{"id":"https://openalex.org/W7160874266","doi":"https://doi.org/10.1093/bib/bbag079","title":"MT-ConBiFormer-GPT: multi-target molecular generation for low-data drug discovery via a contrastive BiFormer-GPT architecture and curriculum learning with cross-domain generalization","display_name":"MT-ConBiFormer-GPT: multi-target molecular generation for low-data drug discovery via a contrastive BiFormer-GPT architecture and curriculum learning with cross-domain generalization","publication_year":2026,"publication_date":"2026-05-01","ids":{"openalex":"https://openalex.org/W7160874266","doi":"https://doi.org/10.1093/bib/bbag079","pmid":"https://pubmed.ncbi.nlm.nih.gov/42114118"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag079","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag079","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag079","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009489625","display_name":"Romina Norouzi","orcid":"https://orcid.org/0009-0004-1220-4374"},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Romina Norouzi","raw_affiliation_strings":["Department of Bioinformatics, Kish International Campus, University of Tehran , 16th Azar St, Kish, 1417935840 ,"],"raw_orcid":"https://orcid.org/0009-0004-1220-4374","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Kish International Campus, University of Tehran , 16th Azar St, Kish, 1417935840 ,","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069064010","display_name":"Karim Abbasi","orcid":"https://orcid.org/0000-0003-2135-8864"},"institutions":[{"id":"https://openalex.org/I181744264","display_name":"Kharazmi University","ror":"https://ror.org/05hsgex59","country_code":"IR","type":"education","lineage":["https://openalex.org/I181744264"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Karim Abbasi","raw_affiliation_strings":["Mosaheb Institute for Mathematical Research, Kharazmi University , South Mofateh St, Tehran, 1571914911 ,"],"raw_orcid":"https://orcid.org/0000-0003-2135-8864","affiliations":[{"raw_affiliation_string":"Mosaheb Institute for Mathematical Research, Kharazmi University , South Mofateh St, Tehran, 1571914911 ,","institution_ids":["https://openalex.org/I181744264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018861719","display_name":"Parvin Razzaghi","orcid":"https://orcid.org/0000-0002-7031-4609"},"institutions":[{"id":"https://openalex.org/I161028277","display_name":"Institute for Advanced Studies in Basic Sciences","ror":"https://ror.org/00bzsst90","country_code":"IR","type":"education","lineage":["https://openalex.org/I161028277"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Parvin Razzaghi","raw_affiliation_strings":["Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS) , Prof Yousef Sobouti Blvd, Zanjan, 4513766731 ,"],"raw_orcid":"https://orcid.org/0000-0002-7031-4609","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Information Technology, Institute for Advanced Studies in Basic Sciences (IASBS) , Prof Yousef Sobouti Blvd, Zanjan, 4513766731 ,","institution_ids":["https://openalex.org/I161028277"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068106181","display_name":"Sajjad Gharaghani","orcid":"https://orcid.org/0000-0001-5468-4258"},"institutions":[{"id":"https://openalex.org/I4210103004","display_name":"Institute of Biochemistry","ror":"https://ror.org/022dvs210","country_code":"HU","type":"facility","lineage":["https://openalex.org/I2800351701","https://openalex.org/I4210103004","https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Sajjad Gharaghani","raw_affiliation_strings":["Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran , Enghelab Square, Tehran, 131451365 ,"],"raw_orcid":"https://orcid.org/0000-0001-5468-4258","affiliations":[{"raw_affiliation_string":"Laboratory of Bioinformatics and Drug Design (LBD), Institute of Biochemistry and Biophysics, University of Tehran , Enghelab Square, Tehran, 131451365 ,","institution_ids":["https://openalex.org/I4210103004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5018861719","https://openalex.org/A5068106181"],"corresponding_institution_ids":["https://openalex.org/I161028277","https://openalex.org/I4210103004"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":12.3448,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.98539206,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":98},"biblio":{"volume":"27","issue":"3","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":0.28519999980926514,"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":0.28519999980926514,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.19050000607967377,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.09210000187158585,"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/generalizability-theory","display_name":"Generalizability theory","score":0.6065999865531921},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.5684999823570251},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5049999952316284},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.491100013256073},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.43540000915527344},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.3971000015735626},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.366100013256073}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7724000215530396},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6504999995231628},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.6065999865531921},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.5684999823570251},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5049999952316284},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.491100013256073},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4699999988079071},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.43540000915527344},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.3971000015735626},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.366100013256073},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.33149999380111694},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.31709998846054077},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.30979999899864197},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.3077999949455261},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.30410000681877136},{"id":"https://openalex.org/C8038995","wikidata":"https://www.wikidata.org/wiki/Q1152135","display_name":"Unsupervised