{"id":"https://openalex.org/W1810249941","doi":"https://doi.org/10.1109/ijcnn.2005.1555824","title":"Predicting sugar regulation in arabidopsis thaliana using kernel learning methods","display_name":"Predicting sugar regulation in arabidopsis thaliana using kernel learning methods","publication_year":2006,"publication_date":"2006-01-05","ids":{"openalex":"https://openalex.org/W1810249941","doi":"https://doi.org/10.1109/ijcnn.2005.1555824","mag":"1810249941"},"language":"en","primary_location":{"id":"doi:10.1109/ijcnn.2005.1555824","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn.2005.1555824","pdf_url":null,"source":{"id":"https://openalex.org/S4363609022","display_name":"Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005.","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005.","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5020035093","display_name":"Kamel Saadi","orcid":"https://orcid.org/0000-0002-3700-8597"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"K. Saadi","raw_affiliation_strings":["School of Computing Sciences, University of East Anglia, Norwich, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045316726","display_name":"Kee-Khoon Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kee-Khoon Lee","raw_affiliation_strings":["School of Computing Sciences, University of East Anglia, Norwich, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063431577","display_name":"Gavin C. Cawley","orcid":"https://orcid.org/0000-0002-4118-9095"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"G.C. Cawley","raw_affiliation_strings":["School of Computing Sciences, University of East Anglia, Norwich, UK"],"affiliations":[{"raw_affiliation_string":"School of Computing Sciences, University of East Anglia, Norwich, UK","institution_ids":["https://openalex.org/I1118541"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029599635","display_name":"Michael Bevan","orcid":"https://orcid.org/0000-0001-8264-2354"},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"M.W. Bevan","raw_affiliation_strings":["John Innes Centre, Norwich Research Park, Norwich, UK"],"affiliations":[{"raw_affiliation_string":"John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020035093"],"corresponding_institution_ids":["https://openalex.org/I1118541"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10909091,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2","issue":null,"first_page":"167","last_page":"172"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9969000220298767,"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":0.9969000220298767,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9934999942779541,"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":0.9869999885559082,"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/upstream","display_name":"Upstream (networking)","score":0.6404432654380798},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6099024415016174},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5540369153022766},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.5489301681518555},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5483428239822388},{"id":"https://openalex.org/keywords/linear-discriminant-analysis","display_name":"Linear discriminant analysis","score":0.5140253305435181},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.501194953918457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.437706857919693},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.43418389558792114},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4167899191379547},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40752774477005005},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37617790699005127},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.31404685974121094},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.30497822165489197}],"concepts":[{"id":"https://openalex.org/C191172861","wikidata":"https://www.wikidata.org/wiki/Q7899321","display_name":"Upstream (networking)","level":2,"score":0.6404432654380798},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6099024415016174},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5540369153022766},{"id":"https://openalex.org/C2775988993","wikidata":"https://www.wikidata.org/wiki/Q158695","display_name":"Arabidopsis thaliana","level":4,"score":0.5489301681518555},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5483428239822388},{"id":"https://openalex.org/C69738355","wikidata":"https://www.wikidata.org/wiki/Q1228929","display_name":"Linear discriminant