{"id":"https://openalex.org/W4220776586","doi":"https://doi.org/10.1109/access.2022.3156888","title":"Solving the Protein Secondary Structure Prediction Problem With the Hessian Free Optimization Algorithm","display_name":"Solving the Protein Secondary Structure Prediction Problem With the Hessian Free Optimization Algorithm","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4220776586","doi":"https://doi.org/10.1109/access.2022.3156888"},"language":"en","primary_location":{"id":"doi:10.1109/access.2022.3156888","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3156888","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09729724.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09729724.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038032119","display_name":"Konstantinos Charalampous","orcid":"https://orcid.org/0000-0002-6885-338X"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Konstantinos Charalampous","raw_affiliation_strings":["Department of Computer Science, University of Cyprus, Nicosia, Cyprus"],"raw_orcid":"https://orcid.org/0000-0002-6885-338X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102885257","display_name":"Michalis Agathocleous","orcid":"https://orcid.org/0000-0003-3557-0196"},"institutions":[{"id":"https://openalex.org/I17389662","display_name":"University of Nicosia","ror":"https://ror.org/04v18t651","country_code":"CY","type":"education","lineage":["https://openalex.org/I17389662"]},{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Michalis Agathocleous","raw_affiliation_strings":["Department of Computer Science, University of Cyprus, Nicosia, Cyprus","Department of Computer Science, University of Nicosia, Nicosia, Cyprus"],"raw_orcid":"https://orcid.org/0000-0003-3557-0196","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]},{"raw_affiliation_string":"Department of Computer Science, University of Nicosia, Nicosia, Cyprus","institution_ids":["https://openalex.org/I17389662"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068564622","display_name":"Chris Christodoulou","orcid":"https://orcid.org/0000-0001-9398-5256"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Chris Christodoulou","raw_affiliation_strings":["Department of Computer Science, University of Cyprus, Nicosia, Cyprus"],"raw_orcid":"https://orcid.org/0000-0001-9398-5256","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070268749","display_name":"Vasilis J. Promponas","orcid":"https://orcid.org/0000-0003-3352-4831"},"institutions":[{"id":"https://openalex.org/I34771391","display_name":"University of Cyprus","ror":"https://ror.org/02qjrjx09","country_code":"CY","type":"education","lineage":["https://openalex.org/I34771391"]}],"countries":["CY"],"is_corresponding":false,"raw_author_name":"Vasilis Promponas","raw_affiliation_strings":["Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus"],"raw_orcid":"https://orcid.org/0000-0003-3352-4831","affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus","institution_ids":["https://openalex.org/I34771391"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.3465,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.54185631,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"10","issue":null,"first_page":"27759","last_page":"27770"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991999864578247,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9991999864578247,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9926999807357788,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9638000130653381,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6310862302780151},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6290774345397949},{"id":"https://openalex.org/keywords/recurrent-neural-network","display_name":"Recurrent neural network","score":0.6025417447090149},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5956932902336121},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5442938208580017},{"id":"https://openalex.org/keywords/hessian-matrix","display_name":"Hessian matrix","score":0.5299378633499146},{"id":"https://openalex.org/keywords/backpropagation","display_name":"Backpropagation","score":0.4593297839164734},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4289684295654297},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.4282605051994324},{"id":"https://openalex.org/keywords/feedforward-neural-network","display_name":"Feedforward