{"meta":{"page":1,"per_page":50,"max_per_page":100,"total":12,"total_is_capped":false,"direct_labels_cover":0,"predictions_cover":12,"direct_label_status":"direct model label, unvalidated","prediction_status":"machine_predicted_unvalidated (Codex and Gemma teacher distillation)","score_status":"score_only:v0-immature-baseline (scores rank; they never assert a category)","snapshot":{"source":"OpenAlex, pinned release, all 482 partitions","release":"2026-06-24","frame_built":"2026-07-12","author_layer_release":"2026-06-26"},"query_hash":"a5c6c3185103","filters":{"venue":"Frontiers in Systems Biology"}},"results":[{"id":"W4380988248","doi":"10.3389/fsysb.2023.1174647","title":"A practical guide for the generation of model-based virtual clinical trials","year":2023,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Mathematical Biology Tumor Growth","field":"Mathematics","cited_by":44,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Toronto Metropolitan University; Université de Montréal; Centre Hospitalier Universitaire Sainte-Justine","funders":"Fonds de Recherche du Québec - Santé; Natural Sciences and Engineering Research Council of Canada","keywords":"Virtual patient; Identifiability; Computer science; Popularity; Variety (cybernetics); Clinical trial; Population; Sensitivity (control systems); Management science; Human–computer interaction; Data science; Machine learning; Artificial intelligence; Medicine; Engineering; Psychology","authors":[{"name":"Morgan Craig","is_ca":true},{"name":"Jana L. Gevertz","is_ca":false},{"name":"Irina Kareva","is_ca":false},{"name":"Kathleen P. Wilkie","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.4461103613928482,"gpt":0.5098891712605287,"spread":0.06377880986768053,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaresearch"],"consensus_categories":[],"category_scores_codex":[0.02082075,0.0001714011,0.00123058,0.0001678893,0.00006132335,0.00001145186,0.0002895214,0.0004424501,0.000006300464],"category_scores_gemma":[0.0382311,0.0001026,0.0002786961,0.0002370259,0.0003332081,0.00003046032,0.00005801988,0.0002137806,0.00001018024],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004737352,"about_ca_system_score_gemma":0.0001972848,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000009172373,"about_ca_topic_score_gemma":0.000007567186,"domain_scores_codex":[0.9945549,0.002385252,0.002238502,0.0003568347,0.0001232647,0.0003412404],"domain_scores_gemma":[0.982688,0.01594444,0.0006968536,0.000486953,0.0001265586,0.00005720233],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002856884,0.000203863,0.004545873,0.0002433151,0.0002378013,0.000003778785,0.00015622,0.0007600425,0.001575117,0.4334246,0.5572531,0.00131066],"study_design_scores_gemma":[0.00132689,0.0003069957,0.00003760742,0.00003815081,0.00009986007,0.000004145599,0.0003911651,0.9367275,0.0002813482,0.05716686,0.003486045,0.0001334709],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.01980763,0.0001326961,0.9739445,0.001169306,0.002829971,0.001764181,0.00009641475,0.00008790247,0.0001674036],"genre_scores_gemma":[0.8066972,0.00006310983,0.1897514,0.0002003972,0.0009171824,0.001218637,0.0000998594,0.00005214683,0.000999981],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.9359674,"threshold_uncertainty_score":0.9698703,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4291149130","doi":"10.3389/fsysb.2022.955611","title":"Metataxonomic insights into the microbial ecology of farm-scale hay, grass or legume, and corn silage produced with and without inoculants","year":2022,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Ruminant Nutrition and Digestive Physiology","field":"Agricultural and Biological Sciences","cited_by":11,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Guelph; Université Laval","funders":"Agriculture and Agri-Food Canada; Natural Sciences and Engineering Research Council of Canada; Novalait","keywords":"Silage; Microbial inoculant; Biology; Forage; Hay; Agronomy; Pediococcus acidilactici; Food science; Lactobacillus plantarum; Lactic acid; Bacteria; Horticulture; Inoculation","authors":[{"name":"Alexandre J. Kennang Ouamba","is_ca":true},{"name":"Mérilie