Penalized logistic normal multinomial factor analyzers for high dimensional compositional data
Bibliographic record
Abstract
Model-based clustering utilizes a finite mixture model to identify underlying patterns or clusters across samples. A finite mixture model is a convex combination of two or more distributions, where appropriate distributions are chosen depending on the type of the data. Recently, there has been a great interest in clustering human microbiome data. Microbiome data are compositional (yielding relative abundance) and are high-dimensional. Previously, a family of logistic normal multinomial factor analyzers (LNM-FA) for model-based clus- tering of high-dimensional microbiome data was proposed via a factor analyzer structure. This reduced the number of parameters and computation overhead compared to a traditional mixtures of logistic normal multinomial models. Here, we propose a penalized LNM-FA (PLNM-FA) model by utilizing lasso regularization to each entry of the loading matrix. This introduces further parsimony compared to LNM-FA and also estimates the number of latent factors simultaneously. Parameter estimation is done using a variational variant of the alternating expectation conditional maximization algorithm to maximize the penalized maximum likelihood. The performance of proposed algorithm is evaluated using simula- tion studies and real data. Journal of Statistical Research 2022, Vol. 56, No. 2, pp.185-216
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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 | 0.009 | 0.020 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.001 | 0.003 |
| Open science | 0.002 | 0.002 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 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".