analysis","level":2,"score":0.5140253305435181},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.501194953918457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.437706857919693},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.43418389558792114},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4167899191379547},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40752774477005005},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37617790699005127},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.31404685974121094},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.30497822165489197},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/ijcnn.2005.1555824","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn.2005.1555824","pdf_url":null,"source":{"id":"https://openalex.org/S4363609022","display_name":"Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005.","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2005 IEEE International Joint Conference on Neural Networks, 2005.","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.418.6025","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.418.6025","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://theoval.cmp.uea.ac.uk/~gcc/publications/pdf/ijcnn2005c.pdf","raw_type":"text"},{"id":"pmh:oai:ueaeprints.uea.ac.uk:3884","is_oa":false,"landing_page_url":"https://ueaeprints.uea.ac.uk/id/eprint/3884/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Conference or Workshop Item"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6700000166893005,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W56062314","https://openalex.org/W327733334","https://openalex.org/W1510073064","https://openalex.org/W1542652324","https://openalex.org/W1554663460","https://openalex.org/W1560724230","https://openalex.org/W1563088657","https://openalex.org/W1946750680","https://openalex.org/W2010874539","https://openalex.org/W2020816856","https://openalex.org/W2024424774","https://openalex.org/W2076118331","https://openalex.org/W2100945610","https://openalex.org/W2107725114","https://openalex.org/W2109363337","https://openalex.org/W2149846618","https://openalex.org/W2150796457","https://openalex.org/W2170960297","https://openalex.org/W2171428093","https://openalex.org/W2548174349","https://openalex.org/W2795536332","https://openalex.org/W3016133651","https://openalex.org/W3144619878","https://openalex.org/W3146003712","https://openalex.org/W4251832462","https://openalex.org/W4298266977","https://openalex.org/W4388297464","https://openalex.org/W6640660124","https://openalex.org/W6655478935","https://openalex.org/W7067627250"],"related_works":["https://openalex.org/W2250488071","https://openalex.org/W2350376142","https://openalex.org/W2356150353","https://openalex.org/W2380744779","https://openalex.org/W1999647744","https://openalex.org/W2967867994","https://openalex.org/W3187420948","https://openalex.org/W2018643641","https://openalex.org/W2469878540","https://openalex.org/W2367057889"],"abstract_inverted_index":{"The":[0,119,148],"ability":[1],"to":[2,50,60,116],"predict":[3,51],"the":[4,11,14,44,63,82,92,95,101,108,130,138,144],"transcriptional":[5],"regulation":[6],"of":[7,13,43,48,76,87,94,103,110,129,140],"genes,":[8],"based":[9],"on":[10],"composition":[12],"upstream":[15,45,145],"promoter":[16,46,78,146],"region,":[17],"would":[18],"be":[19,135],"a":[20,104],"useful":[21],"step":[22],"in":[23,28,58,62,107,117,143,161],"deciphering":[24],"gene":[25],"regulatory":[26,132],"networks":[27],"eukaryotic":[29],"organisms.":[30],"In":[31],"this":[32],"paper":[33],"we":[34],"perform":[35],"optimally":[36],"regularised":[37],"kernel":[38],"Fisher":[39],"discriminant":[40],"(ORKFD)":[41],"analysis":[42,149],"sequences":[47],"genes":[49],"whether":[52],"they":[53],"are":[54,72],"up-":[55],"or":[56],"down-regulated":[57],"response":[59],"glucose":[61],"model":[64,106],"plant":[65],"Arahuiopsis":[66],"thaliana.":[67],"Three":[68],"feature":[69],"selection":[70],"strategies":[71],"investigated,":[73],"namely":[74],"use":[75,93],"known":[77],"motifs":[79,142],"drawn":[80],"from":[81],"PLACE":[83],"database,":[84],"explicit":[85],"enumeration":[86],"all":[88,111],"possible":[89,112],"k-mers":[90,113],"and":[91],"mismatch":[96],"kernels":[97],"(which":[98],"effectively":[99],"permits":[100],"construction":[102],"linear":[105],"space":[109],"with":[114],"up":[115],"mismatches).":[118],"leave-one-out":[120],"cross-validation":[121],"(LOOCV)":[122],"error":[123],"rate":[124],"indicates":[125],"that":[126],"approximately":[127],"two-thirds":[128],"observed":[131],"behaviour":[133],"can":[134],"inferred":[136],"by":[137],"presence":[139],"particular":[141],"sequence.":[147],"has":[150,156],"yielded":[151],"novel":[152],"biological":[153],"insight,":[154],"which":[155],"since":[157],"been":[158],"confirmed":[159],"experimentally":[160],"vivo.":[162]},"counts_by_year":[],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}