{"id":"https://openalex.org/W2912763566","doi":"https://doi.org/10.1109/bibm.2018.8621382","title":"PAAM-ML: A novel Phylogeny and Abundance aware Machine Learning Modelling Approach for Microbiome Classification","display_name":"PAAM-ML: A novel Phylogeny and Abundance aware Machine Learning Modelling Approach for Microbiome Classification","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2912763566","doi":"https://doi.org/10.1109/bibm.2018.8621382","mag":"2912763566"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621382","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621382","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pure.ulster.ac.uk/en/publications/62a68d9f-c8b5-4f10-a59b-ba8f2d63e6a7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007782280","display_name":"Jyotsna Talreja Wassan","orcid":"https://orcid.org/0000-0002-9116-8962"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jyotsna Talreja Wassan","raw_affiliation_strings":["School of Computing, Ulster University Northern Ireland, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing, Ulster University Northern Ireland, United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100379058","display_name":"Haiying Wang","orcid":"https://orcid.org/0000-0001-8358-9065"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Haiying Wang","raw_affiliation_strings":["School of Computing, Ulster University Northern Ireland, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing, Ulster University Northern Ireland, United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024303177","display_name":"Fiona Browne","orcid":"https://orcid.org/0000-0003-0443-4730"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fiona Browne","raw_affiliation_strings":["School of Computing, Ulster University Northern Ireland, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing, Ulster University Northern Ireland, United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024401909","display_name":"Huiru Zheng","orcid":"https://orcid.org/0000-0001-7648-8709"},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Huiru Zheng","raw_affiliation_strings":["School of Computing, Ulster University Northern Ireland, United Kingdom"],"affiliations":[{"raw_affiliation_string":"School of Computing, Ulster University Northern Ireland, United Kingdom","institution_ids":["https://openalex.org/I138801177"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007782280"],"corresponding_institution_ids":["https://openalex.org/I138801177"],"apc_list":null,"apc_paid":null,"fwci":0.4596,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.63932232,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"44","last_page":"49"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9994999766349792,"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/T10066","display_name":"Gut microbiota and health","score":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.986299991607666,"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/T10141","display_name":"Probiotics and Fermented Foods","score":0.9860000014305115,"subfield":{"id":"https://openalex.org/subfields/1106","display_name":"Food Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.8295741081237793},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.6964563131332397},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6843622922897339},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5707643032073975},{"id":"https://openalex.org/keywords/abundance","display_name":"Abundance (ecology)","score":0.5635309219360352},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.5623553395271301},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5566363334655762},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4805239140987396},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4583404064178467},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4553010165691376},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.45047977566719055},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3828642964363098},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2986889183521271},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.1894201636314392},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1601458191871643},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1409292221069336}],"concepts":[{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.8295741081237793},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.6964563131332397},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6843622922897339},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5707643032073975},{"id":"https://openalex.org/C77077793","wikidata":"https://www.wikidata.org/wiki/Q336019","display_name":"Abundance (ecology)","level":2,"score":0.5635309219360352},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.5623553395271301},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5566363334655762},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4805239140987396},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4583404064178467},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4553010165691376},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45047977566719055},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3828642964363098},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2986889183521271},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.1894201636314392},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1601458191871643},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1409292221069336}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm.2018.8621382","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621382","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:pure.atira.dk:openaire/62a68d9f-c8b5-4f10-a59b-ba8f2d63e6a7","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/62a68d9f-c8b5-4f10-a59b-ba8f2d63e6a7","pdf_url":null,"source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Wassan, J