{"id":"W2729511311","doi":"10.1101/158832","title":"<i>PHASIS</i> : A computational suite for <i>de novo</i> discovery and characterization of phased, siRNA-generating loci and their miRNA triggers","year":2017,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Plant Molecular Biology Research","field":"Agricultural and Biological Sciences","cited_by":33,"is_retracted":false,"has_abstract":true,"ca_institutions":"Agriculture and Agri-Food Canada","funders":"National Science Foundation","keywords":"Computational biology; microRNA; Suite; Genome; Biology; Scalability; Computer science; DNA sequencing; Genetics; Gene","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006405405,0.0002997311,0.0004292145,0.00004173372,0.0003299478,0.0003178995,0.0003297706,0.0003278958,0.000003549032],"category_scores_gemma":[0.0001824959,0.0001566494,0.00009832378,0.0001051237,0.0002306486,0.0001614248,0.0002368618,0.0002476772,5.186308e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003833587,"about_ca_system_score_gemma":0.0001209536,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003339231,"about_ca_topic_score_gemma":0.000008700432,"domain_scores_codex":[0.9984125,0.0001344633,0.0003172756,0.0006179654,0.0001563078,0.0003614697],"domain_scores_gemma":[0.9987903,0.0002409934,0.0004200274,0.000155726,0.0002521218,0.0001408969],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.0000710559,0.00005804234,0.0067208,0.0001215433,0.0000645265,0.000004705877,0.000007590558,0.000007970857,0.9927917,0.00006551814,0.00001324527,0.0000733659],"study_design_scores_gemma":[0.0008486092,0.0002265008,0.14414,0.0002677819,0.00006333849,3.540297e-7,0.000005371577,0.002056231,0.8491436,0.00001821167,0.002594395,0.000635643],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9935703,0.0005359213,0.00132631,0.0004263213,0.0001061872,0.0006703153,0.003321334,0.00004184505,0.00000146268],"genre_scores_gemma":[0.9983267,0.0003275211,0.0008273469,0.0001372027,0.0002409383,0.00009776947,0.00003125758,0.000006676436,0.000004593665],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1436481,"threshold_uncertainty_score":0.6387977,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01929355290748657,"score_gpt":0.2298094904919826,"score_spread":0.210515937584496,"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."}}