{"id":"https://openalex.org/W4365456768","doi":"https://doi.org/10.48550/arxiv.2304.05823","title":"DiscoGen: Learning to Discover Gene Regulatory Networks","display_name":"DiscoGen: Learning to Discover Gene Regulatory Networks","publication_year":2023,"publication_date":"2023-04-12","ids":{"openalex":"https://openalex.org/W4365456768","doi":"https://doi.org/10.48550/arxiv.2304.05823"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2304.05823","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2304.05823","pdf_url":"https://arxiv.org/pdf/2304.05823","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2304.05823","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102922377","display_name":"Nan Rosemary Ke","orcid":"https://orcid.org/0009-0003-7647-8449"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ke, Nan Rosemary","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018785790","display_name":"Sara-Jane Dunn","orcid":"https://orcid.org/0000-0003-3062-7923"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dunn, Sara-Jane","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041213674","display_name":"J\u00f6rg Bornschein","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bornschein, Jorg","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087675089","display_name":"Silvia Chiappa","orcid":"https://orcid.org/0000-0002-1882-6842"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chiappa, Silvia","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063369353","display_name":"M\u00e9lanie Rey","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rey, Melanie","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058299981","display_name":"Jean-Baptiste Lespiau","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lespiau, Jean-Baptiste","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030260581","display_name":"Albin Cassirer","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cassirer, Albin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109072714","display_name":"Jane Wang","orcid":"https://orcid.org/0009-0001-2255-6419"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wang, Jane","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005085749","display_name":"Th\u00e9ophane Weber","orcid":"https://orcid.org/0000-0001-6230-952X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Weber, Theophane","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110401550","display_name":"David Barrett","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Barrett, David","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083771180","display_name":"Matthew Botvinick","orcid":"https://orcid.org/0000-0001-7758-6896"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Botvinick, Matthew","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016769717","display_name":"Anirudh Goyal","orcid":"https://orcid.org/0000-0002-4080-1940"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Goyal, Anirudh","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008898050","display_name":"Mike Mozer","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mozer, Mike","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5055733526","display_name":"Danilo Jimenez Rezende","orcid":"https://orcid.org/0000-0003-3184-8509"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rezende, Danilo","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5102922377"],"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T10885","display_name":"Gene expression and cancer classification","score":0.996399998664856,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9944999814033508,"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/computer-science","display_name":"Computer science","score":0.6217966079711914},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5809140205383301},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.574409008026123},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5637851357460022},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5633246898651123},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5604473948478699},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.5253567099571228},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.4342576861381531},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4216150641441345},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.41802671551704407},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3951539993286133},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25332310795783997},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21306633949279785},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20527103543281555},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.10353365540504456},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07524183392524719}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6217966079711914},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5809140205383301},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.574409008026123},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5637851357460022},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5633246898651123},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5604473948478699},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.5253567099571228},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.4342576861381531},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4216150641441345},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.41802671551704407},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3951539993286133},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25332310795783997},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21306633949279785},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20527103543281555},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.10353365540504456},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07524183392524719},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2304.05823","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2304.05823","pdf_url":"https://arxiv.org/pdf/2304.05823","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2304.05823","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2304.05823","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:2304.05823","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2304.05823","pdf_url":"https://arxiv.org/pdf/2304.05823","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4365456768.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2389214306","https://openalex.org/W4375867731","https://openalex.org/W4235240664","https://openalex.org/W2965083567","https://openalex.org/W1838576100","https://openalex.org/W2095886385","https://openalex.org/W2889616422","https://openalex.org/W2089704382","https://openalex.org/W1983399550","https://openalex.org/W97075385"],"abstract_inverted_index":{"Accurately":[0],"inferring":[1],"Gene":[2],"Regulatory":[3],"Networks":[4],"(GRNs)":[5],"is":[6,35,96],"a":[7,85,108],"critical":[8],"and":[9,18,23,67,84,120],"challenging":[10],"task":[11],"in":[12,27,49,65,76],"biology.":[13],"GRNs":[14],"model":[15,128],"the":[16,92],"activatory":[17],"inhibitory":[19],"interactions":[20],"between":[21],"genes":[22],"are":[24],"inherently":[25],"causal":[26,52,58,73,93,133],"nature.":[28],"To":[29],"accurately":[30],"identify":[31],"GRNs,":[32],"perturbational":[33],"data":[34,83],"required.":[36],"However,":[37,69],"most":[38],"GRN":[39,111],"discovery":[40,53,74,94,112,134],"methods":[41,54,75,95],"only":[42],"operate":[43],"on":[44],"observational":[45],"data.":[46,123],"Recent":[47],"advances":[48],"neural":[50,109,131],"network-based":[51,110,132],"have":[55],"significantly":[56],"improved":[57],"discovery,":[59],"including":[60],"handling":[61],"interventional":[62,122],"data,":[63],"improvements":[64],"performance":[66],"scalability.":[68],"applying":[70],"state-of-the-art":[71],"(SOTA)":[72],"biology":[77],"poses":[78],"challenges,":[79],"such":[80],"as":[81],"noisy":[82],"large":[86],"number":[87],"of":[88],"samples.":[89],"Thus,":[90],"adapting":[91],"necessary":[97],"to":[98],"handle":[99,121],"these":[100],"challenges.":[101],"In":[102],"this":[103],"paper,":[104],"we":[105],"introduce":[106],"DiscoGen,":[107],"method":[113],"that":[114,126],"can":[115],"denoise":[116],"gene":[117],"expression":[118],"measurements":[119],"We":[124],"demonstrate":[125],"our":[127],"outperforms":[129],"SOTA":[130],"methods.":[135]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