neural network","score":0.42119747400283813},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21977463364601135}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6310862302780151},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6290774345397949},{"id":"https://openalex.org/C147168706","wikidata":"https://www.wikidata.org/wiki/Q1457734","display_name":"Recurrent neural network","level":3,"score":0.6025417447090149},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5956932902336121},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5442938208580017},{"id":"https://openalex.org/C203616005","wikidata":"https://www.wikidata.org/wiki/Q620495","display_name":"Hessian matrix","level":2,"score":0.5299378633499146},{"id":"https://openalex.org/C155032097","wikidata":"https://www.wikidata.org/wiki/Q798503","display_name":"Backpropagation","level":3,"score":0.4593297839164734},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4289684295654297},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.4282605051994324},{"id":"https://openalex.org/C47702885","wikidata":"https://www.wikidata.org/wiki/Q5441227","display_name":"Feedforward neural network","level":3,"score":0.42119747400283813},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21977463364601135},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2022.3156888","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3156888","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09729724.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:709439a7518a4deb895ed7f79b4128d2","is_oa":true,"landing_page_url":"https://doaj.org/article/709439a7518a4deb895ed7f79b4128d2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 10, Pp 27759-27770 (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2022.3156888","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2022.3156888","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/9668973/09729724.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4220776586.pdf","grobid_xml":"https://content.openalex.org/works/W4220776586.grobid-xml"},"referenced_works_count":81,"referenced_works":["https://openalex.org/W109016873","https://openalex.org/W196761320","https://openalex.org/W1408639475","https://openalex.org/W1499450468","https://openalex.org/W1522301498","https://openalex.org/W1529355025","https://openalex.org/W1597121099","https://openalex.org/W1845127254","https://openalex.org/W1851970720","https://openalex.org/W1873332500","https://openalex.org/W1915676028","https://openalex.org/W1979826517","https://openalex.org/W1987856282","https://openalex.org/W1996073320","https://openalex.org/W2006903949","https://openalex.org/W2008708467","https://openalex.org/W2013136212","https://openalex.org/W2016879831","https://openalex.org/W2022747340","https://openalex.org/W2025634149","https://openalex.org/W2045520172","https://openalex.org/W2045676435","https://openalex.org/W2051812123","https://openalex.org/W2058580716","https://openalex.org/W2064675550","https://openalex.org/W2065000345","https://openalex.org/W2076063813","https://openalex.org/W2079735306","https://openalex.org/W2080603857","https://openalex.org/W2081556853","https://openalex.org/W2087894810","https://openalex.org/W2096495474","https://openalex.org/W2100128988","https://openalex.org/W2100697211","https://openalex.org/W2104893957","https://openalex.org/W2104972430","https://openalex.org/W2107878631","https://openalex.org/W2110425545","https://openalex.org/W2111928547","https://openalex.org/W2119423166","https://openalex.org/W2125036621","https://openalex.org/W2130984546","https://openalex.org/W2131474431","https://openalex.org/W2131774270","https://openalex.org/W2134299061","https://openalex.org/W2142893109","https://openalex.org/W2147905080","https://openalex.org/W2148557779","https://openalex.org/W2153153865","https://openalex.org/W2156798505","https://openalex.org/W2158714788","https://openalex.org/W2166221216","https://openalex.org/W2171865010","https://openalex.org/W2226390861","https://openalex.org/W2234163201","https://openalex.org/W2297901687","https://openalex.org/W2509860925","https://openalex.org/W2567587907","https://openalex.org/W2578980197","https://openalex.org/W2607268717","https://openalex.org/W2622826443","https://openalex.org/W2791790018","https://openalex.org/W2892552174","https://openalex.org/W2952317511","https://openalex.org/W2963457143","https