{"id":"https://openalex.org/W3199294754","doi":"https://doi.org/10.1007/s40747-021-00531-6","title":"Investigating deep feedforward neural networks for classification of transposon-derived piRNAs","display_name":"Investigating deep feedforward neural networks for classification of transposon-derived piRNAs","publication_year":2021,"publication_date":"2021-09-21","ids":{"openalex":"https://openalex.org/W3199294754","doi":"https://doi.org/10.1007/s40747-021-00531-6","mag":"3199294754"},"language":"en","primary_location":{"id":"doi:10.1007/s40747-021-00531-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40747-021-00531-6","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40747-021-00531-6.pdf","source":{"id":"https://openalex.org/S3035462843","display_name":"Complex & Intelligent Systems","issn_l":"2198-6053","issn":["2198-6053","2199-4536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Complex & Intelligent Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://link.springer.com/content/pdf/10.1007/s40747-021-00531-6.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050094609","display_name":"Alisson Hayasi da Costa","orcid":"https://orcid.org/0000-0003-3093-7067"},"institutions":[{"id":"https://openalex.org/I177909021","display_name":"Universidade Federal de S\u00e3o Carlos","ror":"https://ror.org/00qdc6m37","country_code":"BR","type":"education","lineage":["https://openalex.org/I177909021"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Alisson Hayasi da Costa","raw_affiliation_strings":["Department of Computer Science, Federal University of S\u00e3o Carlos, S\u00e3o Carlos, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-3093-7067","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Federal University of S\u00e3o Carlos, S\u00e3o Carlos, Brazil","institution_ids":["https://openalex.org/I177909021"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001692684","display_name":"Renato Santos","orcid":"https://orcid.org/0000-0003-0826-5479"},"institutions":[{"id":"https://openalex.org/I17974374","display_name":"Universidade de S\u00e3o Paulo","ror":"https://ror.org/036rp1748","country_code":"BR","type":"education","lineage":["https://openalex.org/I17974374"]},{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Renato Augusto Corr\u00eaa dos Santos","raw_affiliation_strings":["Institute of Biology, State University of Campinas, Campinas, Brazil","School of Pharmaceutical Sciences of Ribeir\u00e3o Preto, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil"],"raw_orcid":"https://orcid.org/0000-0003-0826-5479","affiliations":[{"raw_affiliation_string":"Institute of Biology, State University of Campinas, Campinas, Brazil","institution_ids":["https://openalex.org/I181391015"]},{"raw_affiliation_string":"School of Pharmaceutical Sciences of Ribeir\u00e3o Preto, University of S\u00e3o Paulo, Ribeir\u00e3o Preto, Brazil","institution_ids":["https://openalex.org/I17974374"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066866262","display_name":"Ricardo Cerri","orcid":"https://orcid.org/0000-0002-2582-1695"},"institutions":[{"id":"https://openalex.org/I177909021","display_name":"Universidade Federal de S\u00e3o Carlos","ror":"https://ror.org/00qdc6m37","country_code":"BR","type":"education","lineage":["https://openalex.org/I177909021"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Ricardo Cerri","raw_affiliation_strings":["Department of Computer Science, Federal University of S\u00e3o Carlos, S\u00e3o Carlos, Brazil"],"raw_orcid":"https://orcid.org/0000-0002-2582-1695","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Federal University of S\u00e3o Carlos, S\u00e3o Carlos, Brazil","institution_ids":["https://openalex.org/I177909021"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5050094609"],"corresponding_institution_ids":["https://openalex.org/I177909021"],"apc_list":{"value":1320,"currency":"GBP","value_usd":1619},"apc_paid":{"value":1320,"currency":"GBP","value_usd":1619},"fwci":0.3254,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.56705644,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"477","last_page":"487"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9993000030517578,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987999796867371,"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":0.9965000152587891,"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/transposable-element","display_name":"Transposable