{"id":"https://openalex.org/W4412823093","doi":"https://doi.org/10.1093/bioinformatics/btag365","title":"BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool","display_name":"BioNeuralNet: a graph neural network based Multi-Omics network data analysis tool","publication_year":2026,"publication_date":"2026-06-01","ids":{"openalex":"https://openalex.org/W4412823093","doi":"https://doi.org/10.1093/bioinformatics/btag365","pmid":"https://pubmed.ncbi.nlm.nih.gov/40740520"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag365","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag365","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag365","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002940251","display_name":"Vicente Ramos\u2010Santillan","orcid":"https://orcid.org/0000-0002-0286-5126"},"institutions":[{"id":"https://openalex.org/I131651094","display_name":"University of Denver","ror":"https://ror.org/04w7skc03","country_code":"US","type":"education","lineage":["https://openalex.org/I131651094"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vicente Ramos","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","Computer Science and Engineering, University of Colorado Denver"],"raw_orcid":"https://orcid.org/0009-0007-9391-6091","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]},{"raw_affiliation_string":"Computer Science and Engineering, University of Colorado Denver","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063249968","display_name":"Sundous Hussein","orcid":null},"institutions":[{"id":"https://openalex.org/I131651094","display_name":"University of Denver","ror":"https://ror.org/04w7skc03","country_code":"US","type":"education","lineage":["https://openalex.org/I131651094"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sundous Hussein","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","Computer Science and Engineering, University of Colorado Denver"],"raw_orcid":"https://orcid.org/0000-0002-5994-7480","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]},{"raw_affiliation_string":"Computer Science and Engineering, University of Colorado Denver","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082003958","display_name":"Mohamed Abdel-Hafiz","orcid":null},"institutions":[{"id":"https://openalex.org/I131651094","display_name":"University of Denver","ror":"https://ror.org/04w7skc03","country_code":"US","type":"education","lineage":["https://openalex.org/I131651094"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohamed Abdel-Hafiz","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","Computer Science and Engineering, University of Colorado Denver"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]},{"raw_affiliation_string":"Computer Science and Engineering, University of Colorado Denver","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Arunangshu Sarkar","orcid":"https://orcid.org/0000-0002-0648-4750"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Arunangshu Sarkar","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO,","Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus"],"raw_orcid":"https://orcid.org/0000-0002-0648-4750","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO,","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]},{"raw_affiliation_string":"Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101689438","display_name":"Weixuan Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Weixuan Liu","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO,","Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus"],"raw_orcid":"https://orcid.org/0009-0005-0222-1784","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO,","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]},{"raw_affiliation_string":"Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022404035","display_name":"Katerina Kechris","orcid":"https://orcid.org/0000-0002-3725-5459"},"institutions":[{"id":"https://openalex.org/I151808059","display_name":"Colorado School of Public Health","ror":"https://ror.org/005x9g035","country_code":"US","type":"education","lineage":["https://openalex.org/I151808059"]},{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Katerina J Kechris","raw_affiliation_strings":["Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO,","Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus"],"raw_orcid":"https://orcid.org/0000-0002-3725-5459","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus , Aurora, CO,","institution_ids":["https://openalex.org/I151808059","https://openalex.org/I51713134"]},{"raw_affiliation_string":"Biostatistics and Bioinformatics, University of Colorado Anschutz Medical Campus","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017665414","display_name":"Russell P. Bowler","orcid":"https://orcid.org/0000-0003-4651-363X"},"institutions":[{"id":"https://openalex.org/I1316902750","display_name":"Cleveland Clinic","ror":"https://ror.org/03xjacd83","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1316902750"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russell P Bowler","raw_affiliation_strings":["Genomic Medicine Institute, Cleveland Clinic Main Campus , Cleveland, OH,","Genomic Medicine Institute, Cleveland Clinic Main Campus"],"raw_orcid":"https://orcid.org/0000-0003-4651-363X","affiliations":[{"raw_affiliation_string":"Genomic Medicine Institute, Cleveland Clinic Main Campus , Cleveland, OH,","institution_ids":["https://openalex.org/I1316902750"]},{"raw_affiliation_string":"Genomic Medicine Institute, Cleveland Clinic Main Campus","institution_ids":["https://openalex.org/I1316902750"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101822172","display_name":"Leslie A. Lange","orcid":"https://orcid.org/0000-0002-4220-6766"},"institutions":[{"id":"https://openalex.org/I51713134","display_name":"University of Colorado Anschutz Medical Campus","ror":"https://ror.org/03wmf1y16","country_code":"US","type":"education","lineage":["https://openalex.org/I51713134"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leslie Lange","raw_affiliation_strings":["Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus , Aurora, CO,","Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus , Aurora, CO,","institution_ids":["https://openalex.org/I51713134"]},{"raw_affiliation_string":"Biomedical Informatics and Personalized Medicine, University of Colorado Anschutz Medical Campus","institution_ids":["https://openalex.org/I51713134"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007232242","display_name":"Farnoush Banaei\u2010Kashani","orcid":"https://orcid.org/0000-0003-4102-9873"},"institutions":[{"id":"https://openalex.org/I131651094","display_name":"University of Denver","ror":"https://ror.org/04w7skc03","country_code":"US","type":"education","lineage":["https://openalex.org/I131651094"]},{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Farnoush