An interpretable stacking ensemble learning framework based on multi-dimensional data for real-time prediction of drug concentration: The example of olanzapine

Enhanced forecasting of emergency department patient arrivals using feature engineering approach and machine learning

BACKGROUND

Emergency department (ED) overcrowding is an important problem in many countries. Accurate predictions of ED patient arrivals can help management to better allocate staff and medical resources. In this study, we investigate the use of calendar and meteorological predictors, as well as feature-engineered variables, to predict daily patient arrivals using datasets from eleven different EDs across three countries.

METHODS

Six machine learning (ML) algorithms were tested on forecasting horizons of 7 and 45 days. Three of them - Light Gradient Boosting Machine (LightGBM), Support Vector Machine with Radial Basis Function (SVM-RBF), and Neural Network Autoregression (NNAR) - were never before reported for predicting ED patient arrivals. Algorithms' hyperparameters were tuned through a grid-search with cross-validation. Prediction performance was assessed using fivefold cross-validation and four performance metrics.

RESULTS

The eXtreme Gradient Boosting (XGBoost) was the best-performing model on both prediction horizons, also outperforming results reported in past studies on ED arrival prediction. XGBoost and NNAR achieved the best performance in nine out of the eleven analyzed datasets, with MAPE values ranging from 5.03% to 14.1%. Feature engineering (FE) improved the performance of the ML algorithms.

CONCLUSION

Accuracy in predicting ED arrivals, achieved through the FE approach, is key for managing human and material resources, as well as reducing patient waiting times and lengths of stay.

Optimizing PGRs for in vitro shoot proliferation of pomegranate with bayesian-tuned ensemble stacking regression and NSGA-II: a comparative evaluation of machine learning models

BACKGROUND

The process of optimizing in vitro shoot proliferation is a complicated task, as it is influenced by interactions of many factors as well as genotype. This study investigated the role of various concentrations of plant growth regulators (zeatin and gibberellic acid) in the successful in vitro shoot proliferation of three Punica granatum cultivars ('Faroogh', 'Atabaki' and 'Shirineshahvar'). Also, the utility of five Machine Learning (ML) algorithms-Support Vector Regression (SVR), Random Forest (RF), Extreme Gradient Boosting (XGB), Ensemble Stacking Regression (ESR) and Elastic Net Multivariate Linear Regression (ENMLR)-as modeling tools were evaluated on in vitro multiplication of pomegranate. A new automatic hyperparameter optimization method named Adaptive Tree Pazen Estimator (ATPE) was developed to tune the hyperparameters. The performance of the models was evaluated and compared using statistical indicators (MAE, RMSE, RRMSE, MAPE, R and R2), while a specific Global Performance Indicator (GPI) was introduced to rank the models based on a single parameter. Moreover, Non‑dominated Sorting Genetic Algorithm‑II (NSGA‑II) was employed to optimize the selected prediction model.

RESULTS

The results demonstrated that the ESR algorithm exhibited higher predictive accuracy in comparison to other ML algorithms. The ESR model was subsequently introduced for optimization by NSGA‑II. ESR-NSGA‑II revealed that the highest proliferation rate (3.47, 3.84, and 3.22), shoot length (2.74, 3.32, and 1.86 cm), leave number (18.18, 19.76, and 18.77), and explant survival (84.21%, 85.49%, and 56.39%) could be achieved with a medium containing 0.750, 0.654, and 0.705 mg/L zeatin, and 0.50, 0.329, and 0.347 mg/L gibberellic acid in the 'Atabaki', 'Faroogh', and 'Shirineshahvar' cultivars, respectively.

CONCLUSIONS

This study demonstrates that the 'Shirineshahvar' cultivar exhibited lower shoot proliferation success compared to the other cultivars. The results indicated the good performance of ESR-NSGA-II in modeling and optimizing in vitro propagation. ESR-NSGA-II can be applied as an up-to-date and reliable computational tool for future studies in plant in vitro culture.

