{"id":"https://openalex.org/W7213864487","doi":"https://doi.org/10.64898/2026.09.14.751453","title":"NeuralRNN: a unified framework for recurrent neural network methods in cognitive neuroscience","display_name":"NeuralRNN: a unified framework for recurrent neural network methods in cognitive neuroscience","publication_year":2026,"publication_date":"2026-09-21","ids":{"openalex":"https://openalex.org/W7213864487","doi":"https://doi.org/10.64898/2026.09.14.751453"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.14.751453","doi":"https://doi.org/10.64898/2026.09.14.751453","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.14.751453","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.09.14.751453.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.09.14.751453.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102708697","display_name":"Honghua Chen","orcid":"https://orcid.org/0009-0001-3009-7128","observed_orcids":["https://orcid.org/0009-0001-3009-7128"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Honghua Chen","raw_affiliation_strings":["Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Sciences, Zhejiang University, Hangzhou, China"],"raw_orcid":"https://orcid.org/0009-0001-3009-7128","affiliations":[{"raw_affiliation_string":"Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008847016","display_name":"Nai Ding","orcid":"https://orcid.org/0000-0003-3428-2723","observed_orcids":["https://orcid.org/0000-0003-3428-2723"]},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nai Ding","raw_affiliation_strings":["Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China","Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Sciences, Zhejiang University, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"Key Laboratory for Biomedical Engineering of Ministry of Education, College of Biomedical Engineering and Instrument Sciences, Zhejiang University, Hangzhou, China","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5102708697"],"corresponding_institution_ids":["https://openalex.org/I76130692"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10320","display_name":"Neural Networks and Applications","score":0.6791999936103821,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.6791999936103821,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10581","display_name":"Neural dynamics and brain function","score":0.2678000032901764,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T14411","display_name":"Undergraduate Neuroscience Education and Research","score":0.0142000000923872,"subfield":{"id":"https://openalex.org/subfields/3304","display_name":"Education"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/recurrent-neural-networks","display_name":"recurrent neural networks","score":0.9819999933242798},{"id":"https://openalex.org/keywords/open-source-framework","display_name":"open source software framework","score":0.6690000295639038},{"id":"https://openalex.org/keywords/dynamical-system-reconstruction","display_name":"dynamical system reconstruction","score":0.8980000019073486},{"id":"https://openalex.org/keywords/gain-modulation","display_name":"gain modulation","score":0.8379999995231628},{"id":"https://openalex.org/keywords/biological-constraints","display_name":"biological constraints","score":0.6039999723434448},{"id":"https://openalex.org/keywords/dynamical-systems-analysis","display_name":"dynamical systems analysis","score":0.8560000061988831},{"id":"https://openalex.org/keywords/computational-neuroscience","display_name":"computational neuroscience","score":0.5460000038146973}],"concepts":[{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.7160000205039978},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6877999901771545},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5771999955177307},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.4957999885082245},{"id":"https://openalex.org/C15286952","wikidata":"https://www.wikidata.org/wiki/Q8037925","display_name":"Computational neuroscience","level":2,"score":0.4410000145435333},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4348999857902527},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.42489999532699585},{"id":"https://openalex.org/C17289045","wikidata":"https://www.wikidata.org/wiki/Q1138951","display_name":"Cognitive neuroscience","level":3,"score":0.4138000011444092},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.39469999074935913},{"id":"https://openalex.org/C169900460","wikidata":"https://www.wikidata.org/wiki/Q2200417","display_name":"Cognition","level":2,"score":0.3831999897956848},{"id":"https://openalex.org/C97541855","wikidata":"https://www.wikidata.org/wiki/Q830687","display_name":"Reinforcement learning","level":2,"score":0.3630000054836273},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.3578999936580658},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.35670000314712524},{"id":"https://openalex.org/C161407221","wikidata":"https://www.wikidata.org/wiki/Q4382939","display_name":"Cognitive model","level":3,"score":0.34860000014305115},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.33379998803138733},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.3294000029563904},{"id":"https://openalex.org/C8521452","wikidata":"https://www.wikidata.org/wiki/Q203790","display_name":"Connectionism","level":3,"score":0.30869999527931213},{"id":"https://openalex.org/C2986342778","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Cognitive