Predicting Serum Levels of Lithium-Treated Patients: A Supervised Machine Learning Approach.
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ABSTRACT:
SUBMITTER: Hsu CW
PROVIDER: S-EPMC8615637 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND:Machine-learning classifiers mostly offer good predictive performance and are increasingly used to support shared decision-making in clinical practice. Focusing on performance and practicability, this study evaluates prediction of patient-reported outcomes (PROs) by eight supervised classifiers including a linear model, following hip and knee replacement surgery. METHODS:NHS PRO data (130,945 observations) from April 2015 to April 2017 were used to train and test eight classifiers to predict binary postoperative improvement based on minimal important differences. Area under the receiver operating characteristic, J-statistic and several other metrics were calculated. The dependent outcomes were generic and disease-specific improvement based on the EQ-5D-3L visual analogue scale (VAS) as well as the Oxford Hip and Knee Score (Q score). RESULTS:The area under the receiver operating characteristic of the best training models was around 0.87 (VAS) and 0.78 (Q score) for hip replacement, while it was around 0.86 (VAS) and 0.70 (Q score) for knee replacement surgery. Extreme gradient boosting, random forests, multistep elastic net and linear model provided the highest overall J-statistics. Based on variable importance, the most important predictors for post-operative outcomes were preoperative VAS, Q score and single Q score dimensions. Sensitivity analysis for hip replacement VAS evaluated the influence of minimal important difference, patient selection criteria as well as additional data years. Together with a small benchmark of the NHS prediction model, robustness of our results was confirmed. CONCLUSIONS:Supervised machine-learning implementations, like extreme gradient boosting, can provide better performance than linear models and should be considered, when high predictive performance is needed. Preoperative VAS, Q score and specific dimensions like limping are the most important predictors for postoperative hip and knee PROMs.
| S-EPMC6325823 | biostudies-other
Project description:Spontaneous activity is a common feature of immature neuronal networks throughout the central nervous system and plays an important role in network development and consolidation. In postnatal rodents, spontaneous activity in the spinal cord exhibits complex, stochastic patterns that have historically proven challenging to characterize. We developed a software tool for quickly and automatically characterizing and classifying episodes of spontaneous activity generated from developing spinal networks. We recorded spontaneous activity from in vitro lumbar ventral roots of 16 neonatal [postnatal day (P)0-P3] mice. Recordings were DC coupled and detrended, and episodes were separated for analysis. Amplitude-, duration-, and frequency-related features were extracted from each episode and organized into five classes. Paired classes and features were used to train and test supervised machine learning algorithms. Multilayer perceptrons were used to classify episodes as rhythmic or multiburst. We increased network excitability with potassium chloride and tested the utility of the tool to detect changes in features and episode class. We also demonstrate usability by having a novel experimenter use the program to classify episodes collected at a later time point (P5). Supervised machine learning-based classification of episodes accounted for changes that traditional approaches cannot detect. Our tool, named SpontaneousClassification, advances the detail in which we can study not only developing spinal networks, but also spontaneous networks in other areas of the nervous system. NEW & NOTEWORTHY Spontaneous activity is important for nervous system network development and consolidation. Our software uses machine learning to automatically and quickly characterize and classify episodes of spontaneous activity in the spinal cord of newborn mice. It detected changes in network activity following KCl-enhanced excitation. Using our software to classify spontaneous activity throughout development, in pathological models, or with neuromodulation, may offer insight into the development and organization of spinal circuits.
| S-EPMC6620704 | biostudies-literature
Project description:BackgroundVirtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites.ResultsWe developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences.In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms.ConclusionOnly a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well in human and drosophila, suggesting that it may be applicable to a broad range of species. Moreover, we have demonstrated that the application of machine learning techniques in combination with upcoming deep sequencing data results in a powerful microRNA target site prediction tool http://www.targetspy.org.
| S-EPMC2889937 | biostudies-literature
Project description:Background: South Africa (SA) has the highest incidence of colorectal cancer (CRC) in Sub-Saharan Africa (SSA). However, there is limited research on CRC recurrence and survival in SA. CRC recurrence and overall survival are highly variable across studies. Accurate prediction of patients at risk can enhance clinical expectations and decisions within the South African CRC patients population. We explored the feasibility of integrating statistical and machine learning (ML) algorithms to achieve higher predictive performance and interpretability in findings. Methods: We selected and compared six algorithms:- logistic regression (LR), naïve Bayes (NB), C5.0, random forest (RF), support vector machine (SVM) and artificial neural network (ANN). Commonly selected features based on OneR and information gain, within 10-fold cross-validation, were used for model development. The validity and stability of the predictive models were further assessed using simulated datasets. Results: The six algorithms achieved high discriminative accuracies (AUC-ROC). ANN achieved the highest AUC-ROC for recurrence (87.0%) and survival (82.0%), and other models showed comparable performance with ANN. We observed no statistical difference in the performance of the models. Features including radiological stage and patient's age, histology, and race are risk factors of CRC recurrence and patient survival, respectively. Conclusions: Based on other studies and what is known in the field, we have affirmed important predictive factors for recurrence and survival using rigorous procedures. Outcomes of this study can be generalised to CRC patient population elsewhere in SA and other SSA countries with similar patient profiles.