element","score":0.7022671103477478},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6804567575454712},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.6476245522499084},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6202213764190674},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5691401958465576},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5616872310638428},{"id":"https://openalex.org/keywords/multilayer-perceptron","display_name":"Multilayer perceptron","score":0.48382869362831116},{"id":"https://openalex.org/keywords/perceptron","display_name":"Perceptron","score":0.45963507890701294},{"id":"https://openalex.org/keywords/computational-intelligence","display_name":"Computational intelligence","score":0.4444500803947449},{"id":"https://openalex.org/keywords/piwi-interacting-rna","display_name":"Piwi-interacting RNA","score":0.43969637155532837},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4294910728931427},{"id":"https://openalex.org/keywords/transposition","display_name":"Transposition (logic)","score":0.4266456067562103},{"id":"https://openalex.org/keywords/feed-forward","display_name":"Feed forward","score":0.4152466356754303},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.27095699310302734},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23066985607147217},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10795709490776062},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09604600071907043},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08619320392608643}],"concepts":[{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.7022671103477478},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6804567575454712},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.6476245522499084},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6202213764190674},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5691401958465576},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5616872310638428},{"id":"https://openalex.org/C179717631","wikidata":"https://www.wikidata.org/wiki/Q2991667","display_name":"Multilayer perceptron","level":3,"score":0.48382869362831116},{"id":"https://openalex.org/C60908668","wikidata":"https://www.wikidata.org/wiki/Q690207","display_name":"Perceptron","level":3,"score":0.45963507890701294},{"id":"https://openalex.org/C139502532","wikidata":"https://www.wikidata.org/wiki/Q1122090","display_name":"Computational intelligence","level":2,"score":0.4444500803947449},{"id":"https://openalex.org/C147724379","wikidata":"https://www.wikidata.org/wiki/Q2367421","display_name":"Piwi-interacting RNA","level":5,"score":0.43969637155532837},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4294910728931427},{"id":"https://openalex.org/C12455157","wikidata":"https://www.wikidata.org/wiki/Q7835331","display_name":"Transposition (logic)","level":2,"score":0.4266456067562103},{"id":"https://openalex.org/C38858127","wikidata":"https://www.wikidata.org/wiki/Q5441228","display_name":"Feed forward","level":2,"score":0.4152466356754303},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.27095699310302734},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23066985607147217},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10795709490776062},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09604600071907043},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08619320392608643},{"id":"https://openalex.org/C133731056","wikidata":"https://www.wikidata.org/wiki/Q4917288","display_name":"Control engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s40747-021-00531-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40747-021-00531-6","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40747-021-00531-6.pdf","source":{"id":"https://openalex.org/S3035462843","display_name":"Complex & Intelligent Systems","issn_l":"2198-6053","issn":["2198-6053","2199-4536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Complex & Intelligent Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s40747-021-00531-6","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40747-021-00531-6","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40747-021-00531-6.pdf","source":{"id":"https://openalex.org/S3035462843","display_name":"Complex & Intelligent Systems","issn_l":"2198-6053","issn":["2198-6053","2199-4536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Complex & Intelligent Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3199294754.pdf","grobid_xml":"https://content.openalex.org/works/W3199294754.