{"id":"W7108598928","doi":"10.5376/cmb.2025.15.0018","title":"Computational Frameworks for Spatial Transcriptomics in Tumor Microenvironment","year":2025,"lang":"","type":"article","venue":"Computational Molecular Biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"","keywords":"Transcriptome; Tumor microenvironment; Function (biology); Spatial analysis; Margin (machine learning); Spatial contextual awareness; Graph; Spatial epidemiology","routes":{"ca_aff":false,"ca_fund":false,"ca_venue":true,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001387328,0.0007726895,0.001014057,0.001068309,0.000814004,0.001678022,0.002200904,0.001539907,0.002151075],"category_scores_gemma":[0.004109547,0.0006395064,0.001990287,0.001298592,0.001439643,0.001644954,0.001870754,0.001470421,0.0003637334],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00145066,"about_ca_system_score_gemma":0.002117513,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01199995,"about_ca_topic_score_gemma":0.01062944,"domain_scores_codex":[0.9994116,0.0002703647,0.00002838641,0.0001219628,0.000115221,0.00005255079],"domain_scores_gemma":[0.9978651,0.001618142,0.0001326098,0.0001303099,0.0001571845,0.00009667027],"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":[0.000007994869,0.00001013211,0.0003775828,0.00003065515,0.00002461757,0.00004036894,0.00003343232,0.9231191,0.0002590924,0.07246193,0.0003717986,0.003263383],"study_design_scores_gemma":[0.000001781076,0.000001669531,0.00003023494,0.000002049228,0.000002214899,0.000004553067,0.00000655673,0.9770401,0.00003411813,0.02253867,0.0003362786,0.000001948836],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.007611244,0.0003544625,0.9888869,0.0006210987,0.00003880773,0.00002421805,0.0002225025,0.0002278083,0.002013077],"genre_scores_gemma":[0.4641542,0.001641753,0.5263029,0.0005028213,0.0002171928,0.0007145022,0.001169336,0.0003743712,0.004922976],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.01199995,"threshold_uncertainty_score":0.02386022,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.007033582086688492,"score_gpt":0.2611081696543777,"score_spread":0.2540745875676892,"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."}}