{"id":"https://openalex.org/W4408352094","doi":"https://doi.org/10.1109/icassp49660.2025.10888039","title":"NanoGen: A High-affinity Nanobody Generation Model with Guided Diffusion","display_name":"NanoGen: A High-affinity Nanobody Generation Model with Guided Diffusion","publication_year":2025,"publication_date":"2025-03-12","ids":{"openalex":"https://openalex.org/W4408352094","doi":"https://doi.org/10.1109/icassp49660.2025.10888039"},"language":"en","primary_location":{"id":"doi:10.1109/icassp49660.2025.10888039","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icassp49660.2025.10888039","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ICASSP 2025 - 2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5052961032","display_name":"Dezhi Wu","orcid":"https://orcid.org/0000-0001-7152-3069"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dezhi Wu","raw_affiliation_strings":["Shanghai Jiao Tong University,Computer Science and Engineering,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Computer Science and Engineering,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100624804","display_name":"Xuejiao Liu","orcid":"https://orcid.org/0000-0002-2713-5779"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuejiao Liu","raw_affiliation_strings":["Fudan University,Institutes of Biomedical Sciences,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fudan University,Institutes of Biomedical Sciences,Shanghai,China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025327117","display_name":"Yiming Qin","orcid":"https://orcid.org/0000-0002-6375-6054"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiming Qin","raw_affiliation_strings":["Tsinghua University,School of Clinical Medicine,Beijing,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tsinghua University,School of Clinical Medicine,Beijing,China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116594287","display_name":"Stephanie M. Linker","orcid":null},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Stephanie M. Linker","raw_affiliation_strings":["Merck KGaA,Digital Chemistry,Darmstadt,Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck KGaA,Digital Chemistry,Darmstadt,Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061940103","display_name":"Karin Hrovatin","orcid":"https://orcid.org/0000-0003-3319-9645"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Karin Hrovatin","raw_affiliation_strings":["Merck KGaA,Digital Chemistry,Darmstadt,Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck KGaA,Digital Chemistry,Darmstadt,Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068029953","display_name":"Alexander V. Hopp","orcid":"https://orcid.org/0000-0003-1729-1046"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alexander V. Hopp","raw_affiliation_strings":["Merck KGaA,AI & Quantum Lab,Darmstadt,Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck KGaA,AI & Quantum Lab,Darmstadt,Germany","institution_ids":["https://openalex.org/I164928964"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052221471","display_name":"Feng Tan","orcid":"https://orcid.org/0009-0001-4754-4641"},"institutions":[{"id":"https://openalex.org/I164928964","display_name":"Merck KGaA, Darmstadt (Germany)","ror":"https://ror.org/04b2dty93","country_code":"DE","type":"company","lineage":["https://openalex.org/I164928964"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Feng Tan","raw_affiliation_strings":["Merck KGaA,AI & Quantum Lab,Darmstadt,Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Merck KGaA,AI & Quantum Lab,Darmstadt,Germany","institution_ids":["https://openalex.org/I164928964"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12224","display_name":"Nanofabrication and Lithography Techniques","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12224","display_name":"Nanofabrication and Lithography Techniques","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9750999808311462,"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/T10131","display_name":"Gold and Silver Nanoparticles Synthesis and Applications","score":0.974399983882904,"subfield":{"id":"https://openalex.org/subfields/2504","display_name":"Electronic, Optical and Magnetic Materials"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.5025520324707031},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.440473735332489},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11049672961235046},{"id":"https://openalex.org/keywords/thermodynamics","display_name":"Thermodynamics","score":0.08877891302108765}],"concepts":[{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5025520324707031},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.440473735332489},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11049672961235046},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.08877891302108765}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/icassp49660.2025.10888039","is_oa":false,"landing_page_url":"https://doi.org/10.1109/icassp49660.2025.10888039","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ICASSP 2025 - 2025 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.46000000834465027,"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W2003150414","https://openalex.org/W2110505462","https://openalex.org/W2950118240","https://openalex.org/W3081714253","https://openalex.org/W3096751000","https://openalex.org/W3125964370","https://openalex.org/W3128431431","https://openalex.org/W3159860348","https://openalex.org/W3214417031","https://openalex.org/W4211045835","https://openalex.org/W4226209114","https://openalex.org/W4283647117","https://openalex.org/W4353090737","https://openalex.org/W4362723204","https://openalex.org/W4390154134","https://openalex.org/W4392168151","https://openalex.org/W4392302569","https://openalex.org/W4392563999","https://openalex.org/W4396662715","https://openalex.org/W6779823529","https://openalex.org/W6783713337","https://openalex.org/W6796411514","https://openalex.org/W6798447524","https://openalex.org/W6852575741"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Nanobodies":[0],"are":[1],"promising":[2],"therapeutic":[3,138],"agents":[4],"due":[5],"to":[6,41,105,133],"their":[7],"superior":[8],"biological":[9],"properties.":[10],"Given":[11],"the":[12,28,49,74,93,108],"importance":[13],"of":[14,21],"binding":[15,103],"affinity,":[16],"a":[17,60,69,98],"computational":[18],"model":[19,64],"capable":[20],"generating":[22],"high-affinity":[23,61],"nanobodies":[24],"can":[25],"significantly":[26],"accelerate":[27],"design":[29,136],"process.":[30],"However,":[31],"two":[32],"key":[33],"challenges":[34],"remain:":[35],"1)":[36],"integrating":[37],"fragmented":[38],"sequence":[39,113,124],"data":[40,88,104],"pre-train":[42],"robust":[43],"nanobody":[44,62,87,112,135],"representations,":[45],"and":[46,86,115,126,137],"2)":[47],"augmenting":[48],"limited":[50],"nanobody-antigen":[51,102],"interaction":[52],"datasets.":[53],"In":[54,73,92],"this":[55],"paper,":[56],"we":[57,77,96],"introduce":[58],"NanoGen,":[59],"generation":[63],"utilizing":[65],"guided":[66],"diffusion":[67],"within":[68],"two-stage":[70],"training":[71],"framework.":[72],"pre-training":[75,114],"phase,":[76],"curate":[78],"large-scale":[79],"datasets":[80],"that":[81,100],"include":[82],"both":[83,123],"heavy-chain":[84],"antibody":[85],"for":[89],"representation":[90],"learning.":[91],"fine-tuning":[94],"stage,":[95],"implement":[97],"pipeline":[99],"augments":[101],"further":[106],"refine":[107],"pre-trained":[109],"model.":[110],"Through":[111],"affinity-specific":[116],"fine-tuning,":[117],"NanoGen":[118],"outperforms":[119],"established":[120],"baselines":[121],"in":[122],"infilling":[125],"affinity":[127],"optimization":[128],"tasks,":[129],"demonstrating":[130],"its":[131],"potential":[132],"advance":[134],"development.":[139]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}