{"id":"https://openalex.org/W3207243472","doi":null,"title":"Image Representations of DNA allow Classification by Convolutional Neural Networks","display_name":"Image Representations of DNA allow Classification by Convolutional Neural Networks","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3207243472","mag":"3207243472"},"language":"en","primary_location":{"id":"pmh:oai:etheses.whiterose.ac.uk:28875","doi":null,"is_oa":true,"landing_page_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","pdf_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","source":{"id":"https://openalex.org/S4306401585","display_name":"White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086453503","display_name":"Joshua Hope","orcid":"https://orcid.org/0000-0003-2742-5538","observed_orcids":["https://orcid.org/0000-0003-2742-5538"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hope, Joshua","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5086453503"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.7842000126838684,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.7842000126838684,"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":0.11100000143051147,"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":0.08869999647140503,"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/dna-sequence-classification","display_name":"DNA sequence classification","score":0.972000002861023},{"id":"https://openalex.org/keywords/convolutional-neural-networks","display_name":"convolutional neural networks","score":0.8640000224113464},{"id":"https://openalex.org/keywords/chaos-game-representation","display_name":"chaos game representation","score":0.7960000038146973},{"id":"https://openalex.org/keywords/archaea","display_name":"archaea","score":0.9269999861717224},{"id":"https://openalex.org/keywords/metagenomics","display_name":"metagenomics","score":0.8240000009536743},{"id":"https://openalex.org/keywords/anaerobic-digestion","display_name":"anaerobic digestion","score":0.8399999737739563},{"id":"https://openalex.org/keywords/sequence-shuffling","display_name":"sequence shuffling","score":0.7020000219345093},{"id":"https://openalex.org/keywords/ensemble-methods","display_name":"ensemble methods","score":0.8920000195503235}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7707842588424683},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.6671290397644043},{"id":"https://openalex.org/C167927819","wikidata":"https://www.wikidata.org/wiki/Q1930567","display_name":"Shuffling","level":2,"score":0.6559818983078003},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6165282726287842},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5928677916526794},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5516850352287292},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5337947607040405},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5158221125602722},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.48276105523109436},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.46554622054100037},{"id":"https://openalex.org/C2279292","wikidata":"https://www.wikidata.org/wiki/Q6322851","display_name":"k-mer","level":4,"score":0.46206578612327576},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4416123330593109},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.427388072013855},{"id":"https://openalex.org/C550995028","wikidata":"https://www.wikidata.org/wiki/Q10872","display_name":"Archaea","level":3,"score":0.41379567980766296},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33462172746658325},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.305229127407074},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2630327641963959},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20268335938453674},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10104283690452576},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08401384949684143},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:etheses.whiterose.ac.uk:28875","doi":null,"is_oa":true,"landing_page_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","pdf_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","source":{"id":"https://openalex.org/S4306401585","display_name":"White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis"}],"best_oa_location":{"id":"pmh:oai:etheses.whiterose.ac.uk:28875","doi":null,"is_oa":true,"landing_page_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","pdf_url":"https://etheses.whiterose.ac.uk/28875/1/Hope_202003443_CorrectedThesisClean.pdf","source":{"id":"https://openalex.org/S4306401585","display_name":"White Rose eTheses Online (University of Leeds, The University of Sheffield, University of York)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2800616092","host_organization_name":"White Rose University