{"id":"https://openalex.org/W4415376293","doi":"https://doi.org/10.1186/s12859-025-06273-3","title":"Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation","display_name":"Topology-aware functional similarity: integrating extended neighborhoods via exponential attenuation","publication_year":2025,"publication_date":"2025-10-21","ids":{"openalex":"https://openalex.org/W4415376293","doi":"https://doi.org/10.1186/s12859-025-06273-3","pmid":"https://pubmed.ncbi.nlm.nih.gov/41120843"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06273-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06273-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06273-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06273-3","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100395912","display_name":"Peng Wang","orcid":"https://orcid.org/0000-0001-6467-1581"},"institutions":[{"id":"https://openalex.org/I145581781","display_name":"Chongqing Technology and Business University","ror":"https://ror.org/05hqf1284","country_code":"CN","type":"education","lineage":["https://openalex.org/I145581781"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Peng Wang","raw_affiliation_strings":["Department of Computer Science, School of Artificial Intelligence, Chongqing Technology and Business University, No.19, Xuefu Ave, Nanan District, Chongqing, 400067, People's Republic of China. pengw@ctbu.edu.cn","Department of Computer Science, School of Artificial Intelligence, Chongqing Technology and Business University, No.19, Xuefu Ave, Nanan District, Chongqing, 400067, People's Republic of China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Artificial Intelligence, Chongqing Technology and Business University, No.19, Xuefu Ave, Nanan District, Chongqing, 400067, People's Republic of China. pengw@ctbu.edu.cn","institution_ids":["https://openalex.org/I145581781"]},{"raw_affiliation_string":"Department of Computer Science, School of Artificial Intelligence, Chongqing Technology and Business University, No.19, Xuefu Ave, Nanan District, Chongqing, 400067, People's Republic of China","institution_ids":["https://openalex.org/I145581781"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100395912"],"corresponding_institution_ids":["https://openalex.org/I145581781"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18130314,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"1","first_page":"255","last_page":"255"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.885200023651123,"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":0.885200023651123,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.040300000458955765,"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/T12536","display_name":"Topological and Geometric Data Analysis","score":0.017799999564886093,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.9211999773979187},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6456999778747559},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.3919999897480011},{"id":"https://openalex.org/keywords/exponential-function","display_name":"Exponential function","score":0.3862999975681305},{"id":"https://openalex.org/keywords/attenuation","display_name":"Attenuation","score":0.3765000104904175},{"id":"https://openalex.org/keywords/functional-data-analysis","display_name":"Functional data analysis","score":0.3138999938964844}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9211999773979187},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6456999778747559},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.559499979019165},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.41339999437332153},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3953999876976013},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39430001378059387},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.3919999897480011},{"id":"https://openalex.org/C151376022","wikidata":"https://www.wikidata.org/wiki/Q168698","display_name":"Exponential function","level":2,"score":0.3862999975681305},{"id":"https://openalex.org/C184652730","wikidata":"https://www.wikidata.org/wiki/Q2357982","display_name":"Attenuation","level":2,"score":0.3765000104904175},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3758000135421753},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3474999964237213},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3269999921321869},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3165999948978424},{"id":"https://openalex.org/C51820054","wikidata":"https://www.wikidata.org/wiki/Q5508814","display_name":"Functional data analysis","level":2,"score":0.3138999938964844},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3125999867916107},{"id":"https://openalex.org/C75235859","wikidata":"https://www.wikidata.org/wiki/Q582659","display_name":"Exponential growth","level":2,"score":0.2980000078678131},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2847000062465668},{"id":"https://openalex.org/C2776477805","wikidata":"https://www.wikidata.org/wiki/Q4460773","display_name":"Topological data