Estimating the volume of penumbra in rodents using DTI and stack-based ensemble machine learning framework

BACKGROUND

This study investigates the potential of diffusion tensor imaging (DTI) in identifying penumbral volume (PV) compared to the standard gadolinium-required perfusion-diffusion mismatch (PDM), utilizing a stack-based ensemble machine learning (ML) approach with enhanced explainability.

METHODS

Sixteen male rats were subjected to middle cerebral artery occlusion. The penumbra was identified using PDM at 30 and 90 min after occlusion. We used 11 DTI-derived metrics and 14 distance-based features to train five voxel-wise ML models. The model predictions were integrated using stack-based ensemble techniques. ML-estimated and PDM-defined PVs were compared to evaluate model performance through volume similarity assessment, the Pearson correlation analysis, and Bland-Altman analysis. Feature importance was determined for explainability.

RESULTS

In the test rats, the ML-estimated median PV was 106.4 mL (interquartile range 44.6-157.3 mL), whereas the PDM-defined median PV was 102.0 mL (52.1-144.9 mL). These PVs had a volume similarity of 0.88 (0.79-0.96), a Pearson correlation coefficient of 0.93 (p < 0.001), and a Bland-Altman bias of 2.5 mL (2.4% of the mean PDM-defined PV), with 95% limits of agreement ranging from -44.9 to 49.9 mL. Among the features used for PV prediction, the mean diffusivity was the most important feature.

CONCLUSIONS

Our study confirmed that PV can be estimated using DTI metrics with a stack-based ensemble ML approach, yielding results comparable to the volume defined by the standard PDM. The model explainability enhanced its clinical relevance. Human studies are warranted to validate our findings.

RELEVANCE STATEMENT

The proposed DTI-based ML model can estimate PV without the need for contrast agent administration, offering a valuable option for patients with kidney dysfunction. It also can serve as an alternative if perfusion map interpretation fails in the clinical setting.

KEY POINTS

• Penumbral volume can be estimated by DTI combined with stack-based ensemble ML. • Mean diffusivity was the most important feature used for predicting penumbral volume. • The proposed approach can be beneficial for patients with kidney dysfunction.

Machine Learning: A New Approach for Dose Individualization

The application of machine learning (ML) has shown promising results in precision medicine due to its exceptional performance in dealing with complex multidimensional data. However, using ML for individualized dosing of medicines is still in its early stage, meriting further exploration. A systematic review of study designs and modeling details of using ML for individualized dosing of different drugs was performed. We have summarized the status of the study populations, predictive targets, and data sources for ML modeling, the selection of ML algorithms and features, and the evaluation and validation of their predictive performance. We also used the Prediction model Risk of Bias Assessment Tool (PROBAST) to assess the risk of bias of included studies. Currently, ML can be used for both a priori and a posteriori dose selection and optimization, and it can also assist the implementation of therapeutic drug monitoring. However, studies are mainly focused on drugs with narrow therapeutic windows, predominantly immunosuppressants (N = 23, 35.9%) and anti-infectives (N = 21, 32.8%), and there is currently only very limited attention for special populations, such as children (N = 22, 34.4%). Most studies showed poor methodological quality and a high risk of bias. The lack of external validation and clinical utility evaluation currently limits the further clinical implementation of ML for dose individualization. We therefore have proposed several ways to improve the clinical relevance of the studies and facilitate the translation of ML models into clinical practice.

Effects of Aripiprazole on Olanzapine Population Pharmacokinetics and Initial Dosage Optimization in Schizophrenia Patients

Objective

Olanzapine has already been used to treat schizophrenia patients; however, the initial dosage recommendation when multiple drugs are used in combination, remains unclear. The purpose of this study was to explore the drug-drug interaction (DDI) of multiple drugs combined with olanzapine and to recommend the optimal administration of olanzapine in schizophrenia patients.

Methods

In this study, we obtained olanzapine concentrations from therapeutic drug monitoring (TDM) database. In addition, related medical information, such as physiological, biochemical indexes, and concomitant drugs was acquired using medical log. Sixty-five schizophrenia patients were enrollmented for analysis using population pharmacokinetic model by means of nonlinear mixed effect (NONMEM).

