Multidimensional scaling improves distance-based clustering for microbiome data
Bibliographic record
Abstract
MOTIVATION: Clustering patients into subgroups based on their microbial compositions can greatly enhance our understanding of the role of microbes in human health and disease etiology. Distance-based clustering methods, such as partitioning around medoids (PAM), are popular due to their computational efficiency and absence of distributional assumptions. However, the performance of these methods can be suboptimal when true cluster memberships are driven by differences in the abundance of only a few microbes, a situation known as the sparse signal scenario. RESULTS: We demonstrate that classical multidimensional scaling (MDS), a widely used dimensionality reduction technique, effectively denoises microbiome data and enhances the clustering performance of distance-based methods. We propose a two-step procedure that first applies MDS to project high-dimensional microbiome data into a low-dimensional space, followed by distance-based clustering using the low-dimensional data. Our extensive simulations demonstrate that our procedure offers superior performance compared to directly conducting distance-based clustering under the sparse signal scenario. The advantage of our procedure is further showcased in several real data applications. AVAILABILITY AND IMPLEMENTATION: The R package MDSMClust is available at https://github.com/wxy929/MDS-project.
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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 | 0.035 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.003 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.002 |
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".