{"id":"W4385173870","doi":"10.1101/2023.07.20.549801","title":"Cellular proliferation biases clonal lineage tracing and trajectory inference","year":2023,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia","funders":"","keywords":"Inference; Tracing; Trajectory; Lineage (genetic); Statistical inference; Probabilistic logic; clone (Java method); Computer science; Simple (philosophy); Cell lineage; Algorithm; Biology; Artificial intelligence; Statistics; Mathematics; Gene; Genetics; Cellular differentiation; Physics","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":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003910894,0.0004769751,0.0003816439,0.0001467703,0.0001694017,0.0001949511,0.0002920871,0.00068623,0.000008145926],"category_scores_gemma":[0.0003154442,0.0005269616,0.0001388601,0.0001570095,0.0001318155,0.00001156623,0.0002371711,0.0005018687,0.00001308264],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004228013,"about_ca_system_score_gemma":0.0004265775,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0000489353,"about_ca_topic_score_gemma":0.0000195109,"domain_scores_codex":[0.9977929,0.0001165131,0.0004518112,0.0009912946,0.000239812,0.0004076531],"domain_scores_gemma":[0.9986387,0.00004773338,0.0002075622,0.0006629548,0.0002416541,0.000201429],"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":[0.00004757898,0.00008566144,0.01388607,0.0002788039,0.00009082596,0.00002190684,0.00001047619,0.0004158823,0.9850274,0.0000267038,0.0001056443,0.000003061467],"study_design_scores_gemma":[0.0004449285,0.0001307556,0.02930307,0.0002730328,0.00008275417,2.504783e-8,0.000002756583,0.001501369,0.9665666,9.507938e-7,0.001028409,0.0006653534],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9888374,0.001377278,0.007920992,0.00006822942,0.0009190727,0.0004766941,0.0002221562,0.0001741186,0.000004053595],"genre_scores_gemma":[0.995497,0.0007626701,0.002285216,0.0001380705,0.001049331,0.0001101362,0.000009131329,0.0001293395,0.000019135],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01846079,"threshold_uncertainty_score":0.9997182,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03117482365183011,"score_gpt":0.238371579869583,"score_spread":0.2071967562177529,"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."}}