{"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/artree-a-deep-autoregressive-model-for-1","title":"ARTree: A Deep Autoregressive Model for Phylogenetic Inference","arxiv_id":"2310.09553","date":"2023-10-14","proceeding":"NeurIPS 2023 11","authors":["Tianyu Xie","Cheng Zhang"],"abstract":"Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic features which would require pre-sampled tree topologies and may suffer from limited approximation capability. In this paper, we propose a deep autoregressive model for phylogenetic inference based on graph neural networks (GNNs), called ARTree. By decomposing a tree topology into a sequence of leaf node addition operations and modeling the involved conditional distributions based on learnable topological features via GNNs, ARTree can provide a rich family of distributions over the entire tree topology space that have simple sampling algorithms and density estimation procedures, without using heuristic features. We demonstrate the effectiveness and efficiency of our method on a benchmark of challenging real data tree topology density estimation and variational Bayesian phylogenetic inference problems.","url_abs":"https://arxiv.org/abs/2310.09553v1","url_pdf":"https://arxiv.org/pdf/2310.09553v1.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":"artree-a-deep-autoregressive-model-for-1","repo_url":"https://github.com/tyuxie/artree","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"density-estimation","task_name":"Density Estimation"},{"task_slug":"model","task_name":"model"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2310.09553","atlas_url":"https://app.syntology.ai/?focus=2310.09553","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2310.09553"}},"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":"deterministic:regex_extraction","url":"https://github.com/tyuxie/ARTree","reach":{"status":"ok"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/tyuxie/artree","reach":{"status":"ok"}}],"summary":{"ran":4,"unverified":3},"by_repo_kind":{"official":{"samples":7,"ran":4,"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":7,"samples":[{"code_sha256_prefix":"6c8d3950e33a69cc","entry":"decompGTR","repo":"tyuxie/ARTree","repo_kind":"official","path":"phyloModel.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/phyloModel.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"6c8d3950e33a69cc"}},{"code_sha256_prefix":"41fac55a2bdf2726","entry":"decompHKY","repo":"tyuxie/ARTree","repo_kind":"official","path":"phyloModel.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/phyloModel.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"41fac55a2bdf2726"}},{"code_sha256_prefix":"b6a7346f405d1e57","entry":"decompJC","repo":"tyuxie/ARTree","repo_kind":"official","path":"phyloModel.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/phyloModel.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"b6a7346f405d1e57"}},{"code_sha256_prefix":"18d34a33e6f67b2e","entry":"namenum","repo":"tyuxie/ARTree","repo_kind":"official","path":"utils.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/utils.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"18d34a33e6f67b2e"}},{"code_sha256_prefix":"f2e729673b621621","entry":"get_dataloader","repo":"tyuxie/ARTree","repo_kind":"official","path":"datasets.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/datasets.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"f2e729673b621621"}},{"code_sha256_prefix":"388f66a5c09d1d92","entry":"node_embedding","repo":"tyuxie/ARTree","repo_kind":"official","path":"datasets.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/datasets.py","link_basis":"plan_row","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"388f66a5c09d1d92"}},{"code_sha256_prefix":"898277507a7f6be6","entry":"node_embedding_forward","repo":"tyuxie/ARTree","repo_kind":"official","path":"datasets.py","file_url":"https://github.com/tyuxie/ARTree/blob/HEAD/datasets.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"898277507a7f6be6"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}