{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/improved-variational-bayesian-phylogenetic-1","title":"Improved Variational Bayesian Phylogenetic Inference with Normalizing Flows","arxiv_id":"2012.00459","date":"2020-12-01","proceeding":"NeurIPS 2020 12","authors":["Cheng Zhang"],"abstract":"Variational Bayesian phylogenetic inference (VBPI) provides a promising general variational framework for efficient estimation of phylogenetic posteriors. However, the current diagonal Lognormal branch length approximation would significantly restrict the quality of the approximating distributions. In this paper, we propose a new type of VBPI, VBPI-NF, as a first step to empower phylogenetic posterior estimation with deep learning techniques. By handling the non-Euclidean branch length space of phylogenetic models with carefully designed permutation equivariant transformations, VBPI-NF uses normalizing flows to provide a rich family of flexible branch length distributions that generalize across different tree topologies. We show that VBPI-NF significantly improves upon the vanilla VBPI on a benchmark of challenging real data Bayesian phylogenetic inference problems. Further investigation also reveals that the structured parameterization in those permutation equivariant transformations can provide additional amortization benefit.","url_abs":"https://arxiv.org/abs/2012.00459v1","url_pdf":"https://arxiv.org/pdf/2012.00459v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"improved-variational-bayesian-phylogenetic-1","repo_url":"https://github.com/zcrabbit/vbpi-nf","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[],"methods":[{"method_slug":"normalizing-flows","method_name":"Normalizing Flows"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2012.00459","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2012.00459"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"deterministic:regex_extraction","url":"https://github.com/zcrabbit/vbpi-nf","reach":null}],"summary":{"ran":1},"by_repo_kind":{"official":{"samples":1,"ran":1,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":1,"samples":[{"code_sha256_prefix":"fa7cf396c54254fc","entry":"PlanarNF","repo":"zcrabbit/vbpi-nf","repo_kind":"official","path":"code/deep_branchModel.py","file_url":"https://github.com/zcrabbit/vbpi-nf/blob/HEAD/code/deep_branchModel.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"fa7cf396c54254fc"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}