{"id":"https://openalex.org/W2079628411","doi":"https://doi.org/10.1137/070688547","title":"Molecular Embedding via a Second Order Dissimilarity Parameterized Approach","display_name":"Molecular Embedding via a Second Order Dissimilarity Parameterized Approach","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W2079628411","doi":"https://doi.org/10.1137/070688547","mag":"2079628411"},"language":"en","primary_location":{"id":"doi:10.1137/070688547","is_oa":false,"landing_page_url":"https://doi.org/10.1137/070688547","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Scientific Computing","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016646160","display_name":"Ian Grooms","orcid":"https://orcid.org/0000-0002-4678-7203"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ian G. Grooms","raw_affiliation_strings":["[email\u00a0protected]#TAB#"],"affiliations":[{"raw_affiliation_string":"[email\u00a0protected]#TAB#","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103333585","display_name":"Robert Michael Lewis","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert Michael Lewis","raw_affiliation_strings":["[email\u00a0protected]#TAB#"],"affiliations":[{"raw_affiliation_string":"[email\u00a0protected]#TAB#","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070192461","display_name":"Michael W. Trosset","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael W. Trosset","raw_affiliation_strings":["[email\u00a0protected]#TAB#"],"affiliations":[{"raw_affiliation_string":"[email\u00a0protected]#TAB#","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5016646160"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.2131,"has_fulltext":false,"cited_by_count":15,"citation_normalized_percentile":{"value":0.78196454,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"31","issue":"4","first_page":"2733","last_page":"2756"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9987999796867371,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9987999796867371,"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/parameterized-complexity","display_name":"Parameterized complexity","score":0.7345647215843201},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.721933126449585},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.5870662331581116},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.5848758816719055},{"id":"https://openalex.org/keywords/optimization-problem","display_name":"Optimization problem","score":0.570644199848175},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.5290747284889221},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.45437902212142944},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.433973491191864},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.43373575806617737},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3779042661190033},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.14173555374145508},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11212590336799622}],"concepts":[{"id":"https://openalex.org/C165464430","wikidata":"https://www.wikidata.org/wiki/Q1570441","display_name":"Parameterized complexity","level":2,"score":0.7345647215843201},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.721933126449585},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.5870662331581116},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.5848758816719055},{"id":"https://openalex.org/C137836250","wikidata":"https://www.wikidata.org/wiki/Q984063","display_name":"Optimization problem","level":2,"score":0.570644199848175},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.5290747284889221},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.45437902212142944},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.433973491191864},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.43373575806617737},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3779042661190033},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.14173555374145508},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11212590336799622},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1137/070688547","is_oa":false,"landing_page_url":"https://doi.org/10.1137/070688547","pdf_url":null,"source":{"id":"https://openalex.org/S165512578","display_name":"SIAM Journal on Scientific Computing","issn_l":"1064-8275","issn":["1064-8275","1095-7197"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320508","host_organization_name":"Society for Industrial and Applied Mathematics","host_organization_lineage":["https://openalex.org/P4310320508"],"host_organization_lineage_names":["Society for Industrial and Applied Mathematics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"SIAM Journal on Scientific Computing","raw_type":"journal-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.156.7622","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.156.7622","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.math.wm.edu/~buckaroo/pubs/GrLeTr09a/GrLeTr09a.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1490549637","https://openalex.org/W1500146304","https://openalex.org/W1505376360","https://openalex.org/W1511973158","https://openalex.org/W1856811566","https://openalex.org/W1975519273","https://openalex.org/W1982819689","https://openalex.org/W1993436046","https://openalex.org/W1995017064","https://openalex.org/W2000389939","https://openalex.org/W2014418975","https://openalex.org/W2020545624","https://openalex.org/W2021001692","https://openalex.org/W2029990042","https://openalex.org/W2037402401","https://openalex.org/W2051434435","https://openalex.org/W2061681393","https://openalex.org/W2068891361","https://openalex.org/W2070876090","https://openalex.org/W2075641155","https://openalex.org/W2092544746","https://openalex.org/W2095888278","https://openalex.org/W2118811613","https://openalex.org/W2124812425","https://openalex.org/W2125947724","https://openalex.org/W2130479394","https://openalex.org/W2147902861","https://openalex.org/W2150381999","https://openalex.org/W2155785386","https://openalex.org/W2163392119","https://openalex.org/W2913650195"],"related_works":["https://openalex.org/W2051058708","https://openalex.org/W154868527","https://openalex.org/W1494268238","https://openalex.org/W1983207144","https://openalex.org/W2171811389","https://openalex.org/W2041837101","https://openalex.org/W1598441350","https://openalex.org/W1539117866","https://openalex.org/W2505728881","https://openalex.org/W2033433656"],"abstract_inverted_index":{"We":[0,85,123],"describe":[1],"a":[2,18,27,95,99,128],"computational":[3,121,148],"approach":[4,14],"to":[5,26,78,98,108],"the":[6,22,47,52,68,113],"embedding":[7],"problem":[8,23,70],"in":[9,57,94,112],"structural":[10],"molecular":[11],"biology.":[12],"The":[13,35,104],"is":[15,38,73],"based":[16],"on":[17,118,139],"dissimilarity":[19],"parameterization":[20],"of":[21,43,50,54,91,130,141],"that":[24,39,67,71,145],"leads":[25],"large-scale":[28],"nonconvex":[29],"bound":[30],"constrained":[31],"matrix":[32,109],"optimization":[33,69,102],"problem.":[34],"underlying":[36],"idea":[37],"an":[40],"increased":[41],"number":[42,129],"independent":[44,92],"variables":[45,93],"decouples":[46],"complicated":[48],"effects":[49],"varying":[51],"location":[53],"individual":[55],"atoms":[56],"coordinate-based":[58],"formulations.":[59],"Numerical":[60],"tests":[61],"support":[62],"this":[63],"hypothesis":[64],"and":[65,76,83,115,132,137],"indicate":[66],"results":[72,126],"relatively":[74],"benign":[75],"easy":[77],"solve,":[79],"despite":[80],"being":[81],"large":[82],"nonconvex.":[84],"can":[86,146],"solve":[87],"problems":[88],"with":[89],"millions":[90],"few":[96,100],"dozen":[97],"score":[101],"iterations.":[103],"nonconvexity":[105],"arises":[106],"due":[107],"rank":[110],"constraints":[111],"problem,":[114],"we":[116],"focus":[117],"their":[119],"efficient":[120],"treatment.":[122],"present":[124],"numerical":[125],"for":[127],"synthetic":[131],"real":[133,142],"protein":[134],"data":[135,144],"sets":[136],"comment":[138],"features":[140],"experimental":[143],"cause":[147],"difficulties.":[149]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":4}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
