Inferring single-cell transcriptomic dynamics with structured latent gene expression dynamics
Bibliographic record
Abstract
Gene expression dynamics provide directional information for trajectory inference from single-cell RNA-sequencing data. Traditional approaches compute local RNA velocity using strict assumptions about the equations describing transcription and splicing of RNA. Not surprisingly, these approaches fail where these assumptions are violated, such as in multiple lineages with distinct gene dynamics or time-dependent kinetic rates of transcription and splicing. In this work we present “LatentVelo”, a novel approach to compute a low-dimensional representation of gene dynamics with deep learning. Our approach embeds cells into a latent space with a variational auto-encoder, and describes differentiation dynamics on this latent space with neural ordinary differential equations. These more general dynamics enable accurate trajectory inference, and the latent space approach enables the generation of a latent “dynamics-based” embedding of cell states. To model multiple distinct lineages, LatentVelo infers a latent regulatory state that controls the dynamics of an individual cell. With these lineage-specific dynamics LatentVelo can predict latent trajectories, describing global inferred developmental path for individual cells, rather than just outputting local RNA velocity vectors. The dynamics-based embedding also enables concurrent batch correction of cell states and RNA velocity, outperforming comparable auto-encoder based batch correction methods that do not consider gene expression dynamics. Finally, the flexible structure of LatentVelo enables additional of new regulatory constraints required to integrate multiomic data. LatentVelo is available at https://github.com/Spencerfar/LatentVelo .
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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 | 0.000 | 0.002 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.002 | 0.001 |
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".