Architecture and implementation of ulrb algorithm in R
Bibliographic record
Abstract
Low-abundance microorganisms, often referred to as the “rare biosphere”, play a crucial role in ecosystem resistance and resilience, but remain challenging to study. One of the main difficulties lies in the lack of an appropriate definition of rare taxa. Most studies use relative abundance thresholds ( e.g. , 0.1 % relative abundance, per sample) to discern rare from abundant taxa within a microbial community. This is inappropriate because such thresholds are arbitrary and lack biological meaning. To solve this problem, we have proposed the utilization of unsupervised machine learning, through the ulrb (“Unsupervised Learning Definition of the Microbial Rare Biosphere”) algorithm, implemented as an R package (v0.1.8). This algorithm applies the partition around medoids (pam) algorithm to cluster taxa based on their abundance, in a community, for any number of samples. Based on the clusters, ulrb automatically classifies taxa into “rare”, “undetermined” or “abundant”, by default. Ulrb includes functions for all analytical steps necessary to define the rare biosphere. Specifically, we include four groups of functions: 1) process data of the user into the correct format for the ulrb algorithm; 2) cluster taxa into abundance classifications; 3) helper functions to evaluate detailed statistics of the clustering steps; and 4) visualization functions, focused on rank abundance curves and Silhouette scores, for assessment of clustering quality. In addition, ulrb allows the user to change the number of classifications obtained and includes options for detailed reporting. In this article, we describe the ulrb R package architecture, coding organization, and strategy. Furthermore, we use a 16S rRNA gene amplicon sequencing dataset from the Arctic Ocean to provide illustrative examples, with code, on how to use and explore ulrb capabilities. By explaining the architecture and implementation of ulrb , this study allows independent groups to integrate an abundance classification step in their data analysis protocols, instead of relying on taxa labeled by inconsistent or manual strategies.
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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 | 0.005 | 0.022 |
| Meta-epidemiology (narrow) | 0.004 | 0.002 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.004 | 0.002 |
| Open science | 0.006 | 0.003 |
| Research integrity | 0.002 | 0.004 |
| Insufficient payload (model declined to judge) | 0.053 | 0.083 |
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".