{"id":"https://openalex.org/W4410536121","doi":"https://doi.org/10.1109/tcbbio.2025.3572178","title":"Multi-Objective Structure-Based Drug Design Using Causal Discovery","display_name":"Multi-Objective Structure-Based Drug Design Using Causal Discovery","publication_year":2025,"publication_date":"2025-05-20","ids":{"openalex":"https://openalex.org/W4410536121","doi":"https://doi.org/10.1109/tcbbio.2025.3572178","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811343"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3572178","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3572178","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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":"Jingyuan Zhou","orcid":"https://orcid.org/0009-0006-2844-4924"},"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":"Jingyuan Zhou","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0006-2844-4924","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003260759","display_name":"Dengwei Zhao","orcid":"https://orcid.org/0000-0003-4764-2759"},"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":"Dengwei Zhao","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0003-4764-2759","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102404029","display_name":"Hao Qian","orcid":"https://orcid.org/0009-0001-7071-3685"},"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":"Hao Qian","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0009-0001-7071-3685","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073963268","display_name":"Shikui Tu","orcid":"https://orcid.org/0000-0001-6270-0449"},"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":"Shikui Tu","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0001-6270-0449","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":null,"display_name":"Lei Xu","orcid":"https://orcid.org/0000-0002-2752-1573"},"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":"Lei Xu","raw_affiliation_strings":["Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0002-2752-1573","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.11387129,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"4","first_page":"1789","last_page":"1800"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9677000045776367,"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/T11663","display_name":"Viral Infectious Diseases and Gene Expression in Insects","score":0.940500020980835,"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/drug-discovery","display_name":"Drug discovery","score":0.596592903137207},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48309803009033203},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4520568251609802},{"id":"https://openalex.org/keywords/causal-structure","display_name":"Causal structure","score":0.4228835105895996},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3458622097969055},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.26106297969818115},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.17153200507164001},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.156742125749588},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13026869297027588},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.06348094344139099}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.596592903137207},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48309803009033203},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4520568251609802},{"id":"https://openalex.org/C163504300","wikidata":"https://www.wikidata.org/wiki/Q2364925","display_name":"Causal structure","level":2,"score":0.4228835105895996},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3458622097969055},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.26106297969818115},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.17153200507164001},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.156742125749588},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13026869297027588},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.06348094344139099},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3572178","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3572178","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811343","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2415283116","display_name":null,"funder_award_id":"62172273","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5453146561","display_name":null,"funder_award_id":"24510714300","funder_id":"https://openalex.org/F4320321885","funder_display_name":"Science and Technology Commission of Shanghai Municipality"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321885","display_name":"Science and Technology Commission of Shanghai