{"id":"W3034015444","doi":"10.3389/fbioe.2020.00534","title":"Automated Hypothesis Generation to Identify Signals Relevant in the Development of Mammalian Cell and Tissue Bioprocesses, With Validation in a Retinal Culture System","year":2020,"lang":"en","type":"article","venue":"Frontiers in Bioengineering and Biotechnology","topic":"Retinal Development and Disorders","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"Alberta Children's Hospital; University of Alberta; University of Calgary","funders":"Natural Sciences and Engineering Research Council of Canada; Alberta Children's Hospital Research Institute; CNIB","keywords":"Biology; Signal transduction; Computational biology; Transcriptome; Receptor; Activin receptor; ACVR2B; Cell biology; Cell type; Immunochemistry; Cell culture; Cell fate determination; Cell; Bioinformatics; Gene expression; Genetics; Gene; TGF beta signaling pathway; Transcription factor","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":[0.0001538688,0.0001108389,0.0001405435,0.0001530524,0.00001988575,0.0000138271,0.0000984369,0.0001809802,2.12819e-7],"category_scores_gemma":[0.00003113698,0.00008395279,0.0000062193,0.0003389649,0.00003261367,0.000004709131,0.00003439518,0.00007723938,2.571423e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001497256,"about_ca_system_score_gemma":0.00002407078,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009730602,"about_ca_topic_score_gemma":0.00003498042,"domain_scores_codex":[0.9993289,0.00002198554,0.0002158614,0.0002343616,0.00006498698,0.0001338684],"domain_scores_gemma":[0.9998508,0.000002807764,0.00003925118,0.00006859939,0.00001500887,0.00002352686],"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":[0.00007276486,0.0000179549,0.008909514,0.00024899,0.000008340817,0.000007744854,0.001073841,0.0005900205,0.986621,0.00001253777,0.0002376994,0.002199647],"study_design_scores_gemma":[0.0005028902,0.000261189,0.009287308,0.00009954737,0.000006398846,0.00001075791,0.002772799,0.004140186,0.9811638,0.000003326215,0.001559052,0.0001927543],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9864315,0.0007328658,0.01169476,0.0008610806,0.00002539817,0.0002167044,0.000002305508,0.00002455937,0.00001080606],"genre_scores_gemma":[0.9585649,0.0001473705,0.04119024,0.00002855982,0.000009115781,0.00002414057,0.000022698,0.000007368593,0.000005535999],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02949549,"threshold_uncertainty_score":0.3423495,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.00878782625307072,"score_gpt":0.2156444993979272,"score_spread":0.2068566731448565,"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."}}