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1477866550","https://openalex.org/W1503398984","https://openalex.org/W1517808374","https://openalex.org/W1569512666","https://openalex.org/W1677182931","https://openalex.org/W1849277567","https://openalex.org/W1901129140","https://openalex.org/W1977733607","https://openalex.org/W1997270596","https://openalex.org/W2083617996","https://openalex.org/W2088338354","https://openalex.org/W2088341630","https://openalex.org/W2095705004","https://openalex.org/W2101234009","https://openalex.org/W2108421854","https://openalex.org/W2118420574","https://openalex.org/W2148105495","https://openalex.org/W2157663132","https://openalex.org/W2160828096","https://openalex.org/W2194775991","https://openalex.org/W2242464395","https://openalex.org/W2261380995","https://openalex.org/W2339812959","https://openalex.org/W2502949459","https://openalex.org/W2531409750","https://openalex.org/W2557283755","https://openalex.org/W2605763657","https://openalex.org/W2608035254","https://openalex.org/W2613718673","https://openalex.org/W2623396617","https://openalex.org/W2625425587","https://openalex.org/W2769569970","https://openalex.org/W2886966121","https://openalex.org/W2889689363","https://openalex.org/W2897418759","https://openalex.org/W2901318957","https://openalex.org/W2914484425","https://openalex.org/W2961926658","https://openalex.org/W2962972936","https://openalex.org/W2999044305","https://openalex.org/W3027555455","https://openalex.org/W3087535133","https://openalex.org/W3134165843","https://openalex.org/W4254965337","https://openalex.org/W4255949318"],"related_works":["https://openalex.org/W2158912913","https://openalex.org/W4221011377","https://openalex.org/W2027956742","https://openalex.org/W2924035798","https://openalex.org/W3192072282","https://openalex.org/W2965423738","https://openalex.org/W2796472296","https://openalex.org/W4366421230","https://openalex.org/W2013814485","https://openalex.org/W2111217101"],"abstract_inverted_index":{"Abstract":[0],"PIWI-interacting":[1],"RNAs":[2,10],"(piRNAS)":[3],"form":[4],"an":[5,68],"important":[6],"class":[7],"of":[8,31,37,47,77,127,138,150,160,178,191],"non-coding":[9],"that":[11,99],"play":[12],"a":[13,83,128,157],"key":[14],"role":[15],"in":[16,40],"gene":[17],"expression":[18],"regulation":[19],"and":[20,33,63,93,123,143,148],"genome":[21],"integrity":[22],"by":[23,96],"silencing":[24],"transposable":[25],"elements.":[26],"However,":[27],"despite":[28],"the":[29,34,115,125,146,176],"importance":[30],"piRNAs":[32,51,169,190],"large":[35],"application":[36],"deep":[38,48,71,90],"learning":[39,49,91],"computational":[41],"biology,":[42],"there":[43],"are":[44],"few":[45],"studies":[46],"for":[50,75,166],"prediction.":[52],"Still,":[53],"current":[54],"methods":[55,165],"focus":[56],"on":[57,70],"using":[58,114],"advanced":[59],"architectures":[60],"like":[61],"CNN":[62],"variations.":[64],"This":[65],"paper":[66],"presents":[67],"investigation":[69],"feedforward":[72],"network":[73],"models":[74],"classification":[76],"human":[78,167],"transposon-derived":[79,168],"piRNAs.":[80],"We":[81],"developed":[82],"lightweight":[84],"predictor":[85,155],"(when":[86],"compared":[87],"to":[88,173],"other":[89,163,192],"methods)":[92],"we":[94,120,181],"show":[95],"practical":[97],"evidence":[98],"simple":[100],"neural":[101,111],"networks":[102,112],"can":[103],"perform":[104],"as":[105,107,136],"well":[106],"better":[108,174],"than":[109],"complex":[110],"when":[113,188],"appropriate":[116],"hyperparameters.":[117],"For":[118],"that,":[119],"train,":[121],"analyze":[122],"compare":[124],"results":[126,187],"multilayer":[129],"perceptron":[130],"with":[131],"different":[132],"hyperparameter":[133],"choices,":[134],"such":[135],"numbers":[137],"hidden":[139],"layers,":[140],"activation":[141],"functions":[142],"optimizers,":[144],"clarifying":[145],"advantages":[147],"disadvantages":[149],"each":[151],"choice.":[152],"Our":[153],"proposed":[154],"reached":[156],"F":[158],"-score":[159],"0.872,":[161],"outperforming":[162],"state-of-the-art":[164],"classification.":[170],"In":[171],"addition,":[172],"access":[175],"generalization":[177],"our":[179],"proposal,":[180],"also":[182],"showed":[183],"it":[184],"achieved":[185],"competitive":[186],"classifying":[189],"species.":[193]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-20T23:13:51.555489","created_date":"2025-10-10T00:00:00"}