{"id":"W3193433935","doi":"10.1038/s41467-021-25133-1","title":"LineageOT is a unified framework for lineage tracing and trajectory inference","year":2021,"lang":"en","type":"article","venue":"Nature Communications","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":96,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of British Columbia; University of British Columbia Hospital","funders":"Royal Commission for the Exhibition of 1851; Natural Sciences and Engineering Research Council of Canada; Burroughs Wellcome Fund","keywords":"Inference; Tracing; Lineage (genetic); Leverage (statistics); Computer science; Trajectory; Computational biology; Theoretical computer science; Biology; Artificial intelligence; Gene; Genetics","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":[],"consensus_categories":[],"category_scores_codex":[0.00009691268,0.00009889826,0.0001072319,0.00002103645,0.0001942018,0.0000370544,0.0003126589,0.0004070428,0.000006665219],"category_scores_gemma":[0.0004263261,0.0001036663,0.00007116325,0.00009911902,0.00007948166,0.000003493122,0.0001058935,0.0004552581,7.842482e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005947883,"about_ca_system_score_gemma":0.00009337262,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000005527961,"about_ca_topic_score_gemma":0.0002268823,"domain_scores_codex":[0.9994287,0.00005280959,0.0001453958,0.0002043952,0.00004889556,0.0001198302],"domain_scores_gemma":[0.9986591,0.0001788275,0.00004362217,0.0008903986,0.000177035,0.00005096726],"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":[0.0001122447,0.0005347112,0.007206429,0.0001266578,0.0002179885,0.000002247418,0.00127366,0.000047513,0.9557052,0.02226902,0.003275554,0.009228817],"study_design_scores_gemma":[0.001233848,0.0002065243,0.005852849,0.000142508,0.0001285117,0.00001900023,0.0004367445,0.002686319,0.5294581,0.001741536,0.4574927,0.0006013379],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7199034,0.07655484,0.1884124,0.01017916,0.0007367451,0.0007840861,0.0005742171,0.000100557,0.002754569],"genre_scores_gemma":[0.9149292,0.00228316,0.08049269,0.001556707,0.0001128083,0.00002559701,0.0003487369,0.00001568912,0.0002354716],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4542172,"threshold_uncertainty_score":0.422739,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03351175915845343,"score_gpt":0.323113493744695,"score_spread":0.2896017345862416,"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."}}