| Literature DB >> 35228820 |
Benjamin Skov Kaas-Hansen1,2,3, Cristina Leal Rodríguez2, Davide Placido2, Hans-Christian Thorsen-Meyer2,4, Anna Pors Nielsen2, Nicolas Dérian5, Søren Brunak2, Stig Ejdrup Andersen1.
Abstract
PURPOSE: Dosing of renally cleared drugs in patients with kidney failure often deviates from clinical guidelines, so we sought to elicit predictors of receiving inappropriate doses of renal risk drugs. PATIENTS AND METHODS: We combined data from the Danish National Patient Register and in-hospital data on drug administrations and estimated glomerular filtration rates for admissions between 1 October 2009 and 1 June 2016, from a pool of about 2.6 million persons. We trained artificial neural network and linear logistic ridge regression models to predict the risk of five outcomes (>0, ≥1, ≥2, ≥3 and ≥5 inappropriate doses daily) with index set 24 hours after admission. We used time-series validation for evaluating discrimination, calibration, clinical utility and explanations.Entities:
Keywords: inappropriate drug dosing; kidney failure; machine learning; predictive modelling; renal risk drugs; risk markers
Year: 2022 PMID: 35228820 PMCID: PMC8881932 DOI: 10.2147/CLEP.S344435
Source DB: PubMed Journal: Clin Epidemiol ISSN: 1179-1349 Impact factor: 4.790
Figure 1Deriving the outcome variables. This exemplary admission is composed of three successive in-patient visits (ie the patient has been transferred twice represented by the arrows). The admission is eligible because it spans more than 24 hours and an eGFR ≤30 was measured before index. Here, apixaban was given while the patient’s eGFR was ≤30, but dose reduction rendered these administrations appropriate.
Univariate Summary Statistics of Select Features. Values are Median (Inter-Quartile Range) and Count (Proportion) as Appropriate. Distinct Patients and Distinct Women Show Counts of Actual Patients (as a Patient Can Contribute More Than One Unit)
| Variate | Development Set (N = 42,250) | Test Set (N = 10,201) | Test Set (Not in Devel. Set) (N = 5980) |
|---|---|---|---|
| Women | 20,743 (49%) | 4854 (48%) | 2940 (49%) |
| Distinct patients | 27,253 | 8412 | 5341 |
| Distinct women | 13,759 (50%) | 4049 (48%) | 2629 (49%) |
| Time at risk, days | 3.5 (1.7–7.7) | 3.5 (1.7–7.2) | 2.9 (1.5–6.4) |
| Inappropriate doses (outcomes) | |||
| >0 (at least one) | 3786 (9.0%) | 1080 (11%) | 740 (12%) |
| ≥1 daily | 2241 (5.3%) | 588 (5.8%) | 333 (5.6%) |
| ≥2 daily | 1236 (2.9%) | 288 (2.8%) | 108 (1.8%) |
| ≥3 daily | 783 (1.9%) | 171 (1.7%) | 56 (0.9%) |
| ≥5 daily | 366 (0.9%) | 64 (0.6%) | 9 (0.2%) |
| Admissions 5 years before admission | |||
| None | 4988 (12%) | 1082 (11%) | 1074 (18%) |
| 1–2 | 10,100 (24%) | 2367 (23%) | 1873 (31%) |
| 3–4 | 7712 (18%) | 1919 (19%) | 1232 (21%) |
| 5–6 | 5490 (13%) | 1303 (13%) | 685 (12%) |
| ≥7 | 13,960 (33%) | 3530 (35%) | 1116 (19%) |
| Drugs used between admission and index | |||
| None | 6165 (15%) | 1228 (12%) | 762 (13%) |
| 1–2 | 9111 (22%) | 1984 (19%) | 1254 (21%) |
| 3–4 | 8761 (21%) | 2078 (20%) | 1355 (23%) |
| 5–6 | 7197 (17%) | 1852 (18%) | 1095 (18%) |
| ≥7 | 11,016 (26%) | 3059 (30%) | 1514 (25%) |
| Any diagnosis of chronic kidney failure | 13,470 (32%) | 3391 (33%) | 732 (12%) |
| Top-5 ICD-10 chapters† | |||
| Cardiovascular (IX) | 25,757 (61%) | 6392 (63%) | 3283 (55%) |
| Genitourinary (XIV) | 23,025 (55%) | 5819 (57%) | 2306 (39%) |
| Lesions, external causes, etc. (XIX) | 20,275 (48%) | 4749 (47%) | 2481 (42%) |
| Metabolic-endocrine (IV) | 19,716 (47%) | 5096 (50%) | 2415 (40%) |
| Symptoms/abnormal findings (XVIII) | 18,663 (44%) | 5711 (56%) | 2882 (48%) |
| Top-5 drug classes‡ | |||
| Analgesics (N02) | 15,740 (37%) | 4367 (43%) | 2506 (42%) |
| Systemic antibacterials (J01) | 14,719 (35%) | 3257 (32%) | 1938 (32%) |
| Diuretics (C03) | 13,966 (33%) | 3672 (36%) | 1951 (33%) |
| Antithrombotics (B01) | 11,842 (28%) | 3181 (31%) | 1795 (30%) |
| Antacids (A02) | 10,635 (25%) | 2776 (27%) | 1407 (24%) |
Notes: †ICD-10 chapters (Roman numbering) of diagnoses recorded in the last 5 years before admission. ‡Drug classes (ATC level 2) administered between admission and index.
