High-dimensional hepatopath data analysis by machine learning for predicting HBV-related fibrosis.
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ABSTRACT:
SUBMITTER: Pu X
PROVIDER: S-EPMC7930086 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Clinical prediction of advanced hepatic fibrosis (HF) and cirrhosis has long been challenging due to the gold standard, liver biopsy, being an invasive approach with certain limitations. Less invasive blood test tandem with a cutting-edge machine learning algorithm shows promising diagnostic potential. In this study, we constructed and compared machine learning methods with the FIB-4 score in a discovery dataset (n = 490) of hepatitis B virus (HBV) patients. Models were validated in an independent HBV dataset (n = 86). We further employed these models on two independent hepatitis C virus (HCV) datasets (n = 254 and 230) to examine their applicability. In the discovery data, gradient boosting (GB) stably outperformed other methods as well as FIB-4 scores (p < .001) in the prediction of advanced HF and cirrhosis. In the HBV validation dataset, for classification between early and advanced HF, the area under receiver operating characteristic curves (AUROC) of GB model was 0.918, while FIB-4 was 0.841; for classification between non-cirrhosis and cirrhosis, GB showed AUROC of 0.871, while FIB-4 was 0.830. Additionally, GB-based prediction demonstrated good classification capacity on two HCV datasets while higher cutoffs for both GB and FIB-4 scores were required to achieve comparable specificity and sensitivity. Using the same parameters as FIB-4, the GB-based prediction system demonstrated steady improvements relative to FIB-4 in HBV and HCV cohorts with different cutoff values required in different etiological groups. A user-friendly web tool, LiveBoost, makes our prediction models freely accessible for further clinical studies and applications.
| S-EPMC6154783 | biostudies-literature
Project description:Automatic boundary detection of 4D ultrasound (4DUS) cardiac data is a promising yet challenging application at the intersection of machine learning and medicine. Using recently developed murine 4DUS cardiac imaging data, we demonstrate here a set of three machine learning models that predict left ventricular wall kinematics along both the endo- and epi-cardial boundaries. Each model is fundamentally built on three key features: (1) the projection of raw US data to a lower dimensional subspace, (2) a smoothing spline basis across time, and (3) a strategic parameterization of the left ventricular boundaries. Model 1 is constructed such that boundary predictions are based on individual short-axis images, regardless of their relative position in the ventricle. Model 2 simultaneously incorporates parallel short-axis image data into their predictions. Model 3 builds on the multi-slice approach of model 2, but assists predictions with a single ground-truth position at end-diastole. To assess the performance of each model, Monte Carlo cross validation was used to assess the performance of each model on unseen data. For predicting the radial distance of the endocardium, models 1, 2, and 3 yielded average R2 values of 0.41, 0.49, and 0.71, respectively. Monte Carlo simulations of the endocardial wall showed significantly closer predictions when using model 2 versus model 1 at a rate of 48.67%, and using model 3 versus model 2 at a rate of 83.50%. These finding suggest that a machine learning approach where multi-slice data are simultaneously used as input and predictions are aided by a single user input yields the most robust performance. Subsequently, we explore the how metrics of cardiac kinematics compare between ground-truth contours and predicted boundaries. We observed negligible deviations from ground-truth when using predicted boundaries alone, except in the case of early diastolic strain rate, providing confidence for the use of such machine learning models for rapid and reliable assessments of murine cardiac function. To our knowledge, this is the first application of machine learning to murine left ventricular 4DUS data. Future work will be needed to strengthen both model performance and applicability to different cardiac disease models.
| S-EPMC8301599 | biostudies-literature
Project description:Data collected from clinical trials and cohort studies, such as dementia studies, are often high-dimensional, censored, heterogeneous and contain missing information, presenting challenges to traditional statistical analysis. There is an urgent need for methods that can overcome these challenges to model this complex data. At present there is no cure for dementia and no treatment that can successfully change the course of the disease. Machine learning models that can predict the time until a patient develops dementia are important tools in helping understand dementia risks and can give more accurate results than traditional statistical methods when modelling high-dimensional, heterogeneous, clinical data. This work compares the performance and stability of ten machine learning algorithms, combined with eight feature selection methods, capable of performing survival analysis of high-dimensional, heterogeneous, clinical data. We developed models that predict survival to dementia using baseline data from two different studies. The Sydney Memory and Ageing Study (MAS) is a longitudinal cohort study of 1037 participants, aged 70-90 years, that aims to determine the effects of ageing on cognition. The Alzheimer's Disease Neuroimaging Initiative (ADNI) is a longitudinal study aimed at identifying biomarkers for the early detection and tracking of Alzheimer's disease. Using the concordance index as a measure of performance, our models achieve maximum performance values of 0.82 for MAS and 0.93 For ADNI.
