Additional file 4 of Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage
Bibliographic record
Abstract
Additional file 4: Fig. S3. Maximum-likelihood phylogeny of Aro10 and Pdc1-like proteins. Phylogeny depicting the relationships between W/S-clade Aro10 proteins and their closest relatives in the Saccharomycotina and between W. versatilis Pdc1 xenologs and the closest related bacterial pyruvate decarboxylase. Branches with bootstrap support higher than 95% are indicated by black dots. Different lineages are represented by different branch colors (red for Saccharomycotina, light brown for other Fungi (i.e., non-Saccharomycotina), orange W/S clade and blue for bacteria). Clades highlighted in grey (Aro10-like and Pdc1-like) were assigned according to the phylogenetic position of functionally characterized Saccharomyces cerevisiae proteins.
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 distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.877 | 0.000 |
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 teacher head, 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".