{"id":"https://openalex.org/W4417062607","doi":"https://doi.org/10.1145/3768322.3769024","title":"From Contrast to Control: Domain Conditioned Masking for Small Molecule Generation of Quaternary Ammonium Compounds","display_name":"From Contrast to Control: Domain Conditioned Masking for Small Molecule Generation of Quaternary Ammonium Compounds","publication_year":2025,"publication_date":"2025-10-11","ids":{"openalex":"https://openalex.org/W4417062607","doi":"https://doi.org/10.1145/3768322.3769024"},"language":null,"primary_location":{"id":"doi:10.1145/3768322.3769024","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3768322.3769024","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3768322.3769024","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Companion Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dl.acm.org/doi/pdf/10.1145/3768322.3769024","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053958994","display_name":"Shiva Ghaemi","orcid":"https://orcid.org/0009-0007-7253-051X"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shiva Ghaemi","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"raw_orcid":"https://orcid.org/0009-0007-7253-051X","affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120715373","display_name":"Rehenuma Tasmin Rodoshi","orcid":"https://orcid.org/0009-0004-8424-9715"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rehenuma Tasmin Rodoshi","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"raw_orcid":"https://orcid.org/0009-0004-8424-9715","affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011677858","display_name":"Shahana Shultana","orcid":"https://orcid.org/0000-0003-2493-4230"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shahana Shultana","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"raw_orcid":"https://orcid.org/0000-0003-2493-4230","affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044722808","display_name":"Amarda Shehu","orcid":"https://orcid.org/0000-0001-5230-4610"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amarda Shehu","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5230-4610","affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089029917","display_name":"Daniel Barbar\u00e1","orcid":"https://orcid.org/0000-0002-2830-1038"},"institutions":[{"id":"https://openalex.org/I162714631","display_name":"George Mason University","ror":"https://ror.org/02jqj7156","country_code":"US","type":"education","lineage":["https://openalex.org/I162714631"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel Barbar\u00e1","raw_affiliation_strings":["George Mason University, Fairfax, VA, USA"],"raw_orcid":"https://orcid.org/0000-0002-2830-1038","affiliations":[{"raw_affiliation_string":"George Mason University, Fairfax, VA, USA","institution_ids":["https://openalex.org/I162714631"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I162714631"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.48869386,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"7"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.654699981212616,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.654699981212616,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.22040000557899475,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.013899999670684338,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/masking","display_name":"Masking (illustration)","score":0.7890999913215637},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.6711999773979187},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.5455999970436096},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.5450000166893005},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5206999778747559},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4973999857902527},{"id":"https://openalex.org/keywords/contrast","display_name":"Contrast (vision)","score":0.49559998512268066},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.47450000047683716}],"concepts":[{"id":"https://openalex.org/C2777402240","wikidata":"https://www.wikidata.org/wiki/Q6783436","display_name":"Masking (illustration)","level":2,"score":0.7890999913215637},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.6711999773979187},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.5455999970436096},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.5450000166893005},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5246000289916992},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5206999778747559},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5112000107765198},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4973999857902527},{"id":"https://openalex.org/C2776502983","wikidata":"https://www.wikidata.org/wiki/Q690182","display_name":"Contrast (vision)","level":2,"score":0.49559998512268066},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.47450000047683716},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4350999891757965},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.41190001368522644},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4081000089645386},{"id":"https://openalex.org/C58103923","wikidata":"https://www.wikidata.org/wiki/Q2286025","display_name":"Silhouette","level":2,"score":0.3831999897956848},{"id":"https://openalex.org/C178910836","wikidata":"https://www.wikidata.org/wiki/Q2196961","display_name":"Molecular model","level":2,"score":0.3695000112056732},{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.3643999993801117},{"id":"https://openalex.org/C53533937","wikidata":"https://www.wikidata.org/wiki/Q185020","display_name":"Histogram","level":3,"score":0.3621000051498413},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.3312999904155731},{"id":"https://openalex.org/C14103023","wikidata":"https://www.wikidata.org/wiki/Q11681459","display_name":"Pairing","level":3,"score":0.32249999046325684},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.30660000443458557},{"id":"https://openalex.org/C179303850","wikidata":"https://www.wikidata.org/wiki/Q4300362","display_name":"Molecular recognition","level":3,"score":0.30390000343322754},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.2921999990940094},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2865999937057495},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.26989999413490295},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2639999985694885}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3768322.3769024","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3768322.3769024","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3768322.3769024","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Companion Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3768322.3769024","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3768322.3769024","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3768322.3769024","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Companion Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417062607.pdf","grobid_xml":"https://content.openalex.org/works/W4417062607.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2080635178","https://openalex.org/W2114704115","https://openalex.org/W3116865743","https://openalex.org/W3174770825","https://openalex.org/W3188458904","https://openalex.org/W3195415198","https://openalex.org/W3209056694","https://openalex.org/W4214868967","https://openalex.org/W4361279210","https://openalex.org/W4391028159","https://openalex.org/W4393185967","https://openalex.org/W4410198195","https://openalex.org/W4412877052"],"related_works":[],"abstract_inverted_index":{"Generative":[0],"models":[1,26,187],"for":[2,27,175],"chemistry":[3],"benefit":[4],"from":[5],"molecular":[6,28,128,140,177],"representations":[7,79,174],"that":[8,40,72,91,162],"reflect":[9],"domain-specific":[10],"targets,":[11],"yet":[12],"most":[13],"contrastive":[14],"learning":[15],"(CL)":[16],"pretraining":[17],"remains":[18],"domain-agnostic.":[19],"We":[20,61,83,179],"survey":[21],"a":[22,35,69,88,136],"range":[23],"of":[24,67],"CL":[25,45,75,171],"representation":[29],"and":[30,77,105,124,138,156],"introduce":[31],"Domain-Conditioned":[32],"Masking":[33],"(DCM),":[34],"simple,":[36],"label-aware":[37],"masking":[38,169],"strategy":[39],"integrates":[41],"seamlessly":[42],"into":[43,184],"existing":[44],"pipelines.":[46],"Using":[47],"binary":[48],"labels":[49],"(target":[50],"vs.":[51],"non-target),":[52],"DCM":[53,63,96],"guides":[54],"view":[55],"construction":[56],"to":[57,80],"emphasize":[58],"domain-relevant":[59],"features.":[60],"implement":[62],"in":[64,190],"the":[65,112,191],"setting":[66],"CONSMI,":[68],"generative":[70,89,186],"model":[71,90],"uses":[73,93],"standard":[74,113],"techniques":[76],"SMILES":[78,94],"generate":[81],"molecules.":[82],"pair":[84],"CONSMI":[85,114,157],"with":[86,99,142,147,167],"MolGPT,":[87],"also":[92],"representations.":[95],"produces":[97],"embeddings":[98,150],"much":[100],"clearer":[101],"separation":[102],"between":[103],"target":[104],"non-target":[106],"molecules":[107],"than":[108],"those":[109],"produced":[110],"by":[111,118],"model,":[115],"as":[116],"evidenced":[117],"histogram":[119],"shifts,":[120],"increased":[121],"centroid":[122],"distances,":[123],"Silhouette":[125],"scores.":[126],"As":[127],"targets":[129],"we":[130],"choose":[131],"Quaternary":[132],"Ammonium":[133],"Compounds":[134],"(QACs)":[135],"rare":[137],"underrepresented":[139],"type":[141],"antibacterial":[143],"properties.":[144],"Injecting":[145],"MolGPT":[146,155],"DCM-trained":[148],"QAC":[149],"improves":[151],"generation":[152],"validity":[153],"over":[154],"baselines.":[158],"Our":[159],"results":[160,183],"show":[161],"minimal":[163],"domain":[164],"supervision":[165],"combined":[166],"targeted":[168],"during":[170],"reliably":[172],"shapes":[173],"domain-aware":[176],"generation.":[178],"will":[180],"expand":[181],"our":[182],"other":[185],"(SimSon,":[188],"MolMCL)":[189],"future.":[192]},"counts_by_year":[],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-12-05T00:00:00"}