{"id":"https://openalex.org/W7138859256","doi":"https://doi.org/10.1016/j.ecoinf.2026.103696","title":"DeepPFT-GANCap: An explainable attention-based hybrid deep learning framework integrating protein language models and wavelet denoising-based evolutionary features for photosystem-II core protein prediction","display_name":"DeepPFT-GANCap: An explainable attention-based hybrid deep learning framework integrating protein language models and wavelet denoising-based evolutionary features for photosystem-II core protein prediction","publication_year":2026,"publication_date":"2026-03-19","ids":{"openalex":"https://openalex.org/W7138859256","doi":"https://doi.org/10.1016/j.ecoinf.2026.103696"},"language":"en","primary_location":{"id":"doi:10.1016/j.ecoinf.2026.103696","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ecoinf.2026.103696","pdf_url":null,"source":{"id":"https://openalex.org/S195809937","display_name":"Ecological Informatics","issn_l":"1574-9541","issn":["1574-9541","1878-0512"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Ecological Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.ecoinf.2026.103696","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5130023311","display_name":"Wajdi Alghamdi","orcid":null},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Wajdi Alghamdi","raw_affiliation_strings":["Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Department of Information Technology, Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126418383","display_name":"Farman Ali","orcid":null},"institutions":[{"id":"https://openalex.org/I59225215","display_name":"Bahria University","ror":"https://ror.org/02v8d7770","country_code":"PK","type":"education","lineage":["https://openalex.org/I59225215"]}],"countries":["PK"],"is_corresponding":true,"raw_author_name":"Farman Ali","raw_affiliation_strings":["Department of Computer Science, Bahria University, Islamabad, Pakistan"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Bahria University, Islamabad, Pakistan","institution_ids":["https://openalex.org/I59225215"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062081377","display_name":"Abdulmohsen Algarni","orcid":"https://orcid.org/0000-0002-7556-958X"},"institutions":[{"id":"https://openalex.org/I82952536","display_name":"King Khalid University","ror":"https://ror.org/052kwzs30","country_code":"SA","type":"education","lineage":["https://openalex.org/I82952536"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Abdulmohsen Algarni","raw_affiliation_strings":["Department of Computer Science, King Khalid University, Abha 61421, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, King Khalid University, Abha 61421, Saudi Arabia","institution_ids":["https://openalex.org/I82952536"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058186043","display_name":"Omar Alghushairy","orcid":"https://orcid.org/0000-0002-7378-5545"},"institutions":[{"id":"https://openalex.org/I4210099699","display_name":"University of Jeddah","ror":"https://ror.org/015ya8798","country_code":"SA","type":"education","lineage":["https://openalex.org/I4210099699"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Omar Alghushairy","raw_affiliation_strings":["Department of Information Systems and Technology, College of Computer Science and Engineering, University of Jeddah, Jeddah, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Department of Information Systems and Technology, College of Computer Science and Engineering, University of Jeddah, Jeddah, Saudi Arabia","institution_ids":["https://openalex.org/I4210099699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130019168","display_name":"Majdi Khalid","orcid":null},"institutions":[{"id":"https://openalex.org/I199693650","display_name":"Umm al-Qura University","ror":"https://ror.org/01xjqrm90","country_code":"SA","type":"education","lineage":["https://openalex.org/I199693650"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Majdi Khalid","raw_affiliation_strings":["Department of Computer Science and Artificial Intelligence, College of Computing, Umm Al-Qura University, Makkah 21955, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Artificial Intelligence, College of Computing, Umm Al-Qura University, Makkah 21955, Saudi Arabia","institution_ids":["https://openalex.org/I199693650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5130127029","display_name":"Meng-Ze Du","orcid":null},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]},{"id":"https://openalex.org/I207528943","display_name":"Chengdu Medical College","ror":"https://ror.org/01c4jmp52","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I207528943"]},{"id":"https://openalex.org/I2800091995","display_name":"West China Medical Center of Sichuan University","ror":"https://ror.org/040nggs60","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I24185976","https://openalex.org/I2800091995"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Meng-Ze Du","raw_affiliation_strings":["Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, B24 Yinquan South Road, Qingyuan 511518, Guang dong Province, People's Republic of China","School of Health and Medical Technology, Chengdu Neusoft University, Chengdu 611844, Sichuan Province, People's Republic of