{"id":"https://openalex.org/W4394907034","doi":"https://doi.org/10.48550/arxiv.2404.10094","title":"Towards DNA-Encoded Library Generation with GFlowNets","display_name":"Towards DNA-Encoded Library Generation with GFlowNets","publication_year":2024,"publication_date":"2024-04-15","ids":{"openalex":"https://openalex.org/W4394907034","doi":"https://doi.org/10.48550/arxiv.2404.10094"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2404.10094","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2404.10094","pdf_url":"https://arxiv.org/pdf/2404.10094","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"","raw_type":null},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2404.10094","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027393953","display_name":"Micha\u0142 Koziarski","orcid":"https://orcid.org/0000-0001-7707-9640"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Koziarski, Micha\u0142","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095767599","display_name":"Mohammed Abukalam","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Abukalam, Mohammed","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044371770","display_name":"Vedant Shah","orcid":"https://orcid.org/0000-0002-4149-4700"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shah, Vedant","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011729655","display_name":"Louis Vaillancourt","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vaillancourt, Louis","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109706327","display_name":"Doris Alexandra Schuetz","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Schuetz, Doris Alexandra","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060689126","display_name":"Moksh Jain","orcid":"https://orcid.org/0000-0002-1513-615X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jain, Moksh","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075445107","display_name":"Almer M. van der Sloot","orcid":"https://orcid.org/0000-0003-0049-2044"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"van der Sloot, Almer","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003541054","display_name":"Mathieu Bourgey","orcid":"https://orcid.org/0000-0002-8432-834X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bourgey, Mathieu","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006793350","display_name":"Anne Marinier","orcid":"https://orcid.org/0000-0002-0116-8345"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Marinier, Anne","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5086198262","display_name":"Yoshua Bengio","orcid":"https://orcid.org/0000-0002-9322-3515"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bengio, Yoshua","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5027393953"],"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.800599992275238,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.800599992275238,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.7813000082969666,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11675","display_name":"Open Source Software Innovations","score":0.7444000244140625,"subfield":{"id":"https://openalex.org/subfields/1706","display_name":"Computer Science Applications"},"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/dna","display_name":"DNA","score":0.5088803768157959},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4372299611568451},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4218483567237854},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.34796541929244995},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2475656270980835},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13744968175888062}],"concepts":[{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5088803768157959},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4372299611568451},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4218483567237854},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.34796541929244995},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2475656270980835},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13744968175888062}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2404.10094","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2404.10094","pdf_url":"https://arxiv.org/pdf/2404.10094","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"","raw_type":null},{"id":"doi:10.48550/arxiv.2404.10094","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2404.10094","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2404.10094","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2404.10094","pdf_url":"https://arxiv.org/pdf/2404.10094","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"","raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320309949","display_name":"Canadian Institute for Advanced Research","ror":"https://ror.org/01sdtdd95"},{"id":"https://openalex.org/F4320330273","display_name":"Institut de Valorisation des Donn\u00e9es","ror":null},{"id":"https://openalex.org/F4320332193","display_name":"Genentech","ror":"https://ror.org/04gndp242"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487","https://openalex.org/W1986764834"],"abstract_inverted_index":{"DNA-encoded":[0],"libraries":[1],"(DELs)":[2],"are":[3,109],"a":[4,74,96,110],"powerful":[5],"approach":[6,112],"for":[7,76,100,113],"rapidly":[8],"screening":[9],"large":[10],"numbers":[11],"of":[12,16,49,87],"diverse":[13,115],"compounds.":[14],"One":[15],"the":[17,29,39,47,66,77,85,101],"key":[18],"challenges":[19],"in":[20],"using":[21,88],"DELs":[22],"is":[23],"library":[24,117],"design,":[25],"which":[26],"involves":[27],"choosing":[28],"building":[30,92],"blocks":[31,93],"that":[32,107],"will":[33],"be":[34],"combinatorially":[35],"combined":[36],"to":[37,94],"produce":[38],"final":[40],"library.":[41],"In":[42],"this":[43,57],"paper":[44],"we":[45,59],"consider":[46],"task":[48,69],"protein-protein":[50],"interaction":[51],"(PPI)":[52],"biased":[53],"DEL":[54],"design.":[55],"To":[56],"end,":[58],"evaluate":[60],"several":[61],"machine":[62],"learning":[63],"algorithms":[64],"on":[65],"PPI":[67],"modulation":[68],"and":[70],"use":[71],"them":[72],"as":[73],"reward":[75],"proposed":[78],"GFlowNet-based":[79],"generative":[80],"approach.":[81],"We":[82],"additionally":[83],"investigate":[84],"possibility":[86],"structural":[89],"information":[90],"about":[91],"design":[95],"hierarchical":[97],"action":[98],"space":[99],"GFlowNet.":[102],"The":[103],"observed":[104],"results":[105],"indicate":[106],"GFlowNets":[108],"promising":[111],"generating":[114],"combinatorial":[116],"candidates.":[118]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
