Development of Machine Learning Models Predicting Estimated Blood Loss during Liver Transplant Surgery.
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ABSTRACT:
SUBMITTER: Park S
PROVIDER: S-EPMC9320884 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:DNA methylation modification plays a vital role in the pathophysiology of high blood pressure (BP). Herein, we applied three machine learning (ML) algorithms including deep learning (DL), support vector machine, and random forest for detecting high BP using DNA methylome data. Peripheral blood samples of 50 elderly individuals were collected three times at three visits for DNA methylome profiling. Participants who had a history of hypertension and/or current high BP measure were considered to have high BP. The whole dataset was randomly divided to conduct a nested five-group cross-validation for prediction performance. Data in each outer training set were independently normalized using a min-max scaler, reduced dimensionality using principal component analysis, then fed into three predictive algorithms. Of the three ML algorithms, DL achieved the best performance (AUPRC = 0.65, AUROC = 0.73, accuracy = 0.69, and F1-score = 0.73). To confirm the reliability of using DNA methylome as a biomarker for high BP, we constructed mixed-effects models and found that 61,694 methylation sites located in 15,523 intragenic regions and 16,754 intergenic regions were significantly associated with BP measures. Our proposed models pioneered the methodology of applying ML and DNA methylome data for early detection of high BP in clinical practices.
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Project description:Mouse efficacy studies are a critical hurdle to advance translational research of potential therapeutic compounds for many diseases. Although mouse liver microsomal (MLM) stability studies are not a perfect surrogate for in vivo studies of metabolic clearance, they are the initial model system used to assess metabolic stability. Consequently, we explored the development of machine learning models that can enhance the probability of identifying compounds possessing MLM stability.Published assays on MLM half-life values were identified in PubChem, reformatted, and curated to create a training set with 894 unique small molecules. These data were used to construct machine learning models assessed with internal cross-validation, external tests with a published set of antitubercular compounds, and independent validation with an additional diverse set of 571 compounds (PubChem data on percent metabolism)."Pruning" out the moderately unstable / moderately stable compounds from the training set produced models with superior predictive power. Bayesian models displayed the best predictive power for identifying compounds with a half-life ?1 h.Our results suggest the pruning strategy may be of general benefit to improve test set enrichment and provide machine learning models with enhanced predictive value for the MLM stability of small organic molecules. This study represents the most exhaustive study to date of using machine learning approaches with MLM data from public sources.
| S-EPMC4712113 | biostudies-literature
Project description:Abstract Background Early diagnosis of liver metastasis is of great importance for enhancing the survival of colorectal adenocarcinoma (CAD) patients, and the combined use of a single biomarker in a classier model has shown great improvement in predicting the metastasis of several types of cancers. However, it is little reported for CAD. This study therefore aimed to screen an optimal classier model of CAD with liver metastasis and explore the metastatic mechanisms of genes when applying this classier model. Methods The differentially expressed genes between primary CAD samples and CAD with metastasis samples were screened from the Moffitt Cancer Center (MCC) dataset GSE131418. The classification performances of six selected algorithms, namely, LR, RF, SVM, GBDT, NN, and CatBoost, for classification of CAD with liver metastasis samples were compared using the MCC dataset GSE131418 by detecting their classification test accuracy. In addition, the consortium datasets of GSE131418 and GSE81558 were used as internal and external validation sets to screen the optimal method. Subsequently, functional analyses and a drug?targeted network construction of the feature genes when applying the optimal method were conducted. Results The optimal CatBoost model with the highest accuracy of 99%, and an area under the curve of 1, was screened, which consisted of 33 feature genes. A functional analysis showed that the feature genes were closely associated with a “steroid metabolic process” and “lipoprotein particle receptor binding” (eg APOB and APOC3). In addition, the feature genes were significantly enriched in the “complement and coagulation cascade” pathways (eg FGA, F2, and F9). In a drug?target interaction network, F2 and F9 were predicted as targets of menadione. Conclusion The CatBoost model constructed using 33 feature genes showed the optimal classification performance for identifying CAD with liver metastasis. APOB, APOC3, FGA, F2, F9, and NKX2?3 were potential biomarkers for classification of CAD with liver metastasis. Menadione might be a promising anti?metastatic drug of CAD cells through functioning its role at sites of F2 and F9. CatBoost model constructed by 33 feature genes showed the optimal classification performance for identifying CAD liver metastasis.