Gagnon","is_ca":true},{"name":"Thibault Varin","is_ca":true},{"name":"P.Y. Chouinard","is_ca":true},{"name":"Gisèle LaPointe","is_ca":true},{"name":"Denis Roy","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01369257161143872,"gpt":0.2084004837911391,"spread":0.1947079121797004,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002735155,0.0001543102,0.0004869039,0.00004795002,0.0002432339,0.00001361537,0.0002139915,0.00009118859,0.00001179476],"category_scores_gemma":[0.00002269325,0.00005225432,0.00002667504,0.0002207106,0.0005156315,0.00003933671,0.0001846817,0.0001557937,6.566062e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000336531,"about_ca_system_score_gemma":0.00001992143,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0009591844,"about_ca_topic_score_gemma":0.002250521,"domain_scores_codex":[0.998386,0.0006209796,0.0002908383,0.0004165205,0.00005173905,0.0002339027],"domain_scores_gemma":[0.9995302,0.0001154976,0.0001929568,0.00008029545,0.00003500612,0.00004607144],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"observational","study_design_scores_codex":[0.0009453733,0.0001124716,0.6727353,0.00003292469,0.00005194012,0.000006015988,0.0006330635,0.000006256881,0.3209553,0.0002439786,0.0008641283,0.003413284],"study_design_scores_gemma":[0.002660395,0.004766914,0.8996263,0.0000482352,0.00006521522,0.0002849244,0.0144982,0.0003842051,0.007293929,0.0008972517,0.06886324,0.0006111771],"study_design_candidate":"observational","study_design_consensus":"observational","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9968896,0.001419176,0.0000111641,0.0004238787,0.000525148,0.0006109281,0.0000476907,0.0000160104,0.00005642986],"genre_scores_gemma":[0.9992156,0.000141066,0.0001342433,0.0001183077,0.00006173452,0.0001526334,0.00005488981,0.000001675775,0.0001198457],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.3136614,"threshold_uncertainty_score":0.2130869,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4399543803","doi":"10.3389/fsysb.2024.1384481","title":"Building an Adverse Outcome Pathway network for COVID-19","year":2024,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Health Systems, Economic Evaluations, Quality of Life","field":"Economics, Econometrics and Finance","cited_by":8,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Ottawa; Health Canada","funders":"Japan Society for the Promotion of Science; Health Canada; Japan Agency for Medical Research and Development; National Science Foundation","keywords":"Adverse Outcome Pathway; Interoperability; Computer science; Usability; Terminology; Coronavirus disease 2019 (COVID-19); Outcome (game theory); Harmonization; Visualization; Data science; Artificial intelligence; World Wide Web; Disease; Medicine; Computational biology; Infectious disease (medical specialty); Biology; Pathology; Human–computer interaction","authors":[{"name":"Penny Nymark","is_ca":false},{"name":"Laure‐Alix Clerbaux","is_ca":false},{"name":"Maria João Amorim","is_ca":false},{"name":"Christos Andronis","is_ca":false},{"name":"F Bernardi","is_ca":false},{"name":"Gillina F. G. Bezemer","is_ca":false},{"name":"Sandra Coecke","is_ca":false},{"name":"Felicity N. E. Gavins","is_ca":false},{"name":"Daniel Jacobson","is_ca":false},{"name":"Eftychia Lekka","is_ca":false},{"name":"Luigi Margiotta‐Casaluci","is_ca":false},{"name":"Marvin Martens","is_ca":false},{"name":"Sally A. Mayasich","is_ca":false},{"name":"Holly M. Mortensen","is_ca":false},{"name":"Young Jun Kim","is_ca":false},{"name":"Magdalini Sachana","is_ca":false},{"name":"Shihori Tanabe","is_ca":false},{"name":"Vassilis Virvilis","is_ca":false},{"name":"Stephen W. Edwards","is_ca":false},{"name":"Sabina