T, Wang, H HY, Fiona, B & Zheng, H 2018, PAAM-ML: A novel Phylogeny and Abundance aware Machine Learning Modelling Approach for Microbiome Classification. in 2018 IEEE International Conference on Bioinformatics and Biomedicine . IEEE, pp. 44-49, 2018 IEEE International Conference on Bioinformatics and Biomedicine, Madrid, Spain, 3/12/18. https://doi.org/10.1109/BIBM.2018.8621382","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"pmh:oai:pure.atira.dk:openaire/62a68d9f-c8b5-4f10-a59b-ba8f2d63e6a7","is_oa":true,"landing_page_url":"https://pure.ulster.ac.uk/en/publications/62a68d9f-c8b5-4f10-a59b-ba8f2d63e6a7","pdf_url":null,"source":{"id":"https://openalex.org/S4306402454","display_name":"Ulster University Research Portal (Ulster University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138801177","host_organization_name":"University of Ulster","host_organization_lineage":["https://openalex.org/I138801177"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Wassan, J T, Wang, H HY, Fiona, B & Zheng, H 2018, PAAM-ML: A novel Phylogeny and Abundance aware Machine Learning Modelling Approach for Microbiome Classification. in 2018 IEEE International Conference on Bioinformatics and Biomedicine . IEEE, pp. 44-49, 2018 IEEE International Conference on Bioinformatics and Biomedicine, Madrid, Spain, 3/12/18. https://doi.org/10.1109/BIBM.2018.8621382","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6899999976158142}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W46659105","https://openalex.org/W1852605861","https://openalex.org/W1996031526","https://openalex.org/W2021276697","https://openalex.org/W2033730546","https://openalex.org/W2035182371","https://openalex.org/W2035720976","https://openalex.org/W2045449780","https://openalex.org/W2059185913","https://openalex.org/W2059237622","https://openalex.org/W2074405982","https://openalex.org/W2075716829","https://openalex.org/W2110300022","https://openalex.org/W2115098873","https://openalex.org/W2127672471","https://openalex.org/W2133057705","https://openalex.org/W2138620443","https://openalex.org/W2170951896","https://openalex.org/W2171571559","https://openalex.org/W2174316710","https://openalex.org/W2395461901","https://openalex.org/W2409427249","https://openalex.org/W2510675082","https://openalex.org/W2794932993","https://openalex.org/W2963546206","https://openalex.org/W2963776453","https://openalex.org/W2999812538","https://openalex.org/W3103144163","https://openalex.org/W6602002561","https://openalex.org/W6680783750","https://openalex.org/W6750320783","https://openalex.org/W6813763326"],"related_works":["https://openalex.org/W638577851","https://openalex.org/W2968354375","https://openalex.org/W2359440920","https://openalex.org/W2889550857","https://openalex.org/W3013372948","https://openalex.org/W3135997498","https://openalex.org/W4242417330","https://openalex.org/W4388282505","https://openalex.org/W3198631238","https://openalex.org/W3139084279"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,16,78,157],"high-throughput":[3],"sequencing":[4],"technologies":[5],"have":[6],"accelerated":[7],"microbiome":[8,121],"studies":[9],"by":[10,174],"profiling":[11],"16S":[12],"rRNA":[13],"genes":[14],"present":[15],"microbial":[17,24,34,54,67,95],"species.":[18],"Identifying,":[19],"analyzing,":[20],"and":[21,44,102,139,192,204],"targeting":[22],"such":[23],"composition":[25],"is":[26,110],"important":[27],"to":[28,98],"provide":[29],"an":[30],"enriched":[31],"analysis":[32,169],"of":[33,66,82,94,128,170,190,196],"samples.":[35],"In":[36],"this":[37],"paper,":[38],"we":[39],"propose":[40],"a":[41,100,167],"novel":[42],"phylogeny":[43,101],"abundance":[45,64,93,103],"aware":[46,104],"machine":[47,116],"learning":[48,117],"modelling":[49],"approach":[50,62,173],"(PAAM-ML)":[51],"for":[52,115,120,185],"classifying":[53],"samples":[55],"into":[56,91],"their":[57,79],"respective":[58],"functional":[59],"phenotypes.":[60],"The":[61,108],"integrates":[63],"count":[65],"species":[68,96],"as":[69,71,113],"well":[70],"relationships":[72],"between":[73],"them,":[74],"which":[75],"are":[76],"encoded":[77],"phylogenetic":[80],"tree":[81,89],"life.":[83],"It":[84,150],"incorporates":[85],"the":[86,92,125,148,171,187,208],"underlying":[87],"structural":[88],"information":[90],"(features)":[97],"create":[99],"matrix":[105,109],"structure":[106],"(PAAM).":[107],"then":[111],"used":[112],"input":[114],"(ML)":[118],"models":[119],"classification.":[122],"We":[123,164],"compared":[124],"classification":[126,183],"performance":[127],"PAAM-ML":[129,145],"with":[130,153,211],"state-of-the-art":[131],"approaches":[132],"using":[133,141],"Phylogenetic":[134],"Isometric":[135],"Log-Ratio":[136],"Transform":[137],"(PhILR)":[138],"MetaPhyl":[140],"three":[142],"use":[143],"cases.":[144],"significantly":[146],"improved":[147],"performance.":[149],"outperformed":[151],"PhILR":[152],"p":[154],"<;":[155],"0.01":[156],"Human":[158,212],"Microbiome":[159],"across":[160],"4":[161],"body":[162],"sites.":[163],"also":[165],"performed":[166],"comprehensive":[168],"proposed":[172],"applying":[175,201],"feature":[176,205],"engineering.":[177],"Our":[178],"experimental":[179],"results":[180],"indicate":[181],"significant":[182],"performance,":[184],"example,":[186],"highest":[188],"accuracy":[189],"0.977":[191],"Mathews":[193],"Correlation":[194],"Coefficient":[195],"0.961":[197],"was":[198],"achieved":[199],"when":[200],"Random":[202],"Forest":[203],"engineering":[206],"over":[207],"PAAM":[209],"associated":[210],"Microbiome.":[213]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
