Cluster Analysis of Microbiome Data by Using Mixtures of Dirichlet–Multinomial Regression Models
Bibliographic record
Abstract
Summary The human gut microbiome is one of the fundamental components of our physiology, and exploring the relationship between biological and environmental covariates and the resulting taxonomic composition of a given microbial community is an active area of research. Previously, a Dirichlet–multinomial regression framework has been suggested to model this relationship, but it did not account for any underlying latent group structure. An underlying group structure of guts (such as enterotypes) has been observed across gut microbiome samples in which guts in the same group share similar biota compositions. In the paper, a finite mixture of Dirichlet–multinomial regression models is proposed that accounts for this underlying group structure and to allow for a probabilistic investigation of the relationship between bacterial abundance and biological and/or environmental covariates within each inferred group. Furthermore, finite mixtures of regression models which incorporate the concomitant effect of the covariates on the resulting mixing proportions are also proposed and examined within the Dirichlet–multinomial framework. We utilize the proposed mixture model to gain insight on underlying subgroups in a microbiome data set comprising tumour and healthy samples and the relationships between covariates and microbial abundance in those subgroups.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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 teacher head, 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".