://openalex.org/W2999044305","https://openalex.org/W3012879224","https://openalex.org/W3021559842","https://openalex.org/W3038831242","https://openalex.org/W3042567394","https://openalex.org/W3083777350","https://openalex.org/W3093108887","https://openalex.org/W3101287485","https://openalex.org/W4239510810","https://openalex.org/W4254816979","https://openalex.org/W6608133726","https://openalex.org/W6628131027","https://openalex.org/W6631190155","https://openalex.org/W6639175750","https://openalex.org/W6639240478","https://openalex.org/W6684470315"],"related_works":["https://openalex.org/W97768505","https://openalex.org/W2918103456","https://openalex.org/W2080531293","https://openalex.org/W4300200276","https://openalex.org/W1856772668","https://openalex.org/W1939602702","https://openalex.org/W2023914354","https://openalex.org/W2540883726","https://openalex.org/W3005666459","https://openalex.org/W4298020725"],"abstract_inverted_index":{"Trying":[0],"to":[1,36,203,238],"extract":[2],"features":[3],"from":[4],"complex":[5],"sequential":[6,67],"data":[7],"for":[8,157,216],"classification":[9],"and":[10,28,77,136,224,262,305],"prediction":[11],"problems":[12],"is":[13,20,34,52,116],"an":[14,175],"extremely":[15],"difficult":[16],"task.":[17],"This":[18],"task":[19],"even":[21],"more":[22,137],"challenging":[23],"when":[24],"both":[25],"the":[26,38,81,95,119,123,144,151,158,169,190,194,199,206,209,258,277,295],"upstream":[27],"downstream":[29],"information":[30],"of":[31,75,108,118,125,146,196,205,208,283,294,309],"a":[32,41,164,298],"time-series":[33],"important":[35,300],"process":[37],"sequence":[39],"at":[40],"specific":[42],"time-step.":[43],"One":[44],"typical":[45],"problem":[46],"which":[47,132,212,234,286],"falls":[48],"in":[49,65,73,99,105,122],"this":[50,106,140,217],"category":[51,107],"Protein":[53],"Secondary":[54],"Structure":[55],"Prediction":[56],"(PSSP).":[57],"Recurrent":[58],"Neural":[59,86,127],"Networks":[60,87],"(RNNs)":[61],"have":[62,213,230],"been":[63,214,232,255],"successful":[64],"handling":[66],"data.":[68],"These":[69],"methods":[70,211],"are":[71,201],"demanding":[72],"terms":[74],"time":[76],"space":[78],"efficiency.":[79],"On":[80],"other":[82,292],"hand,":[83],"simple":[84,147],"Feed-Forward":[85],"(FFNNs)":[88],"can":[89,133,173],"be":[90],"trained":[91,149,167],"really":[92],"fast":[93,307],"with":[94,150,168,226,302],"Backpropagation":[96],"algorithm,":[97],"but":[98],"practice":[100],"they":[101],"give":[102],"poor":[103],"results":[104,200,237],"problems.":[109],"The":[110],"Hessian":[111],"Free":[112],"Optimization":[113],"(HFO)":[114],"algorithm":[115,156,172],"one":[117],"latest":[120],"developments":[121],"field":[124],"Artificial":[126],"Network":[128],"(ANN)":[129],"training":[130,288,308],"algorithms":[131],"converge":[134],"faster":[135,290],"accurately.":[138],"In":[139,161],"paper,":[141],"we":[142],"present":[143],"implementation":[145],"FFNNs":[148],"powerful":[152],"HFO":[153,170,278],"second-order":[154],"learning":[155,171],"PSSP":[159],"problem.":[160,218],"our":[162,197,236,252],"approach,":[163],"single":[165],"FFNN":[166,310],"achieve":[174],"approximately":[176],"79.6%":[177],"per":[178,240,265],"residue":[179,241,266],"(":[180,242,267],"<inline-formula":[181,243,268],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[182,244,269],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">":[183,245,270],"<tex-math":[184,246,271],"notation=\"LaTeX\">$Q_{3}$":[185,247,272],"</tex-math></inline-formula>":[186,248,273],")":[187,249,274],"accuracy":[188],"on":[189,257],"PISCES":[191],"dataset.":[192],"Despite":[193],"simplicity":[195],"method,":[198],"comparable":[202],"some":[204],"state":[207,293],"art":[210,296],"designed":[215],"A":[219],"majority":[220],"voting":[221],"ensemble":[222],"method":[223,253],"filtering":[225],"Support":[227],"Vector":[228],"Machines":[229],"also":[231],"applied,":[233],"increase":[235],"80.4%":[239],"accuracy.":[250,275],"Finally,":[251],"has":[254],"tested":[256],"CASP13":[259],"independent":[260],"dataset":[261],"achieved":[263],"78.14%":[264],"Moreover,":[276],"does":[279],"not":[280],"require":[281],"tuning":[282],"any":[284],"parameters":[285],"makes":[287],"much":[289],"than":[291],"methods,":[297],"very":[299],"feature":[301],"big":[303],"datasets":[304],"facilitates":[306],"ensembles.":[311]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
