Spatial Transcriptomics Brings New Challenges and Opportunities for Trajectory Inference
Bibliographic record
Abstract
Spatial transcriptomics (ST) brings new dimensions to the analysis of single-cell data. While some methods for data analysis can be ported over without major modifications, they are the exception rather than the rule. Trajectory inference (TI) methods in particular can suffer from significant challenges due to spatial batch effects in ST data. These can add independent sources of noise to each time point. Pioneering methods for TI on ST data have focused primarily on addressing the batch effects in physical arrangement, i.e., where tissues are deformed in different ways at different time points. However, other challenges arise due to the measurement granularity of ST technologies, as well as a bias from slicing. In this review, we examine the sources of these challenges, and we explore how they are addressed with current state-of-the-art STTI methods. We conclude by highlighting some opportunities for future method development.
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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 | 0.006 | 0.010 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.003 | 0.002 |
| Bibliometrics | 0.003 | 0.005 |
| Science and technology studies | 0.001 | 0.003 |
| Scholarly communication | 0.004 | 0.005 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.003 | 0.005 |
| Insufficient payload (model declined to judge) | 0.004 | 0.004 |
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".