Type 2 Polarized Memory B cells Hold Allergen-Specific IgE Memory
Bibliographic record
Abstract
R, python and shell code for Science Translational Medicine Manuscript adi0944 Human_10X_PreProcessing_Knudsen.R: Preprocessing of 10x genomics dataset for Seurat analysis, including QC filtering, cleaning, normalization and integration Koenig_Knudsen_Phelps_Bruton_et_al_Revised.R Code for creating the figures of the 10x genomics dataset of memory B cells FigureClusterFinal.csv: Cluster meta data used in Koenig_Knudsen_Phelps_Bruton_et_al_Revised.R tissue_allergy_analysis.R: Reanalysis of the Glass et al mass cytometry dataset IgE-cocluster analysis_long.txt: describes the Bulk IgE to 10x single cell sequencing co-clustering analysis and how the Shell and Python scripts are used in this process
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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 | 0.003 | 0.009 |
| Meta-epidemiology (narrow) | 0.003 | 0.003 |
| Meta-epidemiology (broad) | 0.002 | 0.003 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.004 | 0.003 |
| Research integrity | 0.001 | 0.003 |
| Insufficient payload (model declined to judge) | 0.217 | 0.264 |
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".