{"id":"https://openalex.org/W7114912881","doi":"https://doi.org/10.1007/s41109-025-00764-1","title":"Modeling multi-layer tissue networks in hyperbolic space","display_name":"Modeling multi-layer tissue networks in hyperbolic space","publication_year":2025,"publication_date":"2025-12-12","ids":{"openalex":"https://openalex.org/W7114912881","doi":"https://doi.org/10.1007/s41109-025-00764-1"},"language":"en","primary_location":{"id":"doi:10.1007/s41109-025-00764-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s41109-025-00764-1","pdf_url":null,"source":{"id":"https://openalex.org/S3035517252","display_name":"Applied Network Science","issn_l":"2364-8228","issn":["2364-8228"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Network Science","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1007/s41109-025-00764-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Domonkos Pog\u00e1ny","orcid":null},"institutions":[{"id":"https://openalex.org/I29770179","display_name":"Budapest University of Technology and Economics","ror":"https://ror.org/02w42ss30","country_code":"HU","type":"education","lineage":["https://openalex.org/I29770179"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Domonkos Pog\u00e1ny","raw_affiliation_strings":["Department of Artificial Intelligence and Systems Engineering, Budapest University of Technology and Economics, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence and Systems Engineering, Budapest University of Technology and Economics, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I29770179"]}]},{"author_position":"last","author":{"id":null,"display_name":"P\u00e9ter Antal","orcid":null},"institutions":[{"id":"https://openalex.org/I29770179","display_name":"Budapest University of Technology and Economics","ror":"https://ror.org/02w42ss30","country_code":"HU","type":"education","lineage":["https://openalex.org/I29770179"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"P\u00e9ter Antal","raw_affiliation_strings":["Department of Artificial Intelligence and Systems Engineering, Budapest University of Technology and Economics, Budapest, 1117, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence and Systems Engineering, Budapest University of Technology and Economics, Budapest, 1117, Hungary","institution_ids":["https://openalex.org/I29770179"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I29770179"],"apc_list":{"value":790,"currency":"GBP","value_usd":969},"apc_paid":{"value":790,"currency":"GBP","value_usd":969},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.59025601,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"11","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6152999997138977,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6152999997138977,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.09719999879598618,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.04540000110864639,"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/representation","display_name":"Representation (politics)","score":0.7246999740600586},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6597999930381775},{"id":"https://openalex.org/keywords/geometric-networks","display_name":"Geometric networks","score":0.6531999707221985},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.590499997138977},{"id":"https://openalex.org/keywords/distortion","display_name":"Distortion (music)","score":0.5200999975204468},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.47620001435279846},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4641999900341034},{"id":"https://openalex.org/keywords/hyperbolic-space","display_name":"Hyperbolic space","score":0.45489999651908875},{"id":"https://openalex.org/keywords/hyperbolic-geometry","display_name":"Hyperbolic geometry","score":0.4474000036716461}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7246999740600586},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6597999930381775},{"id":"https://openalex.org/C49777392","wikidata":"https://www.wikidata.org/wiki/Q5535495","display_name":"Geometric networks","level":3,"score":0.6531999707221985},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.590499997138977},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5698999762535095},{"id":"https://openalex.org/C126780896","wikidata":"https://www.wikidata.org/wiki/Q899871","display_name":"Distortion (music)","level":4,"score":0.5200999975204468},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.47620001435279846},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.46720001101493835},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4641999900341034},{"id":"https://openalex.org/C83677898","wikidata":"https://www.wikidata.org/wiki/Q1878538","display_name":"Hyperbolic space","level":2,"score":0.45489999651908875},{"id":"https://openalex.org/C206352148","wikidata":"https://www.wikidata.org/wiki/Q209306","display_name":"Hyperbolic geometry","level":3,"score":0.4474000036716461},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40849998593330383},{"id":"https://openalex.org/C92047909","wikidata":"https://www.wikidata.org/wiki/Q204034","display_name":"Hyperbolic function","level":2,"score":0.3822000026702881},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.36469998955726624},{"id":"https://openalex.org/C114645060","wikidata":"https://www.wikidata.org/wiki/Q5431294","display_name":"Faithful representation","level":2,"score":0.3594000041484833},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.35589998960494995},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3555000126361847},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.35249999165534973},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.3472000062465668},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.3416000008583069},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3001999855041504},{"id":"https://openalex.org/C183322885","wikidata":"https://www.wikidata.org/wiki/Q17007702","display_name":"Context model","level":3,"score":0.29330000281333923},{"id":"https://openalex.org/C167528306","wikidata":"https://www.wikidata.org/wiki/Q5508776","display_name":"Function