Municipality","ror":"https://ror.org/03kt66j61"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":81,"referenced_works":["https://openalex.org/W1975447903","https://openalex.org/W1991111872","https://openalex.org/W2034549041","https://openalex.org/W2052907531","https://openalex.org/W2105649494","https://openalex.org/W2134967712","https://openalex.org/W2143381319","https://openalex.org/W2151697120","https://openalex.org/W2154195147","https://openalex.org/W2160592148","https://openalex.org/W2788775653","https://openalex.org/W2962411443","https://openalex.org/W2962764565","https://openalex.org/W2973114758","https://openalex.org/W2999242200","https://openalex.org/W3013657235","https://openalex.org/W3025593963","https://openalex.org/W3033617045","https://openalex.org/W3082411326","https://openalex.org/W3104956673","https://openalex.org/W3110257065","https://openalex.org/W3116865743","https://openalex.org/W3119872582","https://openalex.org/W3137385578","https://openalex.org/W3153418506","https://openalex.org/W3177533410","https://openalex.org/W3209056694","https://openalex.org/W3209764902","https://openalex.org/W4205773061","https://openalex.org/W4214831389","https://openalex.org/W4242372416","https://openalex.org/W4283804538","https://openalex.org/W4290948309","https://openalex.org/W4298184813","https://openalex.org/W4303431765","https://openalex.org/W4318071656","https://openalex.org/W4318981550","https://openalex.org/W4319869596","https://openalex.org/W4321377212","https://openalex.org/W4323650483","https://openalex.org/W4382182163","https://openalex.org/W4386498912","https://openalex.org/W4388539614","https://openalex.org/W4389257854","https://openalex.org/W4390771096","https://openalex.org/W4392526270","https://openalex.org/W4392653998","https://openalex.org/W4392822048","https://openalex.org/W4393111365","https://openalex.org/W4393153201","https://openalex.org/W4393181728","https://openalex.org/W4393222489","https://openalex.org/W4401102983","https://openalex.org/W4402814842","https://openalex.org/W4404294092","https://openalex.org/W4404781414","https://openalex.org/W4404995526","https://openalex.org/W4405194283","https://openalex.org/W4405194591","https://openalex.org/W4406440058","https://openalex.org/W4409363892","https://openalex.org/W6636400922","https://openalex.org/W6749031613","https://openalex.org/W6779789776","https://openalex.org/W6779823529","https://openalex.org/W6786375611","https://openalex.org/W6788990321","https://openalex.org/W6789109021","https://openalex.org/W6790561777","https://openalex.org/W6796163713","https://openalex.org/W6804214328","https://openalex.org/W6810653082","https://openalex.org/W6838000958","https://openalex.org/W6843880952","https://openalex.org/W6844364769","https://openalex.org/W6850636830","https://openalex.org/W6860306510","https://openalex.org/W6862998299","https://openalex.org/W6863577000","https://openalex.org/W6870521281","https://openalex.org/W6879652996"],"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/W2013003323","https://openalex.org/W1981076832","https://openalex.org/W2024773645","https://openalex.org/W2001717001","https://openalex.org/W2043147644"],"abstract_inverted_index":{"Structure-based":[0],"drug":[1,10,22,34,136,229],"design":[2,23],"(SBDD)":[3],"is":[4,24,123,161,187],"a":[5,18,25,32,119,158,190],"critical":[6],"subtask":[7],"in":[8,100,144,151,189],"the":[9,29,48,89,116,127,164,170,177,181,195,200,209],"discovery":[11,166],"process,":[12,180],"with":[13,227],"deep":[14],"generative":[15],"models":[16],"playing":[17],"pivotal":[19],"role.":[20],"Inherently,":[21],"multi-objective":[26,120],"task":[27],"given":[28],"fact":[30],"that":[31,64,109,217],"promising":[33],"candidate":[35],"must":[36],"satisfy":[37],"multiple":[38,112,222],"properties.":[39,175],"However,":[40],"existing":[41],"SBDD":[42,121],"methods":[43,102],"either":[44],"focus":[45],"solely":[46],"on":[47,126],"binding":[49,132],"affinity":[50,133],"between":[51],"molecules":[52,108,150,226],"and":[53,134,154,157,198],"target":[54,174,185],"proteins":[55],"while":[56],"neglecting":[57],"other":[58,135],"crucial":[59],"properties,":[60,79],"or":[61],"they":[62],"assume":[63],"objective":[65],"properties":[66,137,148,186],"are":[67,74,142,205],"independent":[68],"of":[69,91,95,184,202,212],"each":[70,203],"other.":[71],"Yet":[72],"there":[73],"often":[75],"potential":[76,230],"relationships":[77,99,172],"among":[78,173],"which":[80],"can":[81],"be":[82],"conflicting-improving":[83],"one":[84],"property":[85,204],"may":[86],"lead":[87],"to":[88,106,130,146,168,194,207,232],"deterioration":[90],"another.":[92],"The":[93],"lack":[94],"consideration":[96],"for":[97,149],"these":[98],"current":[101],"makes":[103],"it":[104],"unfeasible":[105],"generate":[107],"simultaneously":[110],"meet":[111],"objectives.":[113],"To":[114],"address":[115],"above":[117],"issues,":[118],"algorithm":[122,167],"proposed":[124],"based":[125],"diffusion":[128],"model":[129,219],"optimize":[131],"simultaneously.":[138],"Multiple":[139],"expert":[140],"networks":[141],"trained":[143],"parallel":[145],"predict":[147],"intermediate":[152],"states":[153],"transmit":[155],"gradients,":[156],"causal":[159,165],"graph":[160],"constructed":[162],"through":[163],"unveil":[169],"underlying":[171],"During":[176],"entire":[178],"generation":[179],"joint":[182],"distribution":[183],"decomposed":[188],"reasonable":[191],"manner":[192],"according":[193],"casual":[196],"graph,":[197],"then":[199],"gradients":[201],"applied":[206],"guide":[208],"optimizing":[210],"direction":[211],"generation.":[213],"Experimental":[214],"results":[215],"indicate":[216],"our":[218],"effectively":[220],"optimizes":[221],"objectives":[223],"simultaneously,":[224],"generating":[225],"greater":[228],"compared":[231],"baseline":[233],"models.":[234]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
