{"id":"https://openalex.org/W4391187291","doi":"https://doi.org/10.1080/10556788.2023.2280784","title":"Predicting pairwise interaction affinities with \u2113 <sub>0</sub> -penalized least squares\u2013a nonsmooth bi-objective optimization based approach*","display_name":"Predicting pairwise interaction affinities with \u2113 <sub>0</sub> -penalized least squares\u2013a nonsmooth bi-objective optimization based approach*","publication_year":2024,"publication_date":"2024-01-24","ids":{"openalex":"https://openalex.org/W4391187291","doi":"https://doi.org/10.1080/10556788.2023.2280784"},"language":"en","primary_location":{"id":"doi:10.1080/10556788.2023.2280784","is_oa":true,"landing_page_url":"https://doi.org/10.1080/10556788.2023.2280784","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/10556788.2023.2280784?needAccess=true","source":{"id":"https://openalex.org/S103047102","display_name":"Optimization methods & software","issn_l":"1026-7670","issn":["1026-7670","1029-4937","1055-6788"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Optimization Methods and Software","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.tandfonline.com/doi/pdf/10.1080/10556788.2023.2280784?needAccess=true","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5092880108","display_name":"Pauliina Paasivirta","orcid":null},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Pauliina Paasivirta","raw_affiliation_strings":["Department of Mathematics and Statistics, University of Turku","Department of Mathematics and Statistics, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Turku","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071510852","display_name":"Riikka Numminen","orcid":"https://orcid.org/0000-0003-2283-6290"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Riikka Numminen","raw_affiliation_strings":["Department of Computing, University of Turku","Department of Computing, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, University of Turku","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Department of Computing, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084144711","display_name":"Antti Airola","orcid":"https://orcid.org/0000-0002-1010-4386"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antti Airola","raw_affiliation_strings":["Department of Computing, University of Turku","Department of Computing, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, University of Turku","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Department of Computing, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062770206","display_name":"Napsu Karmitsa","orcid":"https://orcid.org/0000-0002-8747-4836"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Napsu Karmitsa","raw_affiliation_strings":["Department of Computing, University of Turku","Department of Computing, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, University of Turku","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Department of Computing, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021993986","display_name":"Tapio Pahikkala","orcid":"https://orcid.org/0000-0003-4183-2455"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tapio Pahikkala","raw_affiliation_strings":["Department of Computing, University of Turku","Department of Computing, University of Turku, Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, University of Turku","institution_ids":["https://openalex.org/I155660961"]},{"raw_affiliation_string":"Department of Computing, University of Turku, Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5062770206"],"corresponding_institution_ids":["https://openalex.org/I155660961"],"apc_list":null,"apc_paid":null,"fwci":0.5764,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.65081427,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"41","issue":"2","first_page":"450","last_page":"477"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10848","display_name":"Advanced Multi-Objective Optimization Algorithms","score":0.9851999878883362,"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/T10848","display_name":"Advanced Multi-Objective Optimization Algorithms","score":0.9851999878883362,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9797000288963318,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/affinities","display_name":"Affinities","score":0.8370336294174194},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7515484094619751},{"id":"https://openalex.org/keywords/least-squares-function-approximation","display_name":"Least-squares function approximation","score":0.5229278802871704},{"id":"https://openalex.org/keywords/binding-affinities","display_name":"Binding affinities","score":0.5007455348968506},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4711531400680542},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.37069156765937805},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3533787429332733},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.28167450428009033},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.23339945077896118},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16225942969322205},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.1046912670135498},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07200324535369873}],"concepts":[{"id":"https://openalex.org/C2780283098","wikidata":"https://www.wikidata.org/wiki/Q4688960","display_name":"Affinities","level":2,"score":0.8370336294174194},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7515484094619751},{"id":"https://openalex.org/C9936470","wikidata":"https://www.wikidata.org/wiki/Q6510405","display_name":"Least-squares