{"id":"https://openalex.org/W4416961325","doi":"https://doi.org/10.1109/tcbbio.2025.3639775","title":"FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome","display_name":"FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome","publication_year":2025,"publication_date":"2025-12-03","ids":{"openalex":"https://openalex.org/W4416961325","doi":"https://doi.org/10.1109/tcbbio.2025.3639775","pmid":"https://pubmed.ncbi.nlm.nih.gov/41336154"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3639775","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3639775","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/A5035020838","display_name":"Buchao Zhan","orcid":"https://orcid.org/0009-0008-4129-7281"},"institutions":[{"id":"https://openalex.org/I116265982","display_name":"Qinghai University","ror":"https://ror.org/05h33bt13","country_code":"CN","type":"education","lineage":["https://openalex.org/I116265982"]},{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Buchao Zhan","raw_affiliation_strings":["School of Computer Science, Technology, Hainan University, Haikou, China","School of Computer Science, TechnologyHainan University"],"raw_orcid":"https://orcid.org/0009-0008-4129-7281","affiliations":[{"raw_affiliation_string":"School of Computer Science, Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]},{"raw_affiliation_string":"School of Computer Science, TechnologyHainan University","institution_ids":["https://openalex.org/I116265982"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104234776","display_name":"Dongmei He","orcid":"https://orcid.org/0009-0000-3965-2557"},"institutions":[{"id":"https://openalex.org/I116265982","display_name":"Qinghai University","ror":"https://ror.org/05h33bt13","country_code":"CN","type":"education","lineage":["https://openalex.org/I116265982"]},{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongmei He","raw_affiliation_strings":["School of Computer Science, Technology, Hainan University, Haikou, China","School of Computer Science, TechnologyHainan University"],"raw_orcid":"https://orcid.org/0009-0000-3965-2557","affiliations":[{"raw_affiliation_string":"School of Computer Science, Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]},{"raw_affiliation_string":"School of Computer Science, TechnologyHainan University","institution_ids":["https://openalex.org/I116265982"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025869726","display_name":"Yang Xin","orcid":"https://orcid.org/0000-0002-8315-8000"},"institutions":[{"id":"https://openalex.org/I116265982","display_name":"Qinghai University","ror":"https://ror.org/05h33bt13","country_code":"CN","type":"education","lineage":["https://openalex.org/I116265982"]},{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Yang","raw_affiliation_strings":["School of Computer Science, Technology, Hainan University, Haikou, China","School of Computer Science, TechnologyHainan University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]},{"raw_affiliation_string":"School of Computer Science, TechnologyHainan University","institution_ids":["https://openalex.org/I116265982"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zilong Zhang","orcid":"https://orcid.org/0009-0007-4710-9870"},"institutions":[{"id":"https://openalex.org/I116265982","display_name":"Qinghai University","ror":"https://ror.org/05h33bt13","country_code":"CN","type":"education","lineage":["https://openalex.org/I116265982"]},{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zilong Zhang","raw_affiliation_strings":["School of Computer Science, Technology, Hainan University, Haikou, China","School of Computer Science, TechnologyHainan University"],"raw_orcid":"https://orcid.org/0009-0007-4710-9870","affiliations":[{"raw_affiliation_string":"School of Computer Science, Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]},{"raw_affiliation_string":"School of Computer Science, TechnologyHainan University","institution_ids":["https://openalex.org/I116265982"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016741865","display_name":"Shankai Yan","orcid":"https://orcid.org/0000-0003-0369-4979"},"institutions":[{"id":"https://openalex.org/I116265982","display_name":"Qinghai University","ror":"https://ror.org/05h33bt13","country_code":"CN","type":"education","lineage":["https://openalex.org/I116265982"]},{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]},{"id":"https://openalex.org/I4210145393","display_name":"Hainan Agricultural School","ror":"https://ror.org/04p8ncq94","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210145393"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shankai Yan","raw_affiliation_strings":["School of Computer Science, Technology, Hainan University, Haikou, China","School of Computer Science, TechnologyHainan University"],"raw_orcid":"https://orcid.org/0000-0003-0369-4979","affiliations":[{"raw_affiliation_string":"School of Computer Science, Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203","https://openalex.org/I4210145393"]},{"raw_affiliation_string":"School of Computer Science, TechnologyHainan University","institution_ids":["https://openalex.org/I116265982"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5035020838"],"corresponding_institution_ids":["https://openalex.org/I116265982","https://openalex.org/I20942203","https://openalex.org/I4210145393"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.32342942,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"1","first_page":"247","last_page":"258"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.11410000175237656,"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/T10885","display_name":"Gene expression and cancer classification","score":0.11410000175237656,"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/T10066","display_name":"Gut microbiota and health","score":0.10320000350475311,"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":0.09669999778270721,"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/nat","display_name":"Nat","score":0.8733999729156494},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"Colorectal