Improved high-dimensional prediction with Random Forests by the use of co-data.
Ontology highlight
ABSTRACT:
SUBMITTER: Te Beest DE
PROVIDER: S-EPMC5745983 | biostudies-literature | 2017 Dec
REPOSITORIES: biostudies-literature
Publications
Improved high-dimensional prediction with Random Forests by the use of co-data.
Te Beest Dennis E DE Mes Steven W SW Wilting Saskia M SM Brakenhoff Ruud H RH van de Wiel Mark A MA
BMC bioinformatics 20171228 1
<h4>Background</h4>Prediction in high dimensional settings is difficult due to the large number of variables relative to the sample size. We demonstrate how auxiliary 'co-data' can be used to improve the performance of a Random Forest in such a setting.<h4>Results</h4>Co-data are incorporated in the Random Forest by replacing the uniform sampling probabilities that are used to draw candidate variables by co-data moderated sampling probabilities. Co-data here are defined as any type information t ...[more]
Similar Datasets
Project description:BackgroundIdentifying variants associated with complex human traits in high-dimensional data is a central goal of genome-wide association studies. However, complicated etiologies such as gene-gene interactions are ignored by the univariate analysis usually applied in these studies. Random Forests (RF) are a popular data-mining technique that can accommodate a large number of predictor variables and allow for complex models with interactions. RF analysis produces measures of variable importance that can be used to rank the predictor variables. Thus, single nucleotide polymorphism (SNP) analysis using RFs is gaining popularity as a potential filter approach that considers interactions in high-dimensional data. However, the impact of data dimensionality on the power of RF to identify interactions has not been thoroughly explored. We investigate the ability of rankings from variable importance measures to detect gene-gene interaction effects and their potential effectiveness as filters compared to p-values from univariate logistic regression, particularly as the data becomes increasingly high-dimensional.ResultsRF effectively identifies interactions in low dimensional data. As the total number of predictor variables increases, probability of detection declines more rapidly for interacting SNPs than for non-interacting SNPs, indicating that in high-dimensional data the RF variable importance measures are capturing marginal effects rather than capturing the effects of interactions.ConclusionsWhile RF remains a promising data-mining technique that extends univariate methods to condition on multiple variables simultaneously, RF variable importance measures fail to detect interaction effects in high-dimensional data in the absence of a strong marginal component, and therefore may not be useful as a filter technique that allows for interaction effects in genome-wide data.
| S-EPMC3463421 | biostudies-literature
Project description:MotivationGenome-wide association (GWA) studies have proven to be a successful approach for helping unravel the genetic basis of complex genetic diseases. However, the identified associations are not well suited for disease prediction, and only a modest portion of the heritability can be explained for most diseases, such as Type 2 diabetes or Crohn's disease. This may partly be due to the low power of standard statistical approaches to detect gene-gene and gene-environment interactions when small marginal effects are present. A promising alternative is Random Forests, which have already been successfully applied in candidate gene analyses. Important single nucleotide polymorphisms are detected by permutation importance measures. To this day, the application to GWA data was highly cumbersome with existing implementations because of the high computational burden.ResultsHere, we present the new freely available software package Random Jungle (RJ), which facilitates the rapid analysis of GWA data. The program yields valid results and computes up to 159 times faster than the fastest alternative implementation, while still maintaining all options of other programs. Specifically, it offers the different permutation importance measures available. It includes new options such as the backward elimination method. We illustrate the application of RJ to a GWA of Crohn's disease. The most important single nucleotide polymorphisms (SNPs) validate recent findings in the literature and reveal potential interactions.AvailabilityThe RJ software package is freely available at http://www.randomjungle.org
| S-EPMC2894507 | biostudies-literature
Project description:Clinical research often focuses on complex traits in which many variables play a role in mechanisms driving, or curing, diseases. Clinical prediction is hard when data is high-dimensional, but additional information, like domain knowledge and previously published studies, may be helpful to improve predictions. Such complementary data, or co-data, provide information on the covariates, such as genomic location or P-values from external studies. We use multiple and various co-data to define possibly overlapping or hierarchically structured groups of covariates. These are then used to estimate adaptive multi-group ridge penalties for generalized linear and Cox models. Available group adaptive methods primarily target for settings with few groups, and therefore likely overfit for non-informative, correlated or many groups, and do not account for known structure on group level. To handle these issues, our method combines empirical Bayes estimation of the hyperparameters with an extra level of flexible shrinkage. This renders a uniquely flexible framework as any type of shrinkage can be used on the group level. We describe various types of co-data and propose suitable forms of hypershrinkage. The method is very versatile, as it allows for integration and weighting of multiple co-data sets, inclusion of unpenalized covariates and posterior variable selection. For three cancer genomics applications we demonstrate improvements compared to other models in terms of performance, variable selection stability and validation.
