{"id":"W2119240948","doi":"10.1088/1478-3975/4/4/003","title":"Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites","year":2007,"lang":"en","type":"article","venue":"Physical Biology","topic":"Diffusion and Search Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Alberta","funders":"","keywords":"Jumper; Monte Carlo method; Transcription factor; DNA; Representation (politics); Random walk; Lattice (music); Transcription (linguistics)","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":[0.000119799,0.0001767576,0.0002177714,0.00007576881,0.00009915929,0.00001826916,0.0001159324,0.0001075139,0.00000830381],"category_scores_gemma":[0.00007609431,0.0001298061,0.00009944883,0.0001127915,0.00003815518,0.000007641488,0.00005281344,0.0001288266,0.00001085194],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0000344516,"about_ca_system_score_gemma":0.00001810145,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00003484733,"about_ca_topic_score_gemma":0.00007252667,"domain_scores_codex":[0.9988426,0.0001073743,0.0001722511,0.0004139883,0.0001303519,0.000333417],"domain_scores_gemma":[0.9994969,0.00005180046,0.00004079528,0.0002039398,0.00006485686,0.0001416725],"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":[0.00141269,0.000267031,0.001653512,0.000008197874,0.00004032536,0.000001329753,0.0002083118,0.001278842,0.9936664,0.0001396064,0.000002627609,0.001321145],"study_design_scores_gemma":[0.005486286,0.002397001,0.007431043,0.00007626721,0.00008332718,0.000008654167,0.0004330596,0.1573678,0.8251198,0.0006835893,0.000175207,0.0007379883],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9438437,0.00000773391,0.05563908,0.00007241894,0.00006172715,0.0002686239,0.00002523419,0.00001949578,0.00006196704],"genre_scores_gemma":[0.9989432,0.0000102519,0.0003644462,0.0002084024,0.0001830338,0.0000096816,0.0002116426,0.000018721,0.00005059231],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1685466,"threshold_uncertainty_score":0.5293341,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04793845775479783,"score_gpt":0.3410072124274945,"score_spread":0.2930687546726967,"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."}}