{"id":"https://openalex.org/W7214219086","doi":"https://doi.org/10.48550/arxiv.2609.27349","title":"MolDesignBench: Evaluating LLM-based Agent for Scenario-grounded Molecular Design","display_name":"MolDesignBench: Evaluating LLM-based Agent for Scenario-grounded Molecular Design","publication_year":2026,"publication_date":"2026-09-23","ids":{"openalex":"https://openalex.org/W7214219086","doi":"https://doi.org/10.48550/arxiv.2609.27349"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2609.27349","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.27349","pdf_url":"https://arxiv.org/pdf/2609.27349","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2609.27349","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116176753","display_name":"YongJun Jeong","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Jeong, Yongjun","raw_affiliation_strings":["Department of Artificial Intelligence , Korea University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence , Korea University","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000376670","display_name":"Hanbum Ko","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Ko, Hanbum","raw_affiliation_strings":["Department of Artificial Intelligence , Korea University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence , Korea University","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129585020","display_name":"Ye Rin Kim","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Kim, Ye Rin","raw_affiliation_strings":["Department of Artificial Intelligence , Korea University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence , Korea University","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152639409","display_name":"Chanhui Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Lee, Chanhui","raw_affiliation_strings":["Department of Artificial Intelligence , Korea University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence , Korea University","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024797101","display_name":"Rodrigo Horm\u00e1zabal","orcid":"https://orcid.org/0000-0003-3744-5401","observed_orcids":["https://orcid.org/0000-0003-3744-5401"]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Hormazabal, Rodrigo","raw_affiliation_strings":["LG AI Research"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LG AI Research","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152740295","display_name":"Jaewan Lee","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Lee, Jaewan","raw_affiliation_strings":["LG AI Research"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LG AI Research","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152607947","display_name":"Sehui Han","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258446","display_name":"LG AI Research (South Korea)","ror":"https://ror.org/00nt82y31","country_code":"KR","type":"company","lineage":["https://openalex.org/I4210131320","https://openalex.org/I4405258446"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Han, Sehui","raw_affiliation_strings":["LG AI Research"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LG AI Research","institution_ids":["https://openalex.org/I4405258446"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152740938","display_name":"Sungbin Lim","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Lim, Sungbin","raw_affiliation_strings":["Department of Statistics , Korea University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics , Korea University","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087294413","display_name":"Sungwoong Kim","orcid":"https://orcid.org/0000-0002-2676-9454","observed_orcids":["https://orcid.org/0000-0002-2676-9454"]},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Kim, Sungwoong","raw_affiliation_strings":["Department of Artificial Intelligence , Korea University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence , Korea University","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8833000063896179,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8833000063896179,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.07100000232458115,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T13297","display_name":"History and advancements in chemistry","score":0.006399999838322401,"subfield":{"id":"https://openalex.org/subfields/1207","display_name":"History and Philosophy of Science"},"field":{"id":"https://openalex.org/fields/12","display_name":"Arts and Humanities"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/molecular-design","display_name":"molecular design","score":0.7749999761581421},{"id":"https://openalex.org/keywords/llm-based-agents","display_name":"LLM agents","score":0.7519999742507935},{"id":"https://openalex.org/keywords/benchmark","display_name":"benchmark","score":0.6769999861717224},{"id":"https://openalex.org/keywords/implicit-constraints","display_name":"implicit constraints","score":0.8080000281333923},{"id":"https://openalex.org/keywords/infeasibility-detection","display_name":"infeasibility detection","score":0.9819999933242798},{"id":"https://openalex.org/keywords/failure-mode-analysis","display_name":"failure mode analysis","score":0.7839999794960022},{"id":"https://openalex.org/keywords/chemical-agents","display_name":"chemical agents","score":0.3889999985694885}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6600000262260437},{"id":"https://openalex.org/C31395832","wikidata":"https://www.wikidata.org/wiki/Q1318674","display_name":"Testbed","level":2,"score":0.6312000155448914},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5769000053405762},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.5145000219345093},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4948999881744385},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.4611999988555908},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.42879998683929443},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.3596999943256378},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.3158999979496002},{"id":"https://openalex.org/C31352089","wikidata":"https://www.wikidata.org/wiki/Q3750474","display_name":"Systems