{"id":"W7113894962","doi":"10.2139/ssrn.5894666","title":"Designing Minimal E. coli Genomes Using Variational Autoencoders","year":2025,"lang":"","type":"preprint","venue":"SSRN Electronic Journal","topic":"Bacterial Genetics and Biotechnology","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":false,"ca_institutions":"Institute of Cancer Research","funders":"","keywords":"Genome; Bacterial genome size; Limiting; Synthetic biology; Genomics; Key (lock); Minification","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":[0.0005283895,0.0007638231,0.0009009964,0.0003551812,0.0003207239,0.0005441513,0.0009114271,0.001277229,0.002182134],"category_scores_gemma":[0.002562508,0.0007643375,0.0007876959,0.0002525994,0.0006114962,0.0006522338,0.001375664,0.00103622,0.0003974169],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007634728,"about_ca_system_score_gemma":0.0009851102,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003878429,"about_ca_topic_score_gemma":0.005842334,"domain_scores_codex":[0.9997763,0.00006145495,0.00001005284,0.00006065262,0.00004570984,0.0000458757],"domain_scores_gemma":[0.9992249,0.0005542702,0.00004010815,0.00004856522,0.00008548729,0.00004654908],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00009423863,0.00004027272,0.0005522435,0.0000926721,0.00002912719,0.00005608371,0.00006338894,0.9472982,0.008862928,0.009342455,0.0005662823,0.03300215],"study_design_scores_gemma":[0.000008996802,0.00002918121,0.00006038051,0.000007168294,0.000005758414,0.000008227673,0.00001645813,0.9936399,0.001335008,0.004569272,0.0003163945,0.000003297257],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1415531,0.0003013971,0.8527371,0.000289495,0.0000655368,0.00008094597,0.0001864749,0.000865971,0.003920086],"genre_scores_gemma":[0.691416,0.0001863387,0.3038932,0.000242809,0.00003077197,0.0002441187,0.0005295289,0.000406058,0.003051166],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.003878429,"threshold_uncertainty_score":0.007711709,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01187882088955388,"score_gpt":0.2511697762447061,"score_spread":0.2392909553551522,"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."}}