{"id":"https://openalex.org/W4392516640","doi":"https://doi.org/10.1093/bioinformatics/btae131","title":"Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence","display_name":"Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence","publication_year":2024,"publication_date":"2024-03-01","ids":{"openalex":"https://openalex.org/W4392516640","doi":"https://doi.org/10.1093/bioinformatics/btae131","pmid":"https://pubmed.ncbi.nlm.nih.gov/38444088"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae131","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae131","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae131/56873984/btae131.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae131/56873984/btae131.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088668784","display_name":"Jason Y. Cain","orcid":"https://orcid.org/0000-0001-6124-3637"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason Y Cain","raw_affiliation_strings":["Department of Chemical Engineering, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Department of Chemical Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093711568","display_name":"Jacob I. Evarts","orcid":null},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jacob I Evarts","raw_affiliation_strings":["Department of Biology, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066936754","display_name":"Jessica S. Yu","orcid":"https://orcid.org/0000-0003-4464-904X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jessica S Yu","raw_affiliation_strings":["Department of Biology, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030550883","display_name":"Neda Bagheri","orcid":"https://orcid.org/0000-0003-0146-4627"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neda Bagheri","raw_affiliation_strings":["Department of Biology, University of Washington , Seattle, WA 98195, United States","Department of Chemical Engineering, University of Washington , Seattle, WA 98195, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]},{"raw_affiliation_string":"Department of Chemical Engineering, University of Washington , Seattle, WA 98195, United States","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5088668784"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0346937,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9980000257492065,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","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"}}],"keywords":[{"id":"https://openalex.org/keywords/emulation","display_name":"Emulation","score":0.9436184167861938},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7693301439285278},{"id":"https://openalex.org/keywords/temporal-resolution","display_name":"Temporal resolution","score":0.6400513648986816},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5186383128166199},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4757646918296814},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.47287601232528687},{"id":"https://openalex.org/keywords/feature-engineering","display_name":"Feature engineering","score":0.4684600532054901},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.4423351287841797},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.43781527876853943},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3589806854724884},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.32782232761383057},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.27944254875183105}],"concepts":[{"id":"https://openalex.org/C149810388","wikidata":"https://www.wikidata.org/wiki/Q5374873","display_name":"Emulation","level":2,"score":0.9436184167861938},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7693301439285278},{"id":"https://openalex.org/C119666444","wikidata":"https://www.wikidata.org/wiki/Q5977280","display_name":"Temporal resolution","level":2,"score":0.6400513648986816},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5186383128166199},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4757646918296814},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.47287601232528687},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.4684600532054901},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.4423351287841797},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.43781527876853943},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3589806854724884},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.32782232761383057},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.27944254875183105},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059016","descriptor_name":"Tumor Microenvironment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btae131","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae131","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae131/56873984/btae131.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38444088","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38444088","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae131","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae131","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae131/56873984/btae131.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5899999737739563}],"awards":[{"id":"https://openalex.org/G6266958601","display_name":null,"funder_award_id":"1653315","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6347694119","display_name":null,"funder_award_id":"CBET-1653315","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6671297155","display_name":null,"funder_award_id":"CAREER","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306854","display_name":"Washington Research Foundation","ror":"https://ror.org/00hasdx88"},{"id":"https://openalex.org/F4320337390","display_name":"Division of Chemical, Bioengineering, Environmental, and Transport Systems","ror":"https://ror.org/0471zv972"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392516640.pdf"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1589873300","https://openalex.org/W1966107523","https://openalex.org/W2012757283","https://openalex.org/W2042925520","https://openalex.org/W2063536881","https://openalex.org/W2064675550","https://openalex.org/W2096900000","https://openalex.org/W2097259163","https://openalex.org/W2101234009","https://openalex.org/W2106474670","https://openalex.org/W2109879937","https://openalex.org/W2117692326","https://openalex.org/W2144370915","https://openalex.org/W2150704630","https://openalex.org/W2156638642","https://openalex.org/W2344481922","https://openalex.org/W2503839997","https://openalex.org/W2595828237","https://openalex.org/W2622764401","https://openalex.org/W2751370007","https://openalex.org/W2789705164","https://openalex.org/W2801459582","https://openalex.org/W2806054145","https://openalex.org/W2807369386","https://openalex.org/W2885404336","https://openalex.org/W2886347923","https://openalex.org/W2905576123","https://openalex.org/W2910271149","https://openalex.org/W2911948847","https://openalex.org/W2923643932","https://openalex.org/W2949797623","https://openalex.org/W2951378914","https://openalex.org/W2952966773","https://openalex.org/W2954111351","https://openalex.org/W2968085490","https://openalex.org/W2976185208","https://openalex.org/W3003257820","https://openalex.org/W3003422837","https://openalex.org/W3005127469","https://openalex.org/W3034742379","https://openalex.org/W3038799069","https://openalex.org/W3081825606","https://openalex.org/W3103145119","https://openalex.org/W3106349619","https://openalex.org/W3110430114","https://openalex.org/W3111639496","https://openalex.org/W3117751160","https://openalex.org/W3130323921","https://openalex.org/W3131280372","https://openalex.org/W3133538896","https://openalex.org/W3140926987","https://openalex.org/W3167557279","https://openalex.org/W3169295261","https://openalex.org/W3186633320","https://openalex.org/W3199465333","https://openalex.org/W3210736347","https://openalex.org/W4205409093","https://openalex.org/W4211091012","https://openalex.org/W4211225168","https://openalex.org/W4214594956","https://openalex.org/W4281736568","https://openalex.org/W4285041875","https://openalex.org/W4295605475","https://openalex.org/W4297154457","https://openalex.org/W4309268873","https://openalex.org/W4313584453","https://openalex.org/W4362521490","https://openalex.org/W4389912639","https://openalex.org/W6608852248","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2154523322","https://openalex.org/W2083200807","https://openalex.org/W1603137082","https://openalex.org/W2364195017","https://openalex.org/W2355430452","https://openalex.org/W2049983405","https://openalex.org/W2392315374","https://openalex.org/W1951195060","https://openalex.org/W2351776620","https://openalex.org/W4234346746"],"abstract_inverted_index":{"All":[0],"source":[1],"codes":[2],"for":[3],"the":[4,14],"agent-based":[5],"model,":[6],"emulation,":[7],"and":[8],"analyses":[9],"are":[10],"publicly":[11],"available":[12],"at":[13],"corresponding":[15],"DOIs:":[16],"10.5281/zenodo.10622155,":[17],"10.5281/zenodo.10611675,":[18],"10.5281/zenodo.10621244,":[19],"respectively.":[20]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}