{"id":"https://openalex.org/W3090543969","doi":"https://doi.org/10.1109/access.2020.3027887","title":"Identification of Pathway-Specific Protein Domain by Incorporating Hyperparameter Optimization Based on 2D Convolutional Neural Network","display_name":"Identification of Pathway-Specific Protein Domain by Incorporating Hyperparameter Optimization Based on 2D Convolutional Neural Network","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3090543969","doi":"https://doi.org/10.1109/access.2020.3027887","mag":"3090543969"},"language":"en","primary_location":{"id":"doi:10.1109/access.2020.3027887","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3027887","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09210038.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/ielx7/6287639/8948470/09210038.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5110714403","display_name":"Ali Ghualm","orcid":null},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ali Ghualm","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","School of Computer Science, Shaanxi Normal University, Xi'an, China"],"raw_orcid":"https://orcid.org/0000-0001-5166-2213","affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","institution_ids":["https://openalex.org/I88830068"]},{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi'an, China","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058768577","display_name":"Xiujuan Lei","orcid":"https://orcid.org/0000-0002-9901-1732"},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiujuan Lei","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","School of Computer Science, Shaanxi Normal University, Xi'an, China"],"raw_orcid":"https://orcid.org/0000-0002-9901-1732","affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","institution_ids":["https://openalex.org/I88830068"]},{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi'an, China","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100424310","display_name":"Yuchen Zhang","orcid":"https://orcid.org/0000-0002-1211-2427"},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuchen Zhang","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","School of Computer Science, Shaanxi Normal University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","institution_ids":["https://openalex.org/I88830068"]},{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi'an, China","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024454462","display_name":"Shi Cheng","orcid":"https://orcid.org/0000-0002-5129-995X"},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shi Cheng","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","School of Computer Science, Shaanxi Normal University, Xi'an, China"],"raw_orcid":"https://orcid.org/0000-0002-5129-995X","affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","institution_ids":["https://openalex.org/I88830068"]},{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi'an, China","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102741318","display_name":"Min Guo","orcid":"https://orcid.org/0000-0001-6453-7892"},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Min Guo","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","School of Computer Science, Shaanxi Normal University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi\u2019an, China","institution_ids":["https://openalex.org/I88830068"]},{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University, Xi'an, China","institution_ids":["https://openalex.org/I88830068"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5110714403"],"corresponding_institution_ids":["https://openalex.org/I88830068"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.6669,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.67915749,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"8","issue":null,"first_page":"180140","last_page":"180155"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9966999888420105,"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/hyperparameter","display_name":"Hyperparameter","score":0.6777533888816833},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.637618899345398},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5870789289474487},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5109369158744812},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4866209924221039},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46775388717651367},{"id":"https://openalex.org/keywords/cross-validation","display_name":"Cross-validation","score":0.41775017976760864},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3581366539001465},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20341762900352478}],"concepts":[{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.6777533888816833},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.637618899345398},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5870789289474487},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5109369158744812},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4866209924221039},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46775388717651367},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.41775017976760864},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3581366539001465},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20341762900352478}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2020.3027887","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3027887","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09210038.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:db49238d41ea470cb59c44f656b26011","is_oa":true,"landing_page_url":"https://doaj.org/article/db49238d41ea470cb59c44f656b26011","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 8, Pp 180140-180155 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2020.3027887","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.3027887","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09210038.