Additional file 4 of Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor
Bibliographic record
Abstract
Supplementary Material 4: Figure 3. Family-level collapsed bacterial communities for fecal and fecal-derived chemostats of all seven fecal samples: Relative abundances of amplicon sequence variants (ASV) that represent bacterial composition were identified by Illumina MiSeq 16S rRNA gene sequencing from fecal samples and longitudinal chemostat communities of seven healthy 18-24-month-old participants. ASV relative abundances were collapsed according to highest-likelihood family-level taxanomic classification via BLAST. Alluvial plots show the relative abundance of bacterial families identified on the fecal sample (day 0) and the chemostat culture over time from NS0 (a) and NS1 (b), S2 (c), S3 (d), NS4 (e), S5 (f) and NS6 (g) individuals. Colors represent bacterial families; families are ordered alphabetically by phyla name, then family name. Families appear in each corresponding legend in the same order as in the plot. Families with <1% relative abundance in the samples shown are plotted in grey.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.002 | 0.015 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.001 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.835 | 0.194 |
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".