| S-EPMC9292202 | biostudies-literature
Project description:BackgroundPost translational modifications (PTMs) occur in the vast majority of proteins and are essential for function. Prediction of the sequence location of PTMs enhances the functional characterisation of proteins. Glycosylation is one type of PTM, and is implicated in protein folding, transport and function.ResultsWe use the random forest algorithm and pairwise patterns to predict glycosylation sites. We identify pairwise patterns surrounding glycosylation sites and use an odds ratio to weight their propensity of association with modified residues. Our prediction program, GPP (glycosylation prediction program), predicts glycosylation sites with an accuracy of 90.8% for Ser sites, 92.0% for Thr sites and 92.8% for Asn sites. This is significantly better than current glycosylation predictors. We use the trepan algorithm to extract a set of comprehensible rules from GPP, which provide biological insight into all three major glycosylation types.ConclusionWe have created an accurate predictor of glycosylation sites and used this to extract comprehensible rules about the glycosylation process. GPP is available online at http://comp.chem.nottingham.ac.uk/glyco/.
| S-EPMC2651179 | biostudies-literature
Project description:We present an ensemble tree-based algorithm for variable selection in high dimensional datasets, in settings where a time-to-event outcome is observed with error. The proposed methods are motivated by self-reported outcomes collected in large-scale epidemiologic studies, such as the Women's Health Initiative. The proposed methods equally apply to imperfect outcomes that arise in other settings such as data extracted from electronic medical records. To evaluate the performance of our proposed algorithm, we present results from simulation studies, considering both continuous and categorical covariates. We illustrate this approach to discover single nucleotide polymorphisms that are associated with incident Type II diabetes in the Women's Health Initiative. A freely available R package icRSF (R Core Team, 2018; Xu et al., 2018) has been developed to implement the proposed methods.
| S-EPMC6369914 | biostudies-literature
Project description:Combined focused ion beam and scanning electron microscope (FIB-SEM) tomography is a well-established technique for high resolution imaging and reconstruction of the microstructure of a wide range of materials. Segmentation of FIB-SEM data is complicated due to a number of factors; the most prominent is that for porous materials, the scanning electron microscope image slices contain information not only from the planar cross-section of the material but also from underlying, exposed subsurface pores. In this work, we develop a segmentation method for FIB-SEM data from ethyl cellulose porous films made from ethyl cellulose and hydroxypropyl cellulose (EC/HPC) polymer blends. These materials are used for coating pharmaceutical oral dosage forms (tablets or pellets) to control drug release. We study three samples of ethyl cellulose and hydroxypropyl cellulose with different volume fractions where the hydroxypropyl cellulose phase has been leached out, resulting in a porous material. The data are segmented using scale-space features and a random forest classifier. We demonstrate good agreement with manual segmentations. The method enables quantitative characterization and subsequent optimization of material structure for controlled release applications. Although the methodology is demonstrated on porous polymer films, it is applicable to other soft porous materials imaged by FIB-SEM. We make the data and software used publicly available to facilitate further development of FIB-SEM segmentation methods. LAY DESCRIPTION: For imaging of very fine structures in materials, the resolution limits of, e.g. X-ray computed tomography quickly become a bottleneck. Scanning electron microscopy (SEM) provides a way out, but it is essentially a two-dimensional imaging technique. One manner in which to extend it to three dimensions is to use a focused ion beam (FIB) combined with a scanning electron microscopy and acquire tomography data. In FIB-SEM tomography, ions are used to perform serial sectioning and the electron beam is used to image the cross section surface. This is a well-established method for a wide range of materials. However, image analysis of FIB-SEM data is complicated for a variety of reasons, in particular for porous media. In this work, we analyse FIB-SEM data from ethyl cellulose porous films made from ethyl cellulose and hydroxypropyl cellulose (EC/HPC) polymer blends. These films are used as coatings for controlled drug release. The aim is to perform image segmentation, i.e. to identify which parts of the image data constitute the pores and the solid, respectively. Manual segmentation, i.e. when a trained operator manually identifies areas constituting pores and solid, is too time-consuming to do in full for our very large data sets. However, by performing manual segmentation on a set of small, random regions of the data, we can train a machine learning algorithm to perform automatic segmentation on the entire data sets. The method yields good agreement with the manual segmentations and yields porosities of the entire data sets in very good agreement with expected values. The method facilitates understanding and quantitative characterization of the geometrical structure of the materials, and ultimately understanding of how to tailor the drug release.
| S-EPMC7754501 | biostudies-literature
Project description:BackgroundClinical research and medical practice can be advanced through the prediction of an individual's health state, trajectory, and responses to treatments. However, the majority of current clinical risk prediction models are based on regression approaches or machine learning algorithms that are static, rather than dynamic. To benefit from the increasing emergence of large, heterogeneous data sets, such as electronic health records (EHRs), novel tools to support improved clinical decision making through methods for individual-level risk prediction that can handle multiple variables, their interactions, and time-varying values are necessary.MethodsWe introduce a novel dynamic approach to clinical risk prediction for survival, longitudinal, and multivariate (SLAM) outcomes, called random forest for SLAM data analysis (RF-SLAM). RF-SLAM is a continuous-time, random forest method for survival analysis that combines the strengths of existing statistical and machine learning methods to produce individualized Bayes estimates of piecewise-constant hazard rates. We also present a method-agnostic approach for time-varying evaluation of model performance.ResultsWe derive and illustrate the method by predicting sudden cardiac arrest (SCA) in the Left Ventricular Structural (LV) Predictors of Sudden Cardiac Death (SCD) Registry. We demonstrate superior performance relative to standard random forest methods for survival data. We illustrate the importance of the number of preceding heart failure hospitalizations as a time-dependent predictor in SCA risk assessment.ConclusionsRF-SLAM is a novel statistical and machine learning method that improves risk prediction by incorporating time-varying information and accommodating a large number of predictors, their interactions, and missing values. RF-SLAM is designed to easily extend to simultaneous predictions of multiple, possibly competing, events and/or repeated measurements of discrete or continuous variables over time.Trial registrationLV Structural Predictors of SCD Registry (clinicaltrials.gov, NCT01076660), retrospectively registered 25 February 2010.