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":[{"id":"https://openalex.org/G450443699","display_name":null,"funder_award_id":"61972451","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7417567555","display_name":null,"funder_award_id":"61672334","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7717298466","display_name":null,"funder_award_id":"GK201901010","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8279569169","display_name":null,"funder_award_id":"61902230","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8513270824","display_name":null,"funder_award_id":"61672334","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G8535955237","display_name":null,"funder_award_id":"GK201901010","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3090543969.pdf","grobid_xml":"https://content.openalex.org/works/W3090543969.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1937783148","https://openalex.org/W1981253524","https://openalex.org/W1987482901","https://openalex.org/W2000118138","https://openalex.org/W2000688771","https://openalex.org/W2015805015","https://openalex.org/W2028511475","https://openalex.org/W2035334446","https://openalex.org/W2045389157","https://openalex.org/W2081119171","https://openalex.org/W2092113847","https://openalex.org/W2097606916","https://openalex.org/W2115434912","https://openalex.org/W2134394193","https://openalex.org/W2139754669","https://openalex.org/W2146164120","https://openalex.org/W2147863530","https://openalex.org/W2150398411","https://openalex.org/W2155491969","https://openalex.org/W2159130523","https://openalex.org/W2162491184","https://openalex.org/W2171641243","https://openalex.org/W2401231614","https://openalex.org/W2412782625","https://openalex.org/W2522042227","https://openalex.org/W2539330442","https://openalex.org/W2564018391","https://openalex.org/W2588229031","https://openalex.org/W2651986237","https://openalex.org/W2755930428","https://openalex.org/W2761197040","https://openalex.org/W2770747919","https://openalex.org/W2783839600","https://openalex.org/W2789303432","https://openalex.org/W2798016132","https://openalex.org/W2885808649","https://openalex.org/W2895084243","https://openalex.org/W2914380827","https://openalex.org/W2944764218","https://openalex.org/W2946297791","https://openalex.org/W2951092885","https://openalex.org/W2964121744","https://openalex.org/W2964137095","https://openalex.org/W2965351431","https://openalex.org/W2997405786","https://openalex.org/W3015124682","https://openalex.org/W3037207689","https://openalex.org/W3046219306","https://openalex.org/W6631190155"],"related_works":["https://openalex.org/W4206951940","https://openalex.org/W4293868382","https://openalex.org/W4382602594","https://openalex.org/W2892606308","https://openalex.org/W4387850423","https://openalex.org/W4289492418","https://openalex.org/W3161669023","https://openalex.org/W4388528726","https://openalex.org/W2602382373","https://openalex.org/W3198113463"],"abstract_inverted_index":{"Pathway-specific":[0],"protein":[1,10,84],"domain":[2,85],"(PSPD)":[3],"are":[4,12,21,103],"associated":[5,133,156],"with":[6,81,134,139,157,237,246],"specific":[7,24,310],"pathways.":[8,25,64],"Many":[9,26],"domains":[11,20],"pervasive":[13],"in":[14,221,230,267,285],"various":[15],"biological":[16,277],"processes,":[17],"whereas":[18],"other":[19,238],"linked":[22,104],"to":[23,52,105,166,178,298],"human":[27,61],"disease":[28,62],"pathways,":[29],"such":[30,304],"as":[31,126,305],"cancer":[32],"pathways":[33],"and":[34,63,99,116,146,172,206,225,253,271,294,308],"signaling":[35],"pathway-related":[36],"diseases,":[37],"have":[38],"caused":[39],"the":[40,46,91,106,131,135,140,150,168,174,180,188,195,199,212,228,234,262,268,286,288,291,295],"loss":[41],"of":[42,48,90,93,122,149,198,214,233,264,290,302],"functional":[43],"PSPD.":[44],"Therefore,":[45,209],"creation":[47],"an":[49,258],"accurate":[50],"method":[51,242,260],"predict":[53,299],"its":[54,96,100],"roles":[55],"is":[56,219],"a":[57,70,76,82,94,111,117],"critical":[58],"step":[59],"toward":[60],"In":[65,88],"this":[66],"study,":[67],"we":[68,129,193,210],"proposed":[69,110,159,241,269,282],"deep":[71,215],"learning":[72,216],"model":[73,115,121,145,148,182,201,283],"based":[74,186],"on":[75,187],"two-dimensional":[77],"neural":[78],"network":[79],"(2D-CNN-PSPD)":[80],"pathway-specific":[83],"association":[86,229],"prediction.":[87],"terms":[89],"purposes":[92],"sub-pathway,":[95],"parent":[97],"pathway":[98,102,224,235],"super":[101],"Uni-Pathway.":[107],"We":[108,162,256,279],"also":[109],"dipeptide":[112,118],"composition":[113],"(DPC)":[114],"deviation":[119],"(DDE)":[120],"feature":[123,152],"extraction":[124],"profiles":[125],"PSSM.":[127],"Then,":[128],"predicted":[130],"proteins":[132,266,311],"same":[136,141],"sub-pathway":[137],"or":[138],"organism.":[142],"The":[143],"DDE":[144],"DPC":[147],"PSSM":[151],"profile":[153],"input":[154],"was":[155],"our":[158,184,272,281],"2D-CNN":[160],"method.":[161],"deployed":[163],"several":[164],"parameters":[165],"optimize":[167],"model's":[169],"output":[170],"performance":[171,197],"used":[173],"hyperparameter":[175],"optimization":[176],"approach":[177],"find":[179],"best":[181],"for":[183,261],"dataset":[185],"10-fold":[189],"cross-validation":[190,207],"results.":[191],"Ultimately,":[192],"assessed":[194],"predictive":[196],"current":[200],"by":[202],"using":[203],"independent":[204],"datasets":[205],"datasets.":[208],"enhanced":[211],"efficiency":[213],"methods.":[217],"PSPD":[218,265],"involved":[220],"any":[222],"known":[223],"then":[226],"follow":[227],"different":[231,300],"stages":[232],"hierarchy":[236],"proteins.":[239],"Our":[240],"could":[243],"identify":[244],"2D-CNN-PSPD":[245],"0.83%":[247],"sensitivity,":[248],"0.92%":[249],"specificity,":[250],"87.27%":[251],"accuracy,":[252],"0.75%":[254],"accuracy.":[255],"provided":[257],"important":[259],"analysis":[263],"research,":[270],"achievements":[273],"might":[274],"promote":[275],"computational":[276],"research.":[278],"concluded":[280],"architecture":[284],"future,":[287],"use":[289],"latest":[292],"features,":[293],"multi-one":[296],"structure":[297],"types":[301],"molecules,":[303],"DNA,":[306],"RNA,":[307],"disease-pathway":[309],"associations.":[312]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}