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Project description:The present study investigates the prediction of increased blood pressure by body mass index (BMI), waist (WC) and hip circumference (HC), and waist hip ratio (WHR) using a machine learning technique named classification tree. Data were collected from 400 college students (56.3% women) from 16 to 63 years old. Fifteen trees were calculated in the training group for each sex, using different numbers and combinations of predictors. The result shows that for women BMI, WC, and WHR are the combination that produces the best prediction, since it has the lowest deviance (87.42), misclassification (.19), and the higher pseudo R (2) (.43). This model presented a sensitivity of 80.86% and specificity of 81.22% in the training set and, respectively, 45.65% and 65.15% in the test sample. For men BMI, WC, HC, and WHC showed the best prediction with the lowest deviance (57.25), misclassification (.16), and the higher pseudo R (2) (.46). This model had a sensitivity of 72% and specificity of 86.25% in the training set and, respectively, 58.38% and 69.70% in the test set. Finally, the result from the classification tree analysis was compared with traditional logistic regression, indicating that the former outperformed the latter in terms of predictive power.
| S-EPMC3941962 | biostudies-literature
Project description:BackgroundDays before surgery, add-ons may be scheduled to fill unused surgical block time at an outpatient surgery center. At times, outpatient surgery centers have time limitations for end of block time and discharge from the postanesthesia care unit (PACU). The objective of our study was to develop machine learning models that predicted the following composite outcome: (1) surgery finished by end of operating room block time and (2) patient was discharged by end of recovery room nursing shift. We compared various machine learning models to logistic regression. By evaluating various performance metrics, including F1 scores, we hypothesized that models using ensemble learning will be superior to logistic regression.MethodsData were collected from patients at an ambulatory surgery center. The primary outcome measurement was determined to have a value of 1 (versus 0) if they met both criteria: (1) surgery ends by 5 pm and (2) patient is discharged from the recovery room by 7 pm. We developed models to determine if a procedure would meet both criteria if it were scheduled at 1 pm, 2 pm, 3 pm, or 4 pm. We implemented regression, random forest, balanced random forest, balanced bagging, neural network, and support vector classifier, and included the following features: surgery, surgeon, service line, American Society of Anesthesiologists score, age, sex, weight, and scheduled case duration. We evaluated model performance with Synthetic Minority Oversampling Technique (SMOTE). We compared the following performance metrics: F1 score, area under the receiver operating characteristic curve (AUC), specificity, sensitivity, precision, recall, and Matthews correlation coefficient.ResultsAmong 13,447 surgical procedures, the median total perioperative time (actual case duration and PACU length stay) was 165 minutes. When SMOTE was not used, when predicting whether surgery will end by 5 pm and patient will be discharged by 7 pm, the average F1 scores were best with random forest, balanced bagging, and balanced random forest classifiers. When SMOTE was used, these models had improved F1 scores compared to no SMOTE. The balanced bagging classifier performed best with F1 score of 0.78, 0.80, 0.82, and 0.82 when predicting our outcome if cases were to start at 1 pm, 2 pm, 3 pm, or 4 pm, respectively.ConclusionsWe demonstrated improvement in predicting the outcome at a range of start times when using ensemble learning versus regression techniques. Machine learning may be adapted by operating room management to allow for a better determination whether an add-on case at an outpatient surgery center could be appropriately booked.
| S-EPMC9172889 | biostudies-literature
Project description:The COVID-19 pandemic has had a significant impact on public life and health worldwide, putting the world's healthcare systems at risk. The first step in stopping this outbreak is to detect the infection in its early stages, which will relieve the risk, control the outbreak's spread, and restore full functionality to the world's healthcare systems. Currently, PCR is the most prevalent diagnosis tool for COVID-19. However, chest X-ray images may play an essential role in detecting this disease, as they are successful for many other viral pneumonia diseases. Unfortunately, there are common features between COVID-19 and other viral pneumonia, and hence manual differentiation between them seems to be a critical problem and needs the aid of artificial intelligence. This research employs deep- and transfer-learning techniques to develop accurate, general, and robust models for detecting COVID-19. The developed models utilize either convolutional neural networks or transfer-learning models or hybridize them with powerful machine-learning techniques to exploit their full potential. For experimentation, we applied the proposed models to two data sets: the COVID-19 Radiography Database from Kaggle and a local data set from Asir Hospital, Abha, Saudi Arabia. The proposed models achieved promising results in detecting COVID-19 cases and discriminating them from normal and other viral pneumonia with excellent accuracy. The hybrid models extracted features from the flatten layer or the first hidden layer of the neural network and then fed these features into a classification algorithm. This approach enhanced the results further to full accuracy for binary COVID-19 classification and 97.8% for multiclass classification.
