The maximum entropy principle for compositional data Journal Article
| Authors: | Weistuch, C.; Zhu, J.; Deasy, J. O.; Tannenbaum, A. R. |
| Article Title: | The maximum entropy principle for compositional data |
| Abstract: | Background: Compositional systems, represented as parts of some whole, are ubiquitous. They encompass the abundances of proteins in a cell, the distribution of organisms in nature, and the stoichiometry of the most basic chemical reactions. Thus, a central goal is to understand how such processes emerge from the behaviors of their components and their pairwise interactions. Such a study, however, is challenging for two key reasons. Firstly, such systems are complex and depend, often stochastically, on their constituent parts. Secondly, the data lie on a simplex which influences their correlations. Results: To resolve both of these issues, we provide a general and data-driven modeling tool for compositional systems called Compositional Maximum Entropy (CME). By integrating the prior geometric structure of compositions with sample-specific information, CME infers the underlying multivariate relationships between the constituent components. We provide two proofs of principle. First, we measure the relative abundances of different bacteria and infer how they interact. Second, we show that our method outperforms a common alternative for the extraction of gene-gene interactions in triple-negative breast cancer. Conclusions: CME provides novel and biologically-intuitive insights and is promising as a comprehensive quantitative framework for compositional data. © 2022, The Author(s). |
| Keywords: | proteins; genes; protein; chemistry; bacterium; networks; network; bacteria; inference; entropy; pairwise interaction; geometric structure; compositional data; maximum entropy; maximum entropy methods; basic chemicals; data-driven model; maximum entropy principle; maximum-entropy; modelling tools |
| Journal Title: | BMC Bioinformatics |
| Volume: | 23 |
| ISSN: | 1471-2105 |
| Publisher: | Biomed Central Ltd |
| Date Published: | 2022-10-29 |
| Start Page: | 449 |
| Language: | English |
| DOI: | 10.1186/s12859-022-05007-z |
| PUBMED: | 36309638 |
| PROVIDER: | scopus |
| PMCID: | PMC9617458 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 December 2022 -- Source: Scopus |
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