{"id":"https://openalex.org/W7126030591","doi":"https://doi.org/10.1109/bibm66473.2025.11356250","title":"VQH-AM: Vector Quantization-Augmented Heterogeneous Graph Learning for Antibody Affinity Maturation Prediction","display_name":"VQH-AM: Vector Quantization-Augmented Heterogeneous Graph Learning for Antibody Affinity Maturation Prediction","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126030591","doi":"https://doi.org/10.1109/bibm66473.2025.11356250"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356250","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356250","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 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":null,"display_name":"Zhuowen Zhen","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhuowen Zhen","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124203250","display_name":"Tengfei Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tengfei Ma","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124156189","display_name":"Jiaxuan Li","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Jiaxuan Li","raw_affiliation_strings":["Macao Polytechnic University,Faculty of Applied Sciences,Macao,China"],"affiliations":[{"raw_affiliation_string":"Macao Polytechnic University,Faculty of Applied Sciences,Macao,China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124166898","display_name":"Dashun Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Dashun Zheng","raw_affiliation_strings":["Macao Polytechnic University,Faculty of Applied Sciences,Macao,China"],"affiliations":[{"raw_affiliation_string":"Macao Polytechnic University,Faculty of Applied Sciences,Macao,China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100333835","display_name":"Patrick Cheong\u2010Iao Pang","orcid":"https://orcid.org/0000-0002-8820-5443"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Patrick Cheong-Iao Pang","raw_affiliation_strings":["Macao Polytechnic University,Faculty of Applied Sciences,Macao,China"],"affiliations":[{"raw_affiliation_string":"Macao Polytechnic University,Faculty of Applied Sciences,Macao,China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114549778","display_name":"Yiping Liu","orcid":"https://orcid.org/0000-0002-0924-7339"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiping Liu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052832988","display_name":"X. Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":["College of Computer Science and Electronic Engineering, Hunan University,Changsha,China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering, Hunan University,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I16609230"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.70469086,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"120","last_page":"125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.8367000222206116,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.8367000222206116,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.1306000053882599,"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/T11124","display_name":"Protein purification and stability","score":0.004600000102072954,"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/codebook","display_name":"Codebook","score":0.6449000239372253},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4749999940395355},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4706000089645386},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.446399986743927},{"id":"https://openalex.org/keywords/affinity-maturation","display_name":"Affinity maturation","score":0.4453999996185303},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.3677000105381012},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.33570000529289246}],"concepts":[{"id":"https://openalex.org/C127759330","wikidata":"https://www.wikidata.org/wiki/Q637416","display_name":"Codebook","level":2,"score":0.6449000239372253},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5396000146865845},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4749999940395355},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.47209998965263367},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4706000089645386},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.446399986743927},{"id":"https://openalex.org/C2781377902","wikidata":"https://www.wikidata.org/wiki/Q21418769","display_name":"Affinity maturation","level":3,"score":0.4453999996185303},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42480000853538513},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37720000743865967},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.3677000105381012},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.33570000529289246},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3089999854564667},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.3041999936103821},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.30300000309944153},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.3003999888896942},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.2969000041484833},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2784000039100647},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2702000141143799},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.2639000117778778},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.2612000107765198},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2567000091075897}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356250","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356250","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3466088180","display_name":null,"funder_award_id":"L248013","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"},{"id":"https://openalex.org/G476304118","display_name":null,"funder_award_id":"U22A2037,62425204,62122025,62450002,62432011,62522110,62472152","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1486854136","https://openalex.org/W1969943007","https://openalex.org/W1994891218","https://openalex.org/W2023490488","https://openalex.org/W2031772330","https://openalex.org/W2336509392","https://openalex.org/W2592275197","https://openalex.org/W2766842037","https://openalex.org/W2780523853","https://openalex.org/W2912783011","https://openalex.org/W2920817727","https://openalex.org/W2945403072","https://openalex.org/W2953103783","https://openalex.org/W2965857891","https://openalex.org/W2999958881","https://openalex.org/W3082498841","https://openalex.org/W3146944767","https://openalex.org/W4210658740","https://openalex.org/W4214886481","https://openalex.org/W4391756241","https://openalex.org/W4402322935"],"related_works":[],"abstract_inverted_index":{"Modeling":[0],"the":[1,8,34,95,115,127],"impact":[2,35],"of":[3,36],"amino":[4],"acid":[5],"mutations":[6,37],"on":[7,38],"binding":[9,39,52,89],"affinity":[10,128],"between":[11],"antibodies":[12],"and":[13,82,117,123],"antigens":[14],"plays":[15],"a":[16,42,61,104],"pivotal":[17],"role":[18],"in":[19],"antibody":[20,69],"therapeutics":[21],"development.":[22],"While":[23],"numerous":[24],"deep":[25],"learning-based":[26],"methods":[27,139],"have":[28],"shown":[29],"promising":[30],"results,":[31],"accurately":[32],"modeling":[33],"interfaces":[40],"remains":[41],"significant":[43],"challenge,":[44],"as":[45],"even":[46],"small":[47],"changes":[48],"can":[49],"substantially":[50],"affect":[51],"affinity.":[53],"To":[54],"address":[55],"this":[56],"issue,":[57],"we":[58,74],"propose":[59],"VQH-AM,":[60],"Vector":[62],"Quantization-based":[63],"Heterogeneous":[64],"graph":[65,97],"neural":[66,98],"network":[67],"for":[68,79],"Affinity":[70],"Maturation":[71],"prediction.":[72],"Specifically,":[73],"construct":[75],"atom-level":[76],"heterogeneous":[77,96],"graphs":[78],"both":[80,114],"wild-type":[81],"mutant":[83],"antibody-antigen":[84],"complexes":[85],"to":[86,108,125],"model":[87],"their":[88],"interfaces.":[90],"Atomic":[91],"representations":[92,120],"extracted":[93],"by":[94],"networks":[99],"are":[100,121],"then":[101],"quantized":[102,118],"via":[103],"context-aware":[105],"codebook":[106],"designed":[107],"capture":[109],"semantic":[110],"atomic":[111,119],"patterns.":[112],"Finally,":[113],"original":[116],"integrated":[122],"used":[124],"predict":[126],"maturation":[129],"outcomes.":[130],"Benchmark":[131],"experiments":[132],"demonstrate":[133],"that":[134],"VQH-AM":[135],"consistently":[136],"outperforms":[137],"state-of-the-art":[138],"across":[140],"multiple":[141],"evaluation":[142],"metrics.":[143],"The":[144],"source":[145],"code":[146],"is":[147],"available":[148],"at:":[149],"https://github.com/zwzhen-hnu/VQH-AM.":[150]},"counts_by_year":[],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2026-01-30T00:00:00"}
