{"id":"https://openalex.org/W4408246180","doi":"https://doi.org/10.1109/jbhi.2025.3548263","title":"SecProGNN: Predicting Bronchoalveolar Lavage Fluid Secreted Protein Using Graph Neural Network","display_name":"SecProGNN: Predicting Bronchoalveolar Lavage Fluid Secreted Protein Using Graph Neural Network","publication_year":2025,"publication_date":"2025-03-05","ids":{"openalex":"https://openalex.org/W4408246180","doi":"https://doi.org/10.1109/jbhi.2025.3548263","pmid":"https://pubmed.ncbi.nlm.nih.gov/40042949"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3548263","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3548263","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023665938","display_name":"Dan Shao","orcid":"https://orcid.org/0000-0003-1050-2808"},"institutions":[{"id":"https://openalex.org/I106645853","display_name":"Changchun University of Science and Technology","ror":"https://ror.org/007mntk44","country_code":"CN","type":"education","lineage":["https://openalex.org/I106645853"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dan Shao","raw_affiliation_strings":["School of Computer Science and Technology, Changchun University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0003-1050-2808","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Changchun University, Changchun, China","institution_ids":["https://openalex.org/I106645853"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Guangzhao Zhang","orcid":"https://orcid.org/0009-0003-5428-2875"},"institutions":[{"id":"https://openalex.org/I106645853","display_name":"Changchun University of Science and Technology","ror":"https://ror.org/007mntk44","country_code":"CN","type":"education","lineage":["https://openalex.org/I106645853"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangzhao Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Changchun University, Changchun, China"],"raw_orcid":"https://orcid.org/0009-0003-5428-2875","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Changchun University, Changchun, China","institution_ids":["https://openalex.org/I106645853"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057569181","display_name":"Lin Lin","orcid":"https://orcid.org/0000-0003-1615-6045"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Lin","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0003-1615-6045","affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yucong Xiong","orcid":"https://orcid.org/0009-0009-7049-2788"},"institutions":[{"id":"https://openalex.org/I194450716","display_name":"Jilin University","ror":"https://ror.org/00js3aw79","country_code":"CN","type":"education","lineage":["https://openalex.org/I194450716"]},{"id":"https://openalex.org/I4210134929","display_name":"Jilin Province Science and Technology Department","ror":"https://ror.org/049x38272","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210134929"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yucong Xiong","raw_affiliation_strings":["School of Computer Science and Technology, Jilin University, Changchun, China"],"raw_orcid":"https://orcid.org/0009-0009-7049-2788","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Jilin University, Changchun, China","institution_ids":["https://openalex.org/I4210134929","https://openalex.org/I194450716"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Kai He","orcid":"https://orcid.org/0000-0003-3631-2172"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kai He","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA"],"raw_orcid":"https://orcid.org/0000-0003-3631-2172","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090277607","display_name":"Liyan Sun","orcid":"https://orcid.org/0000-0003-2145-6341"},"institutions":[{"id":"https://openalex.org/I106645853","display_name":"Changchun University of Science and Technology","ror":"https://ror.org/007mntk44","country_code":"CN","type":"education","lineage":["https://openalex.org/I106645853"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liyan Sun","raw_affiliation_strings":["School of Computer Science and Technology, Changchun University, Changchun, China"],"raw_orcid":"https://orcid.org/0000-0003-2145-6341","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Changchun University, Changchun, China","institution_ids":["https://openalex.org/I106645853"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.8663,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.69321329,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"29","issue":"8","first_page":"6114","last_page":"6123"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9939000010490417,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9939000010490417,"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/bronchoalveolar-lavage","display_name":"Bronchoalveolar lavage","score":0.8446478843688965},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5541960000991821},{"id":"https://openalex.org/keywords/secretory-protein","display_name":"Secretory protein","score":0.49339571595191956},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4912535548210144},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4714832305908203},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.45756250619888306},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.41192081570625305},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.34760069847106934},{"id":"https://openalex.org/keywords/lung","display_name":"Lung","score":0.3081304728984833},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3018258810043335},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.20227572321891785},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17254406213760376},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.13426417112350464},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13191446661949158}],"concepts":[{"id":"https://openalex.org/C2777961210","wikidata":"https://www.wikidata.org/wiki/Q927148","display_name":"Bronchoalveolar lavage","level":3,"score":0.8446478843688965},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5541960000991821},{"id":"https://openalex.org/C156399914","wikidata":"https://www.wikidata.org/wiki/Q7444454","display_name":"Secretory