{"id":"https://openalex.org/W7160833817","doi":"https://doi.org/10.48550/arxiv.2605.07838","title":"PPI-Net connects molecular protein interactions to functional processes in disease","display_name":"PPI-Net connects molecular protein interactions to functional processes in disease","publication_year":2026,"publication_date":"2026-05-08","ids":{"openalex":"https://openalex.org/W7160833817","doi":"https://doi.org/10.48550/arxiv.2605.07838"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.07838","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.07838","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.07838","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5135887046","display_name":"Kyle Higgins","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Higgins, Kyle","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052890968","display_name":"Guadalupe Gonzalez","orcid":"https://orcid.org/0000-0002-7650-3056"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gonzalez, Guadalupe","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135883245","display_name":"Dennis Veselkov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Veselkov, Dennis","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050041550","display_name":"Ivan Laponogov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Laponogov, Ivan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135355734","display_name":"Kirill Veselkov","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Veselkov, Kirill","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.968999981880188,"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":0.968999981880188,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0035000001080334187,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.0031999999191612005,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.751800000667572},{"id":"https://openalex.org/keywords/interaction-network","display_name":"Interaction network","score":0.578000009059906},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.510200023651123},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.48590001463890076},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.4846999943256378},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4097999930381775},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.40689998865127563},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.38690000772476196},{"id":"https://openalex.org/keywords/interaction-information","display_name":"Interaction information","score":0.3776000142097473}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.751800000667572},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5920000076293945},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5839999914169312},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.578000009059906},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.510200023651123},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.48590001463890076},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4846999943256378},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4097999930381775},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.40689998865127563},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.38690000772476196},{"id":"https://openalex.org/C38764148","wikidata":"https://www.wikidata.org/wiki/Q17098245","display_name":"Interaction information","level":2,"score":0.3776000142097473},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35179999470710754},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3515999913215637},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3504999876022339},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34450000524520874},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.33379998803138733},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3257000148296356},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.30660000443458557},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.2930999994277954},{"id":"https://openalex.org/C2991772755","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Gene interaction","level":3,"score":0.2818000018596649},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2793000042438507},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.27379998564720154},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.27059999108314514},{"id":"https://openalex.org/C70636015","wikidata":"https://www.wikidata.org/wiki/Q4300350","display_name":"Molecular biophysics","level":2,"score":0.26809999346733093},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.26030001044273376},{"id":"https://openalex.org/C158207573","wikidata":"https://www.wikidata.org/wiki/Q5747224","display_name":"Heterogeneous network","level":4,"score":0.25850000977516174},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2565000057220459},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.25209999084472656},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.25049999356269836},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.2502000033855438}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.07838","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.07838","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.07838","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.07838","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"how":[1],"molecular":[2,57,63],"alterations":[3],"propagate":[4],"across":[5,33],"biological":[6,28,91],"systems":[7],"to":[8,53,59,140,154,198],"drive":[9],"disease":[10,55],"remains":[11],"a":[12,39,68,77,141,157,163],"central":[13],"challenge.":[14],"Although":[15],"high-throughput":[16],"profiling":[17],"enables":[18,210],"comprehensive":[19],"characterization":[20],"of":[21,86,130],"tumor":[22],"states,":[23],"most":[24],"models":[25],"neglect":[26],"structured":[27],"relationships":[29],"or":[30],"lack":[31],"interpretability":[32],"scales.":[34],"Here":[35],"we":[36],"present":[37],"PPI-Net,":[38],"hierarchical":[40,145],"graph":[41,82],"neural":[42],"network":[43,71],"that":[44,127,203],"integrates":[45],"protein-protein":[46],"interaction":[47,70,205],"(PPI)":[48],"networks":[49,206],"with":[50,110,207],"pathway-level":[51],"representations":[52],"model":[54,172],"from":[56,72,96,100,123],"interactions":[58],"functional":[60],"processes.":[61],"Patient-specific":[62],"profiles":[64],"are":[65],"embedded":[66],"within":[67],"shared":[69],"STRING":[73],"and":[74,168,181,195],"propagated":[75],"through":[76],"multi-layer":[78],"Reactome":[79,132],"hierarchy":[80,133],"using":[81,155,166],"attention,":[83],"enabling":[84],"aggregation":[85],"gene-level":[87],"signals":[88],"into":[89,217],"higher-order":[90],"programs.":[92],"Across":[93],"RNA-seq":[94,167],"data":[95,122,170],"ten":[97],"cancer":[98,125,218],"types":[99],"The":[101],"Cancer":[102],"Genome":[103],"Atlas,":[104],"PPI-Net":[105],"achieves":[106],"robust":[107],"predictive":[108],"performance,":[109],"balanced":[111,135,149],"accuracy":[112,136,150],"exceeding":[113],"90%":[114],"in":[115],"multiple":[116],"cohorts.":[117],"Comparative":[118],"analysis":[119],"on":[120],"RNA-Seq":[121],"breast":[124],"demonstrated":[126],"PPI-Net's":[128],"integration":[129],"the":[131],"improved":[134,148],"by":[137,151],"6.7%":[138],"relative":[139,153],"PPI-only":[142],"model,":[143],"while":[144,185,213],"multi-level":[146],"supervision":[147],"12.3%":[152],"only":[156],"single":[158],"top-level":[159],"prediction":[160,212],"head.":[161],"Applying":[162],"multi-omics":[164],"approach":[165],"methylation":[169],"improves":[171],"interpretation,":[173],"recovering":[174],"canonical":[175],"oncogenic":[176],"modules,":[177],"including":[178],"TP53-AKT":[179],"signaling":[180,194],"stress":[182],"response":[183],"pathways,":[184],"revealing":[186],"convergence":[187],"onto":[188],"coherent":[189],"programs":[190],"such":[191],"as":[192],"ion":[193],"cellular":[196],"responses":[197],"stimuli.":[199],"These":[200],"results":[201],"demonstrate":[202],"integrating":[204],"pathway":[208],"hierarchies":[209],"accurate":[211],"providing":[214],"mechanistic":[215],"insight":[216],"biology.":[219]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-05-12T00:00:00"}