{"id":"W4416228481","doi":"10.1021/acs.jcim.5c02266","title":"A Review of Topological Data Analysis and Topological Deep Learning in Molecular Sciences","year":2025,"lang":"en","type":"review","venue":"Journal of Chemical Information and Modeling","topic":"Topological and Geometric Data Analysis","field":"Computer Science","cited_by":16,"is_retracted":false,"has_abstract":true,"ca_institutions":"Toronto Metropolitan University","funders":"Division of Information and Intelligent Systems; Division of Mathematical Sciences; Michigan State University Foundation","keywords":"Topological data analysis; Deep learning; Topology (electrical circuits); Transformative learning; Sequence (biology); TRACE (psycholinguistics); Big data","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":[0.00200186,0.0001709804,0.001552237,0.0010736,0.00004027887,0.0001031755,0.001176962,0.0001819725,0.00001319752],"category_scores_gemma":[0.001771126,0.0001035226,0.0002768014,0.002916683,0.0001268928,0.0009240144,0.001028826,0.0004850423,4.237001e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002190466,"about_ca_system_score_gemma":0.0001168156,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001111554,"about_ca_topic_score_gemma":4.014856e-7,"domain_scores_codex":[0.9975755,0.0001486698,0.001566284,0.0002241832,0.0003235042,0.0001619126],"domain_scores_gemma":[0.9982727,0.0003657998,0.0008578346,0.0002660121,0.0001436708,0.00009396981],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"design_other","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0000017504,0.00002421547,0.00001465151,0.008376026,0.0001674667,0.000004978445,0.00001975024,0.000366374,5.414275e-7,0.00347849,0.00001141272,0.9875343],"study_design_scores_gemma":[0.0005795239,0.0003053101,0.000005870364,0.0507513,0.00553079,0.0003056929,0.0001317088,0.7888534,0.000008649014,0.004390492,0.148298,0.0008392988],"study_design_candidate":"design_other","study_design_consensus":null,"genre_codex":"review","genre_gemma":"review","genre_scores_codex":[0.00004047152,0.6860225,0.3136137,0.0001580971,0.00001460775,0.00005330769,0.000004527485,0.000005013904,0.00008782263],"genre_scores_gemma":[0.0005845515,0.9780632,0.02094633,0.0003559306,0.000009784246,0.000001575723,0.00003625248,8.877984e-7,0.000001521006],"genre_candidate":"review","genre_consensus":"review","teacher_disagreement_score":0.9866951,"threshold_uncertainty_score":0.4221528,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.07976611656877461,"score_gpt":0.3711833016736606,"score_spread":0.291417185104886,"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."}}