Search bioRxiv⌕ Search

bioRxiv · 10.1101/182154

A Methodology for Evaluating the Performance of Alerting and Detection Algorithms Running on Continuous Patient Data

Abstract

ObjectivesClinicians in the intensive care unit (ICU) are presented with a large number of physiological data consisting of periodic and frequently sampled measurements, such as heart rate and blood pressure, as well as aperiodic measurements, such as noninvasive blood pressure and laboratory studies. Because this data can be overwhelming, there is considerable interest in designing algorithms that help integrate and interpret this data and assist ICU clinicians in detecting or predicting in advance patients who may be deteriorating. In order to decide whether to deploy such algorithms in a clinical trial, it is important to evaluate these algorithms using retrospective data. However, the fact that these algorithms will be running continuously, i.e., repeatedly sampling incoming patient data, presents some novel challenges for algorithm evaluation. Commonly used measures of performance such as sensitivity and positive predictive value (PPV) are easily applied to static \"snapshots\" of patient data, but can be very misleading when applied to indicators or alerting algorithms that are running on continuous data. Our objective is to create a method for evaluating algorithm performance on retrospective data with the algorithm running continuously throughout the patients stay as it would in a real ICU.\n\nMethodsWe introduce our evaluation methodology in the context of evaluating an algorithm, a Hemodynamic Instability Indicator (HII), for assisting bedside ICU clinicians with the early detection of hemodynamic instability before the onset of acute hypotension. Each patients ICU stay is divided into segments that are labelled as hemodynamically stable or unstable based on clinician interventions typically aimed at treating hemodynamic instability. These segments can be of varying length with varying degrees of exposure to potential alerts, whether true positive or false positive. Furthermore, to simulate how clinicians might interact with the alerting algorithm, we use a dynamic alert supervision mechanism which suppresses subsequent alerts unless the indicator has significantly deteriorated since the prior alert. Under these conditions determining what counts as a positive or negative instance, and calculations of sensitivity, specificity, and positive predictive value can be problematic. We introduce a methodology for consistently counting positive and negative instances. The methodology distinguishes between counts based on alerting events and counts based on sub-segments, and show how they can be applied in calculating measures of performance such as sensitivity, specificity, positive predictive value.\n\nResultsThe introduced methodology is applied to retrospective evaluation of two algorithms, HII and an alerting algorithm based on systolic blood pressure. We use a database, consisting of data from 41,707 patients from 25 US hospitals, to evaluate the algorithms. Both algorithms are evaluated running continuously throughout each patients stay as they would in a real ICU setting. We show how the introduced performance measures differ for different algorithms and for different assumptions.\n\nDiscussionThe standard measures of diagnostic tests in terms of true positives, false positives, etc. are based on certain assumptions which may not apply when used in the context of measuring the performance on an algorithm running continuously, and thus repeatedly sampling from the same patient. When such measures are being reported it is important that the underlying assumptions be made explicit; otherwise, the results can be very misleading.\n\nConclusionWe introduce a methodology for evaluating how an alerting algorithm or indicator will perform running continuously throughout every patients ICU stay, not just for a subset of patients for selected episodes.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Eshelman, L. J., Xu-Wilson, M., Gross, B., Nielsen, L., Saeed, M., Frassica, J. J.. 2017-09-07. A Methodology for Evaluating the Performance of Alerting and Detection Algorithms Running on Continuous Patient Data. https://doi.org/10.1101/182154

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

The Almond Expression Atlas: A comprehensive multi-tissue transcriptomic resource for almond gene expression

