{"id":"W3200678019","doi":"10.1101/2021.09.11.459915","title":"Predicting long pendant edges in model phylogenies, with applications to biodiversity and tree inference","year":2021,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Evolution and Paleontology Studies","field":"Earth and Planetary Sciences","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Simon Fraser University","funders":"Marsden Fund; Natural Sciences and Engineering Research Council of Canada; National Natural Science Foundation of China","keywords":"Phylogenetic tree; Tree (set theory); Combinatorics; Extinction (optical mineralogy); Extant taxon; Biodiversity; Biology; Clade; Mathematics; Evolutionary biology; Ecology; Paleontology; Genetics; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0001983606,0.0002922556,0.0003679585,0.0002011838,0.0002655365,0.0001251035,0.0002773529,0.0002044309,0.00002627496],"category_scores_gemma":[0.00007821898,0.0002797472,0.00003539382,0.0003933767,0.0001744109,0.0001319689,0.0001649569,0.0004268183,0.00001841887],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002422129,"about_ca_system_score_gemma":0.0003246635,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001197623,"about_ca_topic_score_gemma":0.03588205,"domain_scores_codex":[0.9983854,0.00007655386,0.0002394823,0.0007409315,0.0001973862,0.0003602099],"domain_scores_gemma":[0.9989457,0.00009434349,0.0001364176,0.0004084621,0.0002058067,0.0002092857],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.00001954966,0.00002306596,0.9957073,0.0001023136,0.00005047314,0.00002472983,0.00006787907,0.003464027,0.000486592,0.00001819542,0.00001835565,0.0000175552],"study_design_scores_gemma":[0.0001990027,0.00003286902,0.9937001,0.0001225064,0.00004738002,3.44426e-8,0.00004120826,0.004916673,0.0004966613,9.687695e-7,0.0001058038,0.0003368164],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9904794,0.003119507,0.004934128,0.0002741954,0.0001191444,0.0005141505,0.000400285,0.0001028292,0.00005638522],"genre_scores_gemma":[0.992913,0.000570085,0.006253114,0.0001678155,0.0000521926,0.00003411542,0.000001730781,0.000005300119,0.00000266132],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.03468443,"threshold_uncertainty_score":0.9999655,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02474235599442387,"score_gpt":0.2148530310002476,"score_spread":0.1901106750058237,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}