| S-EPMC8292767 | biostudies-literature
Project description:Geographic patterns of human genetic variation provide important insights into human evolution and disease. A commonly used tool to detect and describe them is principal component analysis (PCA) or the supervised linear discriminant analysis of principal components (DAPC). However, genetic features produced from both approaches could fail to correctly characterize population structure for complex scenarios involving admixture. In this study, we introduce Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC), a supervised non-linear approach for inferring individual geographic genetic structure that could rectify the limitations of these approaches by preserving the multimodal space of samples. We tested the power of KLFDAPC to infer population structure and to predict individual geographic origin using neural networks. Simulation results showed that KLFDAPC has higher discriminatory power than PCA and DAPC. The application of our method to empirical European and East Asian genome-wide genetic datasets indicated that the first two reduced features of KLFDAPC correctly recapitulated the geography of individuals and significantly improved the accuracy of predicting individual geographic origin when compared to PCA and DAPC. Therefore, KLFDAPC can be useful for geographic ancestry inference, design of genome scans and correction for spatial stratification in GWAS that link genes to adaptation or disease susceptibility.
| S-EPMC9294434 | biostudies-literature
Project description:Widely-prescribed prodrug opioids (e.g., hydrocodone) require conversion by liver enzyme CYP-2D6 to exert their analgesic effects. The most commonly prescribed antidepressant, selective serotonin reuptake inhibitors (SSRIs), inhibits CYP-2D6 activity and therefore may reduce the effectiveness of prodrug opioids. We used a machine learning approach to identify patients prescribed a combination of SSRIs and prodrug opioids postoperatively and to examine the effect of this combination on postoperative pain control. Using EHR data from an academic medical center, we identified patients receiving surgery over a 9-year period. We developed and validated natural language processing (NLP) algorithms to extract depression-related information (diagnosis, SSRI use, symptoms) from structured and unstructured data elements. The primary outcome was the difference between preoperative pain score and postoperative pain at discharge, 3-week and 8-week time points. We developed computational models to predict the increase or decrease in the postoperative pain across the 3 time points by using the patient's EHR data (e.g. medications, vitals, demographics) captured before surgery. We evaluate the generalizability of the model using 10-fold cross-validation method where the holdout test method is repeated 10 times and mean area-under-the-curve (AUC) is considered as evaluation metrics for the prediction performance. We identified 4,306 surgical patients with symptoms of depression. A total of 14.1% were prescribed both an SSRI and a prodrug opioid, 29.4% were prescribed an SSRI and a non-prodrug opioid, 18.6% were prescribed a prodrug opioid but were not on SSRIs, and 37.5% were prescribed a non-prodrug opioid but were not on SSRIs. Our NLP algorithm identified depression with a F1 score of 0.95 against manual annotation of 300 randomly sampled clinical notes. On average, patients receiving prodrug opioids had lower average pain scores (p<0.05), with the exception of the SSRI+ group at 3-weeks postoperative follow-up. However, SSRI+/Prodrug+ had significantly worse pain control at discharge, 3 and 8-week follow-up (p < .01) compared to SSRI+/Prodrug- patients, whereas there was no difference in pain control among the SSRI- patients by prodrug opioid (p>0.05). The machine learning algorithm accurately predicted the increase or decrease of the discharge, 3-week and 8-week follow-up pain scores when compared to the pre-operative pain score using 10-fold cross validation (mean area under the receiver operating characteristic curve 0.87, 0.81, and 0.69, respectively). Preoperative pain, surgery type, and opioid tolerance were the strongest predictors of postoperative pain control. We provide the first direct clinical evidence that the known ability of SSRIs to inhibit prodrug opioid effectiveness is associated with worse pain control among depressed patients. Current prescribing patterns indicate that prescribers may not account for this interaction when choosing an opioid. The study results imply that prescribers might instead choose direct acting opioids (e.g. oxycodone or morphine) in depressed patients on SSRIs.