Halappanavar","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.3435554677051489,"gpt":0.4648236614494095,"spread":0.1212681937442605,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.02158647,0.0002515635,0.00137473,0.0006038125,0.0001791765,0.00008296644,0.0004022872,0.0004167945,0.00004945995],"category_scores_gemma":[0.00246982,0.0002981056,0.0001772059,0.0003145993,0.0001063884,0.0003487892,0.00004779231,0.000218225,0.0002334269],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001458928,"about_ca_system_score_gemma":0.0002884082,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001334455,"about_ca_topic_score_gemma":0.0001495129,"domain_scores_codex":[0.9936438,0.0006065998,0.004033362,0.0009425958,0.00004179448,0.0007318413],"domain_scores_gemma":[0.9972546,0.0009872805,0.0008864834,0.0005218987,0.00002909283,0.0003206579],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"theoretical_or_conceptual","study_design_gemma":"not_applicable","study_design_scores_codex":[0.00002610222,0.00002708636,0.3344691,0.001206644,0.00009656985,0.000004966108,0.0008848122,0.005018635,0.000002807733,0.5325248,0.1254629,0.000275596],"study_design_scores_gemma":[0.0006574185,0.000125487,0.001321086,0.00008943257,0.000005933852,0.00001087412,0.001214461,0.0707584,3.65404e-7,0.05497045,0.8704621,0.0003840028],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"empirical","genre_scores_codex":[0.03110643,0.03241361,0.8924167,0.008856479,0.0299948,0.002533175,0.001448135,0.000338248,0.0008923994],"genre_scores_gemma":[0.8797144,0.0002068578,0.09566395,0.0143965,0.005280398,0.001902583,0.0004260286,0.0001613263,0.002247978],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.848608,"threshold_uncertainty_score":0.9999471,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4225140144","doi":"10.3389/fsysb.2022.893007","title":"A Metataxonomic Analysis of Maple Sap Microbial Communities Reveals New Insights Into Maple Syrup Complexity","year":2022,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Plant-Derived Bioactive Compounds","field":"Chemistry","cited_by":8,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":true},"ca_institutions":"Université Laval","funders":"Natural Sciences and Engineering Research Council of Canada; Mitacs","keywords":"Maple; Dormancy; Biology; Maple syrup urine disease; Food science; Botany; Amino acid; Biochemistry","authors":[{"name":"Guillaume Nguyen","is_ca":true},{"name":"Cyril Roblet","is_ca":true},{"name":"Luc Lagacé","is_ca":false},{"name":"Marie Filteau","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.03940597236382851,"gpt":0.2504985329007757,"spread":0.2110925605369472,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow"],"consensus_categories":[],"category_scores_codex":[0.0004049333,0.0002950693,0.001425388,0.0008139088,0.0002323352,0.00002495414,0.001028185,0.000190081,0.0004372813],"category_scores_gemma":[0.00003138575,0.0003073086,0.0002625904,0.0006923515,0.0004100802,0.00007090153,0.0006313584,0.0004729276,0.000004749505],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0007092697,"about_ca_system_score_gemma":0.0001451616,"about_ca_topic_candidate":true,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.02065589,"about_ca_topic_score_gemma":0.002708697,"domain_scores_codex":[0.9974408,0.0007546063,0.000855674,0.0004046889,0.0001426953,0.0004015917],"domain_scores_gemma":[0.9982766,0.0002084203,0.0005736888,0.000787486,0.00005898977,0.00009480407],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0007888977,0.0002925656,0.3576651,0.0004529317,0.007625091,0.0000297094,0.01200125,0.001453641,0.5429002,0.002101252,0.07429062,0.0003987626],"study_design_scores_gemma":[0.008058082,0.0006375477,0.01609384,0.0002863628,0.003404832,0.0001613619,0.1604387,0.0296602,0.02555867,0.01154274,0.7408191,0.003338556],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9877745,0.004471845,0.003443,0.00006602355,0.001201729,0.0002300242,0.001192419,0.0000695464,0.001550892],"genre_scores_gemma":[0.9946321,0.00006282495,0.002289143,0.00006471657,0.00009392088,0.00008449107,0.001992879,0.00002254096,0.0007573917],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6665285,"threshold_uncertainty_score":0.9999379,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4384025388","doi":"10.3389/fsysb.2023.1183868","title":"Contribution of farms to the microbiota in the swine value chain","year":2023,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Meat and Animal Product Quality","field":"Agricultural and Biological Sciences","cited_by":6,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval; Mitel (Canada); Université de Montréal; Centre de Recherche en Sciences Animales de Deschambault","funders":"Agriculture and Agri-Food Canada; Ministère de l'Agriculture, des Pêcheries et de l'Alimentation","keywords":"Biology; Mesophile; Food science; Feces; Biotechnology; Bacteria; Microbiology","authors":[{"name":"Pascal Laforge","is_ca":true},{"name":"Antony T. Vincent","is_ca":true},{"name":"Caroline Duchaine","is_ca":true},{"name":"Perrine Feutry","is_ca":true},{"name":"Annick Dion‐Fortier","is_ca":true},{"name":"Pier-Luc Plante","is_ca":true},{"name":"Éric Pouliot","is_ca":true},{"name":"Sylvain Fournaise","is_ca":true},{"name":"Linda Saucier","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.02569714101950282,"gpt":0.2517785928546019,"spread":0.226081451835099,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002441838,0.0000821765,0.0002287116,0.00002623317,0.00006252444,0.00001219558,0.000386985,0.00009744486,0.000005021397],"category_scores_gemma":[0.0001947439,0.0000220304,0.00004343169,0.0007990006,0.00006802843,0.00001629827,0.00005503617,0.000104287,0.00002030005],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002221593,"about_ca_system_score_gemma":0.000004364382,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001304737,"about_ca_topic_score_gemma":0.0004283288,"domain_scores_codex":[0.9984906,0.0006747926,0.0003018093,0.0002105668,0.00006739471,0.0002548223],"domain_scores_gemma":[0.999647,0.0001449982,0.000073915,0.00008303751,0.00003222877,0.00001886674],"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":[0.0001174826,0.00007994271,0.2850712,0.00002675584,0.0000203314,0.000004632767,0.001377393,0.00008585262,0.6477899,0.008824007,0.04777172,0.008830792],"study_design_scores_gemma":[0.0003314071,0.0004451078,0.7715315,0.00006590453,0.000006338599,0.000007347402,0.007762168,0.0004489218,0.001992871,0.001601286,0.215588,0.0002191708],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9875646,0.0006894926,0.00003870666,0.009988409,0.0009843612,0.0005530289,0.0000583378,0.00001948779,0.0001035586],"genre_scores_gemma":[0.9992192,0.00003412789,0.00001023598,0.0002453937,0.0002678657,0.00003661056,0.00007110591,4.527772e-7,0.0001150126],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.645797,"threshold_uncertainty_score":0.1972381,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4394615787","doi":"10.3389/fsysb.2024.1284668","title":"Forecasting SARS-CoV-2 spike protein evolution from small data by deep learning and regression","year":2024,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"SARS-CoV-2 and COVID-19 Research","field":"Medicine","cited_by":5,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"De Veber; Genome British Columbia; Genome Canada; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada","keywords":"Autoencoder; Spurious relationship; Regression; Computer science; Artificial intelligence; Artificial neural network; Spike (software development); Machine learning; Biology; Computational biology; Mathematics; Statistics","authors":[{"name":"S. B. King","is_ca":true},{"name":"Xinyi E. Chen","is_ca":true},{"name":"Sarah W.S. Ng","is_ca":true},{"name":"Kimia Rostin","is_ca":true},{"name":"Samuel V. Hahn","is_ca":true},{"name":"Tylo Roberts","is_ca":true},{"name":"Janella C. Schwab","is_ca":true},{"name":"Parneet Sekhon","is_ca":true},{"name":"Madina Kagieva","is_ca":true},{"name":"Taylor Reilly","is_ca":true},{"name":"Ruo Chen Qi","is_ca":false},{"name":"Paarsa Salman","is_ca":true},{"name":"Ryan J. Hong","is_ca":true},{"name":"Eric Ma","is_ca":false},{"name":"Steven