learning","level":2,"score":0.27950000762939453},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2786000072956085},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.2597000002861023}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098842","descriptor_name":"Generative Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098842","descriptor_name":"Generative Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098842","descriptor_name":"Generative Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019869","descriptor_name":"Phosphatidylinositol 3-Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051057","descriptor_name":"Proto-Oncogene Proteins c-akt","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051057","descriptor_name":"Proto-Oncogene Proteins c-akt","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D058570","descriptor_name":"TOR Serine-Threonine Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbag079","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag079","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:42114118","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42114118","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13160422","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13160422/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag079","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag079","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W2130479394","https://openalex.org/W2134967712","https://openalex.org/W2144908252","https://openalex.org/W2402506318","https://openalex.org/W2884740260","https://openalex.org/W2923363662","https://openalex.org/W2963028280","https://openalex.org/W3011286504","https://openalex.org/W3159177617","https://openalex.org/W3194855384","https://openalex.org/W3195161349","https://openalex.org/W4200307603","https://openalex.org/W4283811348","https://openalex.org/W4304695118","https://openalex.org/W4313703391","https://openalex.org/W4361000628","https://openalex.org/W4362721142","https://openalex.org/W4385986528","https://openalex.org/W4388464545","https://openalex.org/W4389159869","https://openalex.org/W4392015344","https://openalex.org/W4394994059","https://openalex.org/W4396660597","https://openalex.org/W4399379059","https://openalex.org/W4399608062","https://openalex.org/W4400061043","https://openalex.org/W4400876473","https://openalex.org/W4402441163","https://openalex.org/W4403836322","https://openalex.org/W4406946019","https://openalex.org/W4409652096","https://openalex.org/W4410997516","https://openalex.org/W4411009874","https://openalex.org/W4415053647"],"related_works":[],"abstract_inverted_index":{"Multi-target":[0],"compounds,":[1],"or":[2],"polypharmacological":[3],"agents,":[4],"hold":[5],"significant":[6],"potential":[7],"for":[8,31,48,96,242],"complex":[9],"diseases":[10],"like":[11],"cancer,":[12],"where":[13],"single-target":[14],"therapies":[15],"are":[16],"often":[17],"insufficient.":[18],"A":[19],"lack":[20],"of":[21,176],"high-quality":[22],"bioactivity":[23],"data":[24],"limits":[25],"progress":[26],"in":[27,75,166,204,246],"this":[28],"field,":[29],"especially":[30],"compounds":[32],"interacting":[33],"with":[34,67,84,134],"multiple":[35],"proteins":[36],"simultaneously.":[37],"This":[38,233],"study":[39,154,234],"introduces":[40],"MT-ConBiFormer-GPT,":[41],"a":[42,64,68,93,102,120,135,186,205,236],"deep":[43],"generative":[44],"model":[45,187],"designed":[46],"explicitly":[47],"low-data,":[49],"multi-target":[50,243],"molecular":[51],"generation,":[52],"focusing":[53],"on":[54],"the":[55,79,125,158,174,177,182,190,217],"critical":[56],"PI3K-AKT-mTOR":[57],"cancer":[58],"signaling":[59],"pathway.":[60],"The":[61,114],"framework":[62,126,241],"integrates":[63],"variational":[65],"autoencoder":[66],"BiFormer":[69],"encoder":[70],"to":[71,149],"capture":[72],"long-range":[73],"dependencies":[74],"SMILES":[76],"strings,":[77],"reducing":[78],"quadratic":[80],"computational":[81],"complexity":[82],"associated":[83],"standard":[85],"transformers":[86],"and":[87,100,111,169,192,212,222,238],"mitigating":[88],"semantic":[89],"discontinuities.":[90],"It":[91],"employs":[92],"SMILES-GPT":[94],"decoder":[95],"progressive":[97],"molecule":[98],"generation":[99,171],"follows":[101],"three-phase":[103],"training":[104],"pipeline:":[105],"unsupervised":[106],"pre-training,":[107],"supervised":[108],"contrastive":[109,178,191],"learning,":[110],"curriculum-based":[112],"fine-tuning.":[113],"framework's":[115],"efficacy":[116],"was":[117,127],"evaluated":[118,128],"through":[119,129],"rigorous,":[121],"multi-stage":[122],"assessment.":[123],"First,":[124],"benchmarking":[130],"against":[131],"state-of-the-art":[132],"models,":[133],"specialized":[136],"head-to-head":[137],"variant,":[138],"MT-ConBiFormer-GPT_H2H,":[139],"demonstrating":[140],"superior":[141],"performance,":[142],"thereby":[143],"validating":[144],"its":[145,163,197],"generalizability":[146],"from":[147],"oncology":[148],"neuropsychiatry.":[150],"An":[151],"internal":[152],"ablation":[153],"further":[155],"revealed":[156],"that":[157,216],"full":[159],"MT-ConBiFormer-GPT":[160],"significantly":[161],"outperformed":[162],"baseline,":[164],"MT-BiFormer-GPT,":[165],"both":[167,189],"dual-":[168],"triplet-target":[170],"tasks,":[172],"highlighting":[173],"advantages":[175],"learning":[179,194],"stage.":[180],"Additionally,":[181],"foundational":[183],"Base-BiFormer-GPT":[184],"architecture,":[185],"lacking":[188],"curriculum":[193],"stages,":[195],"highlighted":[196],"intrinsic":[198],"robustness":[199],"by":[200],"achieving":[201],"competitive":[202],"outcomes":[203],"distinct":[206],"omics-driven":[207],"design":[208],"task.":[209],"Docking":[210],"simulations":[211],"mechanistic":[213],"analyses":[214],"show":[215],"generated":[218],"molecules,":[219],"including":[220],"high-fidelity":[221],"scaffold-hopping":[223],"candidates,":[224],"display":[225],"more":[226],"favorable":[227],"binding":[228],"modes":[229],"than":[230],"reference":[231],"inhibitors.":[232],"presents":[235],"flexible":[237],"computationally":[239],"efficient":[240],"drug":[244],"discovery":[245],"data-limited":[247],"settings.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-08-24T07:32:12.397491","created_date":"2026-05-12T00:00:00"}