| S-EPMC7683682 | biostudies-literature
Project description:Having accurate maps depicting the locations of residential buildings across a region benefits a range of sectors. This is particularly true for public health programs focused on delivering services at the household level, such as indoor residual spraying with insecticide to help prevent malaria. While open source data from OpenStreetMap (OSM) depicting the locations and shapes of buildings is rapidly improving in terms of quality and completeness globally, even in settings where all buildings have been mapped, information on whether these buildings are residential, commercial or another type is often only available for a small subset. Using OSM building data from Botswana and Swaziland, we identified buildings for which 'type' was indicated, generated via on the ground observations, and classified these into two classes, "sprayable" and "not-sprayable". Ensemble machine learning, using building characteristics such as size, shape and proximity to neighbouring features, was then used to form a model to predict which of these 2 classes every building in these two countries fell into. Results show that an ensemble machine learning approach performed marginally, but statistically, better than the best individual model and that using this ensemble model we were able to correctly classify >86% (using independent test data) of structures correctly as sprayable and not-sprayable across both countries.
| S-EPMC6150517 | biostudies-other
Project description:BACKGROUND:This paper studies the temporal consistency of health care expenditures in a large state Medicaid program. Predictive machine learning models were used to forecast the expenditures, especially for the high-cost, high-need (HCHN) patients. RESULTS:We systematically tests temporal correlation of patient-level health care expenditures in both the short and long terms. The results suggest that medical expenditures are significantly correlated over multiple periods. Our work demonstrates a prevalent and strong temporal correlation and shows promise for predicting future health care expenditures using machine learning. Temporal correlation is stronger in HCHN patients and their expenditures can be better predicted. Including more past periods is beneficial for better predictive performance. CONCLUSIONS:This study shows that there is significant temporal correlation in health care expenditures. Machine learning models can help to accurately forecast the expenditures. These results could advance the field toward precise preventive care to lower overall health care costs and deliver care more efficiently.
| S-EPMC6245495 | biostudies-other
Project description:This paper considers feature selection for data classification in the presence of a huge number of irrelevant features. We propose a new feature-selection algorithm that addresses several major issues with prior work, including problems with algorithm implementation, computational complexity, and solution accuracy. The key idea is to decompose an arbitrarily complex nonlinear problem into a set of locally linear ones through local learning, and then learn feature relevance globally within the large margin framework. The proposed algorithm is based on well-established machine learning and numerical analysis techniques, without making any assumptions about the underlying data distribution. It is capable of processing many thousands of features within minutes on a personal computer while maintaining a very high accuracy that is nearly insensitive to a growing number of irrelevant features. Theoretical analyses of the algorithm's sample complexity suggest that the algorithm has a logarithmical sample complexity with respect to the number of features. Experiments on 11 synthetic and real-world data sets demonstrate the viability of our formulation of the feature-selection problem for supervised learning and the effectiveness of our algorithm.
| S-EPMC3445441 | biostudies-literature
Project description:Machine learning (ML) may be used to predict mortality. We used claims data from one large German insurer to develop and test differently complex ML prediction models, comparing them for their (balanced) accuracy, but also the importance of different predictors, the relevance of the follow-up period before death (i.e. the amount of accumulated data) and the time distance of the data used for prediction and death. A sample of 373,077 insured very old, aged 75 years or above, living in the Northeast of Germany in 2012 was drawn and followed over 6 years. Our outcome was whether an individual died in one of the years of interest (2013-2017) or not; the primary metric was (balanced) accuracy in a hold-out test dataset. From the 86,326 potential variables, we used the 30 most important ones for modeling. We trained a total of 45 model combinations: (1) Three different ML models were used; logistic regression (LR), random forest (RF), extreme gradient boosting (XGB); (2) Different periods of follow-up were employed for training; 1-5 years; (3) Different time distances between data used for prediction and the time of the event (death/survival) were set; 0-4 years. The mortality rate was 9.15% in mean per year. The models showed (balanced) accuracy between 65 and 93%. A longer follow-up period showed limited to no advantage, but models with short time distance from the event were more accurate than models trained on more distant data. RF and XGB were more accurate than LR. For RF and XGB sensitivity and specificity were similar, while for LR sensitivity was significantly lower than specificity. For all three models, the positive-predictive-value was below 62% (and even dropped to below 20% for longer time distances from death), while the negative-predictive-value significantly exceeded 90% for all analyses. The utilization of and costs for emergency transport as well as emergency and any hospital visits as well as the utilization of conventional outpatient care and laboratory services were consistently found most relevant for predicting mortality. All models showed useful accuracies, and more complex models showed advantages. The variables employed for prediction were consistent across models and with medical reasoning. Identifying individuals at risk could assist tailored decision-making and interventions.
