Dataset Information

Individualized markers optimize class prediction of microarray data.

ABSTRACT:

Background

Identification of molecular markers for the classification of microarray data is a challenging task. Despite the evident dissimilarity in various characteristics of biological samples belonging to the same category, most of the marker--selection and classification methods do not consider this variability. In general, feature selection methods aim at identifying a common set of genes whose combined expression profiles can accurately predict the category of all samples. Here, we argue that this simplified approach is often unable to capture the complexity of a disease phenotype and we propose an alternative method that takes into account the individuality of each patient-sample.

Results

Instead of using the same features for the classification of all samples, the proposed technique starts by creating a pool of informative gene-features. For each sample, the method selects a subset of these features whose expression profiles are most likely to accurately predict the sample's category. Different subsets are utilized for different samples and the outcomes are combined in a hierarchical framework for the classification of all samples. Moreover, this approach can innately identify subgroups of samples within a given class which share common feature sets thus highlighting the effect of individuality on gene expression.

Conclusion

In addition to high classification accuracy, the proposed method offers a more individualized approach for the identification of biological markers, which may help in better understanding the molecular background of a disease and emphasize the need for more flexible medical interventions.

SUBMITTER: Pavlidis P

PROVIDER: S-EPMC1569876 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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Publications

Individualized markers optimize class prediction of microarray data.

Pavlidis Pavlos P Poirazi Panayiota P

BMC bioinformatics 20060714

<h4>Background</h4>Identification of molecular markers for the classification of microarray data is a challenging task. Despite the evident dissimilarity in various characteristics of biological samples belonging to the same category, most of the marker--selection and classification methods do not consider this variability. In general, feature selection methods aim at identifying a common set of genes whose combined expression profiles can accurately predict the category of all samples. Here, we ...[more]

PMID: 16842618

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Project description:BackgroundThe 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.ResultsOur 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.ConclusionsOur 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.

Project description:This study aimed to evaluate whether the combination of inflammatory markers could provide predictive powers for mortality in individual patients on dialysis and develop a predictive model for mortality according to dialysis modality. Data for inflammatory markers were obtained at the time of enrollment from 3,309 patients on dialysis from a prospective multicenter cohort. Net reclassification index (NRI) and integrated discrimination improvement (IDI) were calculated. Cox proportional hazards regression analysis was used to derive a prediction model of mortality and the integrated area under the curve (iAUC) was calculated to compare the predictive accuracy of the models. The incremental additions of albumin, high-sensitive C-reactive protein (hsCRP), white blood count (WBC), and ferritin to the conventional risk factors showed the highest predictive powers for all-cause mortality in the entire population (NRI, 21.0; IDI, 0.045) and patients on peritoneal dialysis (NRI, 25.7; IDI, 0.061). The addition of albumin and hsCRP to the conventional risk factors markedly increased predictive powers for all-cause mortality in HD patients (NRI, 19.0; IDI, 0.035). The prediction model for all-cause mortality using conventional risk factors and combination of inflammatory markers with highest NRI value (iAUC, 0.741; 95% CI, 0.722-0.761) was the most accurate in the entire population compared with a model including conventional risk factors alone (iAUC, 0.719; 95% CI, 0.700-0.738) or model including only significant conventional risk factors and inflammatory markers (iAUC, 0.734; 95% CI, 0.714-0.754). Using multiple inflammatory markers practically available in a clinic can provide higher predictive power for all-cause mortality in patients on dialysis. The predictive model for mortality based on combinations of inflammatory markers enables a stratified risk assessment. However, the optimal combination for the predictive model was different in each dialysis modality.

Dataset Information

Individualized markers optimize class prediction of microarray data.

Background

Results

Conclusion

Publications

Individualized markers optimize class prediction of microarray data.

Similar Datasets

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