Background: Improving crop adaptation and enhancing agronomic and quality traits requires a deeper understanding of gene expression regulation, for which expression atlases are valuable tools. Almond (Prunus dulcis (Mill.) D.A. Webb) is one of the most economically important tree nut crops worldwide. However, an integrated transcriptomic resource for this species is still lacking. Available data remain fragmented across independent studies, limiting their comparability and reuse. Results: Here, we present the first almond gene expression atlas: a comprehensive multi-tissue transcriptomic resource integrating publicly available RNA sequencing data. A total of 142 high-quality untreated and control samples from 17 independent projects were curated through a metadata standardization process and analyzed using a unified bioinformatics pipeline. Standardized expression profiles were generated for 25,225 annotated genes in the Prunus dulcis Texas v2.0 reference genome. The atlas integrates two complementary expression approaches: a median TPM approach capturing quantitative expression levels and a rank-based strategy implemented using the Bgee expression calling method, designed to improve comparability across heterogeneous datasets. This design enables the identification of tissue-specific candidate genes and the exploration of expression patterns across tissues and developmental stages. Its applicability is demonstrated through two use cases, highlighting its ability to identify biologically meaningful gene sets associated with bud dormancy transitions and to prioritize candidate reference genes for RT-qPCR normalization in almond. Conclusions: The Almond Expression Atlas v1.0 is publicly available through FruitDBase (fruitdbase.csic.es), providing an interactive platform for gene expression exploration and visualization. This resource supports functional genomics studies and facilitates candidate gene discovery in almond, while ensuring data traceability and promoting data reusability.

bioinformatics↗

Leakage-Controlled Benchmarking of Variant Effect Predictors and Development of Gradient-Boosting Consensus Model

Single amino acid mutations are among the most common forms of genetic variation, with effects ranging from negligible to severe disruption of protein function. Accurate quantitative evaluation of protein variants therefore represents a key challenge in medicine and protein engineering. Computational variant effect predictors (VEPs) are widely used to prioritize missense variants, yet their fair comparison is hindered by data circularity, benchmarks restricted to human clinical annotations, and limited availability of code and training data, all of which can inflate apparent performance. Here, we reviewed 18 recent and 3 older, widely adopted variant effect predictors for reproducible benchmarking and assembled a rigorously curated, leakage-controlled Benchmark dataset by integrating clinically annotated human variants from ClinVar and Humsavar as well as cross-species variants with functional annotations. The evaluation on this dataset revealed a narrow overall performance range for the benchmarked tools (AUC 0.631-0.758) and a consistent drop from clinical to functional data. Surprisingly, several tools published two decades ago demonstrated comparable performance to mid-ranked modern predictors. Building on these results, we developed a gradient-boosting consensus model, PredictSNPprot, which achieved an AUC of 0.82 on a held-out test set, outperforming the original PredictSNP meta-predictor and the best individual state-of-the-art tool by 13.6 and 5.7 percentage points, respectively. The Benchmark dataset, including the predictions from the evaluated tools, is available at https://doi.org/10.5281/zenodo.23597130 and PredictSNPprot consensus predictor is available at https://github.com/loschmidt/PredictSNPprot.

bioinformatics↗

MaCADEMIA: a software toolbox for single-molecule fluorescence image quantification

Single-molecule localisation microscopy (SMLM) is a powerful tool in molecular and cellular biology and part of the broad umbrella of super-resolution microscopy. A distinct feature of SMLM, is its capacity for deep quantification, beyond just spatial information, to copy number, stoichiometry, molecular interaction and dynamics in living cells. The hardware required is increasingly straightforward to implement. However, complexity remains in the image analysis where much remains fragmented across specialised software tools. Here, we present MaCADEMIA (Matlab Computational Analysis of Diffusion, Emitter Molecular Intensity and Abundance), a simple yet powerful toolbox of MATLAB functions and associated documentation to enable straightforward extraction of quantitative single-molecule information. MaCADEMIA performs ensemble particle detection achieving localisation accuracies down to 0.5 pixels Root mean squared error (RMSE) across wide signal-to-noise (SNR) ranges on standardised particle tracking benchmarks, consistently matching or exceeding the performance of 14 leading methods. Our integrated workflow enables molecular counting and stoichiometry determination through stepwise photobleaching analysis, mobility measurement via mean squared displacement, colocalisaton analysis and absolute protein copy number quantification using three-dimensional cellular models.

bioinformatics↗