Dataset Information

Evaluation of a two-stage framework for prediction using big genomic data.

ABSTRACT: We are in the era of abundant 'big' or 'high-dimensional' data. These data afford us the opportunity to discover predictors of an event of interest, and to estimate occurrence of the event based on values of these predictors. For example, 'genome-wide association studies' examine millions of single-nucleotide polymorphisms (SNPs), along with disease status. We can learn SNPs that affect disease status from these data sets, and use the knowledge learned to predict disease likelihood. Owing to the large number of features, it is difficult for many prediction methods to use all the features directly. The ReliefF algorithm ranks a set of features in terms of how well they predict a target. It can be used to identify good predictors, which can then be provided to a prediction method. We compared the performance of eight prediction methods when predicting binary outcomes using high-dimensional discrete data sets. We performed two-stage prediction, where ReliefF is used in the first stage to identify good predictors. Bayesian network (BN)-based methods performed best overall. Furthermore, ReliefF did not improve their performance. The BN-based methods use the Bayesian Dirichlet Equivalent Uniform score to evaluate candidate models, and use BN inference algorithms to perform prediction. This score and these algorithms were developed for discrete variables. This perhaps explains why they perform better in this domain. Many prediction methods are available, and researchers have little reason for choosing one over the other in the domain of binary prediction using high-dimensional data sets. Our results indicate that the best choices overall are BN-based methods.

SUBMITTER: Jiang X

PROVIDER: S-EPMC4652616 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Evaluation of a two-stage framework for prediction using big genomic data.

Jiang Xia X Neapolitan Richard E RE

Briefings in bioinformatics 20150318 6

We are in the era of abundant 'big' or 'high-dimensional' data. These data afford us the opportunity to discover predictors of an event of interest, and to estimate occurrence of the event based on values of these predictors. For example, 'genome-wide association studies' examine millions of single-nucleotide polymorphisms (SNPs), along with disease status. We can learn SNPs that affect disease status from these data sets, and use the knowledge learned to predict disease likelihood. Owing to the ...[more]

PMID: 25788325

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Project description:BackgroundTraditionally, dengue surveillance is based on case reporting to a central health agency. However, the delay between a case and its notification can limit the system responsiveness. Machine learning methods have been developed to reduce the reporting delays and to predict outbreaks, based on non-traditional and non-clinical data sources. The aim of this systematic review was to identify studies that used real-world data, Big Data and/or machine learning methods to monitor and predict dengue-related outcomes.Methodology/principal findingsWe performed a search in PubMed, Scopus, Web of Science and grey literature between January 1, 2000 and August 31, 2020. The review (ID: CRD42020172472) focused on data-driven studies. Reviews, randomized control trials and descriptive studies were not included. Among the 119 studies included, 67% were published between 2016 and 2020, and 39% used at least one novel data stream. The aim of the included studies was to predict a dengue-related outcome (55%), assess the validity of data sources for dengue surveillance (23%), or both (22%). Most studies (60%) used a machine learning approach. Studies on dengue prediction compared different prediction models, or identified significant predictors among several covariates in a model. The most significant predictors were rainfall (43%), temperature (41%), and humidity (25%). The two models with the highest performances were Neural Networks and Decision Trees (52%), followed by Support Vector Machine (17%). We cannot rule out a selection bias in our study because of our two main limitations: we did not include preprints and could not obtain the opinion of other international experts.Conclusions/significanceCombining real-world data and Big Data with machine learning methods is a promising approach to improve dengue prediction and monitoring. Future studies should focus on how to better integrate all available data sources and methods to improve the response and dengue management by stakeholders.

Dataset Information

Evaluation of a two-stage framework for prediction using big genomic data.

Publications

Evaluation of a two-stage framework for prediction using big genomic data.

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