{"id":"https://openalex.org/W7204196286","doi":"https://doi.org/10.5281/zenodo.22095412","title":"Joint Portal Dynamics on an RNA Neutral Network Improve Prediction of Competing Adaptive Fixations","display_name":"Joint Portal Dynamics on an RNA Neutral Network Improve Prediction of Competing Adaptive Fixations","publication_year":2026,"publication_date":"2026-08-25","ids":{"openalex":"https://openalex.org/W7204196286","doi":"https://doi.org/10.5281/zenodo.22095412"},"language":"en","primary_location":{"id":"doi:10.5281/zenodo.22095412","doi":"https://doi.org/10.5281/zenodo.22095412","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22095412","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"volume":null,"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5281/zenodo.22095412","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5148078153","display_name":"Ryutaro Yonezu","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Yonezu, Ryutaro","raw_affiliation_strings":["Independent researcher"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Independent researcher","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5148078153"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.012299999594688416,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11152","display_name":"Stochastic processes and statistical mechanics","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/2610","display_name":"Mathematical Physics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/wright-fisher-model","display_name":"Wright-Fisher model","score":0.5270000100135803}],"concepts":[{"id":"https://openalex.org/C198125213","wikidata":"https://www.wikidata.org/wiki/Q17155419","display_name":"Neutral network","level":3,"score":0.9014999866485596},{"id":"https://openalex.org/C18555067","wikidata":"https://www.wikidata.org/wiki/Q8375051","display_name":"Joint (building)","level":2,"score":0.5723000168800354},{"id":"https://openalex.org/C18653775","wikidata":"https://www.wikidata.org/wiki/Q1333358","display_name":"Joint probability distribution","level":2,"score":0.5443000197410583},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.5216000080108643},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.512499988079071},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47049999237060547},{"id":"https://openalex.org/C139807058","wikidata":"https://www.wikidata.org/wiki/Q352374","display_name":"Adaptation (eye)","level":2,"score":0.4528999924659729},{"id":"https://openalex.org/C1570309","wikidata":"https://www.wikidata.org/wiki/Q1055017","display_name":"Neutral theory of molecular evolution","level":3,"score":0.4341999888420105},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.39559999108314514},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3711000084877014},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.36880001425743103},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.3652999997138977},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.365200012922287},{"id":"https://openalex.org/C163836022","wikidata":"https://www.wikidata.org/wiki/Q6771326","display_name":"Markov model","level":3,"score":0.3637000024318695},{"id":"https://openalex.org/C171752962","wikidata":"https://www.wikidata.org/wiki/Q255166","display_name":"Kullback\u2013Leibler divergence","level":2,"score":0.32589998841285706},{"id":"https://openalex.org/C192122231","wikidata":"https://www.wikidata.org/wiki/Q4680754","display_name":"Adaptive mutation","level":3,"score":0.3253999948501587},{"id":"https://openalex.org/C2778049214","wikidata":"https://www.wikidata.org/wiki/Q7512234","display_name":"Sigma","level":2,"score":0.31630000472068787},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.3068000078201294},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3061000108718872},{"id":"https://openalex.org/C149129301","wikidata":"https://www.wikidata.org/wiki/Q3883802","display_name":"Neutral mutation","level":3,"score":0.2996000051498413},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.2985000014305115},{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.2944999933242798},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29339998960494995},{"id":"https://openalex.org/C17020691","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operator (biology)","level":5,"score":0.2892000079154968},{"id":"https://openalex.org/C104114177","wikidata":"https://www.wikidata.org/wiki/Q79782","display_name":"Motion (physics)","level":2,"score":0.2773999869823456},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.27149999141693115},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.25360000133514404}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.5281/zenodo.22095412","doi":"https://doi.org/10.5281/zenodo.22095412","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22095412","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"},{"id":"doi:10.5281/zenodo.22095413","doi":"https://doi.org/10.5281/zenodo.22095413","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22095413","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.5281/zenodo.22095412","doi":"https://doi.org/10.5281/zenodo.22095412","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.22095412","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Models":[0],"of":[1,153,253],"mutation-limited":[2],"adaptation":[3],"can":[4,28,249],"fail":[5],"when":[6,233],"access":[7],"to":[8,79,112,120,195,205],"competing":[9,37,80,234],"adaptive":[10,59,115,235],"phenotypes":[11],"is":[12,70,75],"structured":[13,242],"on":[14,83],"the":[15,72,76,90,113,121,165,172,182,187,196,206,213,222,240,254],"same":[16,241],"neutral":[17,54,87,106,243],"genotype":[18],"network.":[19,88],"Martin":[20,173],"et":[21,174],"al.":[22,175],"(2024)":[23],"showed":[24],"that":[25,267],"phenotype":[26,81,116,123],"arrivals":[27],"be":[29],"bursty":[30],"and":[31,56,104,118,125,138,179,201,219],"developed":[32],"a":[33,48,84,148,230,260],"burst-aware":[34,176,198,214],"approximation":[35],"for":[36,164,171,181],"peaks,":[38],"while":[39],"explicitly":[40],"identifying":[41],"dependence":[42],"between":[43],"multiple":[44],"phenotype-introduction":[45],"processes":[46],"as":[47,61],"remaining":[49],"problem.":[50],"Here":[51],"we":[52,142],"represent":[53],"motion":[55],"all":[57],"successful":[58],"exits":[60],"one":[62],"state-resolved":[63],"killed":[64],"continuous-time":[65],"Markov":[66],"process.":[67],"The":[68,227],"mathematics":[69],"standard;":[71],"contribution":[73],"tested":[74],"joint":[77,183,188],"application":[78],"portals":[82],"shared":[85,246],"RNA":[86,94],"In":[89],"published":[91],"focal":[92],"two-peak":[93],"system,":[95],"our":[96],"ViennaRNA":[97],"2.7.2":[98],"reconstruction":[99],"contains":[100],"1,937":[101],"resident":[102],"genotypes":[103],"13,355":[105],"edges,":[107],"with":[108,147],"517":[109],"portal":[110],"edges":[111],"frequent":[114],"p1":[117],"16":[119],"rarer":[122],"p2,":[124],"zero":[126],"portal-genotype":[127],"overlap.":[128],"Under":[129],"N=500,":[130],"per-site":[131],"mutation":[132],"rate":[133],"2":[134],"\u00d7":[135],"10^-5,":[136],"s1=0.005,":[137],"six":[139],"s2":[140],"values,":[141],"compared":[143],"three":[144],"analytic":[145],"predictions":[146],"direct":[149],"count-level":[150],"Wright-Fisher":[151,262],"re-execution":[152],"1,000":[154],"replicates":[155],"per":[156],"condition.":[157],"Mean":[158],"absolute":[159],"error":[160],"(MAE)":[161],"was":[162,210],"0.2220":[163],"simple":[166],"average-rate":[167,207,223],"independent":[168,177,199],"model,":[169,178],"0.0349":[170],"0.01256":[180],"killed-Markov":[184],"model.":[185],"Thus":[186],"model":[189,215,224],"reduced":[190],"MAE":[191],"by":[192,202,259],"64.0%":[193],"relative":[194,204],"stronger":[197],"baseline":[200],"94.3%":[203],"baseline.":[208],"It":[209],"closer":[211,220],"than":[212,221],"in":[216,225],"5/6":[217],"conditions":[218],"6/6.":[226],"result":[228],"supports":[229],"narrow":[231],"conclusion:":[232],"opportunities":[236],"are":[237],"exposed":[238],"along":[239],"trajectory,":[244],"retaining":[245],"state":[247],"information":[248],"materially":[250],"improve":[251],"prediction":[252],"p2-first":[255],"outcome,":[256],"benchmarked":[257],"here":[258],"threshold-based":[261],"takeover":[263],"proxy,":[264],"beyond":[265],"models":[266],"combine":[268],"phenotype-specific":[269],"marginal":[270],"statistics":[271],"independently.":[272],"Research":[273,277],"Inquiries":[274],"\u2014":[275],"Yonezu":[276],"LabContact:":[278],"yonezaemon1+research@gmail.com":[279]},"counts_by_year":[],"updated_date":"2026-10-15T10:00:46.086208","created_date":"2026-08-26T00:00:00"}