Consortium","host_organization_lineage":["https://openalex.org/I2800616092"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3207243472.pdf","grobid_xml":"https://content.openalex.org/works/W3207243472.grobid-xml"},"referenced_works_count":63,"referenced_works":["https://openalex.org/W88991049","https://openalex.org/W1590550687","https://openalex.org/W1686810756","https://openalex.org/W1836465849","https://openalex.org/W1850079471","https://openalex.org/W1904365287","https://openalex.org/W1912338927","https://openalex.org/W1963946970","https://openalex.org/W1976728592","https://openalex.org/W1983540000","https://openalex.org/W1999704304","https://openalex.org/W2014254156","https://openalex.org/W2036145579","https://openalex.org/W2048721314","https://openalex.org/W2049702154","https://openalex.org/W2052903982","https://openalex.org/W2068308871","https://openalex.org/W2069143585","https://openalex.org/W2072812562","https://openalex.org/W2084734290","https://openalex.org/W2112796928","https://openalex.org/W2130942839","https://openalex.org/W2147768505","https://openalex.org/W2161172839","https://openalex.org/W2163605009","https://openalex.org/W2179933869","https://openalex.org/W2210969396","https://openalex.org/W2345658906","https://openalex.org/W2507380695","https://openalex.org/W2519796145","https://openalex.org/W2743255823","https://openalex.org/W2781129742","https://openalex.org/W2782970864","https://openalex.org/W2792919287","https://openalex.org/W2795247881","https://openalex.org/W2798048710","https://openalex.org/W2809485291","https://openalex.org/W2885094215","https://openalex.org/W2887220719","https://openalex.org/W2901438556","https://openalex.org/W2902617128","https://openalex.org/W2906991531","https://openalex.org/W2908510526","https://openalex.org/W2912950612","https://openalex.org/W2917557027","https://openalex.org/W2917563777","https://openalex.org/W2922340657","https://openalex.org/W2953229963","https://openalex.org/W2956911640","https://openalex.org/W2962843949","https://openalex.org/W2963266267","https://openalex.org/W2963600922","https://openalex.org/W2964121744","https://openalex.org/W2981593585","https://openalex.org/W2984353870","https://openalex.org/W3008594856","https://openalex.org/W3030163527","https://openalex.org/W3086177986","https://openalex.org/W3094502228","https://openalex.org/W3177096435","https://openalex.org/W4226318754","https://openalex.org/W4233358305","https://openalex.org/W6982273903"],"related_works":["https://openalex.org/W3178677023","https://openalex.org/W2968770021","https://openalex.org/W2343416635","https://openalex.org/W2555479509","https://openalex.org/W4412655711","https://openalex.org/W3006059006","https://openalex.org/W2587659621","https://openalex.org/W2963600922","https://openalex.org/W7212013114","https://openalex.org/W3120828528"],"abstract_inverted_index":{"In":[0,55],"metagenomic":[1],"analyses":[2],"the":[3,17,35,44,119,125,132,148,163,178,190],"rapid":[4],"and":[5,97,103,121,144,221],"accurate":[6],"identification":[7],"of":[8,19,38,46,74,90,101,124,192,205],"DNA":[9,72,91],"sequences":[10,73,106,154],"is":[11,14],"important.":[12],"This":[13],"confounded":[15],"by":[16,152],"existence":[18],"novel":[20,201],"species":[21],"not":[22],"contained":[23],"in":[24,79,212],"databases.":[25],"There":[26],"exist":[27],"many":[28],"methods":[29,50,217],"to":[30,58,64,70,183,223],"identify":[31,224],"sequences,":[32,92],"but":[33],"with":[34],"increasing":[36],"amounts":[37],"sequencing":[39],"data":[40],"from":[41],"high-throughput":[42],"technologies,":[43],"use":[45,65,191],"new":[47],"deep":[48],"learning":[49,115],"are":[51,77],"made":[52],"more":[53],"viable.":[54],"an":[56,170],"attempt":[57],"address":[59],"this":[60],"it":[61,159],"was":[62,129,147,160,174,181],"decided":[63],"Convolutional":[66],"Neural":[67],"Networks":[68],"(CNNs)":[69],"classify":[71],"archaea,":[75],"which":[76],"important":[78,171],"anaerobic":[80],"digestion.":[81],"CNNs":[82,138],"were":[83,107,110,208],"trained":[84,117,139],"on":[85,118,140,189],"two":[86],"different":[87],"image":[88,142],"representations":[89],"Chaos":[93],"Game":[94],"Representation":[95],"(CGR)":[96],"Reshape.":[98],"Three":[99],"phyla":[100],"archaea":[102],"randomly":[104],"generated":[105],"used.":[108],"These":[109],"compared":[111],"against":[112],"simpler":[113,133],"machine":[114],"models":[116,134,207],"4-mer":[120,157],"7-mer":[122],"frequencies":[123],"same":[126],"sequences.":[127,226],"It":[128,173],"found":[130,161,176],"that":[131,145,162,177,195],"performed":[135],"better":[136],"than":[137],"either":[141],"representation,":[143],"Reshape":[146,164,179],"poorest":[149],"representation.":[150],"However,":[151],"shuffling":[153],"whilst":[155],"preserving":[156],"count":[158],"model":[165,180],"had":[166],"learnt":[167],"4-mers":[168],"as":[169],"feature.":[172],"also":[175,209],"able":[182],"perform":[184],"equally":[185],"well":[186],"without":[187],"depending":[188],"4-mers,":[193],"indicating":[194],"certain":[196],"training":[197],"regimes":[198],"may":[199],"uncover":[200],"features.":[202],"The":[203],"errors":[204],"these":[206],"random":[210],"or":[211],"weak":[213],"disagreement,":[214],"suggesting":[215],"ensemble":[216],"would":[218],"be":[219],"viable":[220],"help":[222],"problematic":[225]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2025-10-10T00:00:00"}
