{"id":"W4401398925","doi":"10.1038/s41540-024-00403-y","title":"On the salient limitations of the methods of assembly theory and their classification of molecular biosignatures","year":2024,"lang":"en","type":"review","venue":"npj Systems Biology and Applications","topic":"Protein Structure and Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":18,"is_retracted":false,"has_abstract":true,"ca_institutions":"Concordia University; McGill Genome Centre","funders":"Fundação de Amparo à Pesquisa do Estado de São Paulo","keywords":"Salient; Coding (social sciences); Computer science; Simple (philosophy); Statistical analysis; Encoding (memory); Scheme (mathematics); Algorithm; Theoretical computer science; Artificial intelligence; Mathematics; Statistics","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":[],"consensus_categories":[],"category_scores_codex":[0.0006145862,0.0001801078,0.000433142,0.00005501048,0.00006610723,0.000006396625,0.0002604064,0.0004001862,3.269947e-7],"category_scores_gemma":[0.0001459798,0.00008337876,0.0001712548,0.0001734637,0.0004014714,9.582401e-7,0.0001113527,0.0001643535,2.714304e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000005014319,"about_ca_system_score_gemma":0.00008041276,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000004029744,"about_ca_topic_score_gemma":0.000001994063,"domain_scores_codex":[0.998485,0.0007242913,0.0004031777,0.0002697057,0.00003928132,0.0000785373],"domain_scores_gemma":[0.9983947,0.0005162951,0.0004417626,0.0005481705,0.0000802772,0.00001877531],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","study_design_scores_codex":[0.000005220058,0.00001974019,0.000002246283,0.001557539,0.000266371,1.489265e-8,0.00003054307,0.000002102936,0.08581339,0.7726877,0.00006930193,0.1395458],"study_design_scores_gemma":[0.000147132,0.0002753689,0.00006326054,0.002383291,0.001420308,0.00003111394,0.0004115558,0.00006285575,0.02527861,0.07591718,0.8936225,0.0003868199],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.0006097769,0.9748281,0.02260297,0.00005797626,0.00008965225,0.001139789,0.0002755067,0.000004140544,0.0003921064],"genre_scores_gemma":[0.1795813,0.8192632,0.0002373564,0.00003240956,0.0000486519,0.0006176641,0.0001440016,0.00001851699,0.00005685267],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.8935532,"threshold_uncertainty_score":0.3400087,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03785111272640172,"score_gpt":0.3571483170269015,"score_spread":0.3192972043004997,"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."}}