{
  "abstract": "Single-cell atlases infer developmental dynamics from destructive snapshots, yet how far realized lineage paths depart from such inferred dynamics has never been measured with controls. We introduce LADD (Least-Action Developmental Dynamics), a measurement framework that learns a stochastic developmental vector field from time-series single-cell RNA-seq and computes minimum-action and minimum-time paths, together with a three-layer calibration protocol that separates genuine path deviation from the generic cost of centroid measurement, and we compare its forecasting component with optimal-transport and flow-matching methods. In the lineage-resolved Caenorhabditis elegans atlas, the raw action ratio of observed lineage-centroid trajectories to optimal paths is 3.79, yet forward-simulated ensembles of the learned model itself score 2.07, leaving a genuine excess of about two-fold. In zebrafish (Danio rerio), the observed ratio sits entirely at the model's floor. Three mechanisms that could explain the residual deviation (detours, flow-opposition, and fate-map complexity) are each excluded; what remains is speed, with lineages moving 30-43% faster along the learned flow. We report validity boundaries for temporal resolution, cross-species comparison, and energetic interpretation, delimiting where action-based trajectory comparisons are meaningful.",
  "abstract_shown": true,
  "affiliations": [
    "Jinan University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "name": "Q. Liu"
    },
    {
      "name": "Y. Zhou"
    },
    {
      "name": "J. Cao"
    },
    {
      "affs": [
        0
      ],
      "name": "Y. Wang"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9pdmsrfms4bdy.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.05.764549",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764549v1.full",
  "id": "9pdmsrfms4bdy",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764549v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "systems biology"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764549v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9pdmsrfms4bdy.ris",
  "sources": [
    {
      "first_seen": "2026-11-10T00:24:51Z",
      "native_id": "10.64898/2026.11.05.764549",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.11.05.764549v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:systems biology",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "Calibrating developmental dynamics from single-cell atlases: lineage paths outrun least-action routes",
  "title_text": "Calibrating developmental dynamics from single-cell atlases: lineage paths outrun least-action routes",
  "type": "preprint",
  "updated_at": "2026-11-10T00:24:51Z",
  "url": "https://research.draconitic.com/paper/9pdmsrfms4bdy",
  "venue": "bioRxiv",
  "versions": []
}