Additional file 5 of Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata
Bibliographic record
Abstract
Additional file 5: Additional Material 5-Supplementary Figure 4. Phylogenetic analyses of the individual SNF7-VPS2 family proteins from ESCRTIII and ESCRTIII-A sub-complexes depicts pan-eukaryotic VPS2/24/46 with Carpediemonas membranifera VPS2 family proteins used as landmark representative for Fornicata. Tree inference was carried out using both Bayesian Inference and Maximum Likelihood analyses. RAxML best model was determined to be LG + G + F while IQ-TREE ModelFinder determined an equivalent LG + G4 + F. Carpediemonas membranifera was determined to have all three components with strong backbone support for VPS24 (1.0/100/100) and VPS46 (1.0/100/100).
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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 | 0.001 | 0.014 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.849 | 0.234 |
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".