systems","level":3,"score":0.305400013923645},{"id":"https://openalex.org/C205427263","wikidata":"https://www.wikidata.org/wiki/Q1931480","display_name":"Neuroinformatics","level":2,"score":0.29739999771118164},{"id":"https://openalex.org/C3832189","wikidata":"https://www.wikidata.org/wiki/Q8588916","display_name":"Models of neural computation","level":3,"score":0.28790000081062317},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.28290000557899475},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.27790001034736633},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.2728999853134155},{"id":"https://openalex.org/C58693492","wikidata":"https://www.wikidata.org/wiki/Q551875","display_name":"Neuroimaging","level":2,"score":0.25679999589920044}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.14.751453","doi":"https://doi.org/10.64898/2026.09.14.751453","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.14.751453","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.09.14.751453.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.14.751453","doi":"https://doi.org/10.64898/2026.09.14.751453","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.14.751453","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/21/2026.09.14.751453.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7213864487.pdf","grobid_xml":"https://content.openalex.org/works/W7213864487.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W1974803102","https://openalex.org/W1980324747","https://openalex.org/W2047125104","https://openalex.org/W2064675550","https://openalex.org/W2099231026","https://openalex.org/W2102701721","https://openalex.org/W2128084896","https://openalex.org/W2157331557","https://openalex.org/W2165150869","https://openalex.org/W2168462263","https://openalex.org/W2280725856","https://openalex.org/W2337492206","https://openalex.org/W2536957931","https://openalex.org/W2561857267","https://openalex.org/W2725150524","https://openalex.org/W2736601468","https://openalex.org/W2794448029","https://openalex.org/W2883380036","https://openalex.org/W2896513464","https://openalex.org/W2908124316","https://openalex.org/W2950800702","https://openalex.org/W2952395051","https://openalex.org/W2969708557","https://openalex.org/W2979826702","https://openalex.org/W3041725488","https://openalex.org/W3112083560","https://openalex.org/W3216796343","https://openalex.org/W4213055974","https://openalex.org/W4281663412","https://openalex.org/W4307583652","https://openalex.org/W4387343609","https://openalex.org/W4388835104","https://openalex.org/W4390113411","https://openalex.org/W4390264077","https://openalex.org/W4396605965","https://openalex.org/W4399437527","https://openalex.org/W4400462656","https://openalex.org/W4407341271","https://openalex.org/W4408591020","https://openalex.org/W4410816687","https://openalex.org/W4411932255","https://openalex.org/W4414552662","https://openalex.org/W4415349358","https://openalex.org/W4415648663","https://openalex.org/W4415798100","https://openalex.org/W7118873358","https://openalex.org/W7127621890","https://openalex.org/W7133189295"],"related_works":["https://openalex.org/W4289653656","https://openalex.org/W3112083560","https://openalex.org/W2725150524","https://openalex.org/W2280725856","https://openalex.org/W4387343609","https://openalex.org/W4307829804","https://openalex.org/W4417087020","https://openalex.org/W2981305449","https://openalex.org/W7015916166","https://openalex.org/W4385715981"],"abstract_inverted_index":{"Abstract":[0],"Recurrent":[1],"neural":[2],"networks":[3],"(RNNs)":[4],"provide":[5],"a":[6,76,90,118,126],"central":[7],"tool":[8],"in":[9,56,75,146],"neuroscience":[10],"to":[11,30,45,139],"optimize":[12],"cognitive":[13],"tasks":[14],"and":[15,50,72,86,99,107,113,122,142],"reconstruct":[16],"dynamical":[17,83,131],"systems.":[18],"Around":[19],"these":[20,70],"two":[21],"paradigms,":[22],"many":[23],"RNN":[24,144],"model":[25,51,73,101],"variants":[26,52,74],"have":[27],"been":[28],"tailored":[29],"capture":[31],"specific":[32],"computations":[33],"of":[34,128],"the":[35,137],"brain.":[36],"In":[37],"practice,":[38],"however,":[39],"this":[40],"methodological":[41],"diversity":[42],"remains":[43],"difficult":[44],"exploit,":[46],"because":[47],"different":[48],"paradigms":[49,71],"are":[53,115,123],"mostly":[54],"implemented":[55],"idiosyncratic,":[57],"study-specific":[58],"code.":[59],"Here":[60],"we":[61],"introduce":[62],"NeuralRNN,":[63],"an":[64,97],"open-source":[65],"Python":[66],"framework":[67],"that":[68],"unifies":[69],"general-purpose":[77],"pipeline.":[78],"NeuralRNN":[79,135],"brings":[80],"task":[81],"optimization,":[82],"system":[84],"reconstruction,":[85],"biological":[87],"constraints":[88],"into":[89],"single":[91],"objective":[92],"interface.":[93],"It":[94],"also":[95],"provides":[96],"integrated":[98],"extensible":[100],"library":[102],"spanning":[103],"generic,":[104],"structure-constrained,":[105],"gain-modulated,":[106],"gated":[108],"RNNs.":[109],"Furthermore,":[110],"data,":[111],"models,":[112],"training":[114],"constructed":[116],"through":[117],"shared":[119],"automated":[120],"pipeline":[121],"equipped":[124],"with":[125],"suite":[127],"tools":[129],"for":[130],"systems":[132],"analysis.":[133],"Together,":[134],"lowers":[136],"barrier":[138],"implementing,":[140],"comparing,":[141],"extending":[143],"methods":[145],"neuroscience.":[147]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-09-22T00:00:00"}