function approximation","level":3,"score":0.5229278802871704},{"id":"https://openalex.org/C3018795828","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Binding affinities","level":3,"score":0.5007455348968506},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4711531400680542},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.37069156765937805},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3533787429332733},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.28167450428009033},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.23339945077896118},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16225942969322205},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.1046912670135498},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07200324535369873},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1080/10556788.2023.2280784","is_oa":true,"landing_page_url":"https://doi.org/10.1080/10556788.2023.2280784","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/10556788.2023.2280784?needAccess=true","source":{"id":"https://openalex.org/S103047102","display_name":"Optimization methods & software","issn_l":"1026-7670","issn":["1026-7670","1029-4937","1055-6788"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Optimization Methods and Software","raw_type":"journal-article"},{"id":"pmh:oai:www.utupub.fi:10024/185907","is_oa":false,"landing_page_url":"https://www.utupub.fi/handle/10024/185907","pdf_url":null,"source":{"id":"https://openalex.org/S4306402470","display_name":"UTUPub (University of Turku)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I155660961","host_organization_name":"University of Turku","host_organization_lineage":["https://openalex.org/I155660961"],"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":null}],"best_oa_location":{"id":"doi:10.1080/10556788.2023.2280784","is_oa":true,"landing_page_url":"https://doi.org/10.1080/10556788.2023.2280784","pdf_url":"https://www.tandfonline.com/doi/pdf/10.1080/10556788.2023.2280784?needAccess=true","source":{"id":"https://openalex.org/S103047102","display_name":"Optimization methods & software","issn_l":"1026-7670","issn":["1026-7670","1029-4937","1055-6788"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320547","host_organization_name":"Taylor & Francis","host_organization_lineage":["https://openalex.org/P4310320547"],"host_organization_lineage_names":["Taylor & Francis"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Optimization Methods and Software","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1218684308","display_name":null,"funder_award_id":"340140","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G123324151","display_name":"AI technologies for interaction prediction in biomedicine","funder_award_id":"345804","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G1320448884","display_name":null,"funder_award_id":"313269","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G1781988190","display_name":null,"funder_award_id":"313266","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G2090226954","display_name":null,"funder_award_id":"345805","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G2852628691","display_name":null,"funder_award_id":"345804","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G2891395848","display_name":null,"funder_award_id":"289500","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G3558297072","display_name":"Machine Learning for Systems Pharmacology","funder_award_id":"340182","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5091040182","display_name":null,"funder_award_id":"311273","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6214043649","display_name":"AI technologies for interaction prediction in biomedicine","funder_award_id":"345805","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7068043672","display_name":null,"funder_award_id":"340182","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G8899941011","display_name":"Machine Learning for Systems Pharmacology","funder_award_id":"340140","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391187291.pdf"},"referenced_works_count":107,"referenced_works":["https://openalex.org/W363319864","https://openalex.org/W613054787","https://openalex.org/W1064564656","https://openalex.org/W1466286227","https://openalex.org/W1511261802","https://openalex.org/W1540155273","https://openalex.org/W1544009106","https://openalex.org/W1551360398","https://openalex.org/W1936663733","https://openalex.org/W1963488456","https://openalex.org/W1971106435","https://openalex.org/W1971387816","https://openalex.org/W1972987731","https://openalex.org/W1984014392","https://openalex.org/W1984084871","https://openalex.org/W1986087295","https://openalex.org/W1996692737","https://openalex.org/W2008840001","https://openalex.org/W2