{"id":"https://openalex.org/W2928148386","doi":"https://doi.org/10.1109/access.2019.2907132","title":"Improved Prediction of Protein-Protein Interactions Using Descriptors Derived From PSSM via Gray Level Co-Occurrence Matrix","display_name":"Improved Prediction of Protein-Protein Interactions Using Descriptors Derived From PSSM via Gray Level Co-Occurrence Matrix","publication_year":2019,"publication_date":"2019-01-01","ids":{"openalex":"https://openalex.org/W2928148386","doi":"https://doi.org/10.1109/access.2019.2907132","mag":"2928148386"},"language":"en","primary_location":{"id":"doi:10.1109/access.2019.2907132","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2019.2907132","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08673760.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/ielx7/6287639/8600701/08673760.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103159012","display_name":"Huijuan Zhu","orcid":"https://orcid.org/0000-0002-5743-4972"},"institutions":[{"id":"https://openalex.org/I115592961","display_name":"Jiangsu University","ror":"https://ror.org/03jc41j30","country_code":"CN","type":"education","lineage":["https://openalex.org/I115592961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui-Juan Zhu","raw_affiliation_strings":["School of Computer Science and Communication Engineering, Jiangsu University, Zhenjiang, China"],"raw_orcid":"https://orcid.org/0000-0002-5743-4972","affiliations":[{"raw_affiliation_string":"School of Computer Science and Communication Engineering, Jiangsu University, Zhenjiang, China","institution_ids":["https://openalex.org/I115592961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019805735","display_name":"Zhu\u2010Hong You","orcid":"https://orcid.org/0000-0003-1266-2696"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106108","display_name":"Xinjiang Technical Institute of Physics & Chemistry","ror":"https://ror.org/00x44h034","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhu-Hong You","raw_affiliation_strings":["Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi, China"],"raw_orcid":"https://orcid.org/0000-0003-1266-2696","affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110605891","display_name":"Wei-Lei Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106108","display_name":"Xinjiang Technical Institute of Physics & Chemistry","ror":"https://ror.org/00x44h034","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei-Lei Shi","raw_affiliation_strings":["Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101900611","display_name":"Shoukun Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210153482","display_name":"Changzhou University","ror":"https://ror.org/04ymgwq66","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210153482"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shou-Kun Xu","raw_affiliation_strings":["School of Information Science and Engineering, Changzhou University, Changzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Changzhou University, Changzhou, China","institution_ids":["https://openalex.org/I4210153482"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Tong-Hai Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106108","display_name":"Xinjiang Technical Institute of Physics & Chemistry","ror":"https://ror.org/00x44h034","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tong-Hai Jiang","raw_affiliation_strings":["Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences, Xinjiang Technical Institute of Physics and Chemistry, Urumqi, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106108"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102212402","display_name":"Lihua Zhuang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210153482","display_name":"Changzhou University","ror":"https://ror.org/04ymgwq66","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210153482"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li-Hua Zhuang","raw_affiliation_strings":["School of Information Science and Engineering, Changzhou University, Changzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Changzhou University, Changzhou, China","institution_ids":["https://openalex.org/I4210153482"]}]}],"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":0.6826,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.66748445,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"7","issue":null,"first_page":"49456","last_page":"49465"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9995999932289124,"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":0.9995999932289124,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991000294685364,"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":0.9965999722480774,"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/computer-science","display_name":"Computer