{"id":"https://openalex.org/W4406658327","doi":"https://doi.org/10.1109/tcbbio.2025.3532256","title":"SMDPG: Identifying Metabolite-Disease Associations via Optimized Negative Sampling and Sparse Graph Convolutional Network","display_name":"SMDPG: Identifying Metabolite-Disease Associations via Optimized Negative Sampling and Sparse Graph Convolutional Network","publication_year":2025,"publication_date":"2025-01-21","ids":{"openalex":"https://openalex.org/W4406658327","doi":"https://doi.org/10.1109/tcbbio.2025.3532256","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811406"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3532256","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3532256","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","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/A5059183788","display_name":"Huang Yi-ran","orcid":"https://orcid.org/0000-0001-6289-8766"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yiran Huang","raw_affiliation_strings":["School of Computer, Electronics and Information, Guangxi University, Nanning, China","School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, China","institution_ids":["https://openalex.org/I150807315"]},{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115965385","display_name":"Qiulong Pu","orcid":"https://orcid.org/0009-0003-5332-5781"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiulong Pu","raw_affiliation_strings":["School of Computer, Electronics and Information, Guangxi University, Nanning, China","School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, China","institution_ids":["https://openalex.org/I150807315"]},{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041285376","display_name":"Wei Lan","orcid":"https://orcid.org/0000-0001-5839-7504"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Lan","raw_affiliation_strings":["School of Computer, Electronics and Information, Guangxi University, Nanning, China","School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, China","institution_ids":["https://openalex.org/I150807315"]},{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China","institution_ids":["https://openalex.org/I150807315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109537668","display_name":"Cuiyu Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cuiyu Huang","raw_affiliation_strings":["College of Chemistry, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Chemistry, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101747550","display_name":"Cheng Zhong","orcid":"https://orcid.org/0000-0002-5560-2151"},"institutions":[{"id":"https://openalex.org/I150807315","display_name":"Guangxi University","ror":"https://ror.org/02c9qn167","country_code":"CN","type":"education","lineage":["https://openalex.org/I150807315"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Zhong","raw_affiliation_strings":["School of Computer, Electronics and Information, Guangxi University, Nanning, China","School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, China","institution_ids":["https://openalex.org/I150807315"]},{"raw_affiliation_string":"School of Computer, Electronics and Information, Guangxi University, Nanning, Guangxi, China","institution_ids":["https://openalex.org/I150807315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5059183788"],"corresponding_institution_ids":["https://openalex.org/I150807315"],"apc_list":null,"apc_paid":null,"fwci":4.1245,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.92964381,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"22","issue":"2","first_page":"672","last_page":"683"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9958999752998352,"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":0.9958999752998352,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9836999773979187,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.9758999943733215,"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/graph","display_name":"Graph","score":0.5420423746109009},{"id":"https://openalex.org/keywords/metabolite","display_name":"Metabolite","score":0.48561564087867737},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48176953196525574},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3235468864440918},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3233356773853302},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3081439137458801},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21136435866355896},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20471304655075073},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.14091089367866516},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.12084227800369263}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5420423746109009},{"id":"https://openalex.org/C2777477808","wikidata":"https://www.wikidata.org/wiki/Q407595","display_name":"Metabolite","level":2,"score":0.48561564087867737},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48176953196525574},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3235468864440918},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3233356773853302},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3081439137458801},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21136435866355896},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20471304655075073},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.14091089367866516},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.12084227800369263}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3532256","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3532256","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811406","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 transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G6754550571","display_name":null,"funder_award_id":"2020GXNSFAA159074","funder_id":"https://openalex.org/F4320322768","funder_display_name":"Natural Science Foundation of Guangxi Province"},{"id":"https://openalex.org/G7386990451","display_name":null,"funder_award_id":"62362004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8262811428","display_name":null,"funder_award_id":"61862006","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322768","display_name":"Natural Science Foundation of Guangxi Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1986386190","https://openalex.org/W1997062226","https://openalex.org/W2018507034","https://openalex.org/W2019696954","https://openalex.org/W2035641101","https://openalex.org/W2053385401","https://openalex.org/W2055773789","https://openalex.org/W2100761975","https://openalex.org/W2108452336","https://openalex.org/W2140099276","https://openalex.org/W2157583521","https://openalex.org/W2510387023","https://openalex.org/W2539120393","https://openalex.org/W2568414132","https://openalex.org/W2749814893","https://openalex.org/W2750245257","https://openalex.org/W2796909069","https://openalex.org/W2809363952","https://openalex.org/W2948946740","https://openalex.org/W2963351448","https://openalex.org/W2983728827","https://openalex.org/W2985331920","https://openalex.org/W3027579288","https://openalex.org/W3092397780","https://openalex.org/W3111441956","https://openalex.org/W3134862445","https://openalex.org/W3135690269","https://openalex.org/W3157237148","https://openalex.org/W3195226391","https://openalex.org/W3197149044","https://openalex.org/W3214608846","https://openalex.org/W4206447491","https://openalex.org/W4283524045","https://openalex.org/W4285076853","https://openalex.org/W4297457250","https://openalex.org/W4297458751","https://openalex.org/W4307502334","https://openalex.org/W4311422829","https://openalex.org/W4313555682","https://openalex.org/W4322754494","https://openalex.org/W4379985215","https://openalex.org/W4384664737","https://openalex.org/W4385442674","https://openalex.org/W4386295460","https://openalex.org/W4389195947","https://openalex.org/W4392266716","https://openalex.org/W4394853685","https://openalex.org/W6602002561","https://openalex.org/W6631190155","https://openalex.org/W6726873649","https://openalex.org/W6745537798","https://openalex.org/W6756748170"],"related_works":["https://openalex.org/W2521903434","https://openalex.org/W1753739957","https://openalex.org/W2085913165","https://openalex.org/W2011282322","https://openalex.org/W2024044986","https://openalex.org/W2005550771","https://openalex.org/W323632276","https://openalex.org/W2418404479","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"Identifying":[0],"disease-associated":[1,22],"metabolites":[2,23,90],"could":[3,45],"provide":[4],"critical":[5],"clues":[6],"for":[7,193],"the":[8,39,48,106,111,126,143,146,150,157,179,183],"diagnosis":[9],"and":[10,29,68,91,93,130],"treatment":[11],"of":[12,41,51,113,145],"diseases.":[13],"Although":[14],"computational":[15],"approaches":[16],"have":[17,34],"been":[18],"proposed":[19],"to":[20,37,63,73,99,109,141,161,178],"predict":[21,74,162],"by":[24],"training":[25],"models":[26],"using":[27],"positive":[28],"negative":[30,42,66,96,102,128],"samples,":[31,43],"few":[32],"efforts":[33],"paid":[35],"attention":[36],"optimize":[38],"reliability":[40],"which":[44],"possibly":[46],"improve":[47],"prediction":[49],"accuracy":[50],"model.":[52],"In":[53,77],"this":[54],"work,":[55],"we":[56,79],"propose":[57,94],"a":[58,82,95,117],"novel":[59],"method":[60,98],"called":[61],"SMDPG":[62,169,188],"leverage":[64],"optimized":[65],"sampling":[67,97],"sparse":[69],"graph":[70,85,108,121,153,158],"convolutional":[71,159],"network":[72,160],"metabolite-disease":[75,83,103,119,132,163,174,196],"associations.":[76,133,164,197],"SMDPG,":[78],"first":[80],"build":[81],"bipartite":[84,107],"based":[86,124],"on":[87,125],"less":[88],"similar":[89],"diseases":[92],"select":[100],"reliable":[101],"samples":[104,129],"from":[105],"reduce":[110],"effect":[112],"noisy":[114],"samples.":[115],"Then":[116],"homogeneous":[118,147,152],"pair":[120],"is":[122,139,154,189],"constructed":[123],"selected":[127],"known":[131],"Further,":[134],"an":[135,190],"edge":[136],"sparseness":[137],"operation":[138],"designed":[140],"simplify":[142],"connection":[144],"graph.":[148],"Finally,":[149],"simplified":[151],"fed":[155],"into":[156],"Experimental":[165],"results":[166],"show":[167],"that":[168,187],"can":[170],"more":[171],"accurately":[172],"predicts":[173],"associations":[175],"as":[176],"compared":[177],"existing":[180],"methods.":[181],"Moreover,":[182],"study":[184],"case":[185],"demonstrates":[186],"effective":[191],"framework":[192],"identifying":[194],"potential":[195]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}
