BIOCURRENT - donor-specific pseudotime coordinate inference

BIOCURRENT is a causal inference framework that reconstructs donor-specific pseudotime geometry in transcriptomic data. By modeling gene expression as a function of baseline characteristics, microenvironmental context, and latent pseudotime, BIOCURRENT enables comparison of compressed or expanded progression intervals across defined transcriptional state transitions. We introduce $\Delta\Delta T$, a geometry-based estimator that quantifies counterfactual changes in pseudotime intervals under hypothetical modulation of microenvironmental programs.
By localizing deviations in pseudotime geometry, BIOCURRENT identifies whether shifts in transcriptomic programs emerge early or later along transcriptomic coordinates and whether upstream or preventive intervention may be feasible. Such localization supports transcriptional stage-aware mechanistic hypotheses and suggests candidate intervention checkpoints in complex biological systems.