Banaei-Kashani","raw_affiliation_strings":["Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","Computer Science and Engineering, University of Colorado Denver"],"raw_orcid":"https://orcid.org/0000-0003-4102-9873","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, University of Colorado Denver , Denver, CO,","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]},{"raw_affiliation_string":"Computer Science and Engineering, University of Colorado Denver","institution_ids":["https://openalex.org/I131651094","https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00429655,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"6","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":0.9980999827384949,"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":0.9980999827384949,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9697999954223633,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9467999935150146,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6190046668052673},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5453353524208069},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5031232237815857},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.43571698665618896},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.43112993240356445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3491109311580658},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3396015167236328},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32245826721191406},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.20316556096076965},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19212442636489868}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6190046668052673},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5453353524208069},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5031232237815857},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43571698665618896},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43112993240356445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3491109311580658},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3396015167236328},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32245826721191406},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.20316556096076965},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19212442636489868}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btag365","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag365","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40740520","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40740520","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ArXiv","raw_type":null},{"id":"pmid:42274222","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42274222","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:arXiv.org:2507.20440","is_oa":true,"landing_page_url":"https://arxiv.org/abs/2507.20440","pdf_url":"https://arxiv.org/pdf/2507.20440","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12310135","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12310135","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:13293062","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13293062/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag365","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag365","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4154720402","display_name":null,"funder_award_id":"R01HL152735","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2391251536","https://openalex.org/W2961085424","https://openalex.org/W2362198218","https://openalex.org/W2019521278","https://openalex.org/W1984922432","https://openalex.org/W2375008505","https://openalex.org/W1982750869","https://openalex.org/W2085756966","https://openalex.org/W2350679292","https://openalex.org/W2086348228"],"abstract_inverted_index":{"SUMMARY:":[0],"Multi-omics":[1],"data":[2,86],"offer":[3],"unprecedented":[4],"insights":[5],"into":[6,108],"complex":[7,105],"biological":[8],"systems,":[9],"yet":[10],"their":[11],"high":[12],"dimensionality,":[13],"sparsity,":[14],"and":[15,77,129,144,156,165,173,199],"intricate":[16],"interactions":[17],"pose":[18],"significant":[19],"analytical":[20,135],"challenges.":[21],"Network-based":[22],"approaches":[23],"have":[24],"advanced":[25],"multi-omics":[26,85,101,117,175],"research":[27],"by":[28],"effectively":[29,59],"capturing":[30],"biologically":[31,96],"relevant":[32],"relationships":[33],"among":[34],"molecular":[35,48,106],"features":[36],"(e.g.,":[37,150],"genes,":[38],"proteins,":[39],"metabolites).":[40],"While":[41],"these":[42,61,104],"methods":[43],"are":[44,201],"powerful":[45],"for":[46,54,82],"representing":[47],"interactions,":[49],"there":[50],"remains":[51],"a":[52,75,130],"need":[53],"tools":[55],"specifically":[56],"designed":[57,169],"to":[58,94,170],"utilize":[60],"network":[62,118,122,176],"representations":[63,99],"across":[64],"diverse":[65,141],"downstream":[66,134],"analyses.":[67],"To":[68],"fulfill":[69],"this":[70],"need,":[71],"we":[72],"introduce":[73],"BioNeuralNet,":[74],"flexible":[76,172],"modular":[78],"Python":[79,148,191],"framework":[80,168],"tailored":[81],"end-to-end":[83],"network-based":[84],"analysis.":[87],"BioNeuralNet":[88,111,160,185],"leverages":[89],"Graph":[90],"Neural":[91],"Networks":[92],"(GNNs)":[93],"learn":[95],"meaningful":[97],"low-dimensional":[98,127],"from":[100],"networks,":[102],"converting":[103],"networks":[107],"versatile":[109],"embeddings.":[110],"supports":[112],"all":[113],"major":[114],"stages":[115],"of":[116,126,133],"analysis,":[119],"including":[120,140],"several":[121],"construction":[123],"techniques,":[124],"generation":[125],"representations,":[128],"broad":[131],"range":[132],"tasks.":[136],"Its":[137],"extensive":[138],"utilities,":[139],"GNN":[142],"architectures,":[143],"compatibility":[145],"with":[146],"established":[147],"packages":[149],"scikit-learn,":[151],"PyTorch,":[152],"NetworkX),":[153],"enhance":[154],"usability":[155],"facilitate":[157],"quick":[158],"adoption.":[159],"is":[161,187],"an":[162],"open-source,":[163],"user-friendly,":[164],"extensively":[166],"documented":[167],"support":[171],"reproducible":[174],"analysis":[177],"in":[178],"precision":[179],"medicine.":[180],"AVAILABILITY":[181],"AND":[182],"IMPLEMENTATION:":[183],"The":[184,190],"library":[186],"available":[188],"via":[189],"Package":[192],"Index":[193],"(PyPI).":[194],"Source":[195],"code,":[196],"documentation,":[197],"tutorials,":[198],"workflows":[200],"hosted":[202],"at":[203,207],"https://bioneuralnet.readthedocs.io.":[204],"Code":[205],"archived":[206],"https://doi.org/10.5281/zenodo.17503083.":[208]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