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Project description:ObjectiveCompare machine learning (ML)-based predictive analytics methods to traditional logistic regression in classification of olfactory dysfunction in chronic rhinosinusitis (CRS-OD) and identify predictors within a large multi-institutional cohort of refractory CRS patients.MethodsAdult CRS patients enrolled in a prospective, multi-institutional, observational cohort study were assessed for baseline CRS-OD using a smell identification test (SIT) or brief SIT (bSIT). Four different ML methods were compared to traditional logistic regression for classification of CRS normosmics versus CRS-OD.ResultsData were collected for 611 study participants who met inclusion criteria between 2011 April and 2015 July. Thirty-four percent of enrolled patients demonstrated olfactory loss on psychophysical testing. Differences between CRS normosmics and those with smell loss included objective disease measures (CT and endoscopy scores), age, sex, prior surgeries, socioeconomic status, steroid use, polyp presence, asthma, and aspirin sensitivity. Most ML methods performed favorably in terms of predictive ability. Top predictors include factors previously reported in the literature, as well as several socioeconomic factors.ConclusionOlfactory dysfunction is a variable phenomenon in CRS patients. ML methods perform well compared to traditional logistic regression in classification of normosmia versus smell loss in CRS, and are able to include numerous risk factors into prediction models. Several actionable features were identified as risk factors for CRS-OD. These results suggest that ML methods may be useful for current understanding and future study of hyposmia secondary to sinonasal disease, the most common cause of persistent olfactory loss in the general population.
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Project description:BackgroundSkeletal muscle loss during treatment is associated with poor survival outcomes in patients with ovarian cancer. Although changes in muscle mass can be assessed on computed tomography (CT) scans, this labour-intensive process can impair its utility in clinical practice. This study aimed to develop a machine learning (ML) model to predict muscle loss based on clinical data and to interpret the ML model by applying SHapley Additive exPlanations (SHAP) method.MethodsThis study included the data of 617 patients with ovarian cancer who underwent primary debulking surgery and platinum-based chemotherapy at a tertiary centre between 2010 and 2019. The cohort data were split into training and test sets based on the treatment time. External validation was performed using 140 patients from a different tertiary centre. The skeletal muscle index (SMI) was measured from pre- and post-treatment CT scans, and a decrease in SMI ≥ 5% was defined as muscle loss. We evaluated five ML models to predict muscle loss, and their performance was determined using the area under the receiver operating characteristic curve (AUC) and F1 score. The features for analysis included demographic and disease-specific characteristics and relative changes in body mass index (BMI), albumin, neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio (PLR). The SHAP method was applied to determine the importance of the features and interpret the ML models.ResultsThe median (inter-quartile range) age of the cohort was 52 (46-59) years. After treatment, 204 patients (33.1%) experienced muscle loss in the training and test datasets, while 44 (31.4%) patients experienced muscle loss in the external validation dataset. Among the five evaluated ML models, the random forest model achieved the highest AUC (0.856, 95% confidence interval: 0.854-0.859) and F1 score (0.726, 95% confidence interval: 0.722-0.730). In the external validation, the random forest model outperformed all ML models with an AUC of 0.874 and an F1 score of 0.741. The results of the SHAP method showed that the albumin change, BMI change, malignant ascites, NLR change, and PLR change were the most important factors in muscle loss. At the patient level, SHAP force plots demonstrated insightful interpretation of our random forest model to predict muscle loss.ConclusionsExplainable ML model was developed using clinical data to identify patients experiencing muscle loss after treatment and provide information of feature contribution. Using the SHAP method, clinicians may better understand the contributors to muscle loss and target interventions to counteract muscle loss.
| S-EPMC10570082 | biostudies-literature
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.
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Project description:Bone is the most common site of distant metastasis from malignant tumors, with the highest prevalence observed in breast and prostate cancers. Such bone metastases (BM) cause many painful skeletal-related events, such as severe bone pain, pathological fractures, spinal cord compression, and hypercalcemia, with adverse effects on life quality. Many bone-targeting agents developed based on the current understanding of BM onset's molecular mechanisms dull these adverse effects. However, only a few studies investigated potential predictors of high risk for developing BM, despite such knowledge being critical for early interventions to prevent or delay BM. This work proposes a computational network-based pipeline that incorporates a ML/DL component to predict BM development. Based on the proposed pipeline we constructed several machine learning models. The deep neural network (DNN) model exhibited the highest prediction accuracy (AUC of 92.11%) using the top 34 featured genes ranked by betweenness centrality scores. We further used an entirely separate, "external" TCGA dataset to evaluate the robustness of this DNN model and achieved sensitivity of 85%, specificity of 80%, positive predictive value of 78.10%, negative predictive value of 80%, and AUC of 85.78%. The result shows the models' way of learning allowed it to zoom in on the featured genes that provide the added benefit of the model displaying generic capabilities, that is, to predict BM for samples from different primary sites. Furthermore, existing experimental evidence provides confidence that about 50% of the 34 hub genes have BM-related functionality, which suggests that these common genetic markers provide vital insight about BM drivers. These findings may prompt the transformation of such a method into an artificial intelligence (AI) diagnostic tool and direct us towards mechanisms that underlie metastasis to bone events.
| S-EPMC8631472 | biostudies-literature