{"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/phylogfn-phylogenetic-inference-with","title":"PhyloGFN: Phylogenetic inference with generative flow networks","arxiv_id":"2310.08774","date":"2023-10-12","proceeding":null,"authors":["Mingyang Zhou","Zichao Yan","Elliot Layne","Nikolay Malkin","Dinghuai Zhang","Moksh Jain","Mathieu Blanchette","Yoshua Bengio"],"abstract":"Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.","url_abs":"https://arxiv.org/abs/2310.08774v2","url_pdf":"https://arxiv.org/pdf/2310.08774v2.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":"phylogfn-phylogenetic-inference-with","repo_url":"https://github.com/zmy1116/phylogfn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"variational-inference","task_name":"Variational Inference"}],"methods":[{"method_slug":"variational-inference","method_name":"Variational Inference"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2310.08774","atlas_url":"https://app.syntology.ai/?focus=2310.08774","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2310.08774"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+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":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/zmy1116/phylogfn","reach":{"status":"ok","spdx":"MIT"}}],"summary":{"ran_fixture":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":0,"samples":[{"code_sha256_prefix":"02566da69866c48c","entry":"trunc_normal_","repo":"zmy1116/phylogfn","repo_kind":"official","path":"src/model/weight_init.py","file_url":"https://github.com/zmy1116/phylogfn/blob/HEAD/src/model/weight_init.py","link_basis":"harvester_set","language":"python","status":"ran_fixture","verification_level":1,"contract_check":"RAISES","metamorphic_tier":"invariant","behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"02566da69866c48c"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}