Mapping lineage-traced cells across time points with moslin
Bibliographic record
Abstract
Abstract Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making beyond simpler pseudotime-based approaches. However, it is currently unclear how lineage and gene expression information across experimental time points can be combined in destructive experiments, which is particularly challenging for in-vivo systems. Here we present moslin, a Fused Gromov-Wasserstein-based model to couple matching cellular profiles across time points. In contrast to existing methods, moslin leverages both intra-individual lineage relations and inter-individual gene expression similarity. We demonstrate on simulated and real data that moslin outperforms state-of-the-art approaches that use either one or both data modalities, even when the lineage information is noisy. On C. elegans embryonic development, we show how moslin, combined with trajectory inference methods, predicts fate probabilities and putative decision driver genes. Finally, we use moslin to delineate lineage relationships among transiently activated fibroblast states during zebrafish heart regeneration. We anticipate moslin to play a crucial role in deciphering complex state change trajectories from lineage-traced single-cell data.
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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 | 0.001 | 0.000 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.000 | 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".