{"id":"W2897133367","doi":"10.1093/bioinformatics/bty878","title":"BMDExpress 2: enhanced transcriptomic dose-response analysis workflow","year":2018,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Gene expression and cancer classification","field":"Biochemistry, Genetics and Molecular Biology","cited_by":227,"is_retracted":false,"has_abstract":true,"ca_institutions":"Health Canada","funders":"National Institute of Environmental Health Sciences; National Institutes of Health","keywords":"Workflow; Computer science; Software; Transcriptome; Software engineering; Data mining; Data science; Database; Operating system; Biology; 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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.005281206,0.002286209,0.001885364,0.002368759,0.001063291,0.00318936,0.003294622,0.001411364,0.06499657],"category_scores_gemma":[0.006553502,0.002293989,0.002740934,0.001638665,0.0007377716,0.001493698,0.003065707,0.003329894,0.05087113],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0012149,"about_ca_system_score_gemma":0.003298285,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00316945,"about_ca_topic_score_gemma":0.004763609,"domain_scores_codex":[0.9971654,0.0003870598,0.00030926,0.0008114321,0.001112213,0.000214657],"domain_scores_gemma":[0.9967468,0.001525474,0.0002463097,0.0005473868,0.0007746271,0.0001593994],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.001776839,0.000222739,0.005765626,0.003781361,0.0004421232,0.0008627956,0.0008289178,0.008913109,0.08538679,0.008693162,0.7721235,0.111203],"study_design_scores_gemma":[0.0006022804,0.0002458098,0.009848394,0.0005684613,0.0002190414,0.0007115974,0.0002124306,0.04551249,0.1324403,0.02106044,0.7880208,0.0005579279],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"software","genre_gemma":"methods","genre_scores_codex":[0.005462926,0.0005293731,0.3830606,0.0008409783,0.00050457,0.000854728,0.2070585,0.3919918,0.009696511],"genre_scores_gemma":[0.02592133,0.0008321633,0.5117707,0.003307418,0.0002152739,0.00673829,0.3180996,0.1121983,0.020917],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.06499657,"threshold_uncertainty_score":0.2174352,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0127195426686106,"score_gpt":0.2668319319701167,"score_spread":0.2541123893015061,"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."}}