Hallam","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.08014831235731062,"gpt":0.3421733725426069,"spread":0.2620250601852963,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0008991653,0.0002114283,0.0004897132,0.0003194312,0.0000894551,0.00006557343,0.0002508242,0.0003683479,0.000001194597],"category_scores_gemma":[0.0004946673,0.0001645792,0.00003885045,0.0003141594,0.0001559237,0.0001175044,0.0002897219,0.0006164616,0.00001459212],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002536926,"about_ca_system_score_gemma":0.0001232203,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002662572,"about_ca_topic_score_gemma":0.0001209126,"domain_scores_codex":[0.9978305,0.0003467888,0.0004120532,0.0007980077,0.000160534,0.0004521584],"domain_scores_gemma":[0.9992964,0.0001183441,0.00008899874,0.0004157819,0.00004833081,0.00003219504],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0003404313,0.00004125141,0.3811506,0.000685335,0.0001343607,0.0001890123,0.0003468104,4.123418e-7,0.5586987,0.00007292366,0.008173211,0.05016691],"study_design_scores_gemma":[0.00179875,0.00054939,0.0006712503,0.00312178,0.00007228264,0.0001406558,0.001605409,0.3511993,0.02295946,0.0005986334,0.6168681,0.0004149619],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8774015,0.07772474,0.0416127,0.0001413262,0.001439658,0.0009161268,0.00006149319,0.000155055,0.0005473518],"genre_scores_gemma":[0.996286,0.0000402933,0.002357043,0.0003530905,0.000460311,0.0001042503,0.0002265405,0.00004359898,0.0001288393],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.6086949,"threshold_uncertainty_score":0.6711345,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4307998948","doi":"10.3389/fsysb.2022.926923","title":"Dual continuum upscaling of liver lobule flow and metabolism to the full organ scale","year":2022,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Mathematical Biology Tumor Growth","field":"Mathematics","cited_by":3,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta; MacEwan University; Virtual Materials Group (Canada)","funders":"Natural Sciences and Engineering Research Council of Canada; MacEwan University","keywords":"Discretization; Lobules of liver; Grid; Mechanics; Biological system; Physics; Geometry; Mathematics; Biology; Mathematical analysis","authors":[{"name":"Dennis Coombe","is_ca":true},{"name":"Vahid Rezania","is_ca":true},{"name":"Jack A. Tuszyński","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01682427704607826,"gpt":0.245873547029763,"spread":0.2290492699836847,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.001637065,0.0001846243,0.0007496934,0.0001713941,0.0001303411,0.00001111342,0.0003606883,0.0001220646,0.00007209196],"category_scores_gemma":[0.0004005216,0.0001291655,0.00006487426,0.0002926258,0.0002172251,0.00002425357,0.0004340235,0.0002791388,0.000008261261],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00005855182,"about_ca_system_score_gemma":0.00003138728,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00007056676,"about_ca_topic_score_gemma":0.00006233625,"domain_scores_codex":[0.9977596,0.0007698907,0.0006182255,0.0003463097,0.0001391045,0.0003668113],"domain_scores_gemma":[0.9988605,0.0003954014,0.0002132459,0.0004037812,0.00005172962,0.00007533145],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"theoretical_or_conceptual","study_design_scores_codex":[0.001102085,0.001310844,0.1145841,0.002211847,0.001269195,0.0001686152,0.04101308,0.0002428963,0.04538451,0.3198658,0.4648639,0.007983077],"study_design_scores_gemma":[0.0108907,0.002963474,0.01600174,0.0005906437,0.001030568,0.002548537,0.05533837,0.05807431,0.01069459,0.4273204,0.4106861,0.003860597],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9533251,0.004005156,0.0367983,0.0006006343,0.002943201,0.001249761,0.0001995156,0.00007236477,0.0008059483],"genre_scores_gemma":[0.9775813,0.00001815182,0.02131659,0.000115818,0.0001807913,0.0002058571,0.00001193101,0.00002861792,0.0005409815],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1074546,"threshold_uncertainty_score":0.5267215,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4321376749","doi":"10.3389/fsysb.2023.1045754","title":"Illuminating HBV with multi-scale modeling","year":2023,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Hepatitis B Virus Studies","field":"Medicine","cited_by":3,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"","funders":"Ministry of Business, Innovation and Employment; York University","keywords":"Immune system; Biology; Terrain; Blood stream; Immunology; Computational biology; Cell biology; Medicine; Ecology; Internal medicine","authors":[{"name":"Shawn Means","is_ca":false},{"name":"Md