representation","level":3,"score":0.29089999198913574},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2906999886035919},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2825999855995178},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26260000467300415},{"id":"https://openalex.org/C2776542497","wikidata":"https://www.wikidata.org/wiki/Q5266672","display_name":"Development (topology)","level":2,"score":0.2581999897956848},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2500999867916107}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s41109-025-00764-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s41109-025-00764-1","pdf_url":null,"source":{"id":"https://openalex.org/S3035517252","display_name":"Applied Network Science","issn_l":"2364-8228","issn":["2364-8228"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Network Science","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:912d1c5f5ac94ff881b95101eec4df66","is_oa":true,"landing_page_url":"https://doaj.org/article/912d1c5f5ac94ff881b95101eec4df66","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Applied Network Science, Vol 11, Iss 1, Pp 1-21 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1007/s41109-025-00764-1","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s41109-025-00764-1","pdf_url":null,"source":{"id":"https://openalex.org/S3035517252","display_name":"Applied Network Science","issn_l":"2364-8228","issn":["2364-8228"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319965","host_organization_name":"Springer Nature","host_organization_lineage":["https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Network Science","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1389815433","display_name":null,"funder_award_id":"OTKA-K139330","funder_id":"https://openalex.org/F4320336675","funder_display_name":"National Research, Development and Innovation Office"},{"id":"https://openalex.org/G3922613009","display_name":null,"funder_award_id":"2024-2.1.1-EK\u00d6P","funder_id":"https://openalex.org/F4320336675","funder_display_name":"National Research, Development and Innovation Office"}],"funders":[{"id":"https://openalex.org/F4320336675","display_name":"National Research, Development and Innovation Office","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1505893511","https://openalex.org/W1971215074","https://openalex.org/W1971421925","https://openalex.org/W1980940295","https://openalex.org/W1981409633","https://openalex.org/W1982803213","https://openalex.org/W1989921625","https://openalex.org/W2008620264","https://openalex.org/W2056782561","https://openalex.org/W2062533676","https://openalex.org/W2072740719","https://openalex.org/W2081306806","https://openalex.org/W2103017472","https://openalex.org/W2112090702","https://openalex.org/W2125414037","https://openalex.org/W2130145803","https://openalex.org/W2138674039","https://openalex.org/W2143746383","https://openalex.org/W2203081190","https://openalex.org/W2588069789","https://openalex.org/W2735272571","https://openalex.org/W2784007581","https://openalex.org/W2889326414","https://openalex.org/W2949564348","https://openalex.org/W2962756421","https://openalex.org/W2971558903","https://openalex.org/W3035102141","https://openalex.org/W3035622618","https://openalex.org/W3096163555","https://openalex.org/W4205175531","https://openalex.org/W4235484205","https://openalex.org/W4296293027","https://openalex.org/W4317036499","https://openalex.org/W4317209905","https://openalex.org/W4353017199","https://openalex.org/W4366777454","https://openalex.org/W4393057656","https://openalex.org/W4395671583","https://openalex.org/W4400869919","https://openalex.org/W4402363891","https://openalex.org/W4409455408"],"related_works":[],"abstract_inverted_index":{"Abstract":[0],"Understanding":[1],"protein":[2,22,63,164],"functions":[3,25,64],"in":[4,50,109,133,162],"a":[5,35,40,127,142],"tissue-specific":[6,30,163,176],"context":[7,111],"is":[8],"essential":[9],"for":[10,83,181],"gaining":[11],"insights":[12,71],"into":[13],"human":[14],"biology,":[15],"disease":[16],"mechanisms,":[17],"and":[18,24,61,125,159,187,196],"potential":[19],"therapeutics.":[20],"Since":[21],"interactions":[23,32],"vary":[26],"across":[27,65],"tissues,":[28],"treating":[29],"protein-protein":[31],"(PPI)":[33],"as":[34],"multi-layer":[36,59,113],"network":[37,73],"has":[38,45,80],"become":[39],"leading":[41],"approach.":[42],"This":[43],"shift":[44],"led":[46],"to":[47,57,86,96],"growing":[48],"interest":[49],"computational":[51],"methods,":[52],"particularly":[53],"unsupervised":[54],"representation":[55,130],"learning,":[56],"model":[58,87],"networks":[60,89,124],"predict":[62],"diverse":[66],"tissue":[67],"types.":[68],"Building":[69],"on":[70,77],"from":[72],"science,":[74],"recent":[75],"research":[76],"non-Euclidean":[78,172],"embeddings":[79,103],"gained":[81],"attention":[82],"their":[84],"ability":[85],"scale-free":[88,150],"with":[90,148],"underlying":[91],"hyperbolic":[92,102,134],"geometry":[93,173],"effectively.":[94],"However,":[95],"the":[97,110,119,149,153,170,175],"best":[98],"of":[99,112,122,152,174],"our":[100,192],"knowledge,":[101],"have":[104],"not":[105],"yet":[106],"been":[107],"explored":[108],"PPI":[114,177],"networks.":[115],"Therefore,":[116],"we":[117,190],"investigate":[118],"geometric":[120,143],"properties":[121],"these":[123],"propose":[126],"contextualized,":[128],"tissue-aware":[129],"learning":[131],"approach":[132],"space.":[135],"Our":[136],"results":[137],"demonstrate":[138],"that":[139],"representations":[140,198],"leveraging":[141],"inductive":[144],"bias":[145],"better":[146],"align":[147],"structure":[151],"networks,":[154],"yielding":[155],"lower":[156],"graph":[157],"distortion":[158],"improved":[160],"performance":[161],"function":[165],"prediction.":[166],"These":[167],"findings":[168],"highlight":[169],"intrinsic":[171],"space,":[178],"providing":[179],"direction":[180],"further":[182,188],"research.":[183],"To":[184],"support":[185],"reproducibility":[186],"exploration,":[189],"made":[191],"PyTorch-based":[193],"embedding":[194],"implementation":[195],"pre-trained":[197],"publicly":[199],"available.":[200]},"counts_by_year":[],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-12-12T00:00:00"}