analysis","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C2780940541","wikidata":"https://www.wikidata.org/wiki/Q1042397","display_name":"Mesa","level":2,"score":0.2750999927520752},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.26510000228881836}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06273-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06273-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06273-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41120843","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41120843","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:0104ee4ee51c4aad9480c70b853f5527","is_oa":true,"landing_page_url":"https://doaj.org/article/0104ee4ee51c4aad9480c70b853f5527","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":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-13 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11346587","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12538863","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06273-3","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06273-3","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06273-3","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4415376293.pdf"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1970697508","https://openalex.org/W1990223774","https://openalex.org/W2075638476","https://openalex.org/W2096358531","https://openalex.org/W2102221598","https://openalex.org/W2103017472","https://openalex.org/W2104097656","https://openalex.org/W2107710781","https://openalex.org/W2111805188","https://openalex.org/W2117486996","https://openalex.org/W2148866736","https://openalex.org/W2166468869","https://openalex.org/W2166542841","https://openalex.org/W2319227129","https://openalex.org/W2470757901","https://openalex.org/W2524896840","https://openalex.org/W2612690371","https://openalex.org/W2624021832","https://openalex.org/W2970771711","https://openalex.org/W2998119497","https://openalex.org/W3022203631","https://openalex.org/W3048475025","https://openalex.org/W3093053585","https://openalex.org/W3103657871","https://openalex.org/W3107527779","https://openalex.org/W4200166788","https://openalex.org/W4284894508","https://openalex.org/W4293046261","https://openalex.org/W4309466794","https://openalex.org/W4391424688","https://openalex.org/W4392600686","https://openalex.org/W4393950665","https://openalex.org/W4400616900","https://openalex.org/W4406002713"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,50,82],"annotation":[2,39],"of":[3,40,44,52,61,92,95,103,146],"protein":[4],"functions":[5],"constitutes":[6],"a":[7,41,58,108,150],"key":[8],"connection":[9],"between":[10],"genetic":[11],"sequences,":[12],"molecular":[13],"conformations,":[14],"and":[15,28,80,107,149,169,178],"biochemical":[16],"roles,":[17],"driving":[18],"progress":[19],"in":[20,46,101,166,190],"biomedical":[21],"studies.":[22],"Traditional":[23],"experimental":[24],"methods":[25,67,165],"are":[26],"time-consuming":[27],"resource-intensive,":[29],"making":[30],"it":[31,98],"difficult":[32],"to":[33,76,141],"meet":[34],"the":[35,47,90,118,144],"demand":[36],"for":[37,187],"functional":[38,86,120,135,188],"vast":[42],"number":[43],"proteins":[45],"post-genomic":[48],"era.":[49],"development":[51],"high-throughput":[53],"sequencing":[54],"technology":[55],"has":[56,99],"generated":[57],"large":[59],"amount":[60],"protein-protein":[62],"interaction":[63],"(PPI)":[64],"data.":[65],"Prediction":[66],"based":[68],"on":[69],"network":[70],"topology":[71],"have":[72],"attracted":[73],"attention":[74],"due":[75],"their":[77],"high":[78],"efficiency":[79],"interpretability.":[81],"FSWeight":[83],"algorithm":[84],"calculates":[85],"similarity":[87,121],"by":[88],"evaluating":[89],"commonality":[91],"second-order":[93],"neighbors":[94],"proteins.":[96],"However,":[97],"limitations":[100],"terms":[102],"insufficient":[104],"local":[105,126],"information":[106,128],"limited":[109],"global":[110,130],"perspective.":[111],"RESULTS:":[112],"In":[113],"this":[114],"study,":[115],"we":[116],"propose":[117],"topology-aware":[119],"(TAFS)":[122],"framework,":[123],"which":[124],"integrates":[125],"neighborhood":[127],"with":[129],"topological":[131,182],"information.":[132],"A":[133],"distance-dependent":[134],"attenuation":[136],"factor":[137],"\u03b3":[138],"is":[139,156],"introduced":[140],"dynamically":[142],"adjust":[143],"weights":[145],"distant":[147],"nodes,":[148],"bidirectional":[151],"joint":[152],"co-function":[153],"probability":[154],"model":[155],"constructed.":[157],"Experiments":[158],"show":[159],"that":[160],"TAFS":[161,173],"outperforms":[162],"traditional":[163],"baseline":[164],"both":[167],"single-species":[168],"cross-species":[170],"evaluations.":[171],"CONCLUSION:":[172],"significantly":[174],"improves":[175],"prediction":[176],"accuracy":[177],"interpretability":[179],"through":[180],"refined":[181],"modeling,":[183],"providing":[184],"new":[185],"insights":[186],"inference":[189],"complex":[191],"biological":[192],"networks.":[193]},"counts_by_year":[],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-21T00:00:00"}