Akkas Ali","is_ca":false},{"name":"Harvey Ho","is_ca":false}],"retraction":null,"screen_n_in":null,"score":{"opus":0.03892652439477444,"gpt":0.2948772754900283,"spread":0.2559507510952539,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003850789,0.0001452647,0.0005255628,0.0002992828,0.00007524126,0.000006580572,0.00007912613,0.0001448968,0.000002307042],"category_scores_gemma":[0.0001235417,0.0001113078,0.0000360101,0.0004177728,0.0001155584,0.0000342956,0.0000576467,0.0001743718,0.00004840217],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001276509,"about_ca_system_score_gemma":0.00004420465,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001753542,"about_ca_topic_score_gemma":0.0006278169,"domain_scores_codex":[0.998743,0.00009952992,0.0003270261,0.0003191886,0.00009782047,0.0004134402],"domain_scores_gemma":[0.9995509,0.00003442869,0.00006422777,0.0002094827,0.00007856745,0.000062377],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00003989279,0.00002533303,0.9920726,0.0001385272,0.00007240984,0.000069936,0.001457989,0.0009758848,0.000790715,0.00002836604,0.002650403,0.001677936],"study_design_scores_gemma":[0.002554327,0.0003579578,0.0285672,0.0006402057,0.00004610014,0.00006361118,0.007828289,0.954562,0.0001054693,0.0000366739,0.0049118,0.0003263837],"study_design_candidate":"observational","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8978497,0.002201777,0.09486438,0.0002704556,0.002109408,0.000717351,0.00002099028,0.0003318131,0.00163414],"genre_scores_gemma":[0.9850041,0.0001701042,0.01324167,0.00005849206,0.0001526388,0.0001354113,0.00003184797,0.00002889335,0.001176835],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9635054,"threshold_uncertainty_score":0.4539001,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4392352117","doi":"10.3389/fsysb.2024.1346076","title":"Pareto task inference analysis reveals cellular trade-offs in diffuse large B-Cell lymphoma transcriptomic data","year":2024,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Protein Degradation and Inhibitors","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval","funders":"","keywords":"Transcriptome; Computational biology; Biology; Phenotype; Pareto principle; Gene; Inference; Computer science; Genetics; Gene expression; Artificial intelligence; Mathematical optimization; Mathematics","authors":[{"name":"Jonatan Blais","is_ca":true},{"name":"Julie Jeukens","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01367718443337682,"gpt":0.2580638127945071,"spread":0.2443866283611303,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0007483206,0.0002624336,0.0005243127,0.0004930855,0.0000390335,0.00005754242,0.0006852341,0.0004646012,0.000006592085],"category_scores_gemma":[0.00007190294,0.000242621,0.0001326182,0.0007327522,0.00009312268,0.00001820796,0.0001419346,0.0001552959,0.00001026897],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00007902383,"about_ca_system_score_gemma":0.0001176623,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002064253,"about_ca_topic_score_gemma":0.0002710835,"domain_scores_codex":[0.9974028,0.0004514702,0.0006431148,0.0009267021,0.0001047315,0.0004712008],"domain_scores_gemma":[0.998842,0.00002255852,0.00009431651,0.000932113,0.00001735827,0.0000916546],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001850774,0.001357531,0.2948916,0.0005007549,0.000872849,0.0001105248,0.0005814447,0.00006874467,0.6379411,0.0007750471,0.05885363,0.003861717],"study_design_scores_gemma":[0.01128779,0.0005023012,0.0085639,0.0003424603,0.0004808312,0.0000199785,0.001734141,0.05521315,0.04877562,0.0004182257,0.8708361,0.001825514],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8511907,0.04729464,0.09621989,0.0001860764,0.002979248,0.0006578406,0.0009870558,0.00005952219,0.0004249951],"genre_scores_gemma":[0.9948618,0.0008392019,0.0003566668,0.0001042723,0.0002023556,0.00007534731,0.003024637,0.00002650952,0.0005091788],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.8119825,"threshold_uncertainty_score":0.9893797,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4389341945","doi":"10.3389/fsysb.2023.1274184","title":"The development