| S-EPMC6364959 | biostudies-literature
Project description:Currently, the identification of stroke patients with an increased suicide risk is mainly based on self-report questionnaires, and this method suffers from a lack of objectivity. This study developed and validated a suicide ideation (SI) prediction model using clinical data and identified SI predictors. Significant variables were selected through traditional statistical analysis based on retrospective data of 385 stroke patients; the data were collected from October 2012 to March 2014. The data were then applied to three boosting models (Xgboost, CatBoost, and LGBM) to identify the comparative and best performing models. Demographic variables that showed significant differences between the two groups were age, onset, type, socioeconomic, and education level. Additionally, functional variables also showed a significant difference with regard to ADL and emotion (p < 0.05). The CatBoost model (0.900) showed higher performance than the other two models; and depression, anxiety, self-efficacy, and rehabilitation motivation were found to have high importance. Negative emotions such as depression and anxiety showed a positive relationship with SI and rehabilitation motivation and self-efficacy displayed an inverse relationship with SI. Machine learning-based SI models could augment SI prevention by helping rehabilitation and medical professionals identify high-risk stroke patients in need of SI prevention intervention.
| S-EPMC9508242 | biostudies-literature
Project description:BACKGROUND:Chronic spinal pain conditions affect millions of US adults and carry a high healthcare cost burden, both direct and indirect. Conservative interventions for spinal pain conditions, including chiropractic care, have been associated with lower healthcare costs and improvements in pain status in different clinical populations, including veterans. Little is currently known about predicting healthcare service utilization in the domain of conservative interventions for spinal pain conditions, including the frequency of use of chiropractic services. The purpose of this retrospective cohort study was to explore the use of supervised machine learning approaches to predicting one-year chiropractic service utilization by veterans receiving VA chiropractic care. METHODS:We included 19,946 veterans who entered the Musculoskeletal Diagnosis Cohort between October 1, 2003 and September 30, 2013 and utilized VA chiropractic services within one year of cohort entry. The primary outcome was one-year chiropractic service utilization following index chiropractic visit, split into quartiles represented by the following classes: 1 visit, 2 to 3 visits, 4 to 6 visits, and 7 or greater visits. We compared the performance of four multiclass classification algorithms (gradient boosted classifier, stochastic gradient descent classifier, support vector classifier, and artificial neural network) in predicting visit quartile using 158 sociodemographic and clinical features. RESULTS:The selected algorithms demonstrated poor prediction capabilities. Subset accuracy was 42.1% for the gradient boosted classifier, 38.6% for the stochastic gradient descent classifier, 41.4% for the support vector classifier, and 40.3% for the artificial neural network. The micro-averaged area under the precision-recall curve for each one-versus-rest classifier was 0.43 for the gradient boosted classifier, 0.38 for the stochastic gradient descent classifier, 0.43 for the support vector classifier, and 0.42 for the artificial neural network. Performance of each model yielded only a small positive shift in prediction probability (approximately 15%) compared to naïve classification. CONCLUSIONS:Using supervised machine learning to predict chiropractic service utilization remains challenging, with only a small shift in predictive probability over naïve classification and limited clinical utility. Future work should examine mechanisms to improve model performance.
| S-EPMC7368704 | biostudies-literature
Project description:Though selective laser melting (SLM) has a rapidly increasing market these years, the quality of the SLM-fabricated part is extremely dependent on the process parameters. However, the current metallographic examination method to find the parameter window is time-consuming and involves subjective assessments of the experimenters. Here, we proposed a supervised machine learning (ML) method to detect the track defect and predict the printability of material in SLM intelligently. The printed tracks were classified into five types based on the measured surface morphologies and characteristics. The classification results were used as the target output of the ML model. Four indicators had been calculated to evaluate the quality of the tracks quantitatively, serving as input variables of the model. The data-driven model can determine the defect-free process parameter combination, which significantly improves the efficiency in searching the process parameter window and has great potential for the application in the unmanned factory in the future.
| S-EPMC7698234 | biostudies-literature
Project description:Background: We sought to test the hypothesis that transcriptome-level gene signatures are differentially expressed between male and female bipolar patients, prior to lithium treatment, in a patient cohort who later were clinically classified as lithium treatment responders. Methods: Gene expression study data was obtained from the Lithium Treatment-Moderate dose Use Study data accessed from the National Center for Biotechnology Information's Gene Expression Omnibus via accession number GSE4548. Differential gene expression analysis was conducted using the Linear Models for Microarray and RNA-Seq (limma) package and the Decision Tree and Random Forest machine learning algorithms in R. Results: Using quantitative gene expression values reported from patient blood samples, the RBPMS2 and LILRA5 genes classify male lithium responders with an area under the receiver operator characteristic curve (AUROC) of 0.92 and the ABRACL, FHL3, and NBPF14 genes classify female lithium responders AUROC of 1. A Decision Tree rule for establishing male versus female samples, using gene expression values were found to be: if RPS4Y1 ≥ 9.643, patient is a male and if RPS4Y1 < 9.643, patient is female with a probability=100%. Conclusions: We developed a pre-treatment gender- and gene-expression-based predictive model selective for classifying male lithium responders with a sensitivity of 96% using 2-genes and female lithium responders with sensitivity=92% using 3-genes.
| S-EPMC6381805 | biostudies-literature