{"id":"W4416616737","doi":"10.1051/limn/2025009","title":"Assigning taxonomy and traits to DNA sequences of river diatoms in a region with limited taxonomic knowledge using the updated and annotated reference library Diat.barcode","year":2025,"lang":"en","type":"article","venue":"International Journal of Limnology","topic":"Diatoms and Algae Research","field":"Materials Science","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Continental (Canada)","funders":"Agencia Nacional de Promoción Científica y Tecnológica; HORIZON EUROPE Framework Programme; Fonds National de la Recherche Luxembourg","keywords":"DNA barcoding; Taxon; Trait; Taxonomy (biology); Taxonomic rank; Mainland; Diatom","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":[0.0002790577,0.00009378965,0.0002186921,0.00045589,0.00003971351,0.00009399701,0.0003754963,0.00005760884,0.00002458469],"category_scores_gemma":[0.00007478613,0.00006137093,0.00001940509,0.0002290571,0.0002880932,0.0004807159,0.000178262,0.000181995,0.000001355542],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000043358,"about_ca_system_score_gemma":0.0002766158,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006817884,"about_ca_topic_score_gemma":0.0000363229,"domain_scores_codex":[0.9989992,0.0001846595,0.0003614296,0.000160022,0.0001356173,0.0001590788],"domain_scores_gemma":[0.9991984,0.0002388953,0.0002443729,0.00006331749,0.00020087,0.0000540874],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"observational","study_design_scores_codex":[0.001551079,0.0002303395,0.1419755,0.00004505689,0.0002040626,0.0002936097,0.001272935,0.001092084,0.8337417,0.004259889,0.0004144828,0.01491931],"study_design_scores_gemma":[0.006099851,0.001531118,0.6147285,0.002459033,0.000110468,0.0011602,0.002853484,0.005079708,0.3532758,0.002654154,0.009426154,0.000621549],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9963245,0.0004809356,0.001443992,0.001220756,0.0001117514,0.0001517352,0.00001072207,0.00000561484,0.0002500031],"genre_scores_gemma":[0.9970418,0.0001185325,0.002656,0.0001014708,0.00003578768,0.000009765255,0.00000165365,0.000005723123,0.00002923465],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4804659,"threshold_uncertainty_score":0.2502634,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0495479786103486,"score_gpt":0.3059096150258714,"score_spread":0.2563616364155228,"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."}}