of an ingestible biosensor for the characterization of gut metabolites related to major depressive disorder: hypothesis and theory","year":2023,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Gut microbiota and health","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"University of Alberta; McMaster University","funders":"McMaster University","keywords":"Major depressive disorder; Computational biology; Biology; Medicine; Mood; Psychiatry","authors":[{"name":"Amanda Densil","is_ca":true},{"name":"Mya Elisabeth George","is_ca":true},{"name":"Hala Mahdi","is_ca":true},{"name":"Andrew Chami","is_ca":true},{"name":"Alyssa Mark","is_ca":true},{"name":"Yifan Wang","is_ca":true},{"name":"Aribah Ali","is_ca":true},{"name":"Pengpeng Tang","is_ca":true},{"name":"A. Dong","is_ca":true},{"name":"Sin Yu Pao","is_ca":true},{"name":"Rubani Singh Suri","is_ca":true},{"name":"Isabella Valentini","is_ca":true},{"name":"Lila Al-Arabi","is_ca":true},{"name":"Fanxiao Liu","is_ca":true},{"name":"Alesha Singh","is_ca":true},{"name":"Linda Wu","is_ca":true},{"name":"Helen Peng","is_ca":true},{"name":"Anjana Sudharshan","is_ca":true},{"name":"Zoha Naqvi","is_ca":true},{"name":"Jayda Hewitt","is_ca":true},{"name":"Catherine M Andary","is_ca":true},{"name":"Vincent Leung","is_ca":true},{"name":"Paul Forsythe","is_ca":true},{"name":"Jianping Xu","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.0101175074221524,"gpt":0.2520068812429772,"spread":0.2418893738208248,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006961829,0.00008917144,0.0001997921,0.00007993007,0.0001272944,0.000006924351,0.0001613112,0.0001318413,2.842716e-7],"category_scores_gemma":[0.0001616229,0.00005392727,0.00002543364,0.0001460357,0.0001101442,0.000002473864,0.00005977598,0.00003431562,4.946536e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000006890861,"about_ca_system_score_gemma":0.00005719271,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001671232,"about_ca_topic_score_gemma":0.00003475994,"domain_scores_codex":[0.9990557,0.0001939677,0.0003418764,0.0001957561,0.00002837396,0.0001843204],"domain_scores_gemma":[0.9994383,0.0001070597,0.0001630558,0.0002029222,0.00006108892,0.00002754058],"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":[0.0001443027,0.00001363807,0.01866295,0.00006214034,0.00008890894,6.004118e-8,0.000578277,0.00000969435,0.9666739,0.0004243949,0.00009046164,0.01325133],"study_design_scores_gemma":[0.001663528,0.0005405763,0.5110736,0.0001025911,0.00007911932,0.000007423655,0.005188174,0.0005333525,0.4026784,0.0008020706,0.07696598,0.0003650844],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9926983,0.00284981,0.003134689,0.0001405415,0.0004237519,0.0006554381,0.00008173685,0.000006904947,0.000008820797],"genre_scores_gemma":[0.9974262,0.0005315941,0.001488581,0.00002461795,0.00002756101,0.0001267936,0.0001259587,0.00001317691,0.0002355296],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5639954,"threshold_uncertainty_score":0.219909,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4390007125","doi":"10.3389/fsysb.2023.1347323","title":"Editorial: Integrative systems biology and big data for agricultural improvement and understanding","year":2023,"lang":"en","type":"editorial","venue":"Frontiers in Systems Biology","topic":"Genetics, Bioinformatics, and Biomedical Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false},"ca_institutions":"Université Laval; Ministry of Agriculture, Fisheries and Food; Ste. Anne's Hospital","funders":"","keywords":"Big data; Agriculture; Volume (thermodynamics); Systems biology; Data science; Computer science; Biology; Computational biology; Ecology; Physics; Data mining","authors":[{"name":"Liliana Fadul-Pacheco","is_ca":true},{"name":"Antony T. Vincent","is_ca":true},{"name":"Éric