| S-EPMC6937754 | biostudies-literature
Project description:BackgroundIn the last years more and more multi-omics data are becoming available, that is, data featuring measurements of several types of omics data for each patient. Using multi-omics data as covariate data in outcome prediction is both promising and challenging due to the complex structure of such data. Random forest is a prediction method known for its ability to render complex dependency patterns between the outcome and the covariates. Against this background we developed five candidate random forest variants tailored to multi-omics covariate data. These variants modify the split point selection of random forest to incorporate the block structure of multi-omics data and can be applied to any outcome type for which a random forest variant exists, such as categorical, continuous and survival outcomes. Using 20 publicly available multi-omics data sets with survival outcome we compared the prediction performances of the block forest variants with alternatives. We also considered the common special case of having clinical covariates and measurements of a single omics data type available.ResultsWe identify one variant termed "block forest" that outperformed all other approaches in the comparison study. In particular, it performed significantly better than standard random survival forest (adjusted p-value: 0.027). The two best performing variants have in common that the block choice is randomized in the split point selection procedure. In the case of having clinical covariates and a single omics data type available, the improvements of the variants over random survival forest were larger than in the case of the multi-omics data. The degrees of improvements over random survival forest varied strongly across data sets. Moreover, considering all clinical covariates mandatorily improved the performance. This result should however be interpreted with caution, because the level of predictive information contained in clinical covariates depends on the specific application.ConclusionsThe new prediction method block forest for multi-omics data can significantly improve the prediction performance of random forest and outperformed alternatives in the comparison. Block forest is particularly effective for the special case of using clinical covariates in combination with measurements of a single omics data type.
| S-EPMC6598279 | biostudies-literature
Project description:BACKGROUND: The goal of class prediction studies is to develop rules to accurately predict the class membership of new samples. The rules are derived using the values of the variables available for each subject: the main characteristic of high-dimensional data is that the number of variables greatly exceeds the number of samples. Frequently the classifiers are developed using class-imbalanced data, i.e., data sets where the number of samples in each class is not equal. Standard classification methods used on class-imbalanced data often produce classifiers that do not accurately predict the minority class; the prediction is biased towards the majority class. In this paper we investigate if the high-dimensionality poses additional challenges when dealing with class-imbalanced prediction. We evaluate the performance of six types of classifiers on class-imbalanced data, using simulated data and a publicly available data set from a breast cancer gene-expression microarray study. We also investigate the effectiveness of some strategies that are available to overcome the effect of class imbalance. RESULTS: Our results show that the evaluated classifiers are highly sensitive to class imbalance and that variable selection introduces an additional bias towards classification into the majority class. Most new samples are assigned to the majority class from the training set, unless the difference between the classes is very large. As a consequence, the class-specific predictive accuracies differ considerably. When the class imbalance is not too severe, down-sizing and asymmetric bagging embedding variable selection work well, while over-sampling does not. Variable normalization can further worsen the performance of the classifiers. CONCLUSIONS: Our results show that matching the prevalence of the classes in training and test set does not guarantee good performance of classifiers and that the problems related to classification with class-imbalanced data are exacerbated when dealing with high-dimensional data. Researchers using class-imbalanced data should be careful in assessing the predictive accuracy of the classifiers and, unless the class imbalance is mild, they should always use an appropriate method for dealing with the class imbalance problem.
| S-EPMC3098087 | biostudies-other
Project description:Extending previous work on quantile classifiers (q-classifiers) we propose the q*-classifier for the class imbalance problem. The classifier assigns a sample to the minority class if the minority class conditional probability exceeds 0 < q* < 1, where q* equals the unconditional probability of observing a minority class sample. The motivation for q*-classification stems from a density-based approach and leads to the useful property that the q*-classifier maximizes the sum of the true positive and true negative rates. Moreover, because the procedure can be equivalently expressed as a cost-weighted Bayes classifier, it also minimizes weighted risk. Because of this dual optimization, the q*-classifier can achieve near zero risk in imbalance problems, while simultaneously optimizing true positive and true negative rates. We use random forests to apply q*-classification. This new method which we call RFQ is shown to outperform or is competitive with existing techniques with respect to tt-mean performance and variable selection. Extensions to the multiclass imbalanced setting are also considered.
| S-EPMC6370055 | biostudies-literature