{"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":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0003376423,0.000623757,0.0006696415,0.0003521071,0.0002135715,0.00007555219,0.0005631555,0.001102808,0.00003631368],"category_scores_gemma":[0.000136874,0.0007574855,0.000493388,0.0002954217,0.0005390963,0.000008153389,0.0001484239,0.0006464181,0.00001037974],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001928847,"about_ca_system_score_gemma":0.0007151789,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00006664387,"about_ca_topic_score_gemma":0.00006202256,"domain_scores_codex":[0.9962986,0.0003084577,0.001116833,0.001315651,0.000184519,0.0007759231],"domain_scores_gemma":[0.998789,0.0002198712,0.0002300797,0.0003729692,0.0002382694,0.0001498614],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.002332178,0.001793826,0.01203003,0.0004262701,0.0008700048,0.00003583684,0.0001715835,0.6378784,0.2540339,0.06453141,0.0007957068,0.02510092],"study_design_scores_gemma":[0.01646098,0.00212551,0.01158995,0.0004882089,0.0003922436,0.00005776547,0.0001269835,0.3810812,0.02733841,0.5254724,0.03253895,0.002327388],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.1918513,0.003770091,0.7995198,0.001761268,0.001268621,0.001123835,0.0004092771,0.00001575132,0.0002800072],"genre_scores_gemma":[0.9482372,0.00008118094,0.04220354,0.005806387,0.000205194,0.0001636755,0.003141894,0.00006499624,0.00009593586],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.7573163,"threshold_uncertainty_score":0.9994876,"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."}}