design","level":2,"score":0.3010999858379364},{"id":"https://openalex.org/C2777466363","wikidata":"https://www.wikidata.org/wiki/Q17008971","display_name":"Design tool","level":2,"score":0.29750001430511475},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.2777999937534332},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.27320000529289246},{"id":"https://openalex.org/C147764199","wikidata":"https://www.wikidata.org/wiki/Q6865248","display_name":"Minification","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25699999928474426},{"id":"https://openalex.org/C80478641","wikidata":"https://www.wikidata.org/wiki/Q195771","display_name":"Sequential analysis","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2506999969482422}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2609.27349","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.27349","pdf_url":"https://arxiv.org/pdf/2609.27349","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2609.27349","doi":"https://doi.org/10.48550/arxiv.2609.27349","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2609.27349","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2609.27349","doi":null,"is_oa":true,"landing_page_url":"https://arxiv.org/abs/2609.27349","pdf_url":"https://arxiv.org/pdf/2609.27349","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1913221277","display_name":null,"funder_award_id":"2022-0-00612","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G4085153280","display_name":null,"funder_award_id":"2022-0-00612","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G4700831490","display_name":null,"funder_award_id":"2022-","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G4734332584","display_name":null,"funder_award_id":"IITP-2026-RS-2025-02304828","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G6038997514","display_name":null,"funder_award_id":"IITP-2026-RS-2025-02304828","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G6969530878","display_name":null,"funder_award_id":"RS-2019-II190079","funder_id":"https://openalex.org/F4320321373","funder_display_name":"Korea University"},{"id":"https://openalex.org/G8458676037","display_name":null,"funder_award_id":"RS-2019-II190079","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G960095468","display_name":null,"funder_award_id":"RS-2019-II190079","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"}],"funders":[{"id":"https://openalex.org/F4320321373","display_name":"Korea University","ror":"https://ror.org/047dqcg40"},{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335489","display_name":"Institute for Information and Communications Technology Promotion","ror":"https://ror.org/01g0hqq23"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214219086.pdf","grobid_xml":"https://content.openalex.org/works/W7214219086.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1500036797","https://openalex.org/W2166550586","https://openalex.org/W4388890648","https://openalex.org/W4405627779","https://openalex.org/W4406779419","https://openalex.org/W4414939355","https://openalex.org/W4415795271","https://openalex.org/W4415797413","https://openalex.org/W4416034236","https://openalex.org/W4416046036","https://openalex.org/W6948247378","https://openalex.org/W7075994024","https://openalex.org/W7077159638","https://openalex.org/W7116045800","https://openalex.org/W7156104865"],"related_works":["https://openalex.org/W7162689699","https://openalex.org/W7162148170","https://openalex.org/W7204181022","https://openalex.org/W4416513658","https://openalex.org/W4416034630","https://openalex.org/W7160719557","https://openalex.org/W7160447078","https://openalex.org/W7141541063","https://openalex.org/W7139964713","https://openalex.org/W4416149808"],"abstract_inverted_index":{"Real-world":[0],"molecular":[1,65],"design":[2,16,66,85],"remains":[3],"challenging":[4],"for":[5,67],"large":[6],"language":[7],"model":[8],"(LLM)-based":[9],"agents.":[10,71,158],"It":[11],"requires":[12],"them":[13],"to":[14,152],"interpret":[15],"contexts,":[17],"satisfy":[18],"multiple":[19],"constraints,":[20,43,92],"identify":[21],"infeasible":[22,94],"specifications,":[23],"and":[24,41,47,76,90,96,127,139,163],"reason":[25],"over":[26],"multi-step":[27],"tool":[28,128,161],"outputs.":[29],"Existing":[30],"benchmarks":[31],"do":[32],"not":[33],"capture":[34],"this":[35,52],"complexity,":[36],"focusing":[37],"instead":[38],"on":[39,156],"explicit":[40,88],"narrow":[42],"only":[44,118],"feasible":[45],"problems,":[46],"single-path":[48],"solutions.":[49],"To":[50],"address":[51],"gap,":[53],"we":[54],"propose":[55],"MolDesignBench,":[56],"a":[57,149],"scenario-grounded":[58],"benchmark":[59],"that":[60,79],"more":[61],"closely":[62],"reflects":[63],"real-world":[64],"evaluating":[68],"tool-augmented":[69],"LLM":[70],"MolDesignBench":[72,147],"comprises":[73],"2K":[74],"generation":[75],"optimization":[77],"instances":[78],"combine":[80],"implicit":[81,136],"requirements":[82],"embedded":[83],"in":[84,122],"narratives":[86],"with":[87],"property":[89],"functional-group":[91],"including":[93],"cases,":[95],"require":[97],"the":[98,115,143],"effective":[99],"use":[100],"of":[101],"17":[102],"specialized":[103],"chemistry":[104],"tools.":[105],"Experiments":[106],"across":[107],"diverse":[108],"frontier":[109],"LLMs":[110],"reveal":[111],"low":[112],"success":[113],"rates--with":[114],"best":[116],"achieving":[117],"$\\sim43$\\%--and":[119],"frequent":[120],"failures":[121],"implicit-constraint":[123],"reasoning,":[124],"infeasibility":[125,140],"detection,":[126],"reasoning.":[129],"The":[130,159],"corresponding":[131],"fine-grained":[132],"failure-mode":[133],"analysis":[134],"identifies":[135],"constraint":[137],"interpretation":[138],"detection":[141],"as":[142,148],"primary":[144],"bottlenecks,":[145],"establishing":[146],"rigorous":[150],"testbed":[151],"guide":[153],"future":[154],"research":[155],"chemical":[157],"benchmark,":[160],"interface,":[162],"evaluation":[164],"code":[165],"are":[166],"publicly":[167],"available.":[168]},"counts_by_year":[],"updated_date":"2026-11-07T11:25:07.637180","created_date":"2026-09-25T00:00:00"}
