{"id":"W6959223318","doi":"10.6084/m9.figshare.c.6714532.v1","title":"An open protocol for modeling T Cell Clonotype repertoires using TCRβ CDR3 sequences","year":2023,"lang":"en","type":"other","venue":"Figshare","topic":"Plant Pathogens and Resistance","field":"Agricultural and Biological Sciences","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université du Québec","funders":"","keywords":"Multiplex; Normalization (sociology); Primer (cosmetics); Concordance; Protocol (science); Spurious relationship; DNA sequencing; T-cell receptor","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":["insufficient_payload"],"consensus_categories":[],"category_scores_codex":[0.00006099982,0.0002197303,0.0002507808,0.00001570068,0.0002016854,0.0002339942,0.0008027712,0.0002844182,0.04313466],"category_scores_gemma":[0.00006993057,0.0000815151,0.00007620662,0.0001482251,0.000005440043,0.0001029905,0.0001387671,0.00009032054,0.0001831154],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002252521,"about_ca_system_score_gemma":0.00003690623,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005514362,"about_ca_topic_score_gemma":0.004524539,"domain_scores_codex":[0.9988613,0.00003517954,0.0001738455,0.0005024351,0.000142267,0.0002849617],"domain_scores_gemma":[0.999508,0.00006562367,0.0001861248,0.0001042378,0.00005152283,0.00008448415],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00004232969,0.00005675995,0.000007984425,0.0003452917,0.0000129494,0.0000272399,0.000006939833,0.0002348958,0.03127009,0.00000477544,0.9638947,0.004096101],"study_design_scores_gemma":[0.0001064382,0.0001213938,0.00002527534,0.002928646,0.000005880663,0.000001864557,0.00002406663,0.006658035,0.0002845898,0.00003414035,0.9894579,0.0003517802],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"dataset","genre_gemma":"protocol","genre_scores_codex":[0.0001014741,0.0001107897,0.000001385121,0.00004711558,0.00009370949,0.121217,0.8079326,0.0007024595,0.06979349],"genre_scores_gemma":[0.0004363242,0.00001301114,0.001982336,0.0002634182,0.003158682,0.5192297,0.1697579,0.0001789381,0.3049797],"genre_candidate":"dataset","genre_consensus":null,"teacher_disagreement_score":0.6381747,"threshold_uncertainty_score":0.9577401,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.1872026503738684,"score_gpt":0.3379973524737304,"score_spread":0.150794702099862,"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."}}