{"id":"https://openalex.org/W4400267221","doi":"https://doi.org/10.48550/arxiv.2407.00236","title":"Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms","display_name":"Closed-Form Test Functions for Biophysical Sequence Optimization Algorithms","publication_year":2024,"publication_date":"2024-06-28","ids":{"openalex":"https://openalex.org/W4400267221","doi":"https://doi.org/10.48550/arxiv.2407.00236"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2407.00236","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.00236","pdf_url":"https://arxiv.org/pdf/2407.00236","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":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2407.00236","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102736359","display_name":"Samuel C. Stanton","orcid":"https://orcid.org/0000-0003-1664-2465"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Stanton, Samuel","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099881278","display_name":"Robert Alberstein","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alberstein, Robert","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090160831","display_name":"Nathan C. Frey","orcid":"https://orcid.org/0000-0001-5291-6131"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Frey, Nathan","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001503348","display_name":"Andrew M. Watkins","orcid":"https://orcid.org/0000-0003-1617-1720"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Watkins, Andrew","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5091175785","display_name":"Kyunghyun Cho","orcid":"https://orcid.org/0000-0003-1669-3211"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cho, Kyunghyun","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5102736359"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T13650","display_name":"Computational Physics and Python Applications","score":0.9031000137329102,"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"}},"topics":[{"id":"https://openalex.org/T13650","display_name":"Computational Physics and Python Applications","score":0.9031000137329102,"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/sequence","display_name":"Sequence (biology)","score":0.6961822509765625},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.6566552519798279},{"id":"https://openalex.org/keywords/test","display_name":"Test (biology)","score":0.5195401310920715},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49419644474983215},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3274857699871063},{"id":"https://openalex.org/keywords/geology","display_name":"Geology","score":0.10484856367111206},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09179922938346863}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6961822509765625},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.6566552519798279},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.5195401310920715},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49419644474983215},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3274857699871063},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.10484856367111206},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09179922938346863},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2407.00236","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.00236","pdf_url":"https://arxiv.org/pdf/2407.00236","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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2407.00236","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2407.00236","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:2407.00236","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.00236","pdf_url":"https://arxiv.org/pdf/2407.00236","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":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W1979597421","https://openalex.org/W2007980826","https://openalex.org/W2051487156","https://openalex.org/W2061531152","https://openalex.org/W3002753104","https://openalex.org/W2077600819","https://openalex.org/W2142036596","https://openalex.org/W2072657027"],"abstract_inverted_index":{"There":[0],"is":[1,74],"a":[2,78,106,141],"growing":[3],"body":[4],"of":[5,12,33,37,48,109,132],"work":[6],"seeking":[7],"to":[8,27,77,90,138],"replicate":[9],"the":[10,34,45],"success":[11],"machine":[13],"learning":[14],"(ML)":[15],"on":[16,81],"domains":[17,69],"like":[18],"computer":[19],"vision":[20],"(CV)":[21],"and":[22,42,134],"natural":[23],"language":[24],"processing":[25],"(NLP)":[26],"applications":[28],"involving":[29],"biophysical":[30,68,85,93,114],"data.":[31],"One":[32],"key":[35,53,99],"ingredients":[36],"prior":[38],"successes":[39],"in":[40],"CV":[41],"NLP":[43],"was":[44],"broad":[46],"acceptance":[47],"difficult":[49],"benchmarks":[50,66,82],"that":[51,58],"distilled":[52],"subproblems":[54],"into":[55,95],"approachable":[56],"tasks":[57],"any":[59],"junior":[60],"researcher":[61],"could":[62],"investigate,":[63],"but":[64],"good":[65],"for":[67,113],"are":[70,129],"rare.":[71],"This":[72],"scarcity":[73],"partially":[75],"due":[76],"narrow":[79],"focus":[80],"which":[83,117],"simulate":[84],"data;":[86],"we":[87,104,118],"propose":[88,105],"instead":[89],"carefully":[91],"abstract":[92],"problems":[94],"simpler":[96],"ones":[97],"with":[98,140],"geometric":[100],"similarities.":[101],"In":[102],"particular":[103],"new":[107],"class":[108],"closed-form":[110],"test":[111],"functions":[112,128],"sequence":[115],"optimization,":[116],"call":[119],"Ehrlich":[120],"functions.":[121],"We":[122],"provide":[123],"empirical":[124],"results":[125],"demonstrating":[126],"these":[127],"interesting":[130],"objects":[131],"study":[133],"can":[135],"be":[136],"non-trivial":[137],"solve":[139],"standard":[142],"genetic":[143],"optimization":[144],"baseline.":[145]},"counts_by_year":[],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2024-07-03T00:00:00"}