| S-EPMC9581892 | biostudies-literature
Project description:Species distribution modeling often involves high-dimensional environmental data. Large amounts of data and multicollinearity among covariates impose challenges to statistical models in variable selection for reliable inferences of the effects of environmental factors on the spatial distribution of species. Few studies have evaluated and compared the performance of multiple machine learning (ML) models in handling multicollinearity. Here, we assessed the effectiveness of removal of correlated covariates and regularization to cope with multicollinearity in ML models for habitat suitability. Three machine learning algorithms maximum entropy (MaxEnt), random forests (RFs), and support vector machines (SVMs) were applied to the original data (OD) of 27 landscape variables, reduced data (RD) with 14 highly correlated covariates being removed, and 15 principal components (PC) of the OD accounting for 90% of the original variability. The performance of the three ML models was measured with the area under the curve and continuous Boyce index. We collected 663 nonduplicated presence locations of Eastern wild turkeys (Meleagris gallopavo silvestris) across the state of Mississippi, United States. Of the total locations, 453 locations separated by a distance of ≥2 km were used to train the three ML algorithms on the OD, RD, and PC data, respectively. The remaining 210 locations were used to validate the trained ML models to measure ML performance. Three ML models had excellent performance on the RD and PC data. MaxEnt and SVMs had good performance on the OD data, indicating the adequacy of regularization of the default setting for multicollinearity. Weak learning of RFs through bagging appeared to alleviate multicollinearity and resulted in excellent performance on the OD data. Regularization of ML algorithms may help exploratory studies of the effects of environmental factors on the spatial distribution and habitat suitability of wildlife.
| S-EPMC6540709 | biostudies-literature
Project description:Parliament dynamics might seem erratic at times. Predicting future voting patterns could support policy design based on the simulation of voting scenarios. The availability of open data on legislative activities and machine learning tools might enable such prediction. In our paper, we provide evidence for this statement by developing an algorithm able to predict party switching in the Italian Parliament with over 70% accuracy up to two months in advance. The analysis was based on voting data from the XVII (2013-2018) and XVIII (2018-2022) Italian legislature. We found party switchers exhibited higher participation in secret ballots and showed a progressive decrease in coherence with their party's majority votes up to two months before the actual switch. These results show how machine learning combined with political open data can support predicting and understanding political dynamics.
| S-EPMC10319836 | biostudies-literature
Project description:BackgroundThe construction of a robust healthcare information system is fundamental to enhancing countries' capabilities in the surveillance and control of hepatitis B virus (HBV). Making use of China's rapidly expanding primary healthcare system, this innovative approach using big data and machine learning (ML) could help towards the World Health Organization's (WHO) HBV infection elimination goals of reaching 90% diagnosis and treatment rates by 2030. We aimed to develop and validate HBV detection models using routine clinical data to improve the detection of HBV and support the development of effective interventions to mitigate the impact of this disease in China.MethodsRelevant data records extracted from the Family Medicine Clinic of the University of Hong Kong-Shenzhen Hospital's Hospital Information System were structuralized using state-of-the-art Natural Language Processing techniques. Several ML models have been used to develop HBV risk assessment models. The performance of the ML model was then interpreted using the Shapley value (SHAP) and validated using cohort data randomly divided at a ratio of 2:1 using a five-fold cross-validation framework.ResultsThe patterns of physical complaints of patients with and without HBV infection were identified by processing 158,988 clinic attendance records. After removing cases without any clinical parameters from the derivation sample (n = 105,992), 27,392 cases were analysed using six modelling methods. A simplified model for HBV using patients' physical complaints and parameters was developed with good discrimination (AUC = 0.78) and calibration (goodness of fit test p-value >0.05).ConclusionsSuspected case detection models of HBV, showing potential for clinical deployment, have been developed to improve HBV surveillance in primary care setting in China. (Word count: 264).
| S-EPMC10860422 | biostudies-literature