{"id":"W2150869900","doi":"10.1093/bioinformatics/btt313","title":"SPANNER: taxonomic assignment of sequences using pyramid matching of similarity profiles","year":2013,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":14,"is_retracted":false,"has_abstract":true,"ca_institutions":"Dalhousie University","funders":"","keywords":"Taxonomic rank; Computer science; Rank (graph theory); Similarity (geometry); Set (abstract data type); Biology; Artificial intelligence; Mathematics; Ecology; Combinatorics","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.003293892,0.001926909,0.001126252,0.005479667,0.001120357,0.001868328,0.002498315,0.001493064,0.01589944],"category_scores_gemma":[0.01203101,0.0009578992,0.001390897,0.00423122,0.0008134611,0.004466005,0.00338746,0.001342084,0.009509721],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008560997,"about_ca_system_score_gemma":0.001249836,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002073698,"about_ca_topic_score_gemma":0.003040768,"domain_scores_codex":[0.9978643,0.0002263779,0.0002299179,0.0009240347,0.0006382485,0.0001172189],"domain_scores_gemma":[0.9972993,0.0007420367,0.0005132868,0.0007572244,0.0004898295,0.0001984155],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.002947028,0.0004631025,0.02083835,0.002776336,0.0006938837,0.0009154664,0.001182406,0.01615419,0.1242286,0.01371795,0.1008845,0.715198],"study_design_scores_gemma":[0.0004224707,0.001184743,0.0192154,0.0004685569,0.0002926545,0.001909714,0.0007035409,0.6461011,0.1351481,0.06445224,0.1297556,0.0003459769],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.03569048,0.0005911146,0.7519349,0.0002619087,0.0002429707,0.0006433722,0.01846627,0.1865238,0.00564522],"genre_scores_gemma":[0.1102877,0.0003131155,0.8417719,0.0002458982,0.00008238679,0.0005100836,0.03518044,0.009137442,0.002471056],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01589944,"threshold_uncertainty_score":0.05318898,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02345590031270034,"score_gpt":0.2388227723223345,"score_spread":0.2153668720096341,"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."}}