Factor augmented inverse regression and its application to microbiome data analysis
Bibliographic record
Abstract
We investigate the relationship between count data that inform the relative abundance of features of a composition, and factors that influence the composition. Our work is motivated from microbiome studies aiming to extract microbial signatures that are predictive of host phenotypes based on data collected from a group of individuals harboring radically different microbial communities. We introduce multinomial Factor Augmented Inverse Regression (FAIR) of the count vector onto response factors as a general framework for obtaining low-dimensional summaries of the count vector that preserve information relevant to the response. By augmenting known response factors with random latent factors, FAIR extends multinomial logistic regression to account for overdispersion and general correlations among counts. The projections of the count vector onto the loading vectors represent additional contribution, in addition to the projections that result from response factors. The method of maximum variational likelihood and a fast variational expectation-maximization algorithm are proposed for approximate inference based on variational approximation, and the asymptotic properties of the resulting estimator are derived. Moreover, a hybrid information criterion and a group-lasso penalized criterion are proposed for model selection. The effectiveness of FAIR is illustrated through simulations and application to a microbiome data set.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.008 | 0.029 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".