Compositional transformations can reasonably introduce phenotype-associated values into sparse features
ABSTRACT Gihawi et al. (mBio 14:e01607-23, 2023, https://doi.org/10.1128/mbio.01607-23) argued that the analysis of tumor-associated microbiome data by Poore et al. (Nature 579:567-574, 2020, https://doi.org/10.1038/s41586-020-2095-1) is invalid because features that were originally very sparse (gen...
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American Society for Microbiology
2025-05-01
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00021-25 |
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| author | George I. Austin Tal Korem |
| author_facet | George I. Austin Tal Korem |
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| collection | DOAJ |
| description | ABSTRACT Gihawi et al. (mBio 14:e01607-23, 2023, https://doi.org/10.1128/mbio.01607-23) argued that the analysis of tumor-associated microbiome data by Poore et al. (Nature 579:567-574, 2020, https://doi.org/10.1038/s41586-020-2095-1) is invalid because features that were originally very sparse (genera with mostly zero read counts) became associated with the phenotype following batch correction. Here, we examine whether such an observation should necessarily indicate issues with processing or machine learning pipelines. We show counterexamples using the centered log ratio (CLR) transformation, which is often used for analysis of compositional microbiome data. The CLR transformation has similarities to voom-SNM, the batch-correction method brought into question by Gihawi et al., and yet is a sample-wise operation that cannot, in itself, “leak” information or invalidate downstream analyses. We show that because the CLR transformation divides each value by the geometric mean of its sample, common imputation strategies for missing or zero values result in transformed features that are associated with the geometric mean. Through analyses of both synthetic and vaginal microbiome data sets, we demonstrate that when the geometric mean is associated with a phenotype, sparse and CLR-transformed features will also become associated with it. We re-analyze features highlighted by Gihawi et al. and demonstrate that the phenomenon of sparse features becoming phenotype-associated can also be observed after a CLR transformation, which serves as a counterexample to the claim that such an observation necessarily means information leakage. While we do not intend to address other concerns regarding tumor microbiome analyses, validate Poore et al.’s results, or evaluate batch-correction pipelines, we conclude that because phenotype-associated features that were initially sparse can be created by a sample-wise transformation that cannot artifactually inflate machine learning performance, their detection is not independently sufficient to demonstrate information leakage in machine learning pipelines. Microbiome data are multivariate, and as such, a value of 0 carries a different meaning for each sample. Many transformations, including CLR and other batch-correction methods, are likewise multivariate, and, as these issues demonstrate, each individual feature should be interpreted with caution.IMPORTANCEGihawi et al. claim that finding that a transformation turned highly sparse (mostly zero) features into features that are associated with a phenotype is sufficient to conclude that there is information leakage and to invalidate an analysis. This claim has critical implications for both the debate regarding The Cancer Genome Atlas (TCGA) cancer microbiome analysis and for interpretation and evaluation of analyses in the microbiome field at large. We show by counterexamples and by reanalysis that such transformations can be valid. |
| format | Article |
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| publishDate | 2025-05-01 |
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| spelling | doaj-art-e802c661eee94325983cd79c1eea4cb12025-08-20T02:32:53ZengAmerican Society for MicrobiologymSystems2379-50772025-05-0110510.1128/msystems.00021-25Compositional transformations can reasonably introduce phenotype-associated values into sparse featuresGeorge I. Austin0Tal Korem1Department of Biomedical Informatics, Columbia University Irving Medical, New York, New York, USAProgram for Mathematical Genomics, Department of Systems Biology, Columbia University Irving Medical Center, New York, New York, USAABSTRACT Gihawi et al. (mBio 14:e01607-23, 2023, https://doi.org/10.1128/mbio.01607-23) argued that the analysis of tumor-associated microbiome data by Poore et al. (Nature 579:567-574, 2020, https://doi.org/10.1038/s41586-020-2095-1) is invalid because features that were originally very sparse (genera with mostly zero read counts) became associated with the phenotype following batch correction. Here, we examine whether such an observation should necessarily indicate issues with processing or machine learning pipelines. We show counterexamples using the centered log ratio (CLR) transformation, which is often used for analysis of compositional microbiome data. The CLR transformation has similarities to voom-SNM, the batch-correction method brought into question by Gihawi et al., and yet is a sample-wise operation that cannot, in itself, “leak” information or invalidate downstream analyses. We show that because the CLR transformation divides each value by the geometric mean of its sample, common imputation strategies for missing or zero values result in transformed features that are associated with the geometric mean. Through analyses of both synthetic and vaginal microbiome data sets, we demonstrate that when the geometric mean is associated with a phenotype, sparse and CLR-transformed features will also become associated with it. We re-analyze features highlighted by Gihawi et al. and demonstrate that the phenomenon of sparse features becoming phenotype-associated can also be observed after a CLR transformation, which serves as a counterexample to the claim that such an observation necessarily means information leakage. While we do not intend to address other concerns regarding tumor microbiome analyses, validate Poore et al.’s results, or evaluate batch-correction pipelines, we conclude that because phenotype-associated features that were initially sparse can be created by a sample-wise transformation that cannot artifactually inflate machine learning performance, their detection is not independently sufficient to demonstrate information leakage in machine learning pipelines. Microbiome data are multivariate, and as such, a value of 0 carries a different meaning for each sample. Many transformations, including CLR and other batch-correction methods, are likewise multivariate, and, as these issues demonstrate, each individual feature should be interpreted with caution.IMPORTANCEGihawi et al. claim that finding that a transformation turned highly sparse (mostly zero) features into features that are associated with a phenotype is sufficient to conclude that there is information leakage and to invalidate an analysis. This claim has critical implications for both the debate regarding The Cancer Genome Atlas (TCGA) cancer microbiome analysis and for interpretation and evaluation of analyses in the microbiome field at large. We show by counterexamples and by reanalysis that such transformations can be valid.https://journals.asm.org/doi/10.1128/msystems.00021-25microbiomecompositional data analysismachine learningimputation |
| spellingShingle | George I. Austin Tal Korem Compositional transformations can reasonably introduce phenotype-associated values into sparse features mSystems microbiome compositional data analysis machine learning imputation |
| title | Compositional transformations can reasonably introduce phenotype-associated values into sparse features |
| title_full | Compositional transformations can reasonably introduce phenotype-associated values into sparse features |
| title_fullStr | Compositional transformations can reasonably introduce phenotype-associated values into sparse features |
| title_full_unstemmed | Compositional transformations can reasonably introduce phenotype-associated values into sparse features |
| title_short | Compositional transformations can reasonably introduce phenotype-associated values into sparse features |
| title_sort | compositional transformations can reasonably introduce phenotype associated values into sparse features |
| topic | microbiome compositional data analysis machine learning imputation |
| url | https://journals.asm.org/doi/10.1128/msystems.00021-25 |
| work_keys_str_mv | AT georgeiaustin compositionaltransformationscanreasonablyintroducephenotypeassociatedvaluesintosparsefeatures AT talkorem compositionaltransformationscanreasonablyintroducephenotypeassociatedvaluesintosparsefeatures |