protein","level":3,"score":0.49339571595191956},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4912535548210144},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4714832305908203},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.45756250619888306},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.41192081570625305},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.34760069847106934},{"id":"https://openalex.org/C2777714996","wikidata":"https://www.wikidata.org/wiki/Q7886","display_name":"Lung","level":2,"score":0.3081304728984833},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3018258810043335},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.20227572321891785},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17254406213760376},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.13426417112350464},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13191446661949158},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077192","descriptor_name":"Adenocarcinoma of Lung","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D000077192","descriptor_name":"Adenocarcinoma of Lung","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D000077192","descriptor_name":"Adenocarcinoma of Lung","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098421","descriptor_name":"Multilayer Perceptrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098421","descriptor_name":"Multilayer Perceptrons","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001992","descriptor_name":"Bronchoalveolar Lavage Fluid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001992","descriptor_name":"Bronchoalveolar Lavage Fluid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D001992","descriptor_name":"Bronchoalveolar Lavage Fluid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D014408","descriptor_name":"Biomarkers, Tumor","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3548263","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3548263","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40042949","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40042949","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4834366915","display_name":null,"funder_award_id":"2021YFA1003003","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G923567926","display_name":null,"funder_award_id":"20230101236JC","funder_id":"https://openalex.org/F4320327282","funder_display_name":"Department of Science and Technology of Jilin Province"}],"funders":[{"id":"https://openalex.org/F4320327282","display_name":"Department of Science and Technology of Jilin Province","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1966327575","https://openalex.org/W1987633528","https://openalex.org/W2004642276","https://openalex.org/W2028232370","https://openalex.org/W2029163288","https://openalex.org/W2043764521","https://openalex.org/W2052685738","https://openalex.org/W2056782561","https://openalex.org/W2072668743","https://openalex.org/W2081375228","https://openalex.org/W2089417302","https://openalex.org/W2095483652","https://openalex.org/W2097606916","https://openalex.org/W2103912979","https://openalex.org/W2118217143","https://openalex.org/W2146512944","https://openalex.org/W2160061958","https://openalex.org/W2405808131","https://openalex.org/W2550451727","https://openalex.org/W2587399783","https://openalex.org/W2752782242","https://openalex.org/W2898402099","https://openalex.org/W2899942534","https://openalex.org/W2915975108","https://openalex.org/W2950764390","https://openalex.org/W2956081200","https://openalex.org/W2962810718","https://openalex.org/W3014323573","https://openalex.org/W3015964336","https://openalex.org/W3029378835","https://openalex.org/W3177828909","https://openalex.org/W3187487600","https://openalex.org/W3195165594","https://openalex.org/W3205873152","https://openalex.org/W3211795435","https://openalex.org/W4200608622","https://openalex.org/W4248510096","https://openalex.org/W4282946910","https://openalex.org/W4285727809","https://openalex.org/W4287093265","https://openalex.org/W4294216483","https://openalex.org/W4294329053","https://openalex.org/W4308834893","https://openalex.org/W4324143928","https://openalex.org/W4377291742","https://openalex.org/W4387701164","https://openalex.org/W4388595306","https://openalex.org/W4390578025","https://openalex.org/W4392544734","https://openalex.org/W4392638831","https://openalex.org/W4396721167","https://openalex.org/W6631190155","https://openalex.org/W6726873649","https://openalex.org/W6754929296"],"related_works":["https://openalex.org/W3030759040","https://openalex.org/W4200419177","https://openalex.org/W2434292116","https://openalex.org/W2475369677","https://openalex.org/W4291181514","https://openalex.org/W2462928754","https://openalex.org/W3022135843","https://openalex.org/W3028827145","https://openalex.org/W4394566403","https://openalex.org/W2000191327"],"abstract_inverted_index":{"Bronchoalveolar":[0],"lavage":[1],"fluid":[2],"(BALF)":[3],"is":[4],"a":[5,50,102],"liquid":[6],"obtained":[7],"from":[8],"the":[9,32,95],"alveoli":[10],"and":[11,44,123],"bronchi,":[12],"often":[13],"used":[14],"to":[15,41,58,90,107],"study":[16],"pulmonary":[17],"diseases.":[18],"So":[19],"far,":[20],"proteomic":[21],"analyses":[22],"have":[23],"identified":[24,124],"over":[25],"three":[26],"thousand":[27],"proteins":[28,37,61,67],"in":[29,62],"BALF.":[30,63,133],"However,":[31],"comprehensive":[33],"characterization":[34],"of":[35],"these":[36,80],"remains":[38],"challenging":[39],"due":[40],"their":[42,77],"complexity":[43],"technological":[45],"limitations.":[46],"This":[47],"paper":[48],"presented":[49],"novel":[51],"deep":[52],"learning":[53],"framework":[54],"called":[55],"SecProGNN,":[56,115],"designed":[57],"predict":[59,108],"secretory":[60],"Firstly,":[64],"SecProGNN":[65],"represented":[66],"as":[68],"graph-structured":[69],"data,":[70],"with":[71],"amino":[72],"acids":[73],"connected":[74],"based":[75],"on":[76],"interactions.":[78],"Then,":[79],"graphs":[81],"were":[82,99],"processed":[83],"through":[84],"graph":[85,92],"neural":[86],"networks":[87],"(GNNs)":[88],"model":[89],"extract":[91],"features.":[93],"Finally,":[94],"extracted":[96],"feature":[97],"vectors":[98],"fed":[100],"into":[101,132],"multi-layer":[103],"perceptron":[104],"(MLP)":[105],"module":[106],"BALF":[109],"secreted":[110,131],"proteins.":[111],"Additionally,":[112],"by":[113],"utilizing":[114],"we":[116],"investigated":[117],"potential":[118],"biomarkers":[119],"for":[120],"lung":[121],"adenocarcinoma":[122],"16":[125],"promising":[126],"candidates":[127],"that":[128],"may":[129],"be":[130]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