China","School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China"],"affiliations":[{"raw_affiliation_string":"Qingyuan People's Hospital, The Sixth Affiliated Hospital of Guangzhou Medical University, B24 Yinquan South Road, Qingyuan 511518, Guang dong Province, People's Republic of China","institution_ids":["https://openalex.org/I92039509"]},{"raw_affiliation_string":"School of Health and Medical Technology, Chengdu Neusoft University, Chengdu 611844, Sichuan Province, People's Republic of China","institution_ids":["https://openalex.org/I207528943","https://openalex.org/I2800091995"]},{"raw_affiliation_string":"School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5126418383","https://openalex.org/A5130127029"],"corresponding_institution_ids":["https://openalex.org/I150229711","https://openalex.org/I207528943","https://openalex.org/I2800091995","https://openalex.org/I59225215","https://openalex.org/I92039509"],"apc_list":{"value":2510,"currency":"USD","value_usd":2510},"apc_paid":{"value":2510,"currency":"USD","value_usd":2510},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.69873474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"95","issue":null,"first_page":"103696","last_page":"103696"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.45399999618530273,"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":0.45399999618530273,"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/T10303","display_name":"Photosynthetic Processes and Mechanisms","score":0.1298000067472458,"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":0.06710000336170197,"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/discriminative-model","display_name":"Discriminative model","score":0.6039999723434448},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.52920001745224},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4973999857902527},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.49140000343322754},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.4578999876976013},{"id":"https://openalex.org/keywords/adaptability","display_name":"Adaptability","score":0.45320001244544983},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.43939998745918274},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.40720000863075256}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7426999807357788},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.729200005531311},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6342999935150146},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6039999723434448},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.52920001745224},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4973999857902527},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.49140000343322754},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.4578999876976013},{"id":"https://openalex.org/C177606310","wikidata":"https://www.wikidata.org/wiki/Q5674297","display_name":"Adaptability","level":2,"score":0.45320001244544983},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.43939998745918274},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.40720000863075256},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.374099999666214},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.3617999851703644},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.3416999876499176},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.3391000032424927},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3224000036716461},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.3215999901294708},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.30000001192092896},{"id":"https://openalex.org/C2776145597","wikidata":"https://www.wikidata.org/wiki/Q25339462","display_name":"Dropout (neural networks)","level":2,"score":0.28949999809265137},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.28279998898506165},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.2809000015258789},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.26930001378059387}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1016/j.ecoinf.2026.103696","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ecoinf.2026.103696","pdf_url":null,"source":{"id":"https://openalex.org/S195809937","display_name":"Ecological Informatics","issn_l":"1574-9541","issn":["1574-9541","1878-0512"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Ecological Informatics","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1016/j.ecoinf.2026.103696","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.ecoinf.2026.103696","pdf_url":null,"source":{"id":"https://openalex.org/S195809937","display_name":"Ecological Informatics","issn_l":"1574-9541","issn":["1574-9541","1878-0512"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Ecological Informatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.42433494329452515}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1485819570","https://openalex.org/W1983729307","https://openalex.org/W1984323311","https://openalex.org/W2008313499","https://openalex.org/W2019610851","https://openalex.org/W2035896978","https://openalex.org/W2089047063","https://openalex.org/W2127928904","https://openalex.org/W2129095580","https://openalex.org/W2135370264","https://openalex.org/W2142097792","https://openalex.org/W2161831550","https://openalex.org/W2171093931","https://openalex.org/W2473156356","https://openalex.org/W2891182582","https://openalex.org/W2945839551","https://openalex.org/W2946492269","https://openalex.org/W2949845722","https://openalex.org/W2980789587","https://openalex.org/W2988542995","https://openalex.org/W2995514860","https://openalex.org/W3112376646","https://openalex.org/W3146944767","https://openalex.org/W3176435454","https://openalex.org/W3177500196","https://openalex.org/W3184871101","https://openalex.org/W3210073584","https://openalex.org/W4214656865","https://openalex.org/W4220900187","https://openalex.org/W4224095040","https://openalex.org/W4293374003","https://openalex.org/W4307818652","https://openalex.org/W4311447039","https://openalex.org/W4317039319","https://openalex.org/W4318773647","https://openalex.org/W4327550249","https://openalex.org/W4367366455","https://openalex.org/W4379876549","https://openalex.org/W4387729411","https://openalex.org/W4390858912","https://openalex.org/W4392906754","https://openalex.org/W4394853710","https://openalex.org/W4396873165","https://openalex.org/W4400624111","https://openalex.org/W4401660158","https://openalex.org/W4402665960","https://openalex.org/W4404171049","https://openalex.org/W4404184058","https://openalex.org/W4408336684","https://openalex.org/W4412170761","https://openalex.org/W4413436017","https://openalex.org/W4414601544","https://openalex.org/W4415390171","https://openalex.org/W7125635194"],"related_works":[],"abstract_inverted_index":{"Functional":[0],"traits":[1,208],"of":[2,9,13,18,22,39,46,52,64,136,163,187,213,219],"plants":[3],"are":[4,56,250],"key":[5],"to":[6,20,116,143,179,209,252,282],"the":[7,16,23,26,50,59,161,164,174,183,211,217],"study":[8,195],"ecological":[10],"processes,":[11],"adaptations":[12],"species,":[14],"and":[15,37,49,62,87,100,149,155,191,216,244,268,286],"responses":[17],"ecosystems":[19],"alterations":[21],"environment.":[24],"Particularly,":[25],"Photosystem-II":[27],"core":[28,236],"protein":[29,95,237,241],"(P-IICP)":[30],"is":[31,231],"vital":[32],"for":[33,204,233],"a":[34,105,126,197,245],"plant's":[35],"adaptability":[36],"efficiency":[38],"photosynthesis":[40,190],"in":[41,58,102,189],"several":[42],"environments.":[43],"The":[44,133,167,194,273],"intricacy":[45],"sequence-function":[47],"relations":[48],"scope":[51],"conventional":[53],"computational":[54,199],"methods":[55],"hurdles":[57],"precise":[60],"characterization":[61],"prediction":[63],"such":[65],"proteins.":[66],"We":[67],"propose":[68],"an":[69],"attention-based":[70],"hybrid":[71,259],"deep":[72,227],"learning":[73,228],"(DL)":[74],"framework,":[75],"DeepPFT-GANCap,":[76],"which":[77],"integrates":[78],"attention":[79],"mechanisms":[80],"with":[81,104,201,221,279],"Generative":[82],"Adversarial":[83],"Network,":[84,86],"Capsule":[85],"Bidirectional":[88],"Temporal":[89],"Convolutional":[90],"Neural":[91],"Network.":[92],"Using":[93],"advanced":[94,202],"language":[96,242],"models":[97,243,263],"(ProtTrans-T5,":[98],"UniRep,":[99],"ESM-2)":[101],"conjunction":[103],"novel":[106,225],"Discrete":[107],"Cosine":[108],"Transform-based":[109],"evolutionary":[110,247],"descriptor":[111,248],"(PsePSSM-DCT)":[112,249],"allows":[113],"our":[114],"model":[115,180],"extract":[117],"highly":[118],"discriminative":[119],"features.":[120],"To":[121],"improve":[122],"interpretability,":[123],"we":[124],"utilized":[125],"wrapper-based":[127],"XGBoost-Forward":[128],"Feature":[129],"Selection":[130],"(XGB-FFS)":[131],"approach.":[132],"experimental":[134],"results":[135],"DeepPFT-GANCap":[137],"demonstrated":[138],"consistently":[139],"superior":[140],"performance":[141],"compared":[142],"competing":[144],"predictors,":[145],"exhibiting":[146],"higher":[147],"accuracy":[148],"good":[150],"generalization":[151],"across":[152],"both":[153],"training":[154],"independent":[156],"test":[157],"datasets,":[158],"thereby":[159],"validating":[160],"effectiveness":[162],"proposed":[165,232],"system.":[166],"SHapley":[168],"Additive":[169],"exPlanations":[170],"(SHAP)":[171],"analysis":[172,289],"revealed":[173],"most":[175],"influential":[176],"features":[177],"contributing":[178],"predictions,":[181],"emphasizing":[182],"critical":[184],"functional":[185,207],"role":[186],"P-IICP":[188],"ecosystem":[192,287],"monitoring.":[193],"provides":[196,275],"scalable":[198],"framework":[200,229,274],"interpretability":[203],"monitoring":[205],"plant":[206,283],"drive":[210],"science":[212],"trait-based":[214],"ecology":[215],"interaction":[218],"climate":[220],"ecosystems.":[222],"\u2022":[223,239,257,272],"A":[224,258],"explainable":[226],"(DeepPFT-GANCap)":[230],"Photosystem":[234],"II":[235],"prediction.":[238],"Multi-source":[240],"frequency-domain":[246],"integrated":[251],"capture":[253],"complementary":[254],"biological":[255],"information.":[256],"GAN\u2013Capsule\u2013BiTCNN":[260],"architecture":[261],"effectively":[262],"class":[264],"imbalance,":[265],"long-range":[266],"dependencies,":[267],"hierarchical":[269],"sequence":[270],"relationships.":[271],"biologically":[276],"interpretable":[277],"predictions":[278],"direct":[280],"relevance":[281],"stress":[284],"adaptation":[285],"productivity":[288]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-03-20T00:00:00"}
