dynamo

中文導讀

dynamo 是少數能做到 metric time 的方法——前提是吃 metabolic-labeling data。有了已知 labeling window,它能估 absolute synthesis/degradation rate,把 splicing-kinetics-ode 的 scale degeneracy 釘住,再用 reconstructed continuous vector field 做 differential geometry(velocity、acceleration、curvature)。沒有 label 時退回 relative。值得記的對照: RegVelo 不用 label,還在 driver prediction AUROC 上贏過用 label 的 dynamo——說明 mechanistic 軸跟 temporal 軸是兩件事。

What it is

An analytical framework that reconstructs a continuous, differentiable vector field of cell-state dynamics from velocity samples, then does vector calculus on it (velocity, acceleration, curvature, divergence). Its distinguishing feature: when fed metabolic-labeling data (scEU-seq, scNT-seq, sci-fate), it estimates absolute kinetic rates and hence physically scaled dynamics.

Physical-time scorecard

Axis	dynamo
Latent time	can be metric (with labels) / ordinal otherwise
Rate scale	absolute when labels present; relative otherwise
External anchor	metabolic-labeling (optional but central)
Verdict	grounded with labeling

It is the wiki’s reference point for what physical-time grounding looks like when an absolute-time signal is available.

Note from RegVelo benchmark

In regvelo, RegVelo out-predicts dynamo on lineage-driver AUROC for hematopoietic lineages even though dynamo uses metabolic-labeling data and RegVelo does not — underscoring that driver/mechanism accuracy and temporal grounding are separable.

Xing’s framing (author’s positioning)

JianhuaXing frames dynamo not as an incremental RNA-velocity improvement but as a new paradigm: it uses ds/dt = βu(α(s)) − γs = f(s) − γs to back out quantitative gene regulation, and recommends metabolic-labeling-derived physical-time velocity — a different level from the scVelo-lineage. Grounded in the dynamical-systems-formulation (Koopman / Zwanzig–Mori projection, manifold vector-field reconstruction). See xing-hu-regvelo-debate.

Related

RNA velocity · metabolic-labeling · physical-time-grounding · splicing-kinetics-ode · latent-time · scVelo · veloVI · RegVelo · CellRank · JianhuaXing · dynamical-systems-formulation · GraphVelo