Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions
Analysis of gene expression data is an attractive topic in the field of bioinformatics, and a typical application is to classify and predict individuals’ diseases or tumors by treating gene expression values as predictors. A primary challenge of this study comes from ultrahigh-dimensionality, which...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477337/?tool=EBI |
| _version_ | 1811267331783917568 |
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| author | Li-Pang Chen |
| author_facet | Li-Pang Chen |
| author_sort | Li-Pang Chen |
| collection | DOAJ |
| description | Analysis of gene expression data is an attractive topic in the field of bioinformatics, and a typical application is to classify and predict individuals’ diseases or tumors by treating gene expression values as predictors. A primary challenge of this study comes from ultrahigh-dimensionality, which makes that (i) many predictors in the dataset might be non-informative, (ii) pairwise dependence structures possibly exist among high-dimensional predictors, yielding the network structure. While many supervised learning methods have been developed, it is expected that the prediction performance would be affected if impacts of ultrahigh-dimensionality were not carefully addressed. In this paper, we propose a new statistical learning algorithm to deal with multi-classification subject to ultrahigh-dimensional gene expressions. In the proposed algorithm, we employ the model-free feature screening method to retain informative gene expression values from ultrahigh-dimensional data, and then construct predictive models with network structures of selected gene expression accommodated. Different from existing supervised learning methods that build predictive models based on entire dataset, our approach is able to identify informative predictors and dependence structures for gene expression. Throughout analysis of a real dataset, we find that the proposed algorithm gives precise classification as well as accurate prediction, and outperforms some commonly used supervised learning methods. |
| first_indexed | 2024-04-12T20:59:25Z |
| format | Article |
| id | doaj.art-b5514281133846e0a9a25715504658b3 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T20:59:25Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-b5514281133846e0a9a25715504658b32022-12-22T03:16:52ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01179Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressionsLi-Pang ChenAnalysis of gene expression data is an attractive topic in the field of bioinformatics, and a typical application is to classify and predict individuals’ diseases or tumors by treating gene expression values as predictors. A primary challenge of this study comes from ultrahigh-dimensionality, which makes that (i) many predictors in the dataset might be non-informative, (ii) pairwise dependence structures possibly exist among high-dimensional predictors, yielding the network structure. While many supervised learning methods have been developed, it is expected that the prediction performance would be affected if impacts of ultrahigh-dimensionality were not carefully addressed. In this paper, we propose a new statistical learning algorithm to deal with multi-classification subject to ultrahigh-dimensional gene expressions. In the proposed algorithm, we employ the model-free feature screening method to retain informative gene expression values from ultrahigh-dimensional data, and then construct predictive models with network structures of selected gene expression accommodated. Different from existing supervised learning methods that build predictive models based on entire dataset, our approach is able to identify informative predictors and dependence structures for gene expression. Throughout analysis of a real dataset, we find that the proposed algorithm gives precise classification as well as accurate prediction, and outperforms some commonly used supervised learning methods.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477337/?tool=EBI |
| spellingShingle | Li-Pang Chen Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions PLoS ONE |
| title | Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions |
| title_full | Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions |
| title_fullStr | Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions |
| title_full_unstemmed | Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions |
| title_short | Classification and prediction for multi-cancer data with ultrahigh-dimensional gene expressions |
| title_sort | classification and prediction for multi cancer data with ultrahigh dimensional gene expressions |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9477337/?tool=EBI |
| work_keys_str_mv | AT lipangchen classificationandpredictionformulticancerdatawithultrahighdimensionalgeneexpressions |