{"id":"W4414915530","doi":"10.1093/narcan/zcaf036","title":"Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment","year":2025,"lang":"en","type":"article","venue":"NAR Cancer","topic":"Cancer Genomics and Diagnostics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Jewish General Hospital","funders":"H2020 European Research Council; Agence Nationale de la Recherche; Fonds de Recherche du Québec-Société et Culture; Fondation du cancer du sein du Québec; Fondation pour la Recherche Médicale; Fonds de Recherche du Québec - Santé; Fondation ARC pour la Recherche sur le Cancer","keywords":"Triple-negative breast cancer; Breast cancer; Transcriptome; Biomarker; Gene expression profiling; Gene signature; Chemotherapy","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":[0.00006280137,0.0002576307,0.0002632207,0.00006408974,0.0001237245,0.00004109688,0.0003152226,0.0001492245,0.0000928122],"category_scores_gemma":[0.0000837171,0.0002344027,0.00009190512,0.0002331712,0.00005759053,0.000004622096,0.0001688933,0.00008944,0.000006879805],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0004244074,"about_ca_system_score_gemma":0.0008622499,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001964995,"about_ca_topic_score_gemma":0.005235366,"domain_scores_codex":[0.9986328,0.00002286123,0.0002491608,0.0005736723,0.0001447997,0.0003766502],"domain_scores_gemma":[0.9989447,0.00002235974,0.00008868454,0.0005830166,0.000213027,0.0001482211],"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":[0.003389028,0.0004048218,0.01500711,0.000166942,0.0008157353,0.00002108323,0.0004702536,0.00404301,0.6467113,0.001387209,0.1638416,0.1637419],"study_design_scores_gemma":[0.003998583,0.0003915807,0.01426936,0.0002480794,0.0001457901,0.000003265102,0.0001571446,0.0001859992,0.7846468,0.0004043629,0.1950161,0.0005329174],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9585423,0.01446041,0.0005404095,0.0057734,0.001697097,0.001455414,0.004894904,0.00005399818,0.01258199],"genre_scores_gemma":[0.9767936,0.008599614,0.00112598,0.002190806,0.0008575638,0.001163814,0.0001094971,0.00004259295,0.009116462],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1632089,"threshold_uncertainty_score":0.9558665,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01321762210894742,"score_gpt":0.2825826608961816,"score_spread":0.2693650387872341,"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."}}