{"paper":{"title":"Gradients do grow on trees: a linear-time ${\\cal O}\\hspace{-0.2em}\\left( N \\right)$-dimensional gradient for statistical phylogenetics","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["q-bio.PE","stat.ME"],"primary_cat":"stat.CO","authors_text":"Akihiko Nishimura, Andrew Holbrook, Andrew Rambaut, Guy Baele, Marc A. Suchard, Philippe Lemey, Xiang Ji, Zhenyu Zhang","submitted_at":"2019-05-29T00:33:42Z","abstract_excerpt":"Calculation of the log-likelihood stands as the computational bottleneck for many statistical phylogenetic algorithms. Even worse is its gradient evaluation, often used to target regions of high probability. Order ${\\cal O}\\hspace{-0.2em}\\left( N \\right)$-dimensional gradient calculations based on the standard pruning algorithm require ${\\cal O}\\hspace{-0.2em}\\left( N^2 \\right)$ operations where N is the number of sampled molecular sequences. With the advent of high-throughput sequencing, recent phylogenetic studies have analyzed hundreds to thousands of sequences, with an apparent trend towar"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"1905.12146","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}