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Phylogenetic variational inference (VI) circumvents this dependency but so far has been limited in speed and scalability. Here we introduce Variational Inference with Node Embeddings (V\n                  <jats:sc>ine<\/jats:sc>\n                  ), a computational method that combines an embedding of taxa in a high-dimensional space and a distance-based \u201cdecoder\u201d with several algorithmic innovations to dramatically improve phylogenetic VI. V\n                  <jats:sc>ine<\/jats:sc>\n                  supports both standard DNA substitution models and CRISPR barcode-mutation models for inference of cell-lineage trees and tissue-migration histories. In extensive simulation experiments, we show that V\n                  <jats:sc>ine<\/jats:sc>\n                  can effectively approximate the results of the best available Bayesian methods with speeds orders of magnitude faster. We then apply V\n                  <jats:sc>ine<\/jats:sc>\n                  to \u223c1,000 complete SARS-CoV-2 genomes and \u223c900 lung-cancer cell barcodes, showing reductions in compute time from days to hours or minutes.\n                <\/jats:p>","DOI":"10.64898\/2025.12.24.696405","type":"posted-content","created":{"date-parts":[[2025,12,26]],"date-time":"2025-12-26T17:50:19Z","timestamp":1766771419000},"source":"Crossref","is-referenced-by-count":3,"title":["VINE: Variational inference for scalable Bayesian reconstruction of species and cell-lineage phylogenies"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3557-7219","authenticated-orcid":false,"given":"Adam","family":"Siepel","sequence":"first","affiliation":[{"name":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca","family":"Hassett","sequence":"additional","affiliation":[{"name":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1746-6320","authenticated-orcid":false,"given":"Stephen J.","family":"Staklinski","sequence":"additional","affiliation":[{"name":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026073111201369000_2025.12.24.696405v3.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-024-00803-0"},{"key":"2026073111201369000_2025.12.24.696405v3.2","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-024-00772-4"},{"key":"2026073111201369000_2025.12.24.696405v3.3","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-022-00483-8"},{"key":"2026073111201369000_2025.12.24.696405v3.4","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaf7907"},{"key":"2026073111201369000_2025.12.24.696405v3.5","doi-asserted-by":"publisher","DOI":"10.1038\/nature20777"},{"key":"2026073111201369000_2025.12.24.696405v3.6","first-page":"D1173","article-title":"scLTdb: a comprehensive single-cell lineage tracing database","volume":"53","year":"2024","journal-title":"Nuc Acids Res"},{"key":"2026073111201369000_2025.12.24.696405v3.7","unstructured":"Askary, A. et al. 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