{"id":"https://openalex.org/W4403487507","doi":"https://doi.org/10.3233/faia240803","title":"Deep Mapper: Efficient Visualization of Plausible Conformational Pathways","display_name":"Deep Mapper: Efficient Visualization of Plausible Conformational Pathways","publication_year":2024,"publication_date":"2024-10-16","ids":{"openalex":"https://openalex.org/W4403487507","doi":"https://doi.org/10.3233/faia240803"},"language":"en","primary_location":{"id":"doi:10.3233/faia240803","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia240803","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA240803","source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["arxiv","crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA240803","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5093952498","display_name":"Ziyad Oulhaj","orcid":null},"institutions":[{"id":"https://openalex.org/I97188460","display_name":"Nantes Universit\u00e9","ror":"https://ror.org/03gnr7b55","country_code":"FR","type":"education","lineage":["https://openalex.org/I97188460"]},{"id":"https://openalex.org/I100445878","display_name":"\u00c9cole Centrale de Nantes","ror":"https://ror.org/03nh7d505","country_code":"FR","type":"education","lineage":["https://openalex.org/I100445878","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I4210153365","display_name":"Laboratoire de Math\u00e9matiques Jean Leray","ror":"https://ror.org/04g1hjn96","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I4210141950","https://openalex.org/I4210153365","https://openalex.org/I97188460"]},{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"funder","lineage":["https://openalex.org/I1294671590"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Ziyad Oulhaj","raw_affiliation_strings":["Nantes Universit\u00e9, \u00c9cole Centrale Nantes, CNRS, Laboratoire de Math\u00e9matiques Jean Leray, UMR\u00a06629, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nantes Universit\u00e9, \u00c9cole Centrale Nantes, CNRS, Laboratoire de Math\u00e9matiques Jean Leray, UMR\u00a06629, France","institution_ids":["https://openalex.org/I97188460","https://openalex.org/I100445878","https://openalex.org/I4210153365","https://openalex.org/I1294671590"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001597037","display_name":"Yoshiyuki Ishii","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshiyuki Ishii","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114301898","display_name":"Kento Ohga","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kento Ohga","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004701153","display_name":"Kimihiro Yamazaki","orcid":"https://orcid.org/0000-0003-4827-9488"},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kimihiro Yamazaki","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049975082","display_name":"Mutsuyo Wada","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Mutsuyo Wada","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021567040","display_name":"Yuhei Umeda","orcid":"https://orcid.org/0000-0001-8244-282X"},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuhei Umeda","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027074375","display_name":"Takashi Katoh","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takashi Katoh","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104262017","display_name":"Yuichiro Wada","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]},{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yuichiro Wada","raw_affiliation_strings":["Fujitsu Limited, Japan","RIKEN Center for Advanced Intelligence Project, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"RIKEN Center for Advanced Intelligence Project, Japan","institution_ids":["https://openalex.org/I4210126580"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103903019","display_name":"Hiroaki Kurihara","orcid":null},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Kurihara","raw_affiliation_strings":["Fujitsu Limited, Japan","Fujitsu Laboratories Ltd. (Japan)"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, Japan","institution_ids":["https://openalex.org/I2252096349"]},{"raw_affiliation_string":"Fujitsu Laboratories