Abbreviations: ICD-10, 10th version of the international classification of disease; ATC, anatomical therapeutic chemical classification of medicines.
Performance Metrics of Final Models and Results of Optuna Hyperparameter Optimization
| Parameter | Daily Rate >0 | Daily Rate ≥1 | Daily Rate ≥2 | Daily Rate ≥3 | Daily Rate ≥5 | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Linear | MLP | Linear | MLP | Linear | MLP | Linear | MLP | Linear | MLP | |
| AUROC† | ||||||||||
| Development set | 0.80 (0.71) | 0.81 (0.73) | 0.81 (0.72) | 0.83 (0.75) | 0.81 | 0.84 | 0.82 | 0.83 | 0.82 | 0.83 |
| Test set | 0.77 (0.70) | 0.79 (0.70) | 0.78 (0.69) | 0.79 (0.70) | 0.79 | 0.79 | 0.81 | 0.81 | 0.78 | 0.80 |
| Test set (new patients) | 0.78 (0.68) | 0.79 (0.68) | 0.82 (0.70) | 0.83 (0.71) | 0.86 | 0.86 | 0.89 | 0.90 | 0.82 | 0.79 |
| Hyperparameters | ||||||||||
| Batch size | 512 | 128 | 512 | 32 | 32 | 64 | 256 | 256 | 64 | 64 |
| Class handling | Undersample | SMOTE | NearMiss | NearMiss | Oversample | SMOTE | Oversample | NearMiss | Oversample | None |
| L2 penalty | 1.28 × 10−6 | 1.66 × 10−6 | 3.02 × 10−6 | 1.43 × 10−6 | 4.38 × 10−6 | 1.39 × 10−6 | 1.43 × 10−6 | 1.30 × 10−6 | 1.09 × 10– | 3.94 × 10−6 |
| Learning rate | 1.79 × 10−2 | 1.20 × 10–4 | 1.92 × 10−2 | 3.45 × 10–4 | 6.73 × 10−3 | 2.71 × 10–4 | 3.76 × 10−2 | 3.08 × 10–4 | 2.11 × 10−2 | 4.86 × 10–4 |
| Optimizer | Adam | Adam | Adam | Adam | Adam | Adam | Adam | Adam | Adam | Adam |
| Activation function | — | tanh | — | sigmoid | — | tanh | — | sigmoid | — | sigmoid |
| No. hidden layers | — | 3 | — | 1 | — | 1 | — | 1 | — | 2 |
| Nodes per hidden layer | — | 8 | — | 8 | — | 32 | — | 32 | — | 8 |
Notes: †Values in parentheses pertain to the reference models (see text for specification). Undersample: random sample of the size of the minority class, from the majority class. Oversample: randomly sample (with replacement) from the minority class until reaching a sample size equal to the size of the majority class.26 NearMiss: a method for non-random, systematic downsampling of the majority class while retaining as much information as possible.27.
Abbreviations: AUROC, area under the receiver operating characteristic curve; MLP, multi-layer perceptron; SMOTE, synthetic minority oversampling technique.
Figure 2Bivariate relationships between values of select features (x axis) and their corresponding shap values (y axis). The continuous features are summarized by locally estimated scatterplot smoothing (LOESS), binary features by vertical density bands.