Journal article
Consistency of feature attribution in deep learning architectures for multi-omics
Scientific reports, Vol.16(1), 25890
08/18/2026
DOI: 10.1038/s41598-026-58312-5
PMID: 42613353
Abstract
Machine and deep learning have grown in popularity and use in biological research over the last decade but still present challenges in interpretability of the fitted model. The development and use of metrics to determine features driving predictions and increase model interpretability continues to be an open area of research. We investigate the use of Shapley Additive Explanations (SHAP) on a multi-view deep learning model applied to multi-omics data for the purposes of identifying biomolecules of interest. Rankings of features via these attribution methods are compared across various architectures to evaluate consistency of the method. We perform multiple computational experiments to assess the robustness of SHAP and investigate modeling approaches and diagnostics to increase and measure the reliability of the identification of important features. Accuracy of a random forest model fit on subsets of features selected as being most influential as well as clustering quality using only these features are used as a measure of effectiveness of the attribution method. Our findings indicate that in the case of our human host cellular response datasets, the rankings of features resulting from SHAP are sensitive to the choice of architecture as well as different random initializations of weights, suggesting caution and a recommendation for further evaluation when using attribution methods on multi-view deep learning models applied to multi-omics data. We present an alternative, simple method to assess the robustness of identification of important biomolecules.
Details
- Title: Subtitle
- Consistency of feature attribution in deep learning architectures for multi-omics
- Creators
- Daniel Claborne - Pacific Northwest National LaboratoryJavier Flores - Pacific Northwest National LaboratorySamantha Erwin - Pacific Northwest National LaboratoryLuke Durell - Pacific Northwest National LaboratoryDavid Degnan - Pacific Northwest National LaboratoryRachel Richardson - Pacific Northwest National LaboratoryRuby Fore - Pacific Northwest National LaboratoryLisa Bramer - Pacific Northwest National Laboratory
- Resource Type
- Journal article
- Publication Details
- Scientific reports, Vol.16(1), 25890
- DOI
- 10.1038/s41598-026-58312-5
- PMID
- 42613353
- NLM abbreviation
- Sci Rep
- ISSN
- 2045-2322
- eISSN
- 2045-2322
- Publisher
- Nature Publishing Group UK
- Grant note
- Defense Threat Reduction Agency (https://doi.org/10.13039/100000774)
- Language
- English
- Date published
- 08/18/2026
- Academic Unit
- Biostatistics
- Record Identifier
- 9985219307802771
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