Ltd. (Japan)","institution_ids":["https://openalex.org/I2252096349"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5093952498"],"corresponding_institution_ids":["https://openalex.org/I100445878","https://openalex.org/I1294671590","https://openalex.org/I4210153365","https://openalex.org/I97188460"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29812207,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9638000130653381,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9638000130653381,"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/visualization","display_name":"Visualization","score":0.6016438603401184},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40802448987960815},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24278846383094788}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6016438603401184},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40802448987960815},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24278846383094788}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.3233/faia240803","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia240803","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA240803","source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},{"id":"pmh:oai:arXiv.org:2402.19177","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.19177","pdf_url":"https://arxiv.org/pdf/2402.19177","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":null,"raw_type":"text"},{"id":"pmh:oai:HAL:hal-05073038v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05073038","pdf_url":"https://hal.science/hal-05073038/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Artificial Intelligence and Applications, 2024, 392, pp2701-2708. &#x27E8;10.3233/faia240803&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"doi:10.3233/faia240803","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia240803","pdf_url":"https://ebooks.iospress.nl/pdf/doi/10.3233/FAIA240803","source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.5299999713897705}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403487507.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2068608913","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890"],"abstract_inverted_index":{"Acquiring":[0],"plausible":[1,118,258],"pathways":[2,61,120,133,165],"on":[3,138,173,238,244],"high-dimensional":[4],"structural":[5,30],"distributions":[6],"is":[7,32,88,105,158,192,222,264],"beneficial":[8],"in":[9,14,52,182,202],"several":[10],"domains.":[11],"For":[12],"example,":[13],"the":[15,38,41,71,93,101,122,139,151,155,164,174,183,203,206,211,216,231,245,249,256,268],"drug":[16,53],"discovery":[17,54],"field,":[18],"a":[19,24,49,106,113,198],"protein":[20,29,39,60,79],"conformational":[21,119],"pathway,":[22],"i.e.":[23],"highly":[25],"probable":[26],"sequence":[27],"of":[28,70,73,154,168,197,215,219],"changes,":[31],"useful":[33],"to":[34,44,78,90,116,162,195,229],"analyze":[35],"interactions":[36],"between":[37],"and":[40,111,213],"ligands,":[42],"helping":[43],"create":[45],"new":[46],"drugs.":[47],"Recently,":[48],"state-of-the-art":[50,270],"method":[51],"was":[55],"presented,":[56],"which":[57,104,209],"efficiently":[58],"computes":[59],"using":[62],"latent":[63,124,241],"variables":[64],"obtained":[65],"from":[66,121],"an":[67,169,239],"isometric":[68,123,240],"auto-encoding":[69],"space":[72,125,242],"3D":[74],"density":[75],"maps":[76],"associated":[77],"conformations.":[80],"However,":[81],"our":[82,220,234,261],"preliminary":[83],"experiments":[84],"show":[85],"that":[86],"there":[87],"room":[89],"significantly":[91],"reduce":[92],"computing":[94],"time.":[95,130],"In":[96,233],"this":[97],"study,":[98],"we":[99],"use":[100],"Mapper":[102,141,156,175,185,217,251],"algorithm,":[103],"Topological":[107],"Data":[108],"Analysis":[109],"method,":[110,208],"present":[112],"novel":[114],"variant":[115],"extract":[117,163],"with":[126,193],"comparatively":[127],"short":[128],"running":[129,262],"The":[131,143,190],"extracted":[132],"are":[134,146,187],"visualized":[135],"as":[136,148,161],"paths":[137],"resulting":[140,250],"graph.":[142],"methodological":[144],"novelties":[145],"described":[147],"follows:":[149],"firstly,":[150],"filter":[152,179],"function":[153],"algorithm":[157,186,221],"optimized":[159],"so":[160],"via":[166],"minimization":[167],"energy":[170],"loss":[171],"defined":[172],"graph":[176,252],"itself,":[177],"while":[178],"functions":[180],"taken":[181],"classical":[184],"fixed":[188],"beforehand.":[189],"optimization":[191],"respect":[194],"parameters":[196],"deep":[199],"neural":[200],"network":[201],"filter.":[204],"Secondly,":[205],"clustering":[207],"defines":[210],"vertices":[212],"edges":[214],"graph,":[218],"designed":[223],"by":[224],"incorporating":[225],"domain":[226],"prior":[227],"knowledge":[228],"assist":[230],"extraction.":[232],"numerical":[235],"experiments,":[236],"based":[237],"built":[243],"common":[246],"50S-ribosomal":[247],"dataset,":[248],"successfully":[253],"includes":[254],"all":[255],"well-recognized":[257],"pathways.":[259],"Moreover,":[260],"time":[263],"much":[265],"shorter":[266],"than":[267],"above":[269],"counterpart.":[271]},"counts_by_year":[],"updated_date":"2026-05-07T13:39:58.223016","created_date":"2025-10-10T00:00:00"}
