{"id":"https://openalex.org/W4313527198","doi":"https://doi.org/10.1109/bibm55620.2022.9995175","title":"Predicting the interactions between plant lncRNA-encoded peptide and protein using domain knowledge-based prototypical network","display_name":"Predicting the interactions between plant lncRNA-encoded peptide and protein using domain knowledge-based prototypical network","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313527198","doi":"https://doi.org/10.1109/bibm55620.2022.9995175"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995175","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9995175","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015704814","display_name":"Siyuan Zhao","orcid":"https://orcid.org/0000-0001-9756-4838"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Siyuan Zhao","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,Liaoning,China,116023"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,Liaoning,China,116023","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008478540","display_name":"Jun Meng","orcid":"https://orcid.org/0000-0002-7357-8562"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Meng","raw_affiliation_strings":["Dalian University of Technology,School of Computer Science and Technology,Dalian,Liaoning,China,116023"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Computer Science and Technology,Dalian,Liaoning,China,116023","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004629036","display_name":"Yushi Luan","orcid":"https://orcid.org/0000-0001-9397-9171"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4210092944","display_name":"Dalian University","ror":"https://ror.org/00g2ypp58","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210092944"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yushi Luan","raw_affiliation_strings":["Dalian University of Technology,School of Bioengineering,Dalian,Liaoning,China,116023"],"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,School of Bioengineering,Dalian,Liaoning,China,116023","institution_ids":["https://openalex.org/I4210092944","https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5015704814"],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.45015823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":null,"first_page":"3328","last_page":"3334"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9987999796867371,"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"}},"topics":[{"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":0.9987000226974487,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9973999857902527,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.7045440077781677},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5814688205718994},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5180418491363525},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5012352466583252},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.49653202295303345},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4535275101661682},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.4484165906906128},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4103570282459259},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33914971351623535},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11992913484573364},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09655994176864624},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08024245500564575}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7045440077781677},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5814688205718994},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5180418491363525},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5012352466583252},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.49653202295303345},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4535275101661682},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.4484165906906128},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4103570282459259},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33914971351623535},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11992913484573364},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09655994176864624},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08024245500564575},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm55620.2022.9995175","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/bibm55620.2022.9995175","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W1689711448","https://openalex.org/W1993220166","https://openalex.org/W2063950568","https://openalex.org/W2087861452","https://openalex.org/W2096945460","https://openalex.org/W2101234009","https://openalex.org/W2104804534","https://openalex.org/W2142580593","https://openalex.org/W2170747616","https://openalex.org/W2170849801","https://openalex.org/W2253429366","https://openalex.org/W2331218777","https://openalex.org/W2339719866","https://openalex.org/W2571814563","https://openalex.org/W2766296277","https://openalex.org/W2770681586","https://openalex.org/W2793168264","https://openalex.org/W2796250155","https://openalex.org/W2799876761","https://openalex.org/W2809712711","https://openalex.org/W2898364362","https://openalex.org/W2900569176","https://openalex.org/W2911424749","https://openalex.org/W2912083425","https://openalex.org/W2914304175","https://openalex.org/W2951162249","https://openalex.org/W2952059807","https://openalex.org/W2994312145","https://openalex.org/W3037563142","https://openalex.org/W3043733133","https://openalex.org/W3081382462","https://openalex.org/W3087692915","https://openalex.org/W3094502228","https://openalex.org/W3097019284","https://openalex.org/W3100057407","https://openalex.org/W3109860017","https://openalex.org/W3127617278","https://openalex.org/W3134111154","https://openalex.org/W3181327235","https://openalex.org/W3184607641","https://openalex.org/W3199607358","https://openalex.org/W3205135608","https://openalex.org/W4200115265","https://openalex.org/W4200351086","https://openalex.org/W4210529848","https://openalex.org/W4214837029","https://openalex.org/W4281742771","https://openalex.org/W4283733459","https://openalex.org/W6675354045","https://openalex.org/W6717697761","https://openalex.org/W6735236233","https://openalex.org/W6743446608","https://openalex.org/W6758126075","https://openalex.org/W6782534648","https://openalex.org/W6784333009"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W2327130486","https://openalex.org/W1583422155","https://openalex.org/W2977618689","https://openalex.org/W1649619740","https://openalex.org/W3213252596","https://openalex.org/W1534006406"],"abstract_inverted_index":{"Long":[0],"noncoding":[1],"RNA(lncRNA)":[2],"has":[3],"been":[4,42,94],"reported":[5],"to":[6,22,27,52,71,110,147,181],"encode":[7],"small":[8],"peptides":[9],"which":[10,103],"play":[11],"key":[12],"roles":[13],"in":[14],"life":[15],"activities":[16],"through":[17],"their":[18],"functions":[19],"by":[20],"binding":[21],"proteins.":[23],"It":[24],"is":[25,62,104,162,213],"crucial":[26],"predict":[28],"the":[29,32,53,77,84,98,111,183,196,207,214,219],"interactions":[30,49,123,220],"between":[31,79,125,222],"lncRNA-encoded":[33,127,223],"peptide":[34,128,224],"and":[35,75,129,145,150,170,225],"protein.":[36,226],"However,":[37,69],"no":[38],"computational":[39,216],"methods":[40],"have":[41,93],"designed":[43],"for":[44,66,106,122,218],"predicting":[45],"this":[46,115],"type":[47],"of":[48,100,209],"directly,":[50],"owing":[51],"few-shot":[54,67],"problem":[55],"causing":[56],"poor":[57],"generalization.":[58],"Prototypical":[59],"network":[60],"(ProtoNet)":[61],"a":[63,119,154],"classic":[64,202],"learner":[65],"learning.":[68],"how":[70],"obtain":[72],"effective":[73],"embedding":[74,169],"measure":[76],"distance":[78],"different":[80],"prototypes":[81],"accurately":[82],"are":[83,142,177],"most":[85],"important":[86],"challenges.":[87],"Although":[88],"some":[89],"improved":[90,164],"prototypical":[91],"networks":[92],"proposed,":[95],"they":[96],"ignore":[97],"role":[99],"domain":[101,112,132,140],"knowledge":[102,141],"helpful":[105],"constructing":[107],"models":[108],"conforming":[109],"mechanism":[113],"In":[114],"study,":[116],"we":[117],"propose":[118],"novel":[120],"method":[121,217],"prediction":[124,221],"plant":[126],"protein":[130],"using":[131,153,166],"knowledge-based":[133],"ProtoNet":[134,165],"(IPLncPP-DKPN).":[135],"Multiple":[136],"features":[137,176],"that":[138,190],"imply":[139],"extracted,":[143],"connected,":[144],"converted":[146,175],"avoid":[148],"sparse":[149],"enhance":[151],"information":[152],"dual-routing":[155],"parallel":[156],"feature":[157],"dimensionality":[158],"reduction":[159],"algorithm":[160],"IProtoNet":[161,180],"an":[163],"capsule":[167],"network-based":[168],"Mahalanobis":[171],"distance-based":[172],"prototype.":[173],"The":[174,186],"fed":[178],"into":[179],"realize":[182],"classification":[184],"task.":[185],"experimental":[187],"results":[188],"manifest":[189],"IPLncPP-DKPN":[191,212],"achieves":[192],"better":[193],"performance":[194],"on":[195],"independent":[197],"test":[198],"set":[199],"compared":[200],"with":[201],"machine":[203],"learning":[204],"models.":[205],"To":[206],"best":[208],"our":[210],"knowledge,":[211],"first":[215]},"counts_by_year":[],"updated_date":"2025-12-23T23:11:35.936235","created_date":"2025-10-10T00:00:00"}