science","score":0.5474368929862976},{"id":"https://openalex.org/keywords/co-occurrence-matrix","display_name":"Co-occurrence matrix","score":0.4960697591304779},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4604192078113556},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45697885751724243},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.42193418741226196},{"id":"https://openalex.org/keywords/gray-level","display_name":"Gray level","score":0.41908252239227295},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3514062762260437},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.21803489327430725},{"id":"https://openalex.org/keywords/image-processing","display_name":"Image processing","score":0.12431281805038452},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08631998300552368},{"id":"https://openalex.org/keywords/image-texture","display_name":"Image texture","score":0.07196357846260071},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.06609952449798584}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5474368929862976},{"id":"https://openalex.org/C117479156","wikidata":"https://www.wikidata.org/wiki/Q1543908","display_name":"Co-occurrence matrix","level":5,"score":0.4960697591304779},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4604192078113556},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45697885751724243},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.42193418741226196},{"id":"https://openalex.org/C2985861186","wikidata":"https://www.wikidata.org/wiki/Q685727","display_name":"Gray level","level":3,"score":0.41908252239227295},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3514062762260437},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.21803489327430725},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.12431281805038452},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08631998300552368},{"id":"https://openalex.org/C63099799","wikidata":"https://www.wikidata.org/wiki/Q17147001","display_name":"Image texture","level":4,"score":0.07196357846260071},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.06609952449798584},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2019.2907132","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2019.2907132","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08673760.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:6bc5d8e2d27a4b2db993535f40ad00b9","is_oa":true,"landing_page_url":"https://doaj.org/article/6bc5d8e2d27a4b2db993535f40ad00b9","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 7, Pp 49456-49465 (2019)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2019.2907132","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2019.2907132","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8600701/08673760.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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6200000047683716}],"awards":[{"id":"https://openalex.org/G2067085294","display_name":null,"funder_award_id":"61802154","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3158980518","display_name":"\u57fa\u4e8e\u6c28\u57fa\u9178\u5e8f\u5217\u53ca\u836f\u7269\u5316\u5408\u7269\u5206\u5b50\u6307\u7eb9\u7684\u836f\u7269\uff0d\u9776\u6807\u76f8\u4e92\u4f5c\u7528\u9884\u6d4b\u7814\u7a76","funder_award_id":"61572506","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G82793888","display_name":null,"funder_award_id":"61722212","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2928148386.pdf","grobid_xml":"https://content.openalex.org/works/W2928148386.