R. Paquet","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.04023510418331774,"gpt":0.3144287603289388,"spread":0.2741936561456211,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":["metaepi_narrow","research_integrity"],"consensus_categories":[],"category_scores_codex":[0.001894432,0.0005293884,0.00101901,0.0003050518,0.0001518597,0.0001557313,0.0008385127,0.002691878,2.542766e-7],"category_scores_gemma":[0.002868263,0.0003755753,0.00007671083,0.0001632845,0.0006908493,0.00000980184,0.001094507,0.0005685393,0.000001612405],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0002102562,"about_ca_system_score_gemma":0.0003655687,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0005690551,"about_ca_topic_score_gemma":0.0002425457,"domain_scores_codex":[0.9965007,0.0002824684,0.0009134313,0.001165676,0.0002966339,0.0008410536],"domain_scores_gemma":[0.9978521,0.0004734517,0.0004109212,0.0007145347,0.0003163696,0.000232581],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.0001366168,0.00001913795,0.0002056365,0.0007439603,0.0003210585,7.840705e-7,0.00007664452,0.000001094717,0.002979254,0.0001137591,0.9938718,0.001530231],"study_design_scores_gemma":[0.001378007,0.001443362,0.000007890665,0.0002244008,0.00005496655,0.000002265531,0.004916035,0.0005087456,0.00004892841,0.0002879377,0.9906458,0.0004817002],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"editorial","genre_gemma":"editorial","genre_scores_codex":[0.0002624474,0.006671841,0.02344798,0.00007147651,0.9617037,0.001471942,0.006280367,0.00002903375,0.00006117732],"genre_scores_gemma":[0.003671512,0.01136599,0.0003645602,0.00001007024,0.9618461,0.0003239695,0.02154145,0.00006058123,0.0008157418],"genre_candidate":"editorial","genre_consensus":"editorial","teacher_disagreement_score":0.02308342,"threshold_uncertainty_score":0.9998696,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null},{"id":"W4307350470","doi":"10.3389/fsysb.2022.1022486","title":"R400: A novel gene signature for dose prediction in radiation exposure studies in humans","year":2022,"lang":"en","type":"article","venue":"Frontiers in Systems Biology","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false},"ca_institutions":"St. Francis Xavier University","funders":"St. Francis Xavier University","keywords":"Toxicogenomics; Computer science; Predictability; Set (abstract data type); Gene signature; Data set; Signature (topology); Computational biology; Machine learning; Data mining; Artificial intelligence; Gene; Biology; Gene expression; Statistics; Mathematics; Genetics","authors":[{"name":"Frederick St. Peter","is_ca":true},{"name":"Srinivas Mukund Vadrev","is_ca":true},{"name":"Othman Soufan","is_ca":true}],"retraction":null,"screen_n_in":null,"score":{"opus":0.01687955306980594,"gpt":0.2576518595735923,"spread":0.2407723065037863,"validation_status":"score_only:v0-immature-baseline"},"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006790984,0.0001363222,0.0002846878,0.000192789,0.00006752901,0.00000709836,0.0001537909,0.0002557868,0.000002005474],"category_scores_gemma":[0.00003491284,0.000137553,0.00005067001,0.0001626643,0.00006650223,0.000004719806,0.0001011236,0.000193643,3.14381e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001660601,"about_ca_system_score_gemma":0.00005343858,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00004262493,"about_ca_topic_score_gemma":0.000128486,"domain_scores_codex":[0.9987912,0.0001167686,0.0004639753,0.0002994786,0.00005284608,0.0002757054],"domain_scores_gemma":[0.9996015,0.00001458547,0.0001438995,0.0001893558,0.00002804123,0.00002265544],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"observational","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001916127,0.0006483077,0.4349828,0.0006101464,0.0005712497,0.0000159667,0.007417846,0.1645008,0.2316082,0.001668032,0.1384072,0.01765341],"study_design_scores_gemma":[0.04022196,0.008229951,0.04825364,0.0003154303,0.0001127368,0.0001277416,0.05127424,0.1104218,0.004407628,0.007005646,0.7267726,0.002856616],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8696869,0.0722314,0.04633344,0.000178645,0.00845571,0.002184151,0.0007167291,0.0000195156,0.0001935118],"genre_scores_gemma":[0.9962244,0.00037718,0.001069686,0.0001104735,0.0002860189,0.0006805924,0.0008884503,0.00001473265,0.0003484479],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.5883654,"threshold_uncertainty_score":0.5609249,"prediction_status":"machine_predicted_unvalidated"},"labels":[],"label_agreement":null}]}