017335040","https://openalex.org/W2018796817","https://openalex.org/W2022623999","https://openalex.org/W2024650813","https://openalex.org/W2028781966","https://openalex.org/W2029348196","https://openalex.org/W2034978228","https://openalex.org/W2041046391","https://openalex.org/W2044002635","https://openalex.org/W2048565304","https://openalex.org/W2057195902","https://openalex.org/W2058839679","https://openalex.org/W2064264167","https://openalex.org/W2066201825","https://openalex.org/W2070664771","https://openalex.org/W2074110893","https://openalex.org/W2074370114","https://openalex.org/W2074522218","https://openalex.org/W2079745490","https://openalex.org/W2082360590","https://openalex.org/W2086286404","https://openalex.org/W2093117046","https://openalex.org/W2095796212","https://openalex.org/W2099862356","https://openalex.org/W2104871495","https://openalex.org/W2106029302","https://openalex.org/W2108153239","https://openalex.org/W2109445534","https://openalex.org/W2109991441","https://openalex.org/W2126671570","https://openalex.org/W2135007932","https://openalex.org/W2139516171","https://openalex.org/W2139736926","https://openalex.org/W2146382443","https://openalex.org/W2152630148","https://openalex.org/W2153838454","https://openalex.org/W2161607603","https://openalex.org/W2166410137","https://openalex.org/W2167212630","https://openalex.org/W2168029744","https://openalex.org/W2177317049","https://openalex.org/W2201551243","https://openalex.org/W2215019161","https://openalex.org/W2259538443","https://openalex.org/W2336207313","https://openalex.org/W2343107734","https://openalex.org/W2398999308","https://openalex.org/W2485305008","https://openalex.org/W2509839093","https://openalex.org/W2556014018","https://openalex.org/W2573312253","https://openalex.org/W2576041084","https://openalex.org/W2580903965","https://openalex.org/W2607497028","https://openalex.org/W2612835976","https://openalex.org/W2738241071","https://openalex.org/W2753953057","https://openalex.org/W2785947426","https://openalex.org/W2795490976","https://openalex.org/W2797260394","https://openalex.org/W2805169807","https://openalex.org/W2808199968","https://openalex.org/W2889321024","https://openalex.org/W2899788782","https://openalex.org/W2900090807","https://openalex.org/W2908760699","https://openalex.org/W2916534270","https://openalex.org/W2952522777","https://openalex.org/W2956769933","https://openalex.org/W2963351303","https://openalex.org/W2964038500","https://openalex.org/W2966273810","https://openalex.org/W2998700652","https://openalex.org/W2999554466","https://openalex.org/W3000043291","https://openalex.org/W3017755410","https://openalex.org/W3034536504","https://openalex.org/W3082511454","https://openalex.org/W3093397714","https://openalex.org/W3111330250","https://openalex.org/W3136918052","https://openalex.org/W3164680581","https://openalex.org/W4212863985","https://openalex.org/W4230819290","https://openalex.org/W4231170962","https://openalex.org/W4238586295","https://openalex.org/W4252076505","https://openalex.org/W4292864963","https://openalex.org/W6732280925"],"related_works":["https://openalex.org/W3187200704","https://openalex.org/W2031259671","https://openalex.org/W3112966125","https://openalex.org/W2108080735","https://openalex.org/W1990832091","https://openalex.org/W2095596733","https://openalex.org/W4240532245","https://openalex.org/W1966443150","https://openalex.org/W4248477353","https://openalex.org/W1532706714"],"abstract_inverted_index":{"In":[0,67],"this":[1],"paper,":[2],"we":[3,59,69],"introduce":[4],"a":[5,31,46,50,63,71,77],"novel":[6],"nonsmooth":[7,64],"optimization-based":[8],"method":[9],"LMBM-Kron\u21130LS":[10,22,96,133],"for":[11,45,56],"solving":[12,62],"large-scale":[13],"pairwise":[14],"interaction":[15,122],"affinity":[16,123],"prediction":[17,81,143],"problems.":[18],"The":[19,129],"aim":[20],"of":[21,53,83,90],"is":[23],"to":[24,75],"produce":[25],"accurate":[26],"predictions":[27],"using":[28,101],"as":[29,33],"sparse":[30,135],"model":[32,86],"possible.":[34],"We":[35,94],"apply":[36,70],"the":[37,80,84,88,91,142],"least":[38],"squares":[39],"approach":[40],"with":[41,97,127],"Kronecker":[42],"product":[43],"kernels":[44],"loss":[47],"function":[48],"and":[49,87,104,120],"continuous":[51,121],"formulation":[52],"\u21130":[54],"pseudonorm":[55],"regularization.":[57],"Thus,":[58],"end":[60],"up":[61],"optimization":[65],"problem.":[66],"addition,":[68],"specific":[72],"bi-objective":[73],"criterion":[74],"strike":[76],"balance":[78],"between":[79],"accuracy":[82],"learned":[85],"sparsity":[89],"obtained":[92],"solution.":[93],"compare":[95],"some":[98],"state-of-the-art":[99],"methods":[100],"three":[102],"benchmark":[103],"two":[105],"simulated":[106],"data":[107],"sets":[108],"under":[109],"four":[110],"distinct":[111],"experimental":[112],"settings,":[113],"including":[114],"zero-shot":[115],"learning.":[116],"Moreover,":[117],"both":[118],"binary":[119],"labels":[124],"are":[125],"considered":[126],"LMBM-Kron\u21130LS.":[128],"results":[130],"show":[131],"that":[132],"finds":[134],"solutions":[136],"without":[137],"sacrificing":[138],"too":[139],"much":[140],"in":[141],"performance.":[144]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
