{"id":"https://openalex.org/W4389712610","doi":"https://doi.org/10.48550/arxiv.2312.07316","title":"GateNet: A novel Neural Network Architecture for Automated Flow Cytometry Gating","display_name":"GateNet: A novel Neural Network Architecture for Automated Flow Cytometry Gating","publication_year":2023,"publication_date":"2023-12-12","ids":{"openalex":"https://openalex.org/W4389712610","doi":"https://doi.org/10.48550/arxiv.2312.07316"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2312.07316","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2312.07316","pdf_url":"https://arxiv.org/pdf/2312.07316","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2312.07316","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007230088","display_name":"L. Fisch","orcid":"https://orcid.org/0000-0001-6424-7676"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Fisch, Lukas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037255370","display_name":"Michael Heming","orcid":"https://orcid.org/0000-0002-9568-2790"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Heming, Michael O.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051643302","display_name":"Andreas Schulte\u2010Mecklenbeck","orcid":"https://orcid.org/0000-0003-3855-4706"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schulte-Mecklenbeck, Andreas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061814062","display_name":"Catharina C. Gro\u00df","orcid":"https://orcid.org/0000-0002-4872-9189"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gross, Catharina C.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092645209","display_name":"Stefan Zumdick","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zumdick, Stefan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077817893","display_name":"Carlotta Barkhau","orcid":"https://orcid.org/0000-0002-7546-9183"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Barkhau, Carlotta","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051242537","display_name":"Daniel Emden","orcid":"https://orcid.org/0000-0001-7459-6634"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Emden, Daniel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047848421","display_name":"Jan Ernsting","orcid":"https://orcid.org/0000-0003-4649-2111"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ernsting, Jan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035949410","display_name":"Ramona Leenings","orcid":"https://orcid.org/0000-0002-9137-7510"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Leenings, Ramona","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037629380","display_name":"Kelvin Sarink","orcid":"https://orcid.org/0000-0002-4840-5619"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sarink, Kelvin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038716495","display_name":"Nils R. Winter","orcid":"https://orcid.org/0000-0002-6241-1492"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Winter, Nils R.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067261122","display_name":"Udo Dannlowski","orcid":"https://orcid.org/0000-0002-0623-3759"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dannlowski, Udo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038373894","display_name":"Heinz Wiendl","orcid":"https://orcid.org/0000-0003-4310-3432"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wiendl, Heinz","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076180609","display_name":"Gerd Meyer zu H\u00f6rste","orcid":"https://orcid.org/0000-0002-4341-4719"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"H\u00f6rste, Gerd Meyer zu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5036108757","display_name":"Tim Hahn","orcid":"https://orcid.org/0000-0002-8929-4134"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hahn, Tim","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5007230088"],"corresponding_institution_ids":[],"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9965999722480774,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9965999722480774,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9352999925613403,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7187191247940063},{"id":"https://openalex.org/keywords/gating","display_name":"Gating","score":0.6627843379974365},{"id":"https://openalex.org/keywords/rendering","display_name":"Rendering (computer graphics)","score":0.6526914238929749},{"id":"https://openalex.org/keywords/flow-cytometry","display_name":"Flow cytometry","score":0.6124667525291443},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.525132417678833},{"id":"https://openalex.org/keywords/cytometry","display_name":"Cytometry","score":0.4470175504684448},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4006957709789276},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3793110251426697},{"id":"https://openalex.org/keywords/neuroscience","display_name":"Neuroscience","score":0.10777199268341064},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1017085611820221},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08827638626098633},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.08425316214561462}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7187191247940063},{"id":"https://openalex.org/C194544171","wikidata":"https://www.wikidata.org/wiki/Q21105679","display_name":"Gating","level":2,"score":0.6627843379974365},{"id":"https://openalex.org/C205711294","wikidata":"https://www.wikidata.org/wiki/Q176953","display_name":"Rendering (computer graphics)","level":2,"score":0.6526914238929749},{"id":"https://openalex.org/C553184892","wikidata":"https://www.wikidata.org/wiki/Q1141429","display_name":"Flow cytometry","level":2,"score":0.6124667525291443},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.525132417678833},{"id":"https://openalex.org/C2780339063","wikidata":"https://www.wikidata.org/wiki/Q5201367","display_name":"Cytometry","level":3,"score":0.4470175504684448},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4006957709789276},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3793110251426697},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.10777199268341064},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1017085611820221},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08827638626098633},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.08425316214561462}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2312.07316","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2312.07316","pdf_url":"https://arxiv.org/pdf/2312.07316","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2312.07316","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2312.07316","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"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":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2312.07316","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2312.07316","pdf_url":"https://arxiv.org/pdf/2312.07316","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G1116979012","display_name":null,"funder_award_id":"Dan3/012/17","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1718956341","display_name":null,"funder_award_id":"ME4050/13-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4266443790","display_name":null,"funder_award_id":"HA7070/2-2","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5106512922","display_name":null,"funder_award_id":"Deutsche Forschungsgemeinschaft (DFG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6024419964","display_name":null,"funder_award_id":"Deutsche Forschungsgemeinschaft (DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6335375501","display_name":null,"funder_award_id":"HA7070/3","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6537435729","display_name":null,"funder_award_id":"Heisenberg","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6732982161","display_name":null,"funder_award_id":"ME4050/12-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6743243744","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8819810260","display_name":null,"funder_award_id":"HA7070/4","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4389712610.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2176701861","https://openalex.org/W3009159775","https://openalex.org/W4251194061","https://openalex.org/W1572687853","https://openalex.org/W3214446176","https://openalex.org/W2538538514","https://openalex.org/W1966652204","https://openalex.org/W2013448542","https://openalex.org/W2002900699","https://openalex.org/W4283393906"],"abstract_inverted_index":{"Flow":[0],"cytometry":[1,29],"is":[2],"widely":[3,157],"used":[4],"to":[5,63,106,113,151],"identify":[6],"cell":[7,33],"populations":[8],"in":[9,23,159],"patient-derived":[10],"fluids":[11],"such":[12],"as":[13],"peripheral":[14],"blood":[15],"(PB)":[16],"or":[17],"cerebrospinal":[18],"fluid":[19],"(CSF).":[20],"While":[21],"ubiquitous":[22],"research":[24],"and":[25,39,79],"clinical":[26],"practice,":[27],"flow":[28,163],"requires":[30,37,148],"gating,":[31],"i.e.":[32],"type":[34],"identification":[35],"which":[36,82],"labor-intensive":[38],"error-prone":[40],"manual":[41],"adjustments.":[42],"To":[43],"facilitate":[44],"this":[45],"process,":[46],"we":[47,110,142],"designed":[48],"GateNet,":[49],"the":[50,61],"first":[51],"neural":[52],"network":[53],"architecture":[54],"enabling":[55],"full":[56],"end-to-end":[57],"automated":[58],"gating":[59,134],"without":[60],"need":[62],"correct":[64],"for":[65,93],"batch":[66],"effects.":[67],"We":[68,90],"train":[69],"GateNet":[70,97,112,146],"with":[71,120],"over":[72],"8,000,000":[73],"events":[74],"based":[75],"on":[76],"N=127":[77],"PB":[78],"CSF":[80],"samples":[81,150],"were":[83],"manually":[84],"labeled":[85],"independently":[86],"by":[87],"four":[88],"experts.":[89],"show":[91,144],"that":[92,145],"novel,":[94],"unseen":[95],"samples,":[96],"achieves":[98],"human-level":[99,153],"performance":[100],"(F1":[101],"score":[102,123],"ranging":[103],"from":[104],"0.910":[105],"0.997).":[107],"In":[108],"addition":[109],"apply":[111],"a":[114],"publicly":[115],"available":[116],"dataset":[117],"confirming":[118],"generalization":[119],"an":[121],"F1":[122],"of":[124,162],"0.936.":[125],"As":[126],"our":[127],"implementation":[128],"utilizes":[129],"graphics":[130],"processing":[131],"units":[132],"(GPU),":[133],"only":[135,147],"needs":[136],"15":[137],"microseconds":[138],"per":[139],"event.":[140],"Importantly,":[141],"also":[143],"~10":[149],"reach":[152],"performance,":[154],"rendering":[155],"it":[156],"applicable":[158],"all":[160],"domains":[161],"cytometry.":[164]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2023-12-14T00:00:00"}