibility of the approach for conservation applications operating on budgets and time lines that can limit in-person meetings of geographically dispersed experts.
| S-EPMC8518685 | biostudies-literature
Project description:The elicitation of scientific and technical judgments from experts, in the form of subjective probability distributions, can be a valuable addition to other forms of evidence in support of public policy decision making. This paper explores when it is sensible to perform such elicitation and how that can best be done. A number of key issues are discussed, including topics on which there are, and are not, experts who have knowledge that provides a basis for making informed predictive judgments; the inadequacy of only using qualitative uncertainty language; the role of cognitive heuristics and of overconfidence; the choice of experts; the development, refinement, and iterative testing of elicitation protocols that are designed to help experts to consider systematically all relevant knowledge when they make their judgments; the treatment of uncertainty about model functional form; diversity of expert opinion; and when it does or does not make sense to combine judgments from different experts. Although it may be tempting to view expert elicitation as a low-cost, low-effort alternative to conducting serious research and analysis, it is neither. Rather, expert elicitation should build on and use the best available research and analysis and be undertaken only when, given those, the state of knowledge will remain insufficient to support timely informed assessment and decision making.
| S-EPMC4034232 | biostudies-literature