Results

Weight and combined use of aripiprazole significantly affected olanzapine clearance. Without aripiprazole, for once-daily olanzapine administration dosages, 0.6, 0.5 mg/kg/day were recommended for 40-70, and 70-100 kg schizophrenia patients, respectively; for twice-daily olanzapine administration dosages, 0.6, 0.5 mg/kg/day were recommended for 40-60, and 60-100 kg schizophrenia patients, respectively. With aripiprazole, for once-daily olanzapine administration dosages, 0.4, 0.3 mg/kg/day were recommended for 40-53, and 53-100 kg schizophrenia patients, respectively; for twice-daily olanzapine administration dosages, 0.4 mg/kg/day was recommended for 40-100 kg schizophrenia patients, respectively.

Conclusion

Aripiprazole significantly affected olanzapine clearance, and when schizophrenia patients use aripiprazole, the olanzapine dosages need adjust. Meanwhile, we firstly recommended the optimal initial dosages of olanzapine in schizophrenia patients.

MolToxPred: small molecule toxicity prediction using machine learning approach

Different types of chemicals and products may exhibit various health risks when administered into the human body. For toxicity reasons, the number of new drugs entering the market through the conventional drug development process has been reduced over the years. However, with the advent of big data and artificial intelligence, machine learning techniques have emerged as a potential solution for predicting toxicity and ensuring efficient drug development and chemical safety. An ML model for toxicity prediction can reduce experimental costs and time while addressing ethical concerns by drastically reducing the need for animals and clinical trials. Herein, MolToxPred, an ML-based tool, has been developed using a stacked model approach to predict the potential toxicity of small molecules and metabolites. The stacked model consists of random forest, multi-layer perceptron, and LightGBM as base classifiers and Logistic Regression as the meta classifier. For training and validation purposes, a comprehensive set of toxic and non-toxic molecules is curated. Different structural and physicochemical-based features in the form of molecular descriptors and fingerprints were employed. MolToxPred utilizes a comprehensive feature selection process and optimizes its hyperparameters through Bayesian optimization with stratified 5-fold cross-validation. In the evaluation phase, MolToxPred achieved an AUROC of 87.76% on the test set and 88.84% on an external validation set. The McNemar test was used as the post-hoc test to determine if the stacked models' performance was significantly different compared to the base learners. The developed stacked model outperformed its base classifiers and an existing tool in the literature, reaffirming its better performance. The hypothesis is that the incorporation of a diverse set of data, the subsequent feature selection, and a stacked ensemble approach give MolToxPred the edge over other methods. In addition to this, an attempt has been made to identify structural alerts responsible for endpoints of the Tox21 data to determine the association of a molecule with a plausible downstream pathway of action. MolToxPred may be helpful for drug discovery and regulatory pipelines in pharmaceutical and other industries for in silico toxicity prediction of small molecule candidates.

Ensemble Learning, Deep Learning-Based and Molecular Descriptor-Based Quantitative Structure-Activity Relationships

A deep learning-based quantitative structure-activity relationship analysis, namely the molecular image-based DeepSNAP-deep learning method, can successfully and automatically capture the spatial and temporal features in an image generated from a three-dimensional (3D) structure of a chemical compound. It allows building high-performance prediction models without extracting and selecting features because of its powerful feature discrimination capability. Deep learning (DL) is based on a neural network with multiple intermediate layers that makes it possible to solve highly complex problems and improve the prediction accuracy by increasing the number of hidden layers. However, DL models are too complex when it comes to understanding the derivation of predictions. Instead, molecular descriptor-based machine learning has clear features owing to the selection and analysis of features. However, molecular descriptor-based machine learning has some limitations in terms of prediction performance, calculation cost, feature selection, etc., while the DeepSNAP-deep learning method outperforms molecular descriptor-based machine learning due to the utilization of 3D structure information and the advanced computer processing power of DL.