cancer","score":0.5723000168800354},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5519000291824341},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.47369998693466187}],"concepts":[{"id":"https://openalex.org/C182516595","wikidata":"https://www.wikidata.org/wiki/Q376660","display_name":"Nat","level":2,"score":0.8733999729156494},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.5723000168800354},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5597000122070312},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5519000291824341},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.47369998693466187},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4462999999523163},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.36059999465942383},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.35010001063346863},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.28760001063346863},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.28540000319480896},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.2583000063896179}],"mesh":[{"descriptor_ui":"D000072761","descriptor_name":"Mycobiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000072761","descriptor_name":"Mycobiome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000072761","descriptor_name":"Mycobiome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000072761","descriptor_name":"Mycobiome","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005658","descriptor_name":"Fungi","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000382","qualifier_name":"microbiology","is_major_topic":false},{"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3639775","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3639775","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:41336154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41336154","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":[],"awards":[{"id":"https://openalex.org/G6297944654","display_name":null,"funder_award_id":"62202128","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6347374521","display_name":null,"funder_award_id":"KYQD(ZR)23125","funder_id":"https://openalex.org/F4320323370","funder_display_name":"Hainan University"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320323370","display_name":"Hainan University","ror":"https://ror.org/03q648j11"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W92469554","https://openalex.org/W1971139108","https://openalex.org/W2008056655","https://openalex.org/W2043175314","https://openalex.org/W2051372177","https://openalex.org/W2058089746","https://openalex.org/W2065581761","https://openalex.org/W2089956125","https://openalex.org/W2108589405","https://openalex.org/W2119387367","https://openalex.org/W2120204563","https://openalex.org/W2128711701","https://openalex.org/W2156555688","https://openalex.org/W2295598076","https://openalex.org/W2465175609","https://openalex.org/W2766676715","https://openalex.org/W2774841093","https://openalex.org/W2799462250","https://openalex.org/W2897124762","https://openalex.org/W2900030356","https://openalex.org/W2942929308","https://openalex.org/W2969604738","https://openalex.org/W2979146632","https://openalex.org/W3015086928","https://openalex.org/W3047536348","https://openalex.org/W3049323167","https://openalex.org/W3105613063","https://openalex.org/W3117063516","https://openalex.org/W3135034938","https://openalex.org/W3146577202","https://openalex.org/W4210569788","https://openalex.org/W4210708031","https://openalex.org/W4298008684","https://openalex.org/W4298008749","https://openalex.org/W4308087740","https://openalex.org/W4372336760","https://openalex.org/W4400762160","https://openalex.org/W4403138830"],"related_works":[],"abstract_inverted_index":{"OBJECTIVE:":[0],"The":[1,144],"role":[2],"of":[3,159],"fungal":[4,36,48,83,110],"microbiota":[5,84],"in":[6,50,140,151],"human":[7],"carcinogenesis":[8],"remains":[9],"largely":[10],"uncharacterized.":[11],"Recent":[12],"evidence":[13],"suggests":[14],"normal":[15],"adjacent":[16],"tissue":[17],"(NAT)":[18],"represents":[19],"an":[20,155],"intermediate":[21],"state":[22],"between":[23,39,56,127],"healthy":[24],"and":[25,41,58,90,129],"malignant":[26],"tissues,":[27],"highlighting":[28],"its":[29],"potential":[30],"for":[31,46,119],"early":[32],"cancer":[33,134,142],"detection.":[34],"Discriminating":[35],"compositional":[37],"profiles":[38],"tumor":[40,57,128],"NAT":[42,59,130],"is":[43],"thus":[44],"critical":[45],"elucidating":[47],"involvement":[49],"oncogenesis.":[51],"However,":[52],"the":[53],"high":[54],"similarity":[55],"mycobiota":[60],"poses":[61],"significant":[62],"analytical":[63],"challenges.":[64],"METHOD:":[65],"To":[66],"overcome":[67],"this":[68],"limitation,":[69],"we":[70],"developed":[71],"a":[72,114],"two-level":[73],"ensemble":[74],"discriminative":[75],"model.":[76],"Base-level":[77],"classifiers,":[78],"trained":[79],"using":[80],"rigorously":[81],"filtered":[82],"data":[85,112],"(based":[86],"on":[87],"prevalence,":[88],"abundance,":[89],"quality":[91],"metrics)":[92],"via":[93],"Random":[94],"Forest,":[95],"generate":[96],"initial":[97],"predictions.":[98],"A":[99],"meta-level":[100],"classifier":[101],"then":[102],"integrates":[103],"these":[104],"base":[105],"predictions,":[106],"transforming":[107],"high-dimensional,":[108],"sparse":[109],"feature":[111],"into":[113],"low-dimensional,":[115],"dense":[116],"representation":[117],"optimized":[118],"discrimination.":[120],"RESULTS:":[121],"Our":[122],"approach":[123],"achieved":[124],"clear":[125],"separation":[126],"mycobiomes":[131],"across":[132],"multiple":[133],"types,":[135],"with":[136],"particularly":[137],"pronounced":[138],"discrimination":[139],"colorectal":[141],"(CRC).":[143],"proposed":[145],"model":[146],"significantly":[147],"outperformed":[148],"existing":[149],"methods":[150],"tumor-NAT":[152],"classification,":[153],"demonstrating":[154],"average":[156],"AUC":[157],"improvement":[158],"approximately":[160],"10%.":[161]},"counts_by_year":[],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-12-03T00:00:00"}
