{"id":"https://openalex.org/W3090791065","doi":"https://doi.org/10.1142/9789811232701_0026","title":"Cross-modal representation alignment of molecular structure and perturbation-induced transcriptional profiles","display_name":"Cross-modal representation alignment of molecular structure and perturbation-induced transcriptional profiles","publication_year":2020,"publication_date":"2020-11-01","ids":{"openalex":"https://openalex.org/W3090791065","doi":"https://doi.org/10.1142/9789811232701_0026","mag":"3090791065","pmid":"https://pubmed.ncbi.nlm.nih.gov/33691024"},"language":"en","primary_location":{"id":"doi:10.1142/9789811232701_0026","is_oa":true,"landing_page_url":"https://doi.org/10.1142/9789811232701_0026","pdf_url":null,"source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2021","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1142/9789811232701_0026","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090442121","display_name":"Samuel G. Finlayson","orcid":"https://orcid.org/0000-0001-7997-5959"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samuel G. Finlayson","raw_affiliation_strings":["Department of EECS, Massachusetts Institute of Technology, Cambridge, MA, USA","Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, MA, USA","Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, MA, USA2Department of EECS, Massachusetts Institute of Technology, Cambridge, MA, USA*Co-first author"],"affiliations":[{"raw_affiliation_string":"Department of EECS, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, MA, USA2Department of EECS, Massachusetts Institute of Technology, Cambridge, MA, USA*Co-first author","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083993242","display_name":"Matthew B. A. McDermott","orcid":"https://orcid.org/0000-0001-6048-9707"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew B.A. McDermott","raw_affiliation_strings":["Department of EECS, Massachusetts Institute of Technology, Cambridge, MA, USA","Dept. of EECS, Massachusetts Inst. of Technol., Cambridge, MA, USA"],"affiliations":[{"raw_affiliation_string":"Department of EECS, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Dept. of EECS, Massachusetts Inst. of Technol., Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076798522","display_name":"Alex Pickering","orcid":null},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alex V. Pickering","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","Department of Biomedical Informatics; Harvard Medical School; Boston MA USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Biomedical Informatics; Harvard Medical School; Boston MA USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061817429","display_name":"Scott Lipnick","orcid":"https://orcid.org/0000-0002-4271-746X"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Scott L. Lipnick","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","Department of Biomedical Informatics; Harvard Medical School; Boston MA USA"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Biomedical Informatics; Harvard Medical School; Boston MA USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088509061","display_name":"Isaac S. Kohane","orcid":"https://orcid.org/0000-0003-2192-5160"},"institutions":[{"id":"https://openalex.org/I2801851002","display_name":"Harvard University Press","ror":"https://ror.org/006v7bf86","country_code":"US","type":"other","lineage":["https://openalex.org/I136199984","https://openalex.org/I2801851002"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Isaac S. Kohane","raw_affiliation_strings":["Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","Harvard University ,"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Harvard University ,","institution_ids":["https://openalex.org/I2801851002"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5090442121"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210098931","https://openalex.org/I63966007"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.16191494,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":null,"first_page":"273","last_page":"284"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9983999729156494,"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":0.9983999729156494,"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/T10252","display_name":"Microbial Natural Products and Biosynthesis","score":0.986299991607666,"subfield":{"id":"https://openalex.org/subfields/2736","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9613999724388123,"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/benchmark","display_name":"Benchmark (surveying)","score":0.7123550772666931},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6864880919456482},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6435548663139343},{"id":"https://openalex.org/keywords/oracle","display_name":"Oracle","score":0.6097994446754456},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5497128367424011},{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.5496727228164673},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.38189584016799927},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3680926561355591},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3603903353214264},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23163187503814697},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08024716377258301}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7123550772666931},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6864880919456482},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6435548663139343},{"id":"https://openalex.org/C55166926","wikidata":"https://www.wikidata.org/wiki/Q2892946","display_name":"Oracle","level":2,"score":0.6097994446754456},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5497128367424011},{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.5496727228164673},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38189584016799927},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3680926561355591},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3603903353214264},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23163187503814697},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08024716377258301},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1142/9789811232701_0026","is_oa":true,"landing_page_url":"https://doi.org/10.1142/9789811232701_0026","pdf_url":null,"source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2021","raw_type":"proceedings-article"},{"id":"pmid:33691024","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33691024","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":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","raw_type":null},{"id":"pmh:oai:arXiv.org:1911.10241","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1911.10241","pdf_url":"https://arxiv.org/pdf/1911.10241","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":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8397230","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8397230","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Pac Symp Biocomput","raw_type":"Text"},{"id":"doi:10.48550/arxiv.1911.10241","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1911.10241","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"},{"id":"mag:3090791065","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1142/9789811232701_0026","is_oa":true,"landing_page_url":"https://doi.org/10.1142/9789811232701_0026","pdf_url":null,"source":null,"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biocomputing 2021","raw_type":"proceedings-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W2101234009","https://openalex.org/W2121604817","https://openalex.org/W2290847742","https://openalex.org/W2404118507","https://openalex.org/W2594183968","https://openalex.org/W2606780347","https://openalex.org/W2612467560","https://openalex.org/W2769760195","https://openalex.org/W2786016794","https://openalex.org/W2795832645","https://openalex.org/W2888905827","https://openalex.org/W2921591500","https://openalex.org/W2970119293","https://openalex.org/W3122451732"],"related_works":["https://openalex.org/W3107798042","https://openalex.org/W82104423","https://openalex.org/W3128075435","https://openalex.org/W1587352276","https://openalex.org/W3109027947","https://openalex.org/W3112351343","https://openalex.org/W2478826238","https://openalex.org/W2967870286","https://openalex.org/W2194985241","https://openalex.org/W3043787172","https://openalex.org/W2033104002","https://openalex.org/W3214494838","https://openalex.org/W2972700488","https://openalex.org/W2952354376","https://openalex.org/W1513074964","https://openalex.org/W2953192678","https://openalex.org/W2783007954","https://openalex.org/W1987741645","https://openalex.org/W3212911837","https://openalex.org/W2333566051"],"abstract_inverted_index":{"Modeling":[0],"the":[1,58,65,124,131],"relationship":[2],"between":[3],"chemical":[4,92],"structure":[5,59,93],"and":[6,79,94,106,109,136,138],"molecular":[7,23],"activity":[8],"is":[9],"a":[10,42,52,61,81],"key":[11],"goal":[12],"in":[13,118,145],"drug":[14],"development.":[15],"Many":[16],"benchmark":[17,100],"tasks":[18,28],"have":[19],"been":[20],"proposed":[21],"for":[22],"property":[24],"prediction,":[25],"but":[26],"these":[27],"are":[29],"generally":[30],"aimed":[31],"at":[32],"specific,":[33],"isolated":[34],"biomedical":[35],"properties.":[36],"In":[37],"this":[38,72,119,127],"work,":[39],"we":[40],"propose":[41],"new":[43,128],"cross-modal":[44],"small":[45,62,146],"molecule":[46,63,147],"retrieval":[47],"task,":[48,129],"designed":[49],"to":[50,54,56,141],"force":[51],"model":[53],"learn":[55],"associate":[57],"of":[60,90,126,133],"with":[64],"transcriptional":[66],"change":[67],"it":[68],"induces.":[69],"We":[70,99],"develop":[71],"task":[73],"formally":[74],"as":[75],"multi-view":[76],"alignment":[77],"problem,":[78],"present":[80],"coordinated":[82],"deep":[83],"learning":[84],"approach":[85],"that":[86,111],"jointly":[87],"optimizes":[88],"representations":[89],"both":[91],"perturbational":[95],"gene":[96],"expression":[97],"profiles.":[98],"our":[101],"results":[102],"against":[103],"oracle":[104],"models":[105],"principled":[107],"baselines,":[108],"find":[110],"cell":[112],"line":[113],"variability":[114],"markedly":[115],"influences":[116],"performance":[117],"domain.":[120],"Our":[121],"work":[122],"establishes":[123],"feasibility":[125],"elucidates":[130],"limitations":[132],"current":[134],"data":[135],"systems,":[137],"may":[139],"serve":[140],"catalyze":[142],"future":[143],"research":[144],"representation":[148],"learning.":[149]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