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1855023611","https://openalex.org/W1886978693","https://openalex.org/W1969051510","https://openalex.org/W1983416467","https://openalex.org/W2024103356","https://openalex.org/W2032408510","https://openalex.org/W2044465660","https://openalex.org/W2056051405","https://openalex.org/W2056990767","https://openalex.org/W2087322782","https://openalex.org/W2105476170","https://openalex.org/W2114535505","https://openalex.org/W2115120876","https://openalex.org/W2118601386","https://openalex.org/W2123525093","https://openalex.org/W2132582966","https://openalex.org/W2143720865","https://openalex.org/W2150757437","https://openalex.org/W2158714788","https://openalex.org/W2171017796","https://openalex.org/W2213532196","https://openalex.org/W2256751779","https://openalex.org/W2280888683","https://openalex.org/W2292990827","https://openalex.org/W2326238091","https://openalex.org/W2340589369","https://openalex.org/W2344144945","https://openalex.org/W2396940995","https://openalex.org/W2405065882","https://openalex.org/W2461435273","https://openalex.org/W2461928526","https://openalex.org/W2464754224","https://openalex.org/W2472057509","https://openalex.org/W2488437997","https://openalex.org/W2528953779","https://openalex.org/W2547150868","https://openalex.org/W2570408261","https://openalex.org/W2590039752","https://openalex.org/W2612020308","https://openalex.org/W2748258175","https://openalex.org/W2750770743","https://openalex.org/W2787229156","https://openalex.org/W2789538492","https://openalex.org/W2790709905","https://openalex.org/W2811374032","https://openalex.org/W2817773239","https://openalex.org/W2908850246","https://openalex.org/W2914883440","https://openalex.org/W4237719354","https://openalex.org/W6720447163","https://openalex.org/W6743337752","https://openalex.org/W6748188947"],"related_works":["https://openalex.org/W1505833044","https://openalex.org/W2617798614","https://openalex.org/W2393987497","https://openalex.org/W2366706511","https://openalex.org/W2358710088","https://openalex.org/W2799833988","https://openalex.org/W2365822921","https://openalex.org/W2085254577","https://openalex.org/W2388086542","https://openalex.org/W1999006669"],"abstract_inverted_index":{"A":[0],"better":[1],"exploring":[2],"biological":[3],"processes,":[4],"means,":[5],"and":[6,32,138,174,180,183,210,225],"functions":[7],"demands":[8],"trusted":[9],"information":[10],"about":[11],"Protein-protein":[12],"interactions":[13],"(PPIs).":[14],"High-throughput":[15],"technologies":[16],"have":[17],"produced":[18,83],"a":[19,50],"large":[20],"number":[21],"of":[22,43,170,192,217],"PPIs":[23,70,218],"data":[24],"for":[25,96,103,124,241],"various":[26],"species,":[27],"however,":[28],"they":[29],"are":[30,82,111,120,205],"resource-expensive":[31],"often":[33],"suffer":[34],"from":[35,122],"high":[36],"error":[37],"rates.":[38],"To":[39],"supplement":[40],"the":[41,44,68,77,86,90,104,114,117,193,197,202,215,233],"limitations":[42],"traditional":[45],"methods,":[46],"in":[47,168],"this":[48],"paper,":[49],"sequence-based":[51],"computational":[52],"method":[53,66,165,204,235],"is":[54,94,166,188,236],"proposed":[55,65,115,164,203,234],"to":[56,145,190],"insight":[57],"whether":[58],"two":[59],"proteins":[60],"interact":[61],"or":[62],"not.":[63],"The":[64,163,228],"divides":[67],"novel":[69,243],"prediction":[71,219],"process":[72],"into":[73],"three":[74],"stages:":[75],"first,":[76],"position-specific":[78],"scoring":[79],"matrices":[80],"(PSSMs)":[81],"by":[84,134,142,154,160,201,220],"incorporating":[85],"evolutionary":[87,118],"information;":[88],"second,":[89],"352-dimensional":[91],"feature":[92],"vector":[93],"constructed":[95,141],"each":[97,125],"protein":[98,126,130],"pair;":[99],"third,":[100],"effective":[101,238],"parameters":[102],"ensemble":[105],"learning":[106],"algorithm":[107,144],"rotation":[108],"forest":[109],"(RF)":[110],"selected.":[112],"In":[113,132],"model,":[116],"features":[119],"extracted":[121],"PSSM":[123],"without":[127],"considering":[128],"any":[129],"annotations.":[131],"addition,":[133],"using":[135,177],"more":[136],"accurate":[137],"diverse":[139],"classifiers":[140],"RF":[143],"avoid":[146],"yielding":[147],"coincident":[148],"errors,":[149],"one":[150,155],"sample":[151],"incorrectly":[152],"divided":[153],"classifier":[156],"will":[157],"be":[158],"corrected":[159],"another":[161],"classifier.":[162],"evaluated":[167],"terms":[169],"accuracy,":[171],"precision,":[172],"sensitivity,":[173],"so":[175],"on":[176],"Yeast,":[178],"Human,":[179],"Pylori":[181],"datasets":[182],"finds":[184],"that":[185,191,232],"its":[186],"performance":[187],"superior":[189],"competing":[194],"methods.":[195],"Specifically,":[196],"average":[198],"accuracies":[199],"achieved":[200],"97.06%":[206],"(Yeast),":[207,222],"98.95%":[208],"(Human),":[209,224],"89.69%":[211],"(H.pylori),":[212],"which":[213],"improves":[214],"accuracy":[216],"0.54%~3.89%":[221],"1.29%~3.85%":[223],"0.22%~4.85%":[226],"(H.pylori).":[227],"experimental":[229],"results":[230],"prove":[231],"an":[237],"alternative